Practical Assignment – Identifying protein interaction interfaces
with Perl scripting.
Calculation of the solvent accessible surface is typically used to identify
interface amino acids in a given protein complex structure. The basic idea
is: amino acids that are exposed in the surface of the unbound protein
and no longer exposed in the complex, are those located in the interface.
The assignment consists in writing a Perl script to automatically identify
the interface residues in the structure of a protein complex.
STEP 1
Protein 1: Arabidopsis Histidine Kinase 4.
File: Arabidopsis_HistidineKinase4.pdb
Protein 2: Arabidopsis Trans Zeatin
File: Arabidopsis_TransZeatin.pdb
Complex: Protein1 in complex with Protein2
File: Arabidopsis_Complex_HistidineHinase4_TransZeatin.pdb
You can use available tools for protein structure visualization (e.g. PyMOL or
RASMOL) to inspect the structures of the proteins and the complex.
STEP 2
We may use the software NACCESS(Hubbard SJ, 1993) to calculate the
residue solvent accessibility (RSA). The basic idea is: we compare the RSA
calculated from the unbound structures (Protein 1 and 2) against the RSA
calculated from the complex structure; then, those residues that show
lower RSA in the complex, are identified as interface residues.
RSA file protein 1: Arabidopsis_HistidineKinase4.rsa
RSA file protein 2: Arabidopsis_TransZeatin.rsa
RSA file complex: Arabidopsis_Complex_HistidineHinase4_TransZeatin.rsa
The beginning and end of an example .rsa file are shown below.
The column 3 (in red) indicates to which protein the residue belongs. Here
we have A=Protein 1, B=Protrein2. For each residue, the amino acid type
is given in the column 1; an integer ID is given in column 4 (in green);
and the absolute RSA is given in column 6 (in blue).
RES
MET
A
126
135.22
69.6
80.60
51.5
54.62
145.6
82.33
52.2
52.89
RES
ASP
A
127
77.65
55.3
75.75
73.8
1.90
5.0
24.29
49.3
53.35
RES
ASP
A
128
108.96
77.6
105.64
102.9
3.33
8.8
38.93
79.1
70.03
RES
ALA
A
129
49.34
45.7
46.49
67.0
2.85
7.4
46.49
65.1
2.85
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RES
ARG
B
390
89.23
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37.4
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89.23
44.3
.00
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.0
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32.58
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41.9
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56.65
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RES
TYR
B
391
26.45
12.4
19.16
10.8
7.29
20.6
17.04
12.5
9.41
STEP 3 – Perl Scripting
First, create a text file with the extension .pl for your script. Then, follow
the steps described in the file ScriptIdentifyInterfaceResidues.pl to finish the
script. The script will read the RSA files (RSA files protein 1, protein 2 and
RSA file complex) to compare the RSA values. The results will be saved in
the output file.
A template script is given in the file ScriptIdentifyInterfaceResidues.pl. Try to
complete the script and execute it to get a list of interface residues. You can use
the visualization tool to verify if the resultant residues are located in the
interface.
Hubbard SJ TJ (1993) ‘NACCESS’, Computer Program. London: Department Molecular Biology.
University College.
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Practical Assignment – Identifying protein interaction interfaces with