Transcript Protein Stucture Database/Structure Analysis

Module 3 Protein Structure
Database/Structure Analysis
Learning objectives
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Understand how information is stored in PDB
Learn how to read a PDB flat file
Become familiar with comparative protein modelling
theories
Learn how to search the PDB for information.
Learn how to download a structure
Learn how to display a structure on the screen
Learn how to compare two structures on the screen.
Primary, secondary, supersecondary, and
tertiary structure
Primary
ACFTYPL …
Secondary
ACFTYPL
sssccss
Supersecondary
Tertiary
Part of a record from the PDB
X
Y
Z
ATOM
1
N
ARG A
14
22.451
98.825
31.990
1.00 88.84
N
ATOM
2
CA
ARG A
14
21.713 100.102
31.828
1.00 90.39
C
ATOM
3
C
ARG A
14
22.583 101.018
30.979
1.00 89.86
C
ATOM
4
O
ARG A
14
22.105 101.989
30.391
1.00 89.82
O
ATOM
5
CB
ARG A
14
21.424 100.704
33.208
1.00 93.23
C
ATOM
6
CG
ARG A
14
20.465 101.880
33.215
1.00 95.72
C
ATOM
7
CD
ARG A
14
20.008 102.147
34.637
1.00 98.10
C
ATOM
8
NE
ARG A
14
18.999 103.196
34.718
1.00100.30
N
ATOM
9
CZ
ARG A
14
18.344 103.507
35.833
1.00100.29
C
ATOM
10
NH1 ARG A
14
18.580 102.835
36.952
1.00 99.51
N
ATOM
11
NH2 ARG A
14
17.441 104.479
35.827
1.00100.79
N
What is PDB?
Protein structure database
Annotated records that represent three
dimensional coordinates of atoms of
biological molecules
Generated from direct submissions of
coordinates from the authors.
In the old days, this was called the
Brookhaven National Database.
3D structure data
The largest 3D structure database is the
Protein Database
It contains over 15,000 records
 Each record contains 3D coordinates for
macromolecules
 80% of the records were obtained from X-ray
diffraction studies, 16% from NMR and the rest
from other methods and theoretical calculations
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Protein structure viewers
RasMol
Deep View
Cn3D
WebLabViewer
Steps to tertiary structure
prediction
Comparative protein modeling

Extrapolates new structure based on related
family members
Steps
1. Identification of modeling templates
2. Alignment
3. Model building
Identification of modeling
templates
One chooses a cutoff value from FastA or
BLAST search
Up to ten templates can be used but the one
with the highest sequence similarity is the
reference template
Ca atoms are selected for superimposition
Alignment
Optimization of superimposition of
templates
“Common core” and conserved loops of
target sequence is threaded onto the
template structure
Building the model
Framework construction

Average the position of each atom in target,
based on the corresponding atoms in template.
Areas that do not match the template are
constructed by using a “spare part” algorithm
Completing the backbone-a library of PDB entries
is consulted
Side chains are added
Model refinement-minimization of energy
Framework construction
Alpha Helix
show all the groups within 8 A of N of NAG202
Comparing similar polypeptides
One of the first structures solved was that of
hemoglobin.
It is composed of 2 alpha and 2 beta chains.
The alpha and beta chains have similar structure.
With Deep View you can superimpose the chains
and locate the amino acids that are near one
another in the two chains.
We will also print out an alignment of the two
polypeptides.
Superimposition of two polypeptides
Workshop for module 3: Download hen lysozyme structure
file from PDB. Show the Ramachandran plot associated
with this structure. Find out the residues that surround
the active site of the enzyme. Download the human
hemoglobin structure from PDB. Separate the alpha chain
and beta chain into two separate files. Compare the structures.
Print out the overlapped structures and print out the
aligned primary sequences.