UNIT II – STRUCTURE PREDICTION AND

DRUG DESIGN

Dr. M Indira
Associate Professor
Department of Biotechnology
Vignan University
 SYLLABUS
 Protein structure prediction;
 Introduction to comparative modeling;
 Sequence alignment;
 Constructing and evaluating a comparative model;
 Predicting protein structures by 'threading';
 Molecular docking - AUTODOCK/EASYMODELLER
and HEX;
 Structure based de novo ligand design;
 Drug discovery;
 Chemoinformatics; QSAR.
INTRODUCTION
 INTRODUCTION
• Proteins are an important class of
biological macromolecules
which are the polymers of amino
acids.
• Biochemists have distinguished
several levels of structural
organization of proteins. They
are:
– Primary structure
– Secondary structure
– Tertiary structure
– Quaternary structure
 PRIMARY STRUCTURE
• The primary structure of protein refers to the sequence of amino
acids present in the polypeptide chain.
• Amino acids are covalently linked by peptide bonds.
• Each component amino acid in a polypeptide is called a
“residue” or
“moiety”
• By convention, the 10 structure of a protein starts from the
amino- terminal (N) end and ends in the carboxyl-terminal (C)
end.
 IMPORTANCE OF PRIMARY STRUCTURE
• To predict 20 and 30 structures from sequence
homologies with related proteins. (Structure prediction)
• Many genetic diseases result from abnormal amino acid
sequences.
• To understand the molecular mechanism of action of
proteins.
• To trace evolutionary paths.

METHODS OF AMINO ACID SEQUENCE

DETERMINATION

• End group analysis – Edman degradation.

• Gene sequencing method.
 SECONDARY STRUCTURE
• Localized arrangement of adjacent amino acids formed as the
polypeptide chain folds.
α-helix
β-pleated sheet
• It consists of β-bends
Non repetitive structures
Super secondary structures
• Linus Pauling proposed some essential features of peptide units
and polypeptide backbone. They are:

– The amide group is rigid and planar as a result of resonance. So

rotation about C-N bond is not feasible.
– Rotation can take place only about N- Cα and Cα – C bonds.
– Trans configuration is more stable than cis for R grps at Cα

• From these conclusions Pauling postulated 2 ordered structures α helix

and
β sheet
 POLYPEPTIDE CHAIN
CONFORMATIONS
• The only reasonably free movements

(measured as ϕ ) and the C α-C

are rotations around the C α-N bond

bond (measured as Ѱ).

• The conformation of the backbone

can therefore be described by the
torsion angles (also called dihedral
angles or rotation angles)
 ALPHA HELIX
• Spiral structure
• Tightly packed, coiled polypeptide
backbone core.
• Side chain extend outwards H bonding
• Stabilized by H bonding b/w
carbonyl oxygen and amide
hydrogen.
• Amino acids per turn – 3.6
• Pitch is 5.4 A
• Alpha helical segments are found
in many globular proteins like
myoglobins, troponin- C etc.
 BETA PLEATED SHEET
• Formed when 2 or more polypeptides
line up side by side.
• Individual polypeptide - β strand
• Each β strand is fully extended.
• They are stabilized by H bond b/w
N-H and carbonyl grps of adjacent
chains.
2 types

Parallel Anti -Parallel

N C N C

N C C N
SECONDARY STRUCTURE
 EXAMPLES

The collagen triple helix.

Silk fibroin beta sheet.
 BETA BENDS
• Permits the change of direction of the
peptide chain to get a folded
structure.
• It gives a protein globularity rather
than
linearity.
• H bond stabilizes the beta bend
structure.
• Proline and Glycine are
frequently found in beta turns.
• Beta turns often promote the formation
of antiparallel beta sheets.
• Occur at protein surfaces.
• Involve four successive aminoacid
residues
 NON REPETITIVE
•
STRUCTURES
A significant portion of globular
protein’s structure may be irregular
or unique.

• They include coils and loops.

• Segments of polypeptide chains

have similar ϕ and Ѱ values are
whose successive residues do not
called coils. Space-filling model of an Ω loop

• Almost all proteins with more than

60 residues contain one or more
loops of 6 to 16 residues, called Ω
loops.
 SUPER SECONDARY STRUCTURES
(MOTIFS)
Certain groupings of secondary structural elements are
called motifs.

beta-alpha-beta motif Greek key motif

β-meander motif Beta barrel

 TERTIARY STRUCTURE
• Tertiary structure is the three-
dimensional conformation of a
polypeptide.

• The common features of protein

tertiary structure reveal much about
the biological functions of the
proteins and their evolutionary
origins.

• The function of a protein depends on

its tertiary structure. If this is disrupted,
it loses its activity.
 DOMAINS
• Polypeptide chains containing more than ,200 residues
usually fold into two or more globular clusters known as
domains.
• Fundamental functional and 3 dimensional structure of
proteins.
• Domains often have a specific function such as the binding
of a small molecule.
• Many domains are structurally independent units that have
the characteristics of small globular proteins.

The two-domain protein glyceraldehyde-

3-phosphate dehydrogenase.
NAD+
 INTERACTIONS STABILIZING 30
STRUCTURE
• This final shape is
determined by a variety of
bonding interactions
between the "side chains"
on the amino acids.
• Hydrogen bonds
• Ionic Bonds
• Disulphide Bridges
• Hydrophobic Interactions:
TERTIARY STRUCTURE
 DETERMINATION OF TERTIARY
STRUCTURE
• The known protein structures have come to light through:
• X-ray crystallographic studies
• Nuclear Magnetic Resonance studies
• The atomic coordinates of most of these structures are
deposited in a database known as the Protein Data
Bank (PDB).
• It allows the tertiary structures of a variety of proteins to
be analyzed and compared.
 QUATERNARY STRUCTURE
• The biological function of some
molecules is determined by multiple
polypeptide chains –
multimeric proteins.
• Arrangement of polypeptide sub unit
is called quaternary structure.
• Sub units are held together by
Quaternary structure of hemoglobin.
non covalent interactions.
• Eg: Hemoglobin has the subunit
composition a2b2
 RECENT DEVELOPMENTS
• A team of scientists at The Scripps Research Institute and the
National Institutes of Health (NIH) has discovered the
structure of a protein – dynamin, that pinches off tiny pouches
from cell’s outer membranes.

• Scientists at the Institute of Structural and Molecular Biology

have revealed the structure of a complex protein called
FimD that acts as an assembly platform for the pili of
cystitis bacteria.

• Researchers from the Walter and Eliza Hall Institute have

found a structural surprise in a type of protein, Bcl-w ,that
encourages cell survival, raising interesting questions about
how the proteins function to influence programmed cell
death.
 Biology/Chemistry of Protein Structure

Primary Assembly
STRUCTURE

PROCESS
Secondary Folding

Tertiary Packing

Quaternary Interaction
 Protein Assembly

• occurs at the ribosome

• involves dehydration
synthesis and
polymerization of amino
acids attached to tRNA:

NH +- {A + B  A-B + H O} -COO -
3 2 n

• thermodynamically
unfavorable, with E =
+10kJ/mol, thus coupled
to reactions that act as
sources of free energy
• yields primary structure
 Primary Structure
primary structure of human insulin
CHAIN 1: GIVEQ CCTSI CSLYQ LENYC N
• linear
CHAIN 2: FVNQH LCGSH LVEAL YLVCG ERGFF YTPKT • ordered
• 1 dimensional
• sequence of amino
acid polymer
• by convention, written
from amino end to
carboxyl end
• a perfectly linear
amino acid polymer is
neither functional nor
energetically
favorable  folding!
 Protein Folding
• occurs in the cytosol • tumbles towards
• involves localized spatial conformations that reduce
interaction among primary E (this process is thermo-
structure elements, i.e. the dynamically favorable)
amino acids • yields secondary structure
• may or may not involve
chaperone proteins
 Secondary Structure
• non-linear
• 3 dimensional
• localized to regions of an
amino acid chain
• formed and stabilized by
hydrogen bonding,
electrostatic and van der
Waals interactions
 Ramachandran Plot
• Pauling built models based on the following
principles, codified by Ramachandran:

(1) bond lengths and angles – should be

similar to those found in individual
amino acids and small peptides
(2) peptide bond – should be planer
(3) overlaps – not permitted, pairs of atoms
no closer than sum of their covalent radii
(4) stabilization – have sterics that permit
hydrogen bonding

• Two degrees of freedom:

(1)  (phi) angle = rotation about N – C
(2)  (psi) angle = rotation about C – C

• A linear amino acid polymer with some folds

is better but still not functional nor
completely energetically favorable  packing!
 Protein Packing
• occurs in the cytosol (~60% bulk
water, ~40% water of hydration)
• involves interaction between
secondary structure elements
and solvent
• may be promoted by
chaperones, membrane proteins
• tumbles into molten globule
states
• overall entropy loss is small
enough so enthalpy determines
sign of E, which decreases
(loss in entropy from packing
counteracted by gain from
desolvation and reorganization
of water, i.e. hydrophobic effect)
• yields tertiary structure
 Tertiary Structure

• non-linear
• 3 dimensional
• global but restricted to the
amino acid polymer
• formed and stabilized by
hydrogen bonding, covalent
(e.g. disulfide) bonding,
hydrophobic packing toward
core and hydrophilic
exposure to solvent
• A globular amino acid
polymer folded and
compacted is somewhat
functional (catalytic) and
energetically favorable 
interaction!
 Protein Interaction
• occurs in the cytosol, in close proximity to other
folded and packed proteins
• involves interaction among tertiary structure
elements of separate polymer chains
• may be promoted by chaperones, membrane
proteins, cytosolic and extracellular elements as
well as the proteins’ own propensities
• E decreases further due to further
desolvation and reduction of surface area
• globular proteins, e.g. hemoglobin,
largely involved in catalytic roles
• fibrous proteins, e.g. collagen,
largely involved in structural roles
• yields quaternary structure
Quaternary Structure
• non-linear
• 3 dimensional
• global, and across
distinct amino acid
polymers
• formed by hydrogen
bonding, covalent
bonding, hydrophobic
packing and hydrophilic
exposure
• favorable, functional
structures occur
frequently and have been
categorized