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Protein Modeling

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26 views17 pages

Protein Modeling

Uploaded by

ManeeshAgrawal
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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HOMOLOGY

MODELING

CHUNMUN KUMARI
M.Sc. BIOTECHNOLOGY 2nd SEM
DEPARTMENT OF BIOTECHNOLOGY
GURU GHASIDAS VISHWAVIDYALAYA,
BILASPUR (C.G.)
WHAT IS HOMOLOGY MODELING ?
Also known as comparative modeling of
protein which is used to build 3D structure of
protein from a polypeptide sequence.
Sequence Structure Function
A T
Y
G
C
A V
W T H P
E
D
K
C
M H
METHODS….
HOMOLOGY MODELING…WHY ?
For constructing error-free protein structure.
Time and cost efficient.
Less labor.
Approach for Computational Modeling
Protein Sequence

TEMPLATE TEMPLATE–FREE
BASED METHOD
HOMOLOGY FOLD RECOGNITION / AB INITIO
MODELING THREADING METHOD

Structure
Generation

Structure
Refinement

Final
Structure
STEPS
STEP 1& 2:-Target –Template search
and sequence alignment
KEY FEATURES……..
Sequence coverage
Sequence similarity
Matching of target predicted secondary structure
with observed template secondary structure.
Structure quality
Known functional relationship.
MODEL BUILDING
The next step is to build the 3D structure of the
target protein sequence using any software.
Consist of 3 steps…

Backbone generation
Loop modeling
Side chain modeling
BACKBONE GENERATION
 When the alignment is
ready, the actual model
building can start.

 If two aligned residues


differ, only the backbone
coordinates (N,Cα,C and O)
can be copied.

 If they are the same, one can


also include the side chain.

Backbone generation
LOOP MODELING
• Loops often play an important
role in defining the functional
specificity of a given protein
framework, forming the active
and binding site.
• Even where loop regions are
conserved in length they can
adopt quite different
conformations.
• Three major approaches have Loop modeling
been used:
1. knowledge-based methods
2. ab initio methods
3. combined approaches
SIDE-CHAIN MODELING
 Use of most probable
ROTAMER for each amino
acid, depending on their
backbone conformation from
library for side chain
modeling.

Side-chain modeling
MODEL EVALUATION
Residues in most favored regions 78.9%
Residues in additional allowed regions 18.80%
Residues in generously allowed regions 1.3%
Residues in disallowed regions 1.0%

94.55% of the residues had an


averaged 3D-1D score > 0.2
RESULT

TARGET PROTEIN SUPERIMPOSITION OF TARGET-


TEMPLET PROTEIN
APPLICATIONS
 There is much information concerning biological
function that can be derived from a 3D protein structure.
1. Amino acid present in the surface and core can be
determined.
2. Protein structures can also be used to explain the
effects of mutations in drug resistance and in genetic
diseases
3. Computer aided drug designing.
REFERENCE
1. Chothia C., and Lesk A.M. (1986).The relation between the
divergence of sequence and structure in proteins. EMBO J5:823–
6.
2. Kendrew J.C., Bodo G., Dinitzis H.M., Parrish R.G., Wyckoff H.
and Phillips D.C. (1958). A three-dimensional model of the
myglobin molecule obtained by Xray analysis. Nature 181, 662666.
3. Kendrew J.C. (1961). The three-dimensional structure of a protein
molecule. Sci. Am. 205(6), 96110.
4. Orengo C.A., Jones D.T., and Thornton J.M. (2003).
Bioinformatics.
5.Vyas V.K., Ukawal R.D., Ghate M., and Chintha C. (2012).
Homology modeling a fast tool for drug discovery:current
perspective. Indian J Pharma Sci. 74(1), 3507339.

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