i

NMR guided approach to evolution of myoglobin protein into a catalyst &

AzulenylAlanine as a probe for mechanistic studies of antimicrobial peptides

A Thesis Submitted in Partial Fulfillment of the Requirements of the Renée Crown University Honors Program at

Syracuse University

Christos P Costeas

Candidate for Bachelor of Science in Biochemistry and Renée Crown University Honors

Spring 2020

Honors Thesis in Biochemistry

Thesis Advisor: _______________________ Dr. Olga Makhlynets

Thesis Reader: _______________________ Dr. Calros A. Castañeda

Honors Director: _______________________ Dr. Danielle Smith, Director

ii

Abstract 1) New catalytic properties have been generally introduced through a “bottom-up” directed evolution-based approach or through a rational design-based approach using structural information of the protein or computational simulation analysis. Recently, Reetz et al. demonstrated the only reported example of a redox mediated Kemp eliminase through coordination of the Kemp substrate to the Fe (II)-heme center using the heme containing cytochrome P450-BM3 which was then improved using rational design. This paper describes NMR-guidance approach as a novel, straightforward method for the design of new enzymes with non-natural functions. We speculated that differences in the HSQC spectra between the substrate analog bound and unbound states of a protein can be used to identify potentially important residue-substrate interactions. We chose, myoglobin as the protein scaffold and Kemp elimination as the novel function to be introduced. Through screening for accelerated formation of a yellow 2-cyano-4-nitrophenol product and based on NMR analysis, mutations were introduced near the heme. NMR successfully predicted T95 as an important residue for directed evolution. Both the facts that T95, is located outside the binding pocket, rendering it not possible to have otherwise been predicted and that the T95V variant showed more than ten-fold improvement in catalysis, underscore NMR-guidance as a simple, logical and powerful strategy for directed evolution. 2) A series of antimicrobial peptides (AMPs) with broad spectrum bactericidal activities have been identified in buffalo species. Buffalo CATHL4s (buCATHL4s) are newly identified AMPs that showed the ability to disrupt the membrane integrity of selected Gram positive (G+) and Gram negative (G-) bacteria and induced specific changes such as budding and pore-like structure formation on the bacterial membrane. Using a phylogenetic analysis, a conserved CATHL4 AMPs sequence was selected, modified and studied in collaboration with Gregory A. Caputo and his group, for its use as a potentially novel antimicrobial therapeutic agent. A therapeutic agent needs to avoid or adequately delay enzymatic degradation in order to act in the human body. This paper demonstrates how the introduction of an unnatural amino acid, β-(1-Azulenyl)-L-Alanine (AzAla) can resolve this issue. It has been previously shown by the Korendovch group that AzAla, a fluorescent pseudoisosteric analog of tryptophan, contrasting other tryprophan analogs, is very minimally affected by its local microenvironment and can be selectively excited at a more distant wavelength (342 nm) than most intrinsic fluorophores. AzAla displays simple single exponential fluorescence decay that allows for easy deconvolution of fluorescence lifetime data. This paper shows that AzAla can successfully replace tryptophan to form a novel peptide with the conserved structure and thus function of the corresponding AMP, but with the added advantages that AzAla has to offer, including its fluorescent properties and proteolytic enzyme resistance.

iii

Executive Summary

One of nature’s benevolent creations are elegantly constructed protein scaffolds made

from strategically placed amino acid residues. The structure and amino acid sequence of many

natural protein catalysts enable the catalysis of several reactions that would generally require

very harsh conditions or that would even be impossible to perform in the laboratory1.

Humans are constantly fascinated by nature’s infinite wisdom and magnificent creations.

Dr. Frances Arnold has dedicated a big part of her career in studying and performing protein

directed evolution. In fact, she was the recipient of the Nobel Prize in Chemistry 2018 for her

work2–5 conducting the directed evolution of enzymes, proteins that catalyze chemical reactions.

The ultimate purpose of protein engineering and evolution is to pioneer or discover proteins that

could, through their properties or function, be important tools for technological, scientific, or

medical applications6.

A protein’s function, its expression level, catalytic activity, and its various properties can

be directly linked to its amino acid sequence. This is therefore precisely what scientists target

when attempting to alter or engineer a protein’s properties and function7.

Different strategies are currently being used in the field for improving a protein’s

enzymatic activity. For instance, Dr. Arnold, inspired by natural evolution, used directed

evolution, entailing sequence diversification to generate a library of modified sequences,

followed by screening to identify variants with improved properties8. Another commonly used

method is computational-aided design, in which residue changes in the protein scaffold of the

wildtype are tested in simulated conditions and then the corresponding mutations are introduced,

and the mutant protein is tested in real life conditions9. The aforementioned methods have been

commonly used in research; however, they have various drawbacks. Concerning directed

iv

evolution, it is worth noting that the cycles of random mutagenesis and screening of all the

variants in each library is time-consuming6. In regard to computational design, very expensive

and high-performance technology is required, as well as highly trained personnel to use the

software. Additionally, simulations may not take into account all real-life conditions, thus not

yielding the same results as the experiments in real-life.

Taking into account the potentials of this upcoming field of protein evolution/design and

the drawbacks of pre-existing methods, we were inspired to find and test a method that will

provide a simple, logical and efficacious strategy for directed evolution, namely using HSQC

(Heteronuclear Single Quantum Correlation Spectroscopy) NMR Spectroscopy10. This NMR

spectroscopic technique allows the detection of interactions at the amino acid residue-specific

level or “atomic level.” When our protein is bound to a substrate or a substrate analog, we

predict that there will be a more significant difference in chemical shifts of free and bound states

in the residues involved with the enzyme substrate interaction, thus indicating the appropriate

protein part(s) to be altered, so as to improve protein activity.

A natural defense mechanism conserved in the innate immune system of all organisms,

including plants, animals and humans, involves antimicrobial peptides (AMPs). Cathelicidins are

AMPs that belong to the large group of positively charged peptides with amphipathic properties

and embody the main part of the immune system in many vertebrates, including humans and

farm animals. Numerous AMPs are stored in secretory granules of certain white blood cells and

can be released to fight against bacteria, enveloped viruses and fungi11.

Until now, several cathelicidins have been identified in cattle, horse, pig, sheep, deer,

chicken and many more species; however, recently new short buffalo cathelicidin peptides with

potent bactericidal properties non-toxic to mammalian cells were identified. These cathelicidins

v

may have potential translational applications for the development of novel antibiotics. However,

most natural peptides are susceptible to enzyme degradation when introduced to the human body.

To counter this issue, studies have shown that the introduction of non-natural amino acids into

peptide sequences inhibit or delay the recognition and subsequent degradation of the peptides by

human enzymes12.

In the development of peptides, studying their environment, structure, location and

properties fluorescent emission characteristics of its amino acid components have been used.

Tryptophan (Trp) has been very useful due to it being excited at different wavelengths than other

amino acids13. However, its emission is highly influenced by its environment which may cause

an issue in the accuracy of certain investigations. This issue14 has also been recently countered

using a non-natural amino acid, β-(1-azulenyl)-L-alanine, (AzAla). AzAla maintains constant

fluorescence properties in various environments and has even more distinct excitation

wavelength than the other natural amino acids. Furthermore, this amino acid mimics

tryptophan’s structure very closely, making it highly probable that if it is used to replace Trp it

may not change the peptide’s original structure15.

Using the newly found buffalo cathelicidins’ most conserved peptide sequences16, a novel

potentially antimicrobial peptide was designed, and AzAla was used to replace Trp at different

positions to investigate if resistance to enzymatic degradation and the fluorescent advantages of

AzAla could be incorporated into this design without altering its structure-dependent

antimicrobial function.

vi

Table of Contents

Abstract……………………………………….……………….………………………………. ii Executive Summary………………………….……………….………………………………. iii Acknowledgements...….…….………………………………………………………………... vii Chapter 1: Introduction………………………...……………………………………………… 1 Chapter 2: Rational Design of a Myoglobin Based Enzyme………………………...……… 10 Chapter 3: Azulenyl-Alanine Modified Antimicrobial Peptide…………………….…….… 22 Chapter 4: Material and Methods.……………….………………………………………...… 29 Chapter 5: Discussion………………………….……………………………………………… 37 References.………………………………...…………………………………………………… 41

vii

Acknowledgements

Research has been a huge part of my time here at Syracuse. I first fell in love with the

laboratory when I started working on the evolution of Myoglobin protein using a novel technique

in order to introduce a new enzymatic function. After my first semester in the lab, I couldn’t get

enough of it. For this I have to first thank Dr. Olga Makhlynets, my PI and mentor who has

welcomed me to work in her Laboratory and has introduced me to the various topics of research

conducted in her lab. I want to thank Dr. Areetha Renita D'Souza, my Post Doc mentor who has

guided me over the years and taught me most of what I know today about lab-etiquette and

research techniques. I also want to thank Mr. Sagar Bhattacharya and Ms. Jennifer Halim Yoon

who have introduced me into the wonders of the biochemistry laboratory when I first started, and

who have collaborated with and supported me throughout various projects. Furthermore, I

would like to thank Dr. Ivan Korendovych and the members of the Korendovych Lab, which

have also guided me throughout my time working in the Laboratory, for their constructive

feedback during lab meetings, and the summers we have spent together in the lab. Finally, I

would like to thank the Honors, Biology and Chemistry Departments for their support, and for

giving me the opportunity to put my research work together and present it in my Biochemistry

thesis.

1

Chapter 1: Introduction

Enzymes are biological protein catalysts defined by their ability to catalyze biochemical

reactions by accelerating the conversion of substrates into products in the active site of the

enzyme. Enzymes have many functional attributes and often evolve from a common ancestor-

sharing sequence and structure similarity. The Enzyme Commission (EC) of the Nomenclature

Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB),

initiated in 1956 by experts in the field, presented a framework for enzyme classification17.

According to the EC enzymes are classified into six different classes according to the type of

chemistry being carried out: 1) oxidoreductases which catalyze oxidation/reduction reactions, 2)

transferases, which transfer a chemical group, for example, a methyl or glycosyl moiety, 3)

hydrolases perform hydrolysis of chemical bonds, 4) lyases which also cleave chemical bonds by

other means than by oxidation or hydrolysis, 5) isomerases that catalyze geometric and structural

changes between isomers and 6), ligases which join two compounds with associated hydrolysis

of a nucleoside triphosphate molecule17. These EC classes are further divided into subclasses and

sub-subclasses in line with a variety of criteria such as the chemical bond cleaved or formed, the

reaction center, the transferred chemical group, and the cofactor used for catalysis. The final

level of classification defines substrate specificity1.

Enzyme evolution is crucial for the ability of organisms to adapt to the changing

environmental conditions and sustenance of their survival and reproduction. The ability to adapt

to chemical changes in the environment drives the gradual modification of enzyme function

through biological selective forces18. On the other hand, laboratory-guided protein evolution

exploits various techniques for the generation of protein variants and selection of desirable

functions. In the last decades, laboratory-directed protein evolution had a significant impact in

2

the chemical, pharmaceutical, and agricultural industries. Many times, enzymatic catalysts are

superior in many industrial processes because of their high selectivity and minimum energy

requirement6.

Directed enzyme evolution is attempting to address many shortcomings of biological

enzymes including the need for high availability at low cost, overcoming product inhibitions or

even design enzymes that are required for specific reactions that have yet to be identified6. In

order to accelerate directed protein evolution, scientists utilize various techniques for generation

of protein mutants and selection of desirable functions6. Protein engineering has grown

considerably with the development of new advanced recombinant DNA technologies and high-

throughput screening technologies6.

A group of enzymes that have been the target of directed evolution are cytochrome P450

enzymes. Cytochrome P450 enzymes is a very diverse set of heme-containing proteins, that

serve a broad spectrum of functions including catalyzing hydroxylation, N oxidation;

sulfoxidation; epoxidation; N, S, and O dealkylation; peroxidation; deamination; desulfuration;

and dehalogenation. In mammals, they catalyse reactions important in drug metabolism, blood

hemostasis, cholesterol biosynthesis, and steroidogenesis19. One example of directed enzyme

evolution of cytochrome P450 enzymes is the modification of the wild-type P450 BM-3, which

is specific for long-chain fatty acids20. Using X-ray crystallography, eight target amino acids

were identified and used for the creation of libraries by site-specific randomization mutagenesis.

Variants of each residue were screened by a spectroscopic assay using omega-p-

nitrophenoxycarboxylic acids as substrates20. Further analysis of the variants generated, led to

the identification of a variant able to efficiently hydroxylate indole, resulting in the formation of

indigo and indirubin20,21. The same variant was later found to be able to hydroxylate several

3

alkanes and alicyclic, aromatic, and heterocyclic compounds, all of which are non-natural

substrates for the wild-type enzyme 20.

Despite the decades of effort and the progress made in directed protein evolution,

designing efficient artificial enzymes remains a big challenge. Recently, Ehud Gazit and

colleagues showeed that supramolecular assemblies formed by a single amino acid residue in the

presence of zinc form incredibly efficient hydrolytic catalysts 22. Currently, all reported examples

of supramolecular catalysts inherently rely on very basic physico-chemical principles and

subunit structures. In general, enzymes rely on precise positioning of multiple amino acid

residues in space, aided by complex dynamics of substrate binding, product formation and

release to perform their functions23. The ability of successfully predicting the structures of

catalytically active assemblies and, subsequently, the necessary building blocks to achieve the

desired structures are of the ad most importance for further advancements in the field 23.

Using a rational design of protein evolution based on a thorough study of the structural

and mechanistic analysis, Makhlynets et al. modified a Due Ferri (DF) metalloenzyme to a single

metal ion-binding protein with zinc affinity that is higher than any other reported model

systems24. Metalloenzymes often utilize radicals in order to facilitate chemical reactions25.

DeGrado and coworkers discovered that model proteins can efficiently stabilize semiquinone

radical anion produced by oxidation of 3,5-di-tert-butylcatechol (DTBC) in the presence of two

zinc ions26,27. Makhlynets et al. showed that the number and the nature of metal ions have a

relatively minor effect on semiquinone stabilization and that a single metal ion can efficiently

stabilize semiquinone radical anion produced by oxidation of 3,5-di-tert-butylcatechol (DTBC)24.

They also demonstrated that hydrophobic sequestration, and interactions with the hydrophilic

residues in the protein interior are critical to create the right conditions for the catechol couple as

4

compared to bulk aqueous solution24. Makhlynets et al. created a modified single metal ion-

binding protein (4G-UFsc) with pM affinity for zinc that is higher than that of any other reported

model systems and comparable to many natural zinc-containing proteins using site-specific

mutagenesis to widen the channel that leads to the metal center and an in-depth structural

characterization of substrate interaction with the apo protein by NMR24.

Heme proteins are the most abundant and most widely used metalloporphyrins in nature.

They are divided in three main categories: 1) those which transport or store oxygen such as

hemoglobins and myoglobins, 2) those which have enzymatic activity such as cytochrome P450s

and 3) those involved in electron transfer as part of the electron transport chain. Natural heme

enzymes are involved in both reductive and oxidative chemistry28. Among those with oxidative

activity are oxygenases that use O2 to oxidize, usually oxygenate, substrates and peroxidases that

use H2O2 to oxidize substrates28.

Because of the diversity of functions of heme proteins and especially cytochrome P450s,

they have been the center of attention for protein engineering. With the development of better

analysis tools such as X-ray crystallography and NMR Spectroscopy, and molecular site specific

mutagenesis, a large number of new genetically encoded cytochrome P450 enzymes were

designed, many of which were adapted to catalyze unnatural reactions such as cyclopropanation,

N–H insertion, C–H amination, sulfimidation, and aziridination reactions, that no other natural

counterparts can2.

5

Figure 1. Natural reactions catalyzed by cytochrome P450s (blue) and new, non-natural reactions catalyzed by enzymes derived from cytochrome P450 by protein engineering and evolution (red). Adopted from Arnold FH. The nature of chemical innovation: new enzymes by evolution2.

The Kemp Elimination reaction is widely used by chemists as a model reaction for proton

transfer. The reaction involves a base-catalyzed ring opening of a benzisoxazole by cleaving a

N−O bond along with the deprotonation of carbon (C-3), producing o-cyano phenol

derivatives29. In the case where a carboxyl group exists on carbon-3, the corresponding reaction

is referred to as Kemp decarboxylation. This simple, one-step transformation without any

intermediate reaction, is highly sensitive to medium effects being over 108 times faster in an

aprotic dipolar solvent (e.g., CH3CN) than that in an aqueous solution29. Those characteristics

made the Kemp Elimination reaction a favorable model for studying many enzyme-catalyzed

proton transfer reactions, in which the carboxylate, amino, and imidazole group of amino acid

residues (histidine) on enzymes can function as general bases 30 (Figure 2).

6

Figure 2. The mechanism of both the Kemp elimination and Kemp decarboxylation. Adopted from Kemp Elimination. (2010). Comprehensive Organic Name Reactions and Reagents30.

In the first part of this study (Chapter 2), we used a rational design of protein

evolution guided by differences in HSQC NMR spectra of the Myoglobin protein in an

attempt to introduce novel Kemp eliminase activity to a non-enzymatic heme-containing

protein.

William F. DeGrado and his team used a computational and NMR guided minimalistic

approach to design a small (75-residue) de-novo Ca2+ dependent Kemp eliminase (AlleyCat for

ALLostEricallY Controlled cATalyst) by introducing a single mutation F92E in Calmodulin C-

terminus31. Calmodulin, a calcium-binding protein, was selected as the backbone because it had

no enzymatic activity and was small enough to facilitate NMR as well as crystallographic studies

and allow for ease in peptide synthesis or E. coli expression31.

One of the challenges of the study of cytochrome P450 protein is the ability to quantify

the amount of active P450 protein in a particular sample. Assays that measure P450 activity by

measurement of the oxidation of substrate drugs or other surrogate compounds are not practical

7

as they do not apply to all the P450 proteins32. Indirect P450 mRNA, or immunochemical

analysis of the samples may not be representative of the heme bound active protein levels33.

Guengerich et al. have recently described an assay of cytochrome P450 proteins based on the

spectral difference of reduced and carbon monoxide bound P450 proteins which is simple and

practical in routine research settings in the context of the stoichiometry of active P450 per unit

protein33.

Kemp elimination is usually catalyzed through an acid base mechanism, however, Reetz

et al. demonstrated the first example of redox catalyzed mechanism of kemp elimination reaction

using a heme containing protein, Cytochrome P450 34. Inspired by this discovery, we decided to

test our NMR guided approach to introduce this reaction mechanism to some protein which did

not previously perform this function. Cytochrome P450 however is a large protein with over 470

amino acid residues making it difficult to characterize by NMR. We selected myoglobin, as it is

a well-studied, small (156 amino acid residues) monomeric hemeprotein with no enzymatic

activity. Myoglobin is an excellent scaffold for NMR studies due to its small size, well-folded

structure and easy purification.

In the second part of this study (Chapter 3), we attempted to use a rational design

approach to make a novel buffalo cathelicidin-based antimicrobial peptide with proteolytic

resistance and solvent-independent emission properties.

Cathelicidins are an ancient class of small, cationic, antimicrobial peptides (AMPs).

These peptides are part of the innate immune system of many vertebrates. A series of new

homologs of cathelicidin4 (CATHL4), which were structurally diverse in their antimicrobial

domain, was identified in buffalo. AMPs of newly identified buffalo CATHL4s (buCATHL4s)

8

displayed potent antimicrobial activity against selected Gram positive (G+) and Gram negative

(G-) bacteria16. The peptides took the form of different secondary structure conformations in

aqueous and membrane-mimicking environments. Simulation studies suggested that the

amphipathic design of buCATHL4 allowed water permeation following membrane disruption.

Biswajit Brahma’s et al. study suggests short buffalo cathelicidin peptides with potent

bactericidal properties and low cytotoxicity have potential translational applications for the

development of novel antibiotics and antimicrobial peptidomimetics16.

Most peptides with natural amino acid sequences are readily degraded by proteolytic

enzymes. A challenge with the use of AMPs as antimicrobial therapeutics in the context of

chronic wounds or eye infections is their susceptibility to proteolytic degradation35. Tryptophan

substitution reduce, through amidation and acetylation, the proteolytic susceptibility of Catenin

derived peptides while also improving antimicrobial performance35. Similarly, the susceptibility

of AMPs to proteolytic degradation as they pass through the gastrointestinal path hinder the

possible use of AMPs in orally administered therapeutic applications35.

Fluorescence spectroscopy is an important tool in the study of proteins and their

interactions with their local environment. Emission characteristics of a protein depends on its

amino acid content and to a great extent on Tryptophan’s (Trp) ability to be excited separately

from all other amino acids36. The fact that Trp emission is highly dependent on solvent exposure

and is influenced by its interactions with neighboring amino acid side chains, complicates the use

of fluorescence spectroscopy in certain experimental settings. Experimental condition shifts due

to solvent changes or peptide interactions can disturb the spectral properties of the protein under

investigation15. It was recently demonstrated that the replacement of Tryptophan with β-(1-

azulenyl)-L-alanine can overcome the solvent sensitivity of spectral emission and introduce a

9

more favorable spectral properties (stable excitation at 342 nm) while retaining the native

protein’s characteristics36.

10

Chapter 2: Rational Design of a Myoglobin Based Enzyme

Replicating Reetz et al. CYT-P450-BM3 data34:

E. coli BL21(DE3) cells were transformed with the plasmids prsfDuet-1 (Novagen)

containing CYT-P450-BM3 and P450-BM3 A82F variant genes. CYT-P450-BM3 and P450-

BM3 A82F variant were produced and purified for biochemical characterization (Figure 3).

Figure 3. SDS (10%) page analysis indicating successful expression of protein expected at 120kDa. SDS page analysis of CYT-P450-BM3 purification using imidazole gradient: Lane 1: marker, 2: after induction, 3: load,4: flow through, 5: 25mM wash (100ml), 6: 50mM wash (100ml), 7-10: 100mM imidazole fractions, 11-14: 250mM imidazole fractions. (Left) SDS page analysis of CYT-P450-BM3 purification using imidazole gradient: 1: marker, 2: after induction, 3: after sonication, supernatant, 4: after sonication pellet, 5: flow-through, 6: wash-50mM imidazole, 7: A82F-250mM imidazole (right). Samples with persistent impurities were further purified through a Q-Sepharose column using FPLC.

To determine the concentration of each protein, carbon monoxide difference spectrum

was performed. Only the reduced ferrous form of the hemeprotein reacted with carbon monoxide

(CO) to form a complex that specifically produces a spectrum with a wavelength maximum at

450 nm. This would serve as an accurate way to establish the amount of functional P450 protein

for kinetic assays.

The reduced state will have a greater absorbance at 450 nm whereas the oxidized state

that will not bind to CO will have greater absorbance at 420 nm evident in both protein in Figure

11

4. Absorbances between 400 nm and 490 nm of the reduced and oxidized proteins were

subtracted and a ferrous CO versus ferrous difference spectrum diagram is prepared (Figure 5).

Figure 4. UV-Vis spectroscopy of CYT-P450-BM3 (right) and P450-BM3 A82F (left) in 50 mM potassium phosphate solution at pH 8.0 (Buffer), oxidized protein with buffer (A82F or P450-BM3 ox), oxidized protein with CO (A82F_CO or P450-BM ox_CO), and reduced protein in buffer with CO (A82F_CO_reduced or P4500BM3 red_CO). 1/10 diluted protein sample used in anaerobic cuvettes, bubbled CO using balloon attached to a syringe and needle, syringe was rinsed with 20mM sodium dithionite (freshly prepared), syringe was used to mix protein with reducing agent.

By subtracting the differences in absorbance at 490 nm of the ferrous CO and ferrous

proteins (ΔA490) from the differences between the two at 450 nm (ΔA450) and divide the answer

by 0.091 nmol/ml (extinction coefficient) the concentrations of each protein were estimated33.

Alternatively, using the ferrous CO versus ferrous difference spectrum (Figure 5), the amplitude

of the positive peak at 450 nm can be used and divided by 0.091nmol/ml to calculate the

concentration of each protein33.

12

Figure 5. Ferrous · CO versus ferrous difference spectrum used for the quantitation of active CYT-P450-BM3 (right) and P450-BM3 A82F (left) concentrations.

In their paper, Reetz et al. had established that CYT-P450-BM3 undergoes Kemp

elimination and then attempted to reshape the large substrate binding pocket of P450-BM3 to

better match the small size of the substrate34. Since the A82F mutation in P450-BM3 was

previously shown to greatly enhance the enzyme’s binding affinity for small molecules, they

decided to introduce the mutation into WT P450-BM3 which showed 129-fold improvement in

the catalytic efficiency (kcat/Km)34. We also found an increase in catalytic efficiency (Figure 6),

a tenfold improvement, which is lower but a significant one non-the-less. The inconsistency

could be due to their WT kinetic values being estimated due to having difficulty in solubilizing

the substrate for that reaction.

13

Table 1. Summary of kinetic parameters for P450 and variant catalyzing Kemp elimination generated by our laboratory and by Reetz et al. (25o C, 50 mM sodium phosphate buffer pH 8.0, 100 mM NaCl, 0.25 mM NADPH, 100 nM or 300 nM purified enzyme, 5% acetonitrile, pH 7.0)34.

Protein kcat (s-1) KM (mM) kcat/KM (M-1s-1)

P450-BM3 WT 0.48 ± 0.08 0.124 ± 0.05 3871

P450-BM3 WT,

Reetz et al. >1.5 >6 240 ± 60

P450-BM3 A82F 7.16 ± 2.02 0.255 ± 0.12 38990

P450-BM3 A82F,

Reetz et al. 8.4 ± 0.4 0.27± 0.03 31,000 ± 1,500

Figure 6. Kemp elimination of P450-BM3 A82F vs P450-BM3 WT.

14

Wildtype Myoglobin Expression and Purification:

Wild-type (WT) myoglobin (mb) cloned into pEXP5-NT/TOPO expression vector, was

expressed in BL21 (DE3) E. coli cells and purified using a nickel affinity column. The

polyhistidine-tag was expressed attached to the protein as it is used to purify the protein from the

bacteria lysate by affinity chromatography due to the histidine’s imidazole ring selectively

binding to the Nickel column. Although, according to literature this method could be used for

the purification of Myoglobin, after several attempts, it was found that the his-tag tagged

Myoglobin protein was difficult to elute from the column. It was speculated that the twelve

surface histidine residues in Myoglobin’s structure (Figure 7) might be sufficient, without a

polyhistidine-tag, for the protein to attach to the nickel affinity column. Therefore, the WT-mb

gene was cloned into a pET-28a(+) vector (without a his-tag) and competent BL21 E. coli cells

were used for transformation and expression of the protein.

Figure 7. Myoglobin with twelve surface histidines (blue) can bind to the nickel column without any His6-tag requirement. (PDB ID: 1MBN)

15

Myoglobin H64V Mutagenesis

The first mutation introduced to WT-mb was a valine substitution at position 64 (Figure

8). His64 is a distal histidine that helps myoglobin stabilize bound oxygen molecules. Thus, in

order to inhibit mb from performing its current activity –storing oxygen by binding it to heme-

we wanted to free up the heme containing site. Furthermore, valine being a smaller, hydrophobic

residue was selected to provide easier access of the substrate to the heme binding site.

Figure 8. Myoglobin H64V in pET28a (+) Colony screen. 1%agarose, 150V, TaqPCR protocol, Lane (1): 200 bp O’range Ruler DNA marker. Lane (2)-(16): Colonies mixed with GoTaQ-Green Master Mix. Colonies in lanes (6)-(16) show successful expression of H64V-mb gene. Colony represented in Lane (14) was selected for transformation.

Upon protein purification of the WT-mb and H64V mutant UV Vis absorbance was used

to measure concentrations. The spectrum of reduced Mb has prominent peaks (Q bands) in the

visible range at about 540 and 580 nm, and its Soret band is at 417 nm with ε417 = 128,000 M−1

cm−1 37. It was observed however that the heme iron was oxidized from Fe(II) to Fe(III) from

the sharp soret band at 409 nm, Q bands at 504 and 535 nm, and a CT1 band at 634 nm,

characteristic of a six-coordinated high-spin heme with a histidine residue (His-93) and a water

molecule bound at the fifth and the sixth coordination position of the iron atom, respectively37.

For the redox mediated kemp elimination Fe (II) iron is required. To reverse iron oxidation and

reduce it back to Fe (II), dithionite was used as a reducing agent as indicated by the red shifts of

16

the soret band from 409 nm 417 nm (Figure 9). Even though 3 equivalence of dithionite was

sufficient to completely reduce WT-mb, H64V proved to be very easily self-oxidized upon

exiting the glove box thus ascorbic acid was used as a co-reducing agent to stabilize it during the

progression of Kemp elimination assay. Kemp elimination failed to show any significant

catalytic activity in either the WT-mb (Kcat/KM of 13 M-1s-1 ) or the H64 mutant (kcat/KM of 18 M-

1s-1 ) (Table 2).

Figure 9. UV-Vis analyses of oxidized (red circles) and reduced (blue squares) forms of WT myoglobin (left). UV-Vis analyses of oxidized (red circles) and reduced (blue squares) forms of Mb-H64V variant (right). Myoglobin H64V/V68A Mutagenesis:

Without serving any significant catalytic activity in either WT or H64V mb, a second

mutation was introduced by SOE PCR at position 68 changing the wild type valine into an

alanine. Egeberg et al. (1990) proposed that the naturally occurring Val residue indirectly

stabilizes bound O2 by orienting the ligand for more efficient hydrogen bonding to His6438.

Steric considerations indicate that this residue itself actually hinders oxygen binding by

restricting the rotational freedom of the bound O2 and distorting the Fe-O-O bonds38. The latter

17

effects serve to explain why the V68A substitution would further increase the size of the binding

pocket allowing for easier access of the substrate. The V68A was introduced at to the H64V

mutant creating a H64V/V68A Double mutant Myoglobin.

Kemp Elimination of Myoglobin H64V vs H64V/V68A:

Upon successful purification and reduction of the H64V/V68A double mutant by

dithionite, a Kemp elimination assay was performed as described in the materials and methods.

Preliminary results demonstrated an improvement in increased Kemp elimination rate of the

double mutant compared to the H64V mutant and the V68A mutant (Figure 10).

Figure 10. Kemp elimination of Myoglobin H64V vs H64V/V68A. HSQC NMR titration of H64V/V68A:

HSQC NMR titration was performed using 1H-15N double-labeled H64V/V68A-mb

protein expressed in BL21 (DE3) E. coli cells. Comparison between the free and bound state (to

a non-catalyzable substrate analog of Kemp) showed some shifts in residue peaks, indicating

18

possible interaction between the substrate and some residues. After assignment of the amino

acid residues, it was observed that the residues with greatest chemical shifts were T95 and K96

(Figure 11).

Figure 11. HSQC NMR titration of Myoglobin H64V variant (reduced form) in absence of substrate analog (blue) and Myoglobin in presence of two equivalents of analog (red). (left) T95 and K96 residues presented the greatest shifts (right).

After further investigation of the 3D structure of the protein, it was found that the T95

and K96 residues were situated around the outside of the heme binding pocket (Figure 12). This

displays the incompatibility of the heme binding site with the Kemp substrate supporting the low

Kemp elimination results.

19

Figure 12. Residues (T95 and K96) with the greatest shifts from NMR titration (red) shown in sticks (right) are located on the outside of the binding pocked as shown on the surface representation (blue) of Myoglobin (left) (PDB ID: 1MBN). Myoglobin T95 and K96 Random Mutagenesis:

Using the H64V/V68A double mutated Myoglobin plasmid as template, the codons of the

T95 and K96 residues were randomized using an NNK library, to investigate if a different

residue at that position could provide a substrate interaction that would improve the proteins

ability for Kemp elimination.

Bacterial colonies generated from the NNK library were picked to perform a crude

extract screening to test the speed of the production of Kemp catalysis product. The crude

screening of the T95 NNK library indicated two colonies which demonstrated a significantly

greater Kemp elimination activity compared to the H64V/ V68A controls (Figure 13). On the

contrary none of the K96 showed any significant activity increase.

After sequencing, both T95 NNK library “hits,” they turned out to both be valine mutants

at the 95th position. Thus, the triple mutant H64V/V68A/T95V protein was then expressed and

purified, reduced and tested for a Kemp elimination assay. It was found that the triple mutant

had a ten-fold increase in activity compared to the H64V/V68A double mutant (Table 2).

20

Figure 13. Representative sequencing results of the NNK libraries of Myoglobin, showing the randomization of the codons (black:G, Blue:C, Red:C, Green:A) for the selected residues (right). T95NNK library crude lysate screening: Column 1: Blank, 11 (A,B,C,D): Sacrificed, 2 (A,B,C,D): H64V/V68A (control), Rest: T95NNK Clones (left). Table 2. Kinetic parameters of the Myoglobin variants (Kcat, KM and kcat/KM values are reported at pH 7.0).

Mb-Variants WT H64V H64V/V68A H64V/V68A/T95V

kcat/KM, M-1s-1 (pH 7.0) 13 18 199 2660

Mb-Variants kcat (s-1) KM (M) kcat/KM (M-1s-1)

H64V/V68A 0.394 0.00198 199 H64V/V68A/T95V 1.011 0.00038 2660

Conclusions:

Firstly, through generating comparable Kemp assay data for CYT-P450-BM3 and P450-

BM3 A82F, we were able to replicate and confirm Reetz et al.’s findings34 that heme containing

proteins can undergo directed evolution towards improved Kemp catalytic activity. Furthermore,

in our paper we present the first ever report on Kemp eliminase activity of myoglobin, and the

second example of redox-mediated Kemp eliminase. Furthermore, we have shown how NMR

successfully predicted T95 as an important residue for directed evolution, a residue that is found

outside the binding pocket and could not have been otherwise predicted by any other method. By

21

evolving the identified residue and producing the T95V containing triple mutant we have showed

more than ten-fold improvement in catalysis (Figure 14), a clear display of the capabilities of our

novel NMR-guidance method as a simple, logical and powerful strategy for Directed Evolution.

Figure 14. Kemp elimination catalyzed by Myoglobin H64V/V68A (red) and H64V/V68A/T95V (blue) variants. Conditions: 20 mM HEPES; pH 7.0; 0.25 μM protein.

22

Chapter 3: Azulenyl-Alanine Modified Antimicrobial Peptide

Reasoning for the chosen sequence:

Based on consensus determined after phylogenetic analysis of the conserved CATHL4

AMPs sequence (Figure 1) the peptide sequence A-I-P-W-I-W-I-W-R-L-L-R-K-G (AG14) was

selected (in collaboration with Gregory A. Caputo and his group) for the basis of the

development of a potentially novel antimicrobial therapeutic agent (Figure 15).

Figure 15: Phylogenetic relationship and consensus of amino acid residues of the 12 CATHL4 AMPs. The Neighbor-joining tree construction was based on complete nucleotide sequences of the CATHL4 variants (NCBI Accession ID: KJ173930—KJ173976). The compiled most conserved amino acid sequence reads as: AIPWIL(/W)IWW(/R)LLF(/R)KG.

Most peptide with natural amino acid sequences are readily degraded by proteolytic

enzymes. The susceptibility of peptide-based materials to proteolytic degradation as they pass

through the gastrointestinal path are a challenge for therapeutic applications. Thus, we will be

investigating the introduction of artificial amino acids in order to reduce the susceptibility of the

potential therapeutic peptide to trypsin proteolytic degradation without compromising its

structure and therefore without its function being altered.

AzulenylAlanine substitution of tryptophan-containing peptides:

The tryptophan (Trp) residues in the initial sequence of the peptide AG14 to

accommodate a tryptophan mimic: AzulenylAlanine (AzAla, Z) (Figure 16). Substitution of Trp

to AzAla has been shown to have a minimal effect on properties of peptides. Furthermore,

23

AzAla also has a rich absorption and fluorescence spectra (340nm) with bands distinctly

different from those of tryptophan (280 nm) useful for monitoring protein interactions.

Figure 16. Structures of Trp and AzAla.

Three different AG14 variants, AG14W4Z, AG14W6Z and AG14W8Z (in which in the

fourth, sixth and eighth position respectively tryptophan was substituted with AzAla) were

synthesized as per the materials and methods (Figure 17).

Figure 17. Primary structures of AG14 peptide and its Az-Ala variants.

In order to check if there is a change in the protease susceptibility of the peptide before

and after the introduction of AzAla enzyme digestion experiments were performed using HPLC

(High Performance Liquid Chromatography) and MALDI-TOF (Matrix-assisted laser

desorption/ionization - time-of-flight mass spectrometer) to closely monitor the rate digestion of

each (Figure 18).

A-I-P-W-I-W-I-W-R-L-L-R-K-G (AG14) A-I-P-Z-I-W-I-W-R-L-L-R-K-G (AG14W4Z) A-I-P-W-I-Z-I-W-R-L-L-R-K-G (AG14W6Z) A-I-P-W-I-W-I-Z-R-L-L-R-K-G (AG14W8Z)

24

Figure 18. Overlay of chromatograms acquired at various time points after peptide and trypsin were mixed. The inset graph shows the percentage of undigested peptide peak area monitored over time. Identity of peaks was established by MALDI-TOF using the sample that was digested for 4 hours (top). MALDI-TOF analysis of trypsin digest product at retention time of 8.1 min for AG14 collected after 4 hours. The peak at 1237 Da corresponds to AIPWIWIWR peptide segment (grey). MALDI-TOF analysis of the trypsin digest product at retention time of 8.4 min collected for AG14 after 4 hours. The peak at 1801.6 Da corresponds to the undigested peptide(pink). MALDI-TOF analysis of the trypsin digest product at retention time of 8.7 min for AG14 collected after 4 hours. The peak at 1617.9 Da corresponds to AIPWIWIWRLLR peptide segment (blue). Table 3. MALDI-TOF signal and expected mass of digested peptide sequences.

Peptide sequence Position of the peak in

the chromatogram

MALDI-TOF

signal, Da

Expected

mass, Da

AIPWIWIWR 1 1237 1240

AIPWIWIWRLLRKG* 2 1801 1806

AIPWIWIWRLLR 3 1618 1622 * amide at C-term

25

Trypsin is an endopeptidase the carboxyl side (or "C-terminal side") of the amino acids

lysine and arginine except when either is bound to a C terminal proline. The aspartate residue

(Asp 189) located in the catalytic pocket (S1) of trypsin is responsible for attracting and

stabilizing positively charged lysine and/or arginine, and is, thus, responsible for the specificity

of the enzyme.

AG14 and AzAla variants were incubated with trypsin and samples were taken at regular

time points and identified by HPLC and MALDI. The mass spectrometry results suggest that the

peptide (AG14) was cleaved between R9 and L10 (AIPWIWIWR- 1244Da, LLRKG 587 Da)

and between R12 and K13 (AIPWIWIWRKKR- 1628 Da). Trypsin digestion of the AzAla

variants suggests that the Z substitution served as a way to reduce the proteolytic susceptibility

of AG14 as shown by AG14 (Figure 18). The greatest decrease in susceptibility was observed in

AG14W8Z where the location of the unnatural amino acid is closest to the expected sites of

cleavage (Figure 19).

Figure 19. Absorbance of AG14 and AzAla variants monitored over time on the analytical HPLC in the presence the lower decrease of the integrated HPLC of trypsin (0.1 µg) for 2.5 hours, integrated for the peptides at peptide peaks over 2.5 hours compared to Abs 220 nm.

26

In order to test whether the structure of AG14 was retained by the modified peptides as

well, which could play an important role in their potential antimicrobial properties, Circular

Dichroism (CD) spectroscopy experiment was performed. Briefly, CD is defined as the unequal

absorption of left-handed and right-handed circularly polarized light. Based on the polarization

pattern observed we can determine information regarding the secondary structure of the peptide.

Figure 20. CD Spectra of AG14 and AzAla variants in 5mM phosphate, 10mM NaCl pH 7.0 (left). CD Spectra of AG14 and AzAla variants in POPC vesicles (250uM) (right). The pathlength was 1cm for both.

Circular Dichroism (CD) spectroscopy of AG14 and its AzAla variants was performed in

aqueous conditions as well as within POPC vesicles. The CD spectra showed the replacement of

W with Z at the aforementioned positions did not alter the original structure of AG14, and the

peptides maintained the same structure they had in the aqueous buffer, within the vesicles as

well. Furthermore, the absorption patterns of the peptides: negative bands at 222 nm and 208 nm

and a positive band at 193 nm, are characteristic of the expected alpha helical structure (Figure

20).

27

Figure 21. AzAla: Fluorescent spectra of excitation wavelength 342 nm and emission recorded over the range of 355 nm − 455 nm (left). Tryptophan: Fluorescent spectra of excitation wavelength 280 nm and emission recorded over the range of 300-400 nm (right).

Going from Z4 to Z6 and Z8 we observe a red shift in the peak of Trp’s spectral

maximum emissions. This is consistent with changing the microenvironment of Trp towards

more polar conditions. Based on this observation (Figure 21) we can postulate the possibility that

Trp’s in Z4 are found more buried and inside the peptides’ conformation and being somewhat

isolated from the hydrophilic solvent. Conversely, the AzAla spectral fluorescence indicate

possible quenching of signal emissions from the AzAla amino acid of Z4 as indicated by the

lowest peak (Figure 21). This supports that the AzAla amino acid of Z4 may be found on the

outer side of the peptide exposed by possible surrounding quenchers. This speculation is in

accordance with the earlier one giving us possible insight to the folding of the peptide.

Conclusions:

Introduction of AzAla in the place of Trp has decreased the peptide’s susceptibility to

trypsin digestion with the greatest effect observed in AG14W8Z where the location of the

unnatural amino acid is closest to the expected sites of cleavage. Through CD analysis, we have

28

observed that the replacement of Trp by AzAla did not cause change in the peptide structure

compared with the original AG14, nor in hydrophilic (5mM phosphate), neither in hydrophobic

(POPC vesicles) environments, thus it is expected that the antimicrobial function of the peptide

will also remain intact.

29

Chapter 4: Material and Methods (adopted from the Makhlynets Lab)

Cloning and mutagenesis:

WT Myoglobin gene (cloned into pET22b(+) vector from Novagen) was a generous gift

from the Fasan lab (University of Rochester). All myoglobin mutants reported here were cloned

into pET28a vector using NcoI and XhoI restriction enzymes. pET28a contains both N-terminal

and C-terminal His6-tag. However, mutant genes were cloned into that expression vector without

any His6-tag since the gene with twelve histidine residues was found to bind to Ni-NTA column

itself without any requirement of His6-tag. Saturation mutagenesis to generate all possible

mutants at a specific position (NNK libraries) was done using megaprimer protocol with Phusion

DNA polymerase (New England Biolabs).

Megaprimer protocol is based on two-step PCR. First PCR with T7 forward or T7 reverse

and mutagenic primer combination (as appropriate) generates the megaprimer which comprises

the desired NNK library. Temperature gradient is decided based on the melting temperatures of

the primers used. Generally, annealing at a temperature 5ºC above the lower Tm primer for 30 s

works very well. Extension is performed at 72ºC for 60 s. Once the megaprimer is generated

successfully, it can be used directly for the second PCR without any purification step. Annealing

is performed with temperature gradient from 75ºC to 65ºC for 30 s. Extension time generally

varies from 5 min to 7 min at 72ºC. After the PCR reaction, the template was digested with

restriction enzyme Dpn-I (1 L per 25 μL reaction, incubation for 6-7 h at 37ºC) to eliminate

parental DNA and then transformed into E. coli commercial C2987H cell (NEB5). Sequences of

the mutated genes were confirmed by Sanger sequencing (Genewiz, Inc.).

Site-directed mutagenesis to generate a specific mutant at a specific site was performed

by using SOE PCR protocol instead of megaprimer PCR. The second step of megaprimer PCR

30

did not work efficiently for Myoglobin (DNA template size: ~6000 bp). SOE PCR is also a two-

step PCR (like megaprimer PCR already discussed above). In this protocol, first PCR generates

two fragments, which comprise the mutation at desired position. Annealing temperature is

decided based on the melting temperatures of the primer pair and following GoTaq polymerase

protocol. Generally, annealing at 60ºC for 30 s works well for the first step. Extension is

performed at 72ºC for 45 s. Once the mutant fragments are designed successfully, they act as

templates for the second PCR, where the fragments are mixed well in the same PCR tube.

Annealing is performed for 30 s with step-gradient from 58°C to 63°C with 1°C increment of

temperature. Rest of the conditions for extension remain the same as for the first PCR. Purified

PCR products are directly used for cloning into pET28a vector using NcoI and XhoI restriction

enzymes and cloning mixture is transformed into E. coli commercial C2987H cell (NEB5α).

Colony screening is done with at least ten colonies to find positive hits. Sanger sequencing

(Genewiz, Inc.) confirmed sequences of the mutated genes.

Library screening:

Individual clones obtained after transformation of the NNK libraries into the BL21

(DE3) pLysS cells were inoculated into 200 μL of Luria Bertani (LB) supplemented with 50

μg/mL of kanamycin and 34 μg/mL of chloramphenicol in 96-well plates and grown for 6-7

hours at 37°C with shaking at 230 rpm. Aliquots of 20 μL of the resulting cultures were added to

400 μL of the 1X LB medium (supplemented with 50 μg/mL of kanamycin, 34 μg/mL of

chrolamphenicol) in deep well plates. 0.3 mM of δ-aminolevulinic acid was added as heme

precursor and overexpression was induced by adding 0.25 mM IPTG (isopropyl-β-D-1-

thiogalactopyranoside) when OD600 of cultures reached ~0.8. The cultures were grown at 25ºC

for 20 h and centrifuged at 2,000 g for 15 min; the pellets were lysed with a buffer containing 20

31

mM HEPES, pH 7.0, 0.5% triton X and centrifuged again for 15 min to clarify the lysates. The

activities of the crude lysates were tested with Kemp (0.4 mM) in 20 mM HEPES, pH 7.0 buffer

containing 1 mM of ascorbate, 1 μM of SOD and 20 nM of catalase maintaining reducing

condition. Absorbance of the product was monitored at 380 nm. The plasmids for the most active

clones were extracted and re-transformed into BL21 pLysS. The positive hits were confirmed in

triplicate in confirmation screening under the same conditions as described above. The plasmids

for the clones with higher activity were extracted and sequenced using T7 or T7 term primers (as

appropriate).

Protein expression:

A plasmid encoding a gene with the desired protein sequence was transformed into E.

coli BL21 (DE3) cells and grown overnight at 37°C on an agar plate containing kanamycin (50

μg/mL). Growth media described below was also supplemented with kanamycin. The next day, a

single colony from a fresh agar plate was grown in 50 mL Luria Bertani (LB) medium overnight.

The next morning 10 mL of the overnight culture was diluted with 1 L of 1X LB media and

incubated at 37°C until OD600 reached 0.8. Then the culture was cooled down to room

temperature on ice and δ-aminolevulinic acid (0.3 mM) was added as heme precursor. After 15

min, IPTG (isopropyl-β-D-1-thiogalactopyranoside) was added to a final concentration of 0.25

mM for induction. After incubation at 25ºC for 20 h, the cells were harvested by centrifugation

(4,000 g for 30 min). The typical yield of wet cell paste was ~5.0 g per 1 L of culture. The cell

paste was flash frozen in liquid nitrogen and preserved at -80°C until further use.

Protein purification:

Cells were resuspended in buffer containing 25 mM TRIS (pH 8.0) on ice with a protease

inhibitor phenylmethylsulfonyl fluoride (PMSF) (0.5 mM final concentration) added. Cells were

32

lysed by sonication on ice for 10 min (20 s pulse, 20 s rest). The crude cell lysate was

centrifuged at 20,000 g for 30 min and the lysate was loaded onto Ni-NTA column (2 mL,

Clontech) pre-equilibrated with resuspension buffer and the resin was then washed with 50 mL

of the same buffer. The protein was eluted with 25 mM TRIS (pH 8.0) buffer with gradient

addition of imidazole from 20 mM to 250 mM. Fractions containing the protein were identified

by the UV-Vis analysis, combined and exchanged into a buffer containing 20 mM HEPES (pH

7.0) using a desalting column (BioRad, Econo-Pac 10G). Protein samples were concentrated

down to 500-700 µM using 5 MWCO spin filter (CORNING>>431482).

The reduction of protein samples was performed by bringing the degassed, pure protein

samples into the glovebox (MBRAUN) and addition of five equivalents of freshly prepared

dithionite solution under anaerobic condition. Protein was degassed using a Schlenk line and

three one-minute cycles.

For standardization of dithionite, 20-30 mg of solid dithionite was brought into the glovebox.

Next, 1 mL of degassed milliQ water was added to that. Following the same way, potassium

ferricyanide solution was prepared. Dithionite stock was diluted 10-fold with milliQ water. Next,

two solutions were prepared in the following way:

(a) 990 μL water + 10 μL potassium ferricyanide

(b) 980 μL water + 10 μL potassium ferricyanide + 10 μL 1/10 sodium dithionite

Absorbances of both the solutions were measured at ε= 420 nm using diode array instrument.

Since, the extinction coefficient of potassium ferricyanide is ε420 = 1020 M-1cm-1, ΔA420/1020

gives the concentration of reduced iron. From this information, the reducing equivalence of 1/10

dithionite solution was calculated.

33

Kinetic assays of Kemp elimination:

Measurement of enzymatic activities of all the Myoglobin variants discussed here, were

performed at 22°C in a BioTek Eon3 plate reader monitoring absorbance of the product at 380

nm using 96-well plates. The molar extinction coefficient for the product 2-hydroxybenzonitrile

at 380 nm (15,800 M-1cm-1) was taken from the literature. Eight different concentrations of the

Kemp substrate between 50 and 1000 μM were used in these assays while maintaining a constant

2% concentration of acetonitrile. The reaction was monitored in triplicate for 900 s with pure,

reduced protein in 200 μL of buffer (20 mM HEPES, pH 7.0). To maintain reducing condition,

ascorbate (1 mM), SOD (1 µM) and catalase (10 nM) were added to the buffer before the

dilution of reduced protein to the desired concentration. Since, this reducing buffer is stable

enough in aerobic condition at least for 1 h, ascorbate, SOD and catalase are added immediately

before the assay experiment. Next, a 50 μL portion of reduced protein solution in buffer was

added first to each of wells of the 96-well plate and subsequently, 150 μL of substrate solution

was added. The obtained kinetic traces were analyzed using the Michaelis-Menten kinetic

equation {v0=kcat[E]0[S]0/(KM+[S]0)} to obtain kcat and KM values. Individual kcat and KM

parameters could not be obtained for some variants as KM values were exceedingly high. In those

cases, the data points were fit to a linear regime of the Michaelis-Menten model using the

equation {v0=kcat[E]0[S]0/(KM)}.

Expression and purification of isotopically labelled protein:

Transformation was done as described in the “protein expression” section. Overnight

culture (10 mL) was used to inoculate 2L of 1X Terrific Broth (TB) media containing the

antibiotics and incubated at 37°C until OD600 reached 0.8. Then the cells were harvested by

centrifugation (4,000 g for 30 min) at room temperature and washed with unlabelled M9 minimal

34

medium (30 mL).The cell pellet was then resuspended in M9 medium (1 L) containing 15NH4Cl

(1 g) as a nitrogen source and 13C-labelled glucose (2.5 g) as the carbon source. The culture was

incubated at 37ºC for 3 hours to allow for recovery of growth. δ-aminolevulinic acid (0.3 mM)

was added as heme precursor and after 15 mins protein expression was induced by addition of

0.25 mM IPTG and the culture was further incubated at 25ºC for 20 h. Cells were harvested by

centrifugation at 4˚C, 4,000 rpm for 30 min with typical yield of 2 g of wet cell pellet per 1 L of

culture. Pellets were flash frozen in liquid nitrogen and preserved at -80ºC until needed.

Purification of isotopically labelled protein was done as described under “Protein purification”

section.

NMR experiments:

All NMR experiments were carried out at 25°C on a Bruker AVANCE III HD 800 MHz,

equipped with a Triple Resonance Inverse (TCI) Detection CryoProbe.

Spectral data were acquired and processed using Topspin 3.0 (Bruker), NMRPipe and

analysed using Sparky 3.113 and CCPN. For reduced myoglobin H64V (850 μM), backbone

resonance assignments were obtained using a series of three-dimensional NMR experiments:

HNCACB, HN(CO)CACB, HNCO and HN(CA)CO. Chemical shifts were directly/indirectly

referenced to DSS (4,4-dimethyl-4-silapentane-1-sulfonic acid).

Interaction studies of Myoglobin H64V (350 µM) were performed by acquiring 15N-1H

HSQC spectra with either Kemp substrate/inhibitor at 1:0, 1:0.5, 1:1 and 1:2 stoichiometric

ratios. Both Kemp substrate (5-nitrobenzisoxazole) and inhibitor (5-nitrobenzotriazole) solutions

were prepared by dissolving solid substrates in 100% acetonitrile.

Trypsin digestion:

35

Pure lyophilized AG14 peptides were dissolved in MilliQ water and syringe filtered (0.2-

micron, 6500 rpm 10 mins) prior to checking concentration. The concentration of AG14 peptide

was determined by measuring absorbance at 280 nm on an UV-Vis spectrophotometer using

ɛ280= 16,500 M-1cm-1. The concentrations of AzAla variants were determined by measuring

absorbance at 342 nm on an UV-Vis spectrophotometer using ɛ342= 4,212 M-1cm-1. The peptide

stocks of 2mM concentration were prepared in buffer (50 mM sodium phosphate, 100mM NaCl,

pH 7.0). Trypsin (1 mg/ml, Ameresco) stock was prepared fresh in buffer and serial dilutions

were done: 0.1 mg/ml, 0.01 mg/ml, 0.001 mg/ml for the assay. The reaction samples (500 µL)

were prepared in triplicate by mixing AG14 (500 µM final concentration), trypsin (50 µL of

0.001 mg/ml solution) in buffer (50 mM sodium phosphate, 100mM NaCl, pH 7.0). The trypsin

digest was monitored on the HPLC every 15 min at room temperature by following the peak of

undigested peptide. Identity of various peaks in HPLC chromatogram were identified by

MALDI-TOF. For this, fractions containing peptides corresponding to different peaks on HPLC

were collected, lyophilised and re-dissolved in 10 µL of solvent B; 10 µL of solvent A, and 2 µL

of CHCA matrix was added (1:10 proportion) and the mixture was loaded onto the MALDI

target.

Preparation of Vesicles:

Solid POPC (12.5 mg, Avanti Polar Lipids) was dissolved in chloroform (0.5 mL) to

make a lipid stock (16.5 mM). This stock (303 µL) was pipetted into a glass vial and dried with

nitrogen gas and then under a vacuum for 1 hr. The resulting film was resuspended with PBS

buffer (5 mM sodium phosphate, 10 mM NaCl, pH 7.0) containing peptide (final concentration -

2 µM).

36

Circular dichroism spectroscopy:

The CD spectra were acquired on the Jasco J-715 CD spectrometer collecting 64 scans (4

s averaging time) for each spectrum and using a quartz cuvette with a 1 cm path length. The

measurements were performed on samples containing peptides (10 µM) in buffer (5 mM

phosphate,10 mM NaCl, pH 7.0) in the presence and in the absence of vesicles (250 µM of 100%

POPC). Care was taken that the sample absorbance never exceeded 1.5 at all wavelengths to

produce reliable ellipticity values. Mean residue ellipticity (MRE, deg*cm2*dmol-1) values were

calculated using the following equation, where q is ellipticity (mdeg), l is pathlength (cm), C is

peptide concentration (M), N is number of residues. MRE=θ/(10*C*l*N)

Fluorescence:

Fluorescence data for the peptides were obtained on a JY-Horiba fluoromax-2 spectro-

fluorometer at room temperature. Emission spectra measurements were taken in Spectrosil quartz

cuvettes (1 cm path length cuvette, sample volume 2 ml) using a 5 mm excitation slit width and 5

mm emission slit width for spectra. The measurements were performed on samples containing

peptides (2 µM) in buffer (50 mM sodium phosphate,150 mM NaCl, pH 7.0). The excitation

wavelength used to excite AzAla was 342 nm. Fluorescence emission spectra were recorded over

the range of 355 nm − 455 nm. To excite tryptophan, the excitation wavelength used was 280

nm. Fluorescence emission spectra were recorded over the range of 300-400 nm.

37

Chapter 5: Discussion

Protein evolution is a continuous process in nature as a result of random mutation

acquisition and Darwinian39 selection of the fittest in a constantly changing environment,

however in nature it may take a long period of time for an advantageous mutation to appear by

chance. Manmade directed evolution is a rather faster method, and it did not actually first start in

the laboratory. Since the introduction of agriculture and farming40, humans were indirectly

practicing selection of mutants through crop selection based on the quality and quantity of grains

produced and selective crossbreeding animals for many generations for better meat or milk

production or even better hunting dog skills resulted in systematic selection of favorable

combinations of genetic mutants41. Protein mutagenesis in nature however should not only be

seen as in the light of a positive natural selection pathway, as it is also responsible for the

pathogenesis of cancer where many mutants in oncogenes result in their constitutive activation

and give a growth advantage at the cellular level but with devastating effect at the organism

level. Mutants that are resistant to chemotherapeutic agents are often selected as an adverse

response to cancer treatment. In different types of cancer, such as leukemia, translocation of

different genes creates novel chimeric proteins with catastrophic effects42.

In the laboratory even faster, more sophisticated and effective directed evolution

techniques have been developed6, and in this paper we have shown how this new NMR-guided

approach allowed the evolution of a scaffold with no previous Kemp catalytic capabilities, to

incorporate and be efficient in conducting this novel catalytic function. In the laboratory,

directed protein evolution, which is the manipulation and selection of specific molecules instead

of organisms, has developed over the years and had a great impact in many industries including

agriculture, the pharmaceutical industry, the chemical industry and others. Scientists employed

38

many strategies to introduce and select favorable single or combinations of mutant proteins with

new or improved phenotypes and physical properties43. Random mutagenesis and selection of

specific favorable mutants, DNA shuffling of libraries of mutants and combination of related

proteins, exon shuffling of non-homologous genes or even whole genomic shuffling of different

strains are just a few of the methods used6. The improvement and modification of many nucleic-

acid modification enzymes such as polymerases, restriction endonucleases and many other

biological reagents led to the explosive development of molecular biology. In turn, the

development of molecular biology techniques and especially genomics and proteomics

accelerated the industry of directed protein evolution44 with an incredible impact in

pharmacology through the design of protein pharmaceuticals, antibodies, vaccines and many

therapeutic chemicals.

In this study we used a combination of rational design-based site-specific mutagenesis of

myoglobin to modify the heme binding pocket to inhibit its previous activity and make the heme

more easily accessible. Its low catalytic efficiency even after the initial mutations (kcat/KM WT:

13 M-1s-1, H64V: 18 M-1s-1) demonstrated how myoglobin’s original scaffold was not intended

for Kemp catalysis. We then used HSQC NMR-analysis followed by random mutagenesis and

enzymatic screening to establish and enhance the enzymatic activity of the protein (H64V/V68A:

199 M-1s-1, H64V/V68A/T95V: 2660 M-1s-1). We have therefore demonstrated that HSQC NMR

guided evolution can be used successfully in the introduction of a desired novel enzymatic

activity to non-protein scaffolds and provide a direction for improving the catalytic efficiency of

an enzyme.

Briefly, after successful expression of WT mb, we used side specific mutagenesis to

accommodate access of the substrate to the heme binding site. The first mutation introduced was

39

the substitution of His64 with valine, a smaller hydrophobic residue. His64 is a distal histidine

that helps myoglobin stabilize bound oxygen molecules. To further increase the size of the

binding pocket allowing for easier access of the substrate a second mutation was introduced in

position 68, replacing valine into an alanine. A Kemp elimination assay demonstrated a modest

increase in the Kemp elimination activity of the H64V/V68A double mutant compared to the

H64V and V68A mutants.

In order to determine which residues are involved in protein substrate interaction, we

performed HSQC NMR analysis of the H64V/V68A double mutant protein in the presence and

absence of a non-catalyzable substrate. HSQC NMR studies identified residues at the positions

T95 and K96 as the ones having the greatest chemical shifts as a result of substrate binding. In

an attempt to further enhance substrate binding and increase enzymatic activity, targeted random

mutagenesis of these two residues and crude lysate screening with Kemp elimination was carried

out. Random mutagenesis screening resulted in the identification of two identical constructs

with a T95V substitution which had increased enzymatic activity. Enzymatic studies of the

triple mutant H64V/V68A/T95V protein demonstrated a ten-fold increase in activity compared

to the H64V/V68A double mutant.

Since this novel NMR-guided approach has successfully predicted important residues to

be modified outside of the binding pocket, which would not have been speculated by any other

rational design method, we have established this technique as a powerful new approach in the

quest for designing and improving protein catalysts. Furthermore, we postulate that myoglobin, a

small, heme containing protein can serve as a suitable template for NMR-guided evolution of a

multitude of novel enzyme catalysts with different substrate specificities and enzymatic

activities.

40

Through incorporation of the non-natural amino acid into the small antimicrobial

peptides, we have demonstrated successful introduction of the proteolytic resistance without

altering the peptide conformation and have shown the unique ability of AzAla to serve as an

environment-insensitive and non-disruptive biochemical probe that can be selectively excited at

342 nm. The minimal changes in quantum yield and emission maxima in different

microenvironments allowed for observations of subtle effects caused by weak quenchers

inherently present in proteins.

The next step for the antimicrobial peptides, would be a comparison between AG14 and

AG14WZ fluorescent spectra in different environments to further investigate the structures of the

different peptides at various conditions and compare what information they can provide

regarding the microenvironment they are located in. Furthermore, the effectiveness of the

antimicrobial properties of AG14WZ peptides should be compared with the original AG14

peptides to further look into how well they retain their antimicrobial function. If the peptides

pass cytotoxicity testing in mammalian cells, further proteolytic analysis should be performed to

see how they would hold up against other endogenous human enzymes in addition to studies

regarding methods of oral or blood administration and the lifetime and tracking of the peptides

inside the human body.

Finally, it would be interesting to investigate the incorporation of AzAla into larger

proteins such as enzymes as an approach to introduce proteolytic resistance and spectral

enhancement without altering their structure and their natural properties. Combining our

understanding of protein enzyme structure and function in combination with new molecular

biology techniques will lead to an explosion of discoveries and the development of many

designer proteins for a multitude of applications.

41

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