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computer programs Journal of

Applied Crystallography

RPMS: Ramachandran plot for multiple structures

ISSN 0021-8898

K. Gopalakrishnan,a S. Saravanan,a R. Sarania and K. Sekara,b*

Received 23 July 2007 Accepted 27 October 2007

a Bioinformatics Centre (Centre of Excellence in Structural Biology and Bio-computing), Indian Institute of Science, Bangalore 560 012, India, and bSupercomputer Education and Research Centre, Indian Institute of Science, Bangalore 560 012, India. Correspondence e-mail: sekar@physics.iisc.ernet.in

# 2008 International Union of Crystallography Printed in Singapore – all rights reserved

An interactive internet computing server, RPMS (Ramachandran plot for multiple structures) has been developed to visualize the Ramachandran angles of several highly homologous protein structures in a single plot. Options are provided for users to locate the amino acid residues in various regions of the plot. To perform the above, users need to enter the Protein Data Bank (PDB) identification codes. In addition, users can upload the atomic coordinates from the local machine. A Java graphics interface has been deployed and the server has been interfaced with a locally maintained PDB anonymous FTP server, which is updated weekly. The server RPMS can be accessed through the Bioinformatics web server at http://cluster.physics.iisc.ernet.in/rpms/.

1. Introduction The conformation angles that main-chain amino acids make with preceding and succeeding residues play a crucial role in the folding process of the polypeptide chain. The Ramachandran plot is a unique tool to display the conformational angles (’ and ) of the polypeptide chain in a given protein structure (Ramachandran & Sasisekharan, 1968). Structural crystallographers and protein modellers use the Ramachandran plot during every stage of model building for the analysis of stereochemical feasibility. Extensive research has been carried out on conformation angles, based on the concept of steric hindrance (Richardson, 1981; Hooft et al., 1997). Knowledge of amino acid backbone interactions can improve current force fields and enhance the understanding of residues contained in structural motifs (Bosco & Robert, 2005). The existing programs, PROCHECK (Laskowski et al., 1993), WHATIF (Vriend, 1990), Ramachandran plot on the web (Sheik et al., 2002), STING (Neshich et al., 2006) and WEBMOL (Walter, 1997) can be used to generate the Ramachandran plot for only a single protein structure. To the best knowledge of the authors, there is no program available to study the conformation angles (’ and ) of several highly homologous structures (for example, phospholipase A2 and its various mutant and inhibitor complex structures) in a single plot. Thus, an interactive internet computing server to compute and display the conformation angles of multiple structures has been created. The utilities of the server are discussed below.

2. Utilities and perspectives The user must provide the PDB ID codes or upload the threedimensional atomic coordinates in the PDB format of all the desired protein structures from the client machine. The server is interfaced with a locally maintained worldwide remediated PDB anonymous FTP server. The atomic coordinates are updated every week from the parent RCSB-PDB server, and hence the users access up-to-date information available in its archive. Due to computational complexity, the number of protein structures displayed in a single plot is restricted to ten. The proposed server RPMS displays the Ramachandran plot for: J. Appl. Cryst. (2008). 41, 219–221

(i) all the residues of all polypeptide chains of the specified structures; (ii) a particular region thereof (for example, residues 60 to 70); or (iii) a particular chain in the multi-subunit protein structures. The user can compare different chains of a homopolymer, or homologous X-ray structures. Furthermore, the conformational angles of homologous structures solved using both X-ray and NMR data can be seen on a single plot (see the case study below for details). In addition, the server can be used to visualize the distribution of conformation angles of various models available in a particular NMR structure. Options are provided for the user to select a particular model among the ensemble, up to a maximum of ten. Further, it is possible to view the conformation angles in each of the various types of allowed regions (fully, additionally or generously allowed and disallowed), in specific secondary structural element regions (-helical, -sheet or 310-helical), and within the specified limits of ’ and . In addition, the server is able to display the ’ and values for either all the residues in the structure, or a specific residue in the plot. Finally, if the user specifies the preceding (n 1)th residue and/or the succeeding (n + 1)th residue, the conformational angles of the middle (nth) residue can be plotted. In the output screen, the user can click a particular amino acid residue from the list of amino acids provided in a box on the right to highlight the corresponding point in the plot, and vice versa. Thus, the structural biologist can interpret the location of different residues in various homologous structures. The user can zoom into the plot by selecting a rectangular area with the mouse. Clicking the ‘Refresh’ button returns the entire plot. A useful option is provided to display the alignment of amino acid residues available in all the uploaded structures using ClustalW (Thompson et al., 1994). Furthermore, the detailed analysis option displays the statistics and distribution of the conformation angles in various regions (fully, additionally and generously allowed and disallowed regions) of the plot. The web interface of the tool is user-friendly and was developed using HTML and JavaScript. The server software was written using the Java programming language and it runs on an Intel-based Solaris server (3.0 GHz Pentium IV processor, 2 Gbyte of RAM). This operating system was chosen for security, scalability and reliability. Java Servlets and Applets have been used to create the Ramachandoi:10.1107/S0021889807053708

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computer programs dran plot. The server and its utilities have been tested on Windows 95/98/2007 and on the Linux operating system. The server has been validated and the response time is found to be very fast. However, the response time varies depending upon the network speed. The described server is freely accessible over the web for academic and research institutions at http://cluster.physics.iisc.ernet.in/rpms/. Users are requested to send their suggestions and comments to sekar@ physics.iisc.ernet.in or sekar@serc.iisc.ernet.in.

3. Case study Three case studies are outlined below to demonstrate some of the useful various options incorporated in the interactive internet server. A sample output plot for a loop (residues 60 to 70) region containing 11 residues from ten highly homologous structures of bovine pancreatic phospholipase A2 is shown in Fig. 1. The PDB structures include 1IRB (Huang et al., 1996), 1FDK (Sekar et al., 1997a), 1MKS (Sekar et al., 1997b), 1MKV (Sekar et al., 1998a), 1MKT (Sekar et al., 1998b), 1UNE (Sekar & Sundaralingam, 1999), 1KVX, 1KVW (Sekar et al., 1999), 1GH4 (Rajakannan et al., 2002) and 1O2E (Sekar et al., 2003). All the structures consist of a single polypeptide chain of 123 amino acid residues. For clarity, each structure is represented by a different colour in the plot. The surface loop residues (60 to 70) show large conformational differences in their actual three-dimensional structures and in many structures, these residues have weak electron density, suggesting a high degree of flexibility. Even though the structures considered are highly homologous, the surface loop residues seem to adopt completely different conformations. For example, the Val65 residue in 1MKT, 1UNE and 1FDK adopts different conformations, lying in the -sheet, 310-helical and -helical regions, respectively, of the plot. Fig. 2 is a screen shot of the output page from the comparison of three phospholipase A2 structures, two solved by X-ray crystallography (1UNE and 1MKT), the other being a model (model seven) from the ensemble of 20 models available for the NMR structure 1BVM (Yuan et al., 1999). In phospholipase A2 proteins, it was found that the catalytically important His48 residue has very similar

Figure 2 Ramachandran plot for the residue His48 of bovine pancreatic phospholipase A2 from 1UNE (orthorhombic form), 1MKT (trigonal form) and model seven from the ensemble of models from the NMR structure 1BVM.

Figure 3 Ramachandran plot for the four chains of the homopolymeric lectin structure, 1J4S.

conformational angles, as seen in the Ramachandran plot. Thus, the residues have highly rigid conformations, which may be required for enzymatic activity. On the other hand, Fig. 3 shows the screenshot of the conformation angles of all the chains of a homopolymeric tetramer of 1J4S (Pratap et al., 2002) solved using X-ray crystallography. Contrary to expectation, the Ramachandran plot of the four chains of the artocarpin, 1J4S, shows that there exists a variation in the conformation angles between the chains (for example, see Phe71 in all four chains). This flexibility may have implications for the structure–function relationship of this particular lectin. Thus, the server enables the comparison of the conformational angles of residues in highly homologous protein structures. This would help structural biologists to analyse the cause and effects of such differences in conformation.

Figure 1

4. Conclusion

Ramachandran plot for the surface loop region (residues 60–70) in the polypeptide chain of ten highly homologous structures of bovine pancreatic phospholipase A2. Sequence alignment, performed using ClustalW (Thompson et al., 1994), is inset.

It is now possible to analyse the conformational angles of multiple homologous protein structures using this server, which will be useful

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computer programs to the research community working in the area of structural bioinformatics, computational biology and bioinformatics. Further, the server described will be improved in accordance with the progress of, and requests from, the structural biology and bioinformatics communities around the world. The Ramachandran Plot for Multiple Structures computing server is developed and maintained at the Indian Institute of Science, Bangalore 560 012, India, with support from the Department of Biotechnology (DBT), Government of India. Part of this work is supported by the National Bioscience award grant to KS. Finally, KS would like to thank the anonymous referees for their constructive suggestions.

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