Design of a novel globular protein with atomic-level

accuracy

NOVEL METHODS

• Computational methods

• New developments in the making

• Opening of a new field of science

Ideas

• Redesign naturally occurring proteins so that they have enhanced stability or new functionality

This group

• Found a procedure for the development of low free energy structures

• Led them to the creation of the protein TOP7

• A 93 residue protein with topology that is not present in the Protein Structure Data Base

Design Protocol

• Critical is cycling between seequence design and backbone optimization. The goal is to find the lowest free energy backbone conformation for a fixed amino acid sequence

Some more Top7 features

• Highly soluble protein

• Monomeric structure

• Thermally stable

• More stable than most proteins of its size

Conclusion

• Top7 shows that the design of globular proteins not yet observed in nature is possible but can be extremely stable

• The methods used to design TOp7 are applicable to any globular protein structure

• This may open the door for exploration of new protein strucutres and architectures

A few more signaling things

• EGF receptor dimerizes when ligand binds and then causes signaling cascade for cell division

uses covalent linkage of phosphate to

downstream proteins to carry on signal

Continued

• SH molecules (SH2 SH3) are adaptor proteins.

• They will recognize specific parts of target molecule and bind and now the phosphate will be transferred on to the target molecule

Calmodulin

• Helix loop helix (EF Hand)

• Important in many signal transduction pathways

• Charged glu and asp bind Ca2+

• Unbound state resembles a dumbbell

• Bound state it becomes very compact

Myoglobin/Hemoglobin

Globin Fold

• Made up of alpha helices

• Hemoglobin and myoglobin are examples

Oxygen is not soluble in blood so it needs carriers

• Myoglobin• One subunit• Transports oxygen in

muscle

• Hemoglobin• 4 subunits• Transports oxygen all

over body• Four oxygen binding

sites

Hemoglobin

• Oxygen binds to heme group

• No oxygen bound called T state

• Oxygen bound called R

Binding of Oxygen

• When shifts from T to R the iron moves to the center of the heme plane because an overall structural shift. This shift then gets propagated throughout the structure and leads to the change in other subunits

COOPERATIVE BINDING: with the binding of the firstThe others will bind much easier

Sickle Cell

• Base pair change in hemoglobin from glu to val

Makes hemoglobin sticky and red blood cells will clump together and cause all sorts of problems

Enzymes

• Enzymes speeds things up substantially

Enzymes

• Have high specificity for their substrate

How they speed things up

• Increase substrate at catalytic site

• Physically bring molecules to the right place and increase local concentration

• Selectively stabalize by binding to TRANSITION STATE

• Lower the activation energy by stabalizing the transition state

ACTIVE SITE

• Pocket or groove lined with specific amino acid residues

• Here is where the substrate goes and undergoes some sort of chemical transformation

• Therefore it can be seen that the enzyme is playing the role in this chemical modification

Serine Proteases

4 aspects for serine proteases

• Catalytic Triad

• Oxyanion hole

• Specific binding

• Non-specific binding

Catalytic TriadAlways see these three particular side chains: ASP 102, His 57, and Ser 195

All spread out in primary sequence

Come together at active site in binding pocket

Continued

His residue accepts proton from reactive serine and helps stabalize the transition state

Ser forms covalent bond with substrate

Oxyanion holeVery important in stabalizing the transition state by Forming H Bonds

Allows for nonspecific substrate binding to the main chain of the substrate

This is the region of the enzyme that is non specific

Specific parts are taken care of with the specificity pocket

Specificity binding pocket

Accepts different side chains from different substrates dependingOn the member of the serine protease family

Specificity Pocket

Specificity PocketChymotrypsin cleaves bulky aromatic side chains: Serine at the Bottom of the pocket which wont interfere too much with largeAromatic side chain

Trypsin cleaves next to large positively charged side chains; AspAt bottom which will attract positive side chain from substrate

Elastase cleaves small uncharged sidechains:

Two Phase Reaction

First: acylation in which the peptide bond gets cleaved

When the substrate comes close, the oxygen of serine 195Bends to interact with substrateRESULTS in bond between the reactive serineAnd carboxly or substrate

Proton of serine is donated to His

Peptide bond goes from planar to tetrahedral state

This state is unstable and very short lived

First Phase

Continued

This then allows for peptide to be released and the end of the first step

Phase 2

Enzyme still attached to remaining part of peptide

Deacylation: water comes along and forms a new tetrahedralTransition state which is also unstable

A covalent bond is formed between C and O and the fragment isreleased

Hydrgoen then goes back to serine and enzyme can be used again

Second phase