Structure and Function of Proteins Ora Schueler-Furman 2009-2010 1.

Structure and Function Structure and Function of Proteinsof Proteins

Ora Schueler-Furman2009-2010

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PROTEINSPROTEINS

From the Greek word From the Greek word

“Proteios”“Proteios”- first rank, most important- first rank, most important

Play central roles in all biological processesPlay central roles in all biological processes

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Introduction into Introduction into Protein StructureProtein Structure

• The chemical nature of polypeptides

• Forces that determine protein structure

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The 4 Hierarchical Levels of Protein Structure

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Primary Structure: Sequence

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Formation of a Peptide Bond

O - oxygen

N - nitrogen

O-+H3N

R

H

CO

C||

H - hydrogen

C - carbon

cpk colors

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Dihedral Angles and define Backbone Geometry

The peptide bond is planar and polar9

Basic Facts

Polypeptide chain: 50-10’000 aa But also >20000 aa: 34’350 aa (Titin)

Average MW of aa : 110 daltonsAverage MW of a protein of length n aa:

n X110Distance (Ci – Ci+1) <=3.63Ǻaa – amino acid

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Basic Terms

Main chain, backbone, side chain, residue bb scPeptide: a small # of connected aa

Polypeptide: a longer chain of aa

Protein: polypeptide chain with defined aa sequence & conformation

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The Protein Alphabet: 20 lettersA Ala AlanineC Cys CysteineD Asp AspartateE Glu GlutamateF Phe PhenylalanineG Gly GlycineH His HistidineI Ile IsoleucineK Lys LysineL Leu Leucine

M Met MethionineN Asn AspargineP Pro ProlineQ Gln GlutamineR Arg ArginineS Ser SerineT Thr ThreonineV Val ValineW Trp TryptophaneY Tyr Tyrosine

amino acids vary in: volume, shape, chemical nature(charge, hydrogen bonding capability, etc.)

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• The simplest aa• No sc• Very flexible bb

Special Amino Acids

• Cyclic aa• sc Connects bb N• Very constrained bb

N

CO

C H

HH

N

CO

C H

CH2

CH2H2C

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Aliphatic Amino Acids

• sc contains only carbon and hydrogen atoms• hate water 14

Amino Acids with Hydroxyl Group

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Negatively Charged Amino Acids

different size → different tendency for 2. structure

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Amide Amino Acids

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Positively Charged Amino Acids

• large sc

• pKa 11.1 • pKa 12

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Aromatic Amino Acids

• sc contains aromatic ring

• pKa 7

• benzene ring

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Amino Acids with Sulfur

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Cystine

Oxidation of Sulfur atoms creates covalent disulfide bond (S-S bond)between two cysteines

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S-S Bonds Stabilize the Protein

A chain

G I V E Q C C A S V C S L Y Q L E N E N Y C N

s

s

s

s

B chainF V N Q H L C G S H L V E A L Y L V C G E R G F..

s

s

InsulinA chain

NN

CC

B chain22

Post-Translational Post-Translational Modifications Modifications

• Processing (pro-insulin/insulin)– control of protein activity

• Glycosylation– protein trafficking

• Phosphorylation (Tyr, Ser, Thr) – regulation of signaling

• Methylation, Acetylation – histone tagging

• ….

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Metal Binding ProteinsMetal Binding Proteins

• aa: HCDE• Fe, Zn, Mg, Ca• Fe

– blood: red hemoglobin– electro-transfer: cytochrome c

• Zn – in DNA-binding “Zn-finger” proteins– Alcohol dehydrogenase: oxidation of alcohol

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Forces that Determine Protein

Structure

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Non-Covalent Forces Add up

Each bond is weak

Large number of bonds

From: the Molecular Biology of the Cell, 4th ed.

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Attractions between moleculesAttractions between molecules

E(r) = K/rp

p=1: Coulomb interactionbetween two charges

p>1: delocalized charges – weaker interactionsp=6: interaction between neutral molecules

Short-range interactions: p>=3

p=1

p=6

r – distance between molecules

E(r

) –

ener

gy o

f at

trac

tion

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1. Van der Waals Interactions (Lennard Jones Potential)

From: the Molecular Biology of the Cell, 4th ed.

rij

Attractive: weak, due to transient dipoles

Repulsive:Atoms do not penetrate each others →

spheres (VdW-radii)

0.5-1kcal/mol1Ǻ = 0.1nm

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2. Hydrogen Bonds

Hydrogen “shared” between two electronegative atoms

Important for 2nd struct.Interaction with water

1-3kcal/mol

NH

O Cd

Acceptor

Donor

From: the Molecular Biology of the Cell, 4th ed. 29

3. Electrostatic Forces (Salt Bridges)

Coulomb’s law:

E = kqAqB/Dr

qA, qB : point chargesr: distance k=332 (for units of kcal/mol) D: dielectric constant

(water:80; protein: ~4)Solvent screening: D’ = DrAB

qBqA

r

3Ǻ: ~1.4 kcal/mol

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4. Aromatic Rings: and Cation- Interactions

Aromatic ring: cloud of electrons: negative charge

Can interact with • positive charge of Lys, Arg, His• edge of other aromatic ring

From: wikipedia.

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5. Water

• polar• cohesive

•competes with interactions in the protein (Hb, SB)• high D – reduces electrostatic forces

• hydrophobic effect• explicit modeling difficult

From: the Molecular Biology of the Cell, 4th ed. 32

Accessible Surface Area

• Roll ball (radius = 1.4Ǻ; H2O) over molecule

• polar vs apolar: well solvated protein – polar atoms at surface, apolar atoms in the core

Van der Waals surface

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Non-Covalent Forces: Summary

• VdW: Many small contributions sum up to significant energy• Salt bridges and hydrogen bonds: polar interactions are reduced by competing water at the surface• Surface of protein: hydrophobic atoms should be all buried

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