Topic 3

A brief refresher on protein structure
Topic 3
Perhaps the most important structural bioinformatics
result ever published…
Chothia, C. & Lesk, A. M. (1986). The relation
between the divergence of sequence and structure
in proteins. EMBO J., 5(4):823-826.
Starting now, the relationships
identified by this simple graph will
impact everything we do throughout
the remainder of the class.
Levels of Protein Structures
Levels of Protein Structures
primary structure
(set of covalent bonds within the structure)
 secondary structure (helices, strands, coils/loops)
 tertiary structure (3D packing of secondary structures)
 quaternary structure
(spatial arrangements of multiple chains)
The three most common classes of proteins
Globular protein
Fibrous protein
Membrane protein
Formation of a Peptide Bond by Condensation
Amino Acid
Amino Acid
Note: this
chemistry will not
work as drawn!
Peptide bond
Peptide bond is the amide linkage that is formed between two amino
acids, which results in (net) release of a molecule of water (H2O).
The four atoms in the yellow box form a rigid planar unit and, as we will
see next, there is no rotation around the C-N bond.
The primary structure is the set of all covalent bonds within the protein, which is approximated
by the sequence (-CSS). Note: Primary structure or sequence, but not primary sequence.
Q: why is the pentapeptide SGYAL different than LAYGS?
A Closer Look at the Peptide Bond
 The carbonyl group has a partial negative charge and the amide nitrogen
has a partial positive charge, which set up a small electric dipole.
 The peptide C-N bond has a partial double-bond character (partial
sharing of two pairs of electrons between O and N.
 The peptide bond is planar and rigid, cannot rotate freely (see next slide).
 Resonance: delocalization of bonding electrons over more than one
chemical bond.
Lehninger Principles of Biochemistry
A Closer Look at the Peptide Bond
But, bonds N-C and C -C can rotate, which can be described by two torsion
angles:  (phi) and (psi).
(phi): C-N-C-C
(psi): N-C-C-N
 (omega): C-C-N- C
In principle,  and  can have any value between -180O and +180O. But due
to steric interference……
A Closer Look at the Peptide Bond
Bond lengths : C -C
Note the differences between C-N and N-C
The peptide bond is normally in the trans configuration (~99.6% of the time)
  = 180O
One exception is for proline. The fraction of X-Pro peptide bonds in the cis isomer
under unstrained conditions ranges from 10-40%. The fraction depends slightly on the
preceding amino acid X.
An (a.) unstable vs. (b.) the most stable Ala-Ala dipeptide conformation
The rotatable backbone torsion angles
Rotation of phi
Rotation of psi
The Ramachandran plot
With a molecular modeling kit, prove to yourself that (0,0) is an unallowable due to a steric
Prolyl cis-trans isomerization as a molecular switch
“The local environment of proline within
a protein can influence the relative free
energies of the cis and trans isomeric
states, leading to wide variations in the
ratio of cis:trans populations in different
proteins. Although most structures
require proline to adopt one or the other
isomer in the context of native protein
folds, several recent structures show the
presence of both populations for specific
proline residues.”
Liu et al. Nature Chemical Biology. 3, 619 629 (2007)
Final thoughts on primary structure
-- The primary structure is a complete description of the covalent
bond network within a protein.
-- This is almost(!) completely described by the sequence of amino
-- If you know that the protein is AVG…, you can look up the
structures of A, V and G, plus what you know about peptide
bonding allows you to complete the covalent bond structure.
-- So, when does the primary structure not fully describe the
covalent bond network?
Secondary structure = local regions of proteins characterized by (i.) similar / values and (ii.)
backbone hydrogen bonding
Proteins are composed of repeating structural elements
Hydrogen Bond
H-bond donor
H-bond acceptor
 A weak bond involving the sharing of an electron with a hydrogen atom
Common hydrogen bonds in
biological systems
Directionality of the H-bond
Secondary Structure:-helix
5.4 Å
3.6 residue
 = -57O,  = -47O
Hydrogen bond pattern: C=O (i) and N-H (i+4)
Image from “Protein Structure and Function” by Gregory A Petsko and Dagmar Ringe
The -helix
Protein Secondary Structure: helices
 Other helical conformations
310 helix,
=-49O, =-26O
Hydrogen bond pattern: C=O (i) and N-H (i+3)
Residues per turn: 3
 helix
=-57O, =-70O
Hydrogen bond pattern: C=O (i) and N-H (i+5)
Residue per turn: 4.4
Amphipathic helix
protein packing and function
Image from “Protein Structure and Function” by Gregory A Petsko and Dagmar Ringe
-sheet (Pleated Sheet)
Anti-parallel -sheet
 = -139O,  = +135O
Parallel -sheet
 = -119O,  = +113O
Lehninger Principles of Biochemistry
The -pleated sheet
Amino acid propensity
Used in the first generation of secondary structure prediction methods, e.g. Chou-Fasman
• the distance between the C atom of residue i and the C atom of residue i+3
is less than 7Å
• the central two residues are not helical
• on the basis of the phi, psi angles of residues i+1 and i+2
Turn propensities (Ft/Fb)
Lehninger Principles of Biochemistry
Ramachandran Plot
Red: allowed regions
Yellow: additionally allowed regions
White: disallowed regions
Relating the Ramachandran plot to secondary structures
Not all Ramachandran plots are created equal.
Tertiary structure = the 3D shape of a single protein chain, which is stabilized by a large
number of noncovalent interactions.
Ruminations on protein stability...
• Protein stability is a small difference of large numbers.
• Proteins are stable (G < 0) only over a narrow environmental range.
• In fact, there are forces pushing the equilibrium between folded and unfolded in
both directions.
Stabilizing forces: Intraprotein salt bridges, hydrogen bonds, dipole-dipole interactions and VDW
interactions (all of which are electrostatic in nature).
Destabilizing forces: Primarily electrostatic interactions with solvent and conformational entropy
SCOP = structure classification of proteins
SCOP = structure classification of proteins
SCOP = structure classification of proteins
SCOP = structure classification of proteins
Motif vs. Domain vs. Tertiary structure
There are many different ways to represent a protein structure
It is common, and sometimes useful, to think of protein structures as scaffolding upon which
‘active sites’ are attached.
Conformational changes within the tetramer structure underlie the differences in oxygen affinity
between oxy- and deoxy-hemoglobin.
Monoclonal antibodies.

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