Practical Assignment Protein Interface word document

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Practical Assignment



Identifying protein interaction interfaces
with Perl scripting.

C
alculation

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 residu
es

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
tool
s

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 accessib
ility

(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 p
rotein 1:

Arabidopsis_HistidineKinase4.
rsa


RSA file p
rotein
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

37.4

89.23

44.3

.00

.0

32.58

41.9

56.65

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
value
s.

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.