(2) How to get lecture slides (2) How to get lecture slidesstructure.yonsei.ac.kr/File name: AMB_Ch3

structure.yonsei.ac.kr/File name: AMB_Ch3

AnnouncementAnnouncement

Advanced Molecular Biology course 2015 is Essential

(1) Syllabus (1) Syllabus Two parts (Dr Cho, Dr Kim) First part covers three themes - Protein Structure and Function (Ch3) - RTK strcuture and anti-cancer monoclonal antibody drugs - Biophysical techniques for experiments

Two parts (Dr Cho, Dr Kim) First part covers three themes - Protein Structure and Function (Ch3) - RTK strcuture and anti-cancer monoclonal antibody drugs - Biophysical techniques for experiments

(4) Interviewing with me (4) Interviewing with me You may see me during this course if you want My office hours: AM 10:00-11:00 on Thursday How: First, Contact me by E-mail or telephone E-mail address: hscho8@yonsei.ac.kr, 2123-5651

You may see me during this course if you want My office hours: AM 10:00-11:00 on Thursday How: First, Contact me by E-mail or telephone E-mail address: hscho8@yonsei.ac.kr, 2123-5651

Announcement (continued)Announcement (continued)

(3) Exam and Grading (3) Exam and Grading2 times (Dr Cho (45%), Dr Kim (45%), attendance(10%) ) Problem types: Short or long answer with figures100% Place: Lecture Room S118A Posting of score in Exam: on the board at room SB134,

2 times (Dr Cho (45%), Dr Kim (45%), attendance(10%) ) Problem types: Short or long answer with figures100% Place: Lecture Room S118A Posting of score in Exam: on the board at room SB134,

Molecular Cell BiologyFifth Edition

Chapter 3:Protein Structure and Function

Copyright © 2004 by W. H. Freeman & Company

Harvey Lodish • Arnold Berk • Paul Matsudaira • Chris A. Kaiser • Monty Krieger • Matthew P. Scott •

Lawrence Zipursky • James Darnell

F1-ATPase

•Function is derived from three-dimensional structure ; - Structures define the functions of proteins

•Only when a protein is in its correct three-dimensional structure, it is able to function

Protein Structure and Function

Principles of Biology

•Living organisms are subject to basic laws of chemistry and physics

• Major difference between general chemistry and biology; they include more than 70% waters. so biological molecules are always surrounded by waters• Four of water’s properties for life

– Cohesive behavior– High heat capacity– Expansion upon freezing– Versatility as a solvent

• H-bonds

• Peptide bond is plane!• the size of protein; dalton• average MW of amino acids in protein : 113

Secondary structure : alpha helix, beta sheet60% polypeptide chain, H-bond

Alpha helix : (n, n+4) carbonyl oxygen, amide hydrogen atomDirection : where is the N-terminal ?

Beta sheet : Parallel, antiparallelpleated sheet

Turns : 3-4 residues, glycine, proline common

Top view

Side view

Motifs : paticular Combinations of Secondary Structures

Structural and functional domains are modules of tertiary structure

Structural domain : proline-rich domain, acidic domain, SH3, zinc-finger motif

Functional domain : kinase domain, DNA-binding domain

Heamagglutinin – Surface protein in influenza virus

Epidermal growth factor

Proteins Associate into multimeric structures and Macromelecular assemblies

RNA polymerase II : 12 subunits(Dr. Roger kornberg)

Mediator : 20 subunits

Members of protein families have a common evolutionary ancestor

Homologous proteins belongs to a family

Non-homologous protein : similar structure, similar function

4 subnits

* Oxygen-binding globinPlant Blood Muscle

Folding, Modification, and Degradation of proteins

• The information for protein folding is encoded in the amino acid sequence

• Folding of proteins in vivo is promoted by chaperone95% proteins within cells are in native conformation despite of high concentration (200-300mg/ml), which favor the precification of proteins in vitro. This can be explained by chaperones. (above 85% protein folding)

- Molecular chaperone : bind to exposed hydrophobic regions and stabilize them, thereby preventing these proteins from aggregating and being degraded. (Hsp70+Hsp40, GrpE+DnaK)

- Chaperonins directly facilitate the folding of proteins (TriC, GroEL)

TriC

ATP X, ADP binding ; bind to misfolded protein

ATP binding, GroES ;Releases the folded proteinCavity twofold increase

Chemical Modification of amino acid residues

80% proteins are acetylated ; lifetime control,Nonacetylated protein – short lifetime

Nearly every protein in a cell is chemically modified after its synthesis.This may alter the activity, life span, or cellular location of proteins.

Phosporylation : Serine, threonine, tyrosine, histidineGlycosylation : asparagine, serine, threonineLipid attachment :

prothrombin

Membrane receptors

collagen

Repression by nucleosomes

Coiling of DNA around a histone octamer in the nucleosome isnow recognized as a cornerstone of transcriptional control.

Nucleosomes repress transcription in at least three different ways.

First, they occlude sites of protein binding to DNA, thereby interferingwith the interaction of activator and repressor proteins,polymerases and transcription factors, DNA-modifying enzymes.

Second, chains of nucleosomes can become furthercoiled or folded, and this higher-order coiling represses transcriptionof entire chromosomal domains.

Finally, interactions ofnucleosomes with additional chromosomal proteins in heterochromatinrepress gene expression in a hereditary manner6.

Each histone is organizedin two domains, a characteristic ‘histone fold’ and an unstructuredN-terminal ‘tail’. The histone-fold domains constrain theDNA in a central core particle and, thereby, restrict access ofDNA-binding proteins.

This histone tail is a flexible amino terminus of 11-37 residues.

Several positively charged lysine side chains in the histone tail may Interact with linker DNA, and the tails of one nucleosome likely interact with Neighboring nucleosomes higher-order coiling.

The histone tail lysine, especially those in H3 and H4, undergo reversible acetylation and deacetylation by enzymes such as CBP (P300) and HDACs

In the acetylated form, the positve charge of the lysine e-amino group is neuralized. This eliminate its interaction with a DNA phosphate group.

So the greater the acetylation of histone N-terminus, the less likely chromatinis to form condensed 30-nm fibers and possibly higher-order folded structures.

Sites of Histone Tail Modifications

Epigenetics edited by Allis et al. (2007)

Distinction between Euchromatic and Heterochromatic Domains

H3K9-Me, H3K27-Me

H3K4-Me

Heterochromatic Hallmarks

Euchromatic Hallmarks

Epigenetics edited by Allis et al. (2007)

Proteolytic cleavage : blood coagulation, digestion and apoptosis EGF, insulin

Protein self-splicing : internal segment is removed. Hedgehog.

Serine is part of a catalytic triad that also includes histidine and aspartate

-The three-dimensional structure of chymotrypsin was solved by David Blow in 1967.

-It is synthesized as a single polypeptide, termed Chymotrypsinogen, which is activated by the proteolytic cleavage to yield the three chains.

[1GCT.pdb]

-The active site of chymotrypsin, marked by serine 195, lies in a cleft on the surface of the enzyme.

-This side chain of serine 195 is hydrogen bonded to the imidazole ring of histidine 57.

cleft

Substrate binding

Nucleophilic attack

Tetrahedral intermediate(acyl-enzyme)

Amine is free

Water mediated deacylation

OH- Attacks the carbonyl carbon

Carboxylic acid product

Burst phase

Steady-state phase

Degradation of proteinLysosomal pathway : extracellular proteins, hydrolytic enzyme and acidic sol’nUbiquitination : lysine residue attached 76-residue peptide.

E1,E2 : thioester bond

E3 : specific substrate binding protein isopeptide bond

Cytosolic protein ; cyclinMisfolded in ERImmune system

N-terminal rule : stabilizing (Met, pro), destabilizing (Arg, leu)E3 enzyme read N-terminal residue; cell cyclin (internal sequence) misfolded protein (hydrophobic sequence)

26S proteasome • 20S proteasome (CP) : 700kD, catalytic (7-9 a.a)• 19S proteasome (RP) : 700kD, 6 ATPase+isopeptidase

Digestive Proteases Degrade Dietary Proteins

Zymogen, stomoch (pepsin, F,L), pancrease (trypsin, chymotrypsine; basic, aromatic)

Misfolding not only leads to a loss of the normal function of the protein but alsoMarks it for proteolytic degradation.

The proteolytic fragments filamentous plaquesdegenerative disease ; Alzheimer’s disease, Parkinson’s disease, mad cow disease

Amyloid precursor beta amyloid helix sheet)

MW ?

Kd ?

High shap complementarity :