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Dep. of Chemistry & Biochemistry Prof. Indig. Chemistry 501 Handout 4 The Three-Dimensional Structure of Proteins Chapter 4. Lehninger. Principles of Biochemistry. by Nelson and Cox, 5 th Edition; W.H. Freeman and Company. A protein’s conformation is stabilized

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Dep. of Chemistry & Biochemistry

Prof. Indig

Chemistry 501 Handout 4The Three-Dimensional Structure of ProteinsChapter 4

Lehninger. Principles of Biochemistry.

by Nelson and Cox, 5th Edition; W.H. Freeman and Company


A protein’s conformation is stabilized

largely by weak interactions

Proteins in any of their functional, folded conformations are called native proteins.


Quaternary structure of deoxyhemoglobin

(a) A ribbon representation

(b)A space-filling model

Structure of the enzyme

chymotrypsin, a globular protein

(PDB file 6GCH)

The known 3-D structures of proteins are archived in the Protein Data Bank (PDB). Each structure

is assigned a four-character identifier, or PDB ID.


Protein Architecture - Primary Structure

The planar peptide bond

Each peptide bond has some double

bond character due to resonance and

cannot rotate

Series of rigid planes sharing a common point of rotation at Ca

Three bonds separate

the a carbons in a

polypeptide chain

 =  = 180o when the peptide is in its fully extended conformation and all peptide groups are

in the same plane


Convention: In this conformation,f = y = 0o

In a protein, this conformation is prohibited

by steric overlap between an a-carbonyl

oxygen and an a-amino hydrogen atom

Ramachandran plot for L-Ala residues

Conformations deemed possible are those that

involve little or no steric interference, based

on calculations using known van der Walls

Radii and bond angles


Protein Architecture - Secondary Structure

A few types of secondary structures are particularly stable and occur

widely in proteins. Most prominent: a helix and b conformations.



Note: The a helix

is not hollow



Ball-and-stick model of a

right-handed a helix, showing

the intrachain H bonds

The a helix as viewed

from one end, looking

down the longitudinal axis

The atoms in the center

of the a helix are in

very close contact

Helical wheel

representation of an

a helix.


Not all polypeptides can form a stable a helix.

Interactions between side chains can stabilize

of destabilize this structure

The identity of the amino acid residues

near the ends of the a-helical segment

also affects the stability of the helix



Interaction between R groups

of amino acids three residues

apart in an a helix

Troponin C

(shown: a helix segment 13 residues long)

The four amino acid residues at each end

of the helix do not participate fully in the

helix hydrogen bonds


b turns are common in proteins

The b conformation organizes

polypeptide chains into sheets

180o turn involving four amino acid residues

Gly and Pro residues often occur in b turns

Gly - small and flexible

Pro - the cis configuration is particularly

amenable to a tight turn

b sheets


Common secondary structures have characteristic bond angles and amino acid content

Ramachandran plots for

a variety of structures

Common secondary structures can be assessed

by circular dichroism (CD) spectroscopy

Pyruvate kinase (all amino acid residues except Gly)


Protein tertiary and quaternary structures

a helix



b conformation

Tertiary structure includes long-range

aspects of amino acid sequence

Quaternary structure includes the three-dimensional

arrangement of polypeptide chains in multisubunit proteins


Example of

quaternary structure

Fibrous Proteins

(structure, support, shape, protection)

- Polypeptide chains arranged in long strands of sheets



coiled coil

Disulfide (-S-S-) bonds stabilize

the quarternary structure

Permanent waving




(connective tissue, tendons, cartilage, organic matrix of bone, cornea)

Structure of collagen fibrils

The three-stranded collagen superhelix shown from one end (ball-and-stick representation)

Three helix wrap around one

another with a right-handed twist

  • chain: repeating tripeptide sequence (generally Gly-X-Y, where X is often
  • Pro and Y is often 4-Hyp)adopts a left-handed helical structure with three residues per turn

Structure of silk

Fibroin : layers of antiparallel b sheets rich in

Ala and Gly residues

Permits close packing

and interlocking of R groups

Sheets held together by numerous weak interactions, rather than covalent bonds such as disulfide bonds in a-keratin

Strands of fibroin (blue) emerge from the

spinnerets of a spider (colorized electron micrograph)


Globular Proteins

Structures compact and varied

Tertiary structure of a small globular

protein:sperm whale myoglobin

e.g. human serum albumin

585 residues in a single chain (Mr 64,500)

Approximate dimensions its single polypeptide chain

would have if it occurred entirely in:

a) Polypeptide backbone shown in a ribbon representation

b) Surface contour image: useful for visualizing

pockets in the protein

c) Ribbon representation including side chains

for the hydrophobic residues Leu, Ile, Val, and Phe

d) Space-filling model with all amino acid side chains

The heme group


Supersecondary structures (motifs, or simply folds)

Particularly stable arrangements of several elements

of secondary structure and the connections between them.



Protein motifs are the basis for protein structural classification

Constructing large motifs from smaller ones

The Structural Classification of Proteins (SCOP) database.

Protein structures divided into four classes:

all a

all b

a/b (a and b segments interspersed or alternate)

a+b (a and b regions are somewhat segregated)

Within each class: tens to hundreds of different folding arrangements,

built up form increasingly identifiable structures.


Protein quaternary structures range from simple dimers to large complexes

Viral capsids

Quaternary structure of deoxyhemoglobin

a) The coat protein of poliovirus assemble into an icosahedron 300 Angstrons in diameter

b) Tabaco mosaic virus: rod-shaped virus 3,000 Angstrons long and 180 Angstrons in diameter

with helical symmetry


Protein denaturation and folding

Loss of protein structure results in loss of function


The thermodynamics of protein folding

depicted as a free-energy funnel

Polypeptides fold rapidly by a stepwise process


Folding for many proteins is facilitated by the action of specialized proteins (chaperones)

E. Coli chaperone proteins DnaK and DnaJ


Chaperonins in protein folding

GroEL/GroES complex

Proposed pathway for the action of the

E. coli chaperonins GroEL and GroES.


Defects in protein folding may be the molecular basis for a wide range of genetic disorders

Formation of disease-causing

amyloid fibrils


Prion Diseases

Stained section of cerebral cortex from autopsy of a patient with

Creutzfeldt-Jakob disease shows spongiform (vacuolar)

degeneration, the most characteristic neurohistological feature.

Structure of the globular domain of human PrP

in monomeric (left) and dimeric (right) forms.

Proteinaceousinfectiousonlyprotein (PrP)