Nucleic Acids Research 2006 34(Web Server issue):W128-W132; doi:10.1093/nar/gkl036
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3dSS: 3D structural superposition
K. Sumathi1,
P. Ananthalakshmi1,
M. N. A. Md. Roshan1 and
K. Sekar1,2,*
1 Bioinformatics Centre, Indian Institute of Science Bangalore 560 012, India
2 Supercomputer Education and Research Centre, Indian Institute of Science Bangalore 560 012, India
*To whom correspondence should be addressed. Tel: +91 080 23601409; Fax: +91 080 23600085; Email: sekar{at}physics.iisc.ernet.in, sekar{at}serc.iisc.ernet.in
Received October 6, 2005. Revised November 28, 2005. Accepted November 28, 2005.
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ABSTRACT
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3dSS is a web-based interactive computing server, primarily
designed to aid researchers, to superpose two or several 3D
protein structures. In addition, the server can be effectively
used to find the invariant and common water molecules present
in the superposed homologous protein structures. The molecular
visualization tool RASMOL is interfaced with the server to visualize
the superposed 3D structures with the water molecules (invariant
or common) in the client machine. Furthermore, an option is
provided to save the superposed 3D atomic coordinates in the
client machine. To perform the above, users need to enter Protein
Data Bank (PDB)-id(s) or upload the atomic coordinates in PDB
format. This server uses a locally maintained PDB anonymous
FTP server that is being updated weekly. This program can be
accessed through our Bioinformatics web server at the URL
http://cluster.physics.iisc.ernet.in/3dss/ or
http://10.188.1.15/3dss/.
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INTRODUCTION
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In the post-genome era, the structural and conformational properties
of the 3D protein molecules are of considerable interest owing
to its importance in various biological processes. Owing to
the recent technological advances like high power tunable synchrotron
radiation, powerful number crunching computers and due to ambitious
structural genomics programs in different parts of the world,
there has been a tremendous increase in the number of protein
structures in the Protein Data Bank (PDB) (
1). Now there are
34 000 3D structures available in this entity. Analysis of the
3D structure of protein molecules is greatly enhanced by understanding
the relationship between the individual protein molecules. Furthermore,
knowledge of the 3D structural relationship between different
protein molecules is a key issue in understanding the structure
and function. In order to find the common structural region,
one need to lay one molecule over the other by appropriate rotation
and translation and this process is termed as superposition
of the 3D structures. Several programs are available in the
literature (
2–
9) for this purpose. Most of these programs
are stand-alone versions and have their own merits and demerits.
Two most recent ones are web-based servers, namely, SSM (
8)
and SuperPose (
9). The program SSM uses the procedure of matching
graphs generated using the secondary structural elements followed
by the alignment of C
atoms of the protein molecule. Using one
of the programs (
9), SuperPose, we experienced problems while
trying to superpose multiple structures as well as portions
of molecules. In fact, it was difficult to superpose different
subunits available in multi-subunit protein structures. In addition,
most of the existing programs use only the first model of the
ensemble in the case of structures solved using NMR technique
and there is no provision for the users to superpose all the
models in the ensemble.
It is well known that water molecules play a vital role in protein structures, aiding in stabilizing the protein fold and in ligand design (10–14). In addition, investigations on the invariant water molecules in several well studied homologous protein structures shed light on the specific roles of water molecules such as catalytic, structural and functional (15–18).Thus, it is necessary to find the invariant and common water molecules (for definition see below) in homologous protein structures, for which 3D structural superposition step is crucial. But the existing programs do not have provisions for the users to identify the invariant and common water molecules. Hence, we created a unique computing server to superpose the three-dimensional structures and to find the invariant and common water molecules in homologous protein structures.
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BACKGROUND
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The water molecules present in two highly similar (the best
example is native structure and its mutant structure) or highly
homologous structures (the inhibitor free and inhibitor bound
structure) are known as invariant water molecules. Further,
such situation is also possible in multi-subunit protein structures.
For example, if a molecule has four identical subunits, the
water molecules that interact with the residues in the same
position in different subunits (e.g. subunit A and B) can be
considered as invariant water molecules. On the other hand,
common water molecules are those, which lie at the interface
and interact with the selected subunits.
In the computing server, two widely recognized programs STAMP (19) and ProFit (A. C. R. Martin, http://www.bioinf.org.uk/software/profit/) are deployed for superposition purposes. The program STAMP uses multiple sequence alignment using the amino acid sequence information followed by an initial superposition of structures. In contrast, the program ProFit uses the McLachlan fitting algorithm, essentially a steepest descent minimization (3). The user-friendly molecular visualization tool RASMOL (20) is interfaced to view the superposed molecules in the client machine. This server is developed using PERL, HTML and JAVASCRIPT. Ploticus [Copy right 1998–2002, Stephan C. Grugg (scg{at}jax.org)], a data display engine is used for generating plots to display root mean square deviation (r.m.s.d.) graphically.
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DATA PRESENTATION AND AVAILABILITY
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The software is developed and optimized for Intel based Solaris
(Version 10.0) and is driven by 3.0 GHz pentium IV processor
equipped with 2 GB RD RAM. This operating system is chosen for
better security, scalability and reliability. The software and
its functionalities are well tested on Windows 95/98/2000, Linux
and SGI platforms. During validation of the software, we realized
that two web browsers, namely, NETSCAPE (version 4.7 and 7.2)
and MOZILLA behaved well. To visualize the superposed 3D structures
in the client machine, user needs to interface the molecular
visualization tool RASMOL (only for the first time usage of
the software) and the necessary instructions are provided in
the link (
http://cluster.physics.iisc.ernet.in/3dss/rasmol.html).
The following are the four major options provided in the proposed
computing server.
- Superpose only two structures,
- Superpose several structures,
- Superpose subunits within a structure, and
- Superpose different models present in NMR ensemble.
All the above options, allow users to select the structures
available in the PDB by providing its unique PDB-id or by up-loading
the 3D atomic coordinates (PDB format) from the local hard disk
of the client machine. Once the file is uploaded, the program
automatically culls the input PDB file and displays all the
chain details of the structure in a convenient form. Using the
check box, users can select the entire file, a particular chain
or a portion of the chain(s) for superposition. For the option
(b), firstly the user needs to provide the number of molecules
to be superposed on the fixed molecule. Based on this number,
provisions will be available to the user to either supply the
PDB-id's or upload the 3D atomic coordinates from the client
machine. By default, the server produces only the structural
superposition output. It is worth mentioning that necessary
check boxes are provided in the options (a) and (b) to find
the invariant water molecules present in the structures. Owing
to computational complexity, the number of structures to be
superposed on the fixed molecule is limited to 20 at any given
time. For option (c), the molecule needs to contain more than
one copy of the same polypeptide chain. Using this option, the
users can perform three different calculations: (i) superpose
different subunits present in a selected structure, (ii) superpose
and identify the invariant water molecules and (iii) identify
the common water molecules. The option (d) performs structural
superposition of various models present in a NMR ensemble and
the user can select the models of interest. Here again, the
number of mobile molecules is limited to 20 for superposition.
In the first three major options, the server displays all models
of NMR structure so that the users can select any particular
model using the pull-down menu. As mentioned above, two superposition
programs (STAMP and ProFit) are deployed for structural superposition
and the user has the freedom to choose a program of interest.
A detailed output containing r.m.s.d. values, sequence identity,
rotation matrix, translation vector and so on will be displayed.
Most importantly, users can save the superposed atomic coordinates
in the local client machine for further analysis. The users
of the program are requested to cite this article and the URL
address in their research proceedings.
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CASE STUDY
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The output of a typical superposition of 12 (native, mutants
and inhibitor complexes) structures of recombinant phospholipase
A
2 (
21–
23) (1VL9, 1UNE, 1MKS, 1FDK, 1MKV, 1MKT, 1KVX,
1O2E, 1VKQ, 1IRB, 1GH4 and 1C74 solved using X-ray crystallography
is shown in
Figure 1. The PDB-id 1VL9 is used as a fixed molecule
and the remaining 11 structures are treated as mobile molecules
(molecules to be superposed on the fixed molecule). The program
STAMP is used for superposition. The top panel shows a detailed
output like status of superposition, sequence identity, stamp
score and r.m.s.d. values. The RASMOL graphics panel on the
right shows the superposition of all the structures in different
colors.
Figure 2 displays the invariant water molecules in six
different crystal structures of Oligo-peptide binding proteins
(OppA) (
24). The structure (1B4Z {457}) is used as fixed molecule
and the remaining five (1B32 {437}, 1B3F {455}, 1B3G {356},
1B46 {374} and 1B51 {433}) are treated as mobile molecules.
The number within braces represents the number of water molecules
present in the 3D structures. The server reports 209 invariant
water molecules in all the structures. It is interesting to
note that 58.7% (209/356) of the water molecules is invariant.
The invariant water molecules are identified after superposition
within a distance of 1.8 Å (between the water molecules).
Figure 3 shows the invariant water molecules between different
subunits of a tetramer. The PDB-id used here is 1JAC (
25) and
it has eight different chains [four heavy chains (A, C, E, G)
and four light chains (B, D, F, H)]. The superposition of different
chains A, B, C, D (green) and E, F, G, H (red) along with 36
invariant water molecules and their interactions with the subunits
are shown. The calculation is performed using the options ‘Superpose
subunits within a structure’ and ‘identify invariant
water molecules’. The common water molecules between two
different subunits (only subunit A and B are used) of a tetrameric
protein [PDB-id 1J4S (
26)] are shown in
Figure 4. Here, the
options (c), ‘Superpose subunits within a structure’
and ‘Identify common water molecules’ are used.
The subunits A and B are shown in green and red colors, respectively.
There are eight water molecules (blue), which are common between
the chains A and B.
View larger version (56K):
[in this window]
[in a new window]
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Figure 1 The screen snapshot shows the superposition of 12 structures of recombinant phospholipase A2. The top panel shows the status of superposition and the right RASMOL graphics panel displays the superposition in different colors (see the last column of the top panel for coloring scheme). The bottom left panel shows the graphical display of the r.m.s.d. values of the 12 structures and is generated using the data display engine, Ploticus. It is clear from the plot that the region 60–70 is having large deviations compared with the remaining portion of the molecule.
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View larger version (59K):
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[in a new window]
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Figure 2 The screen shot displays the superposition of six OppA along with 209 invariant water molecules. This is carried out using the option (b), ‘Superpose several structures’ and ‘Superpose and identify invariant water molecules’.
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View larger version (47K):
[in this window]
[in a new window]
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Figure 3 The output panel depicts the superposition of eight different chains along with 36 invariant water molecules in PDB-id: 1JAC. The chains A, B, C, D (fixed) are colored green and the color red is used for the chains E, F, G, H (mobile). The invariant water molecules are having the same color as the corresponding subunits.
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View larger version (36K):
[in this window]
[in a new window]
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Figure 4 The output shows the common water molecules between the subunits A and B. The RASMOL panel shows eight common water molecules (blue color). This is carried out using the option (c) ‘Superpose subunits within a structure and ‘identify common water molecules’.
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CONCLUSIONS
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At the outset, 3dSS is created to better serve the research
community working in the area of structural bioinformatics.
This computing server is very useful to superpose either complete
or partial structures. Furthermore, the server can effectively
be used to identify the invariant and common water molecules.
The knowledge base (PDB) used by the server is up-to-date and
hence the user will be able to access the latest information
available in the PDB. As described, it is tempting to conclude
that the software will certainly be beneficial for many macromolecular
crystallographers and the undergraduate/graduate students working
in the area of structural bioinformatics.
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ACKNOWLEDGEMENTS
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The corresponding author (K.S.) thanks Dr Geoffrey Barton and
Dr Andrew Martin for permitting to use their superposition programs
in the computing server. The authors thank Ch. Kiran Kumar for
his help at the initial stages of this work. One of the authors
(K.S.) thanks Ms P. Mridula for critical manuscript reading.
The proposed search engine is developed and maintained at the
Bionformatics Centre, Indian Institute of Science, Bangalore
560 012, India. All the contributing authors acknowledge the
use of the facilities: the Interactive Graphics Based Molecular
Modeling, Bioinformatics centre and the Supercomputer Education
and Research Centre. The first two facilities are supported
by the Department of Biotechnology (DBT), Government of India.
We are grateful for the individual (K.S.) project support from
DBT. A part of this work is supported by the Institute wide
Computational Genomics Program. The Open Access publication
charges for this article were waived by Oxford University Press.
Conflict of interest statement. None declared.
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Footnotes
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This work is dedicated to the late professor M. Sundaralingam
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors
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