RIBFIND: a web server for identifying rigid bodies in protein structures and to aid flexible fitting into cryo EM maps

Arun Prasad Pandurangan,Maya Topf

doi:10.1093/bioinformatics/bts446

Arun Prasad Pandurangan, Maya Topf

Open Access

https://doi.org/10.1093/bioinformatics/bts446

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Abstract

To better analyze low-resolution cryo electron microscopy maps of macromolecular assemblies, component atomic structures frequently have to be flexibly fitted into them. Reaching an optimal fit and preventing the fitting process from getting trapped in local minima can be significantly improved by identifying appropriate rigid bodies (RBs) in the fitted component. Here we present the RIBFIND server, a tool for identifying RBs in protein structures. The server identifies RBs in proteins by calculating spatial proximity between their secondary structural elements. The RIBFIND web server and its standalone program are available at http://ribfind.ismb.lon.ac.uk. a.pandurangan@mail.cryst.bbk.ac.uk Supplementary data are available at Bioinformatics online.

Highlights

Studying the structure and function of macromolecular assemblies using cryo electron microscopy techniques is becoming increasingly popular (Orlova and Saibil, 2011)
To use RIBFIND a web server has been set up. It accepts the following It worth noting that in cases where the ‘close’ conformation is inputs (Fig. 1a): (i) the protein coordinates in PDB file format; (ii) a may not result in the ‘open’ conformation during flexible fitting description of the protein secondary structural elements (SSEs) in DSSP (Kabsch and Sander, 1983) format into the corresponding ‘open’ map (e.g. Actin subunit,; (iii) the Pandurangan and Topf, 2012)
The rigid bodies (RBs) set that is displayed by default is the one that contains the maximal number of clusters identified by RIBFIND (we previously showed that using this set in cryo electron microscopy (cryo EM) flexible fitting produced the best results in most cases (Pandurangan and Topf, 2012))

Summary

INTRODUCTION

Studying the structure and function of macromolecular assemblies using cryo electron microscopy (cryo EM) techniques is becoming increasingly popular (Orlova and Saibil, 2011). When the assembly components in the density map are in a different conformation from their corresponding atomic structures (Orlova and Saibil, 2011), fitting the components rigidly may not result in a satisfying pseudo-atomic model. These compact units can be arranged hierarchically, which can lead to the prediction of a comprehensive set of protein dynamic pathways (Lesk and Rose, 1981) One such program uses a graph theory-based approach to model the atomic structure of the molecule as a bondbending network and applies a fast combinatorial algorithm to determine the rigidity of this network, thereby the RBs of the molecule (FIRST) (Jacobs, et al, 2001). We present a web server and a standalone tool for RIBFIND

METHODS

CASE STUDY

Findings

CONCLUSION