1

Distribution of the amino acids in Nature

2.4Methionine

1.7Cysteine

3.2Tyrosine

3.9Phenylalanine

4.0Glutamine

5.1Proline

5.2Isoleucine

5.3Aspartic acid

5.7Lysine

5.8Threonine

6.2Glutamic acid

6.6Valine

7.2Glycine

6.9Serine

9.0Leucine

1.3Tryptophan

2.2Histidine

4.4Asparagine

5.7Arginine

8.3Alanine

Frequency in proteins (%)Amino Acid

Incr

easin

g Fr

eque

ncy

Four special amino acids

glycine proline cysteine histidine

H2N

O

H

OHH2N

O

OH

SH

H2N

O

OH

N

HN

HN

C OH

O

H

2

• First amino aciddiscovered in 1820 fromgelatin.

• “R” = hydrogen• Reduced steric

hindrance: can adopt awider range of peptideconformationscompared to otheramino acids.

Glycine: The Smallest Amino Acid

H2N

O

H

OH

H

NH

NH

O

O

NH

OH

O

NH

OH

O

NH

O

In proline, the trans isomer is only slightly favoredover the cis isomer. Thus, proline can readilyadopt the cis conformation.

Proline Trans Cis

N

C

OO

N

O

CO

!

!

!!

N

O

N

O

!

!

!!

O

H

HO

Slightly favored

Heavily favored

3

Cysteine and Cystine

NH

SH

O

NH

S

O

HN

S

O

cysteine cystine

• Disulfide bonds constrain protein conformation

SH

HS

S S

Disulfide Bonds and “Perms”

S

S

S

S

S

S

S

S

S

S

S

S

SH

SH

SH

SH

SH

SH

HS

HS

HS

HS

HS

HS

Reduce Curl

SH

SH

HS

SH

HS

HS

HS

HS

SH

HS

SH

HS

S

S

HS

S

HS

HS

S

S

SH

S

S

S

Oxidize

4

What is pKa ?

NH

O

NH

HN

NH

O

NH

N

+ H

pKa = - log Ka

NH

O

NH

HN

NH

O

NH

N

Ka =

H Ka = H

pKa = - log [H+] = pH

Titration Curve of Histidine

4

4.5

5

5.5

6

6.5

7

7.5

1 1.2 1.4 1.6 1.8 2

Volume of Base (mL)p

H

Histidine can shuffle between forms

H2NOH

O

NH

HN

slight decrease in physiological pH(more acidic)

H2NOH

O

NH

Nslight increase in physiological pH(more basic)

5

Hydrolysis of a peptide bond

chymotrypsin acrosin Factor X

Enzymes make the rate of reactions go faster.

Uncatalyzed rate 7-400 years

NH

N

O

R

R'

H

+ H2O NH

H2N

O

R

R'

H

O +

Amino acids cooperate in catalysis

chymotrypsin

The catalytic triad: serine, histidine, and aspartic acidwork together to cleave amide bonds

The aspartate H-bonds to the histidine side chain,perturbing its pKa and making it more basic. This

makes it easier for histidine to remove a proton fromserine during the reaction.

Ser 195His 57

Asp 102

N

NOO

O

HH

SerHis

Asp

6

Take home messages• Proteins are polymers of amino acids.• Amino acids are connected through peptide bonds.• The nature of the peptide bond constrains the shape of the

polymer.• Nonbonded interactions between side chains also constrain the

shape of the peptide backbone.• There are twenty amino acids, each containing unique side

chains.• Amino acids can work in concert in a polypeptide chain to

generate new functions.

• Question: How does a straight chain polymer of amino acidsfold??

HUMPTY DUMPTY SAT ON A WALL. HUMPTY DUMPTYHAD A GREAT FALL. ALL THE KING’S HORSES AND ALLTHE KING’S MEN, COULDN’T PUT HUMPTY TOGETHERAGAIN.

Protein Structure and Folding

Life Sciences 1aLecture Notes Set 5Fall 2006Prof. Daniel Kahne

7

Lectures 7-8: The Molecular Basis of Translation:Proteins: The Workhorses of Biology

a. A chemical look at proteinsi. Introduction to proteins and amino acidsii. Conformational peculiarities of peptide bondsiii. Structures and properties of the twenty natural amino acidsiv. A closer look at four special amino acids -- Gly, Pro, Cys, and His.v. Collaborations between amino acids in proteins

b. Protein structurei. The four levels of structureii. A closer look at secondary structure

c. Protein folding:i. Anfinsen’s experimentii. Thermodynamic forces involved in protein structures.iii. Thermodynamics of protein foldingiv. The Levinthal paradox (the kinetics of protein folding)v. Molecular chaperones

Alberts pp. 119-128;McMurry: pp. 182-192,233-238

Lecture Readings

Four Levels of Protein Structure

8

Different Proteins Contain DifferentSecondary Structural Elements

Cytochrome b562 LDH Antibody

Secondary Structure

SinglePolypeptide Domain

Protein Molecule

Hierarchical Organization ofProtein Structure

9

Only some peptide backboneconformations are sterically allowed

A Ramachandran plot shows the allowedcombinations of the dihedral angles.

phiHH

CC’’NN

HH

OO

psipsi22

phiphi33

psipsi11

phiphi11 RR

psipsi33

phiphi22

peptide planepeptide plane

CCαα

CCαα

Secondary Structure: α-helices

NH2

O

acetamide

Linus Pauling and Robert B. Corey, Proc Nat Acad Sci, 1951, 37, 235.

10

Details about α-helices

CCαα11

CC’’11

CC’’22CCαα

22

CCαα44 CCαα33

CCαα55

CCαα66

CCαα88

CCαα77

CC’’55

CC’’33

CC’’44

CC’’66CC’’77

CC’’88

99

8877

55

66

44

22

33

Secondary Structure: β-sheets

CC’’NN

OO

RR

CC

NN

NNCCαα

CCαα

CC

RR

RRRR

11

Christian Anfinsen, NobelPrize in Chemistry 1972

Thermodynamic Hypothesis: The informationcontained in the primary amino acid sequence leadsto the correct protein fold. (or in other words . . .Could you put Humpty Dumpty back togetheragain?)

Test: Will a denatured protein (RibonucleaseA)refold to its native conformation?

Does primary sequence determineprotein conformation?

Conclusion: The information required to fold a protein is contained within its sequence.

Anfinsen’s protein folding experiment