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. 2017 Nov 20:5:e4013.
doi: 10.7717/peerj.4013. eCollection 2017.

PBxplore: a tool to analyze local protein structure and deformability with Protein Blocks

Jonathan Barnoud #  1   2   3   4   5 , Hubert Santuz #  1   2   3   4   6 , Pierrick Craveur  1   2   3   4   7 , Agnel Praveen Joseph  1   2   3   4   8 , Vincent Jallu  9 , Alexandre G de Brevern #  1   2   3   4 , Pierre Poulain #  1   2   3   4   10
Affiliations

PBxplore: a tool to analyze local protein structure and deformability with Protein Blocks

Jonathan Barnoud et al. PeerJ. .

Abstract

This paper describes the development and application of a suite of tools, called PBxplore, to analyze the dynamics and deformability of protein structures using Protein Blocks (PBs). Proteins are highly dynamic macromolecules, and a classical way to analyze their inherent flexibility is to perform molecular dynamics simulations. The advantage of using small structural prototypes such as PBs is to give a good approximation of the local structure of the protein backbone. More importantly, by reducing the conformational complexity of protein structures, PBs allow analysis of local protein deformability which cannot be done with other methods and had been used efficiently in different applications. PBxplore is able to process large amounts of data such as those produced by molecular dynamics simulations. It produces frequencies, entropy and information logo outputs as text and graphics. PBxplore is available at https://github.com/pierrepo/PBxplore and is released under the open-source MIT license.

Keywords: Deformability; Protein; Protein blocks; Python; Structural alphabet; Structure.

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Conflict of interest statement

The authors declare there are no competing interests.

Figures

Figure 1
Figure 1
(A) The 16 protein blocks (PBs) represented in balls with carbon atoms in gray, oxygen atoms in red and nitrogen atoms in purple (hydrogen atoms are not represented). (B) The barstar protein (PDB ID 1AY7 (Sevcík et al., 1998)) represented in cartoon with alpha-helices in blue, beta-strands in red and coil in pink. These representations were generated using PyMOL software (DeLano, 2002) (C) PBs sequence obtained from PBs assignment. Z is a dummy PB, meaning that no PB can be assigned to this position.
Figure 2
Figure 2. PBxplore is based on 3 programs that can be chained to build a structure analysis pipeline.
Main input file types (.pdb, MD trajectory, MD topology), output files (.fasta, .png, .Neq, .pdf) and parameters (beginning with a single or double dash) are indicated.
Figure 3
Figure 3. Distribution of PBs for the β3 integrin along the protein sequence.
On the x-axis are found the 690 position residues and on the y-axis the 16 consecutive PBs from a to p (the two first and two last positions associated to “Z” have no assignment): (A) for the entire protein; (B) for the PSI domain only (residues 1 to 56). The dashed zone pinpoints residue 33 to 35.
Figure 4
Figure 4. (A) Neq versus residue number for the PSI domain (residues 1 to 56); (B) comparison between RMSF and Neq.
Figure 5
Figure 5. WebLogo-like representation of PBs for the PSI domain of the β3 integrin.
PBs in red roughly correspond to α-helices, PBs in blue to β-sheets and PBs in green to coil.
See this image and copyright information in PMC

References

    1. Ascher D, Dubois PF, Hinsen K, James JH, Oliphant T. Numerical Python. Lawrence Livermore National Laboratory, Livermore, CATechnical Report UCRL-MA-128569. 1999
    1. Atilgan AR, Turgut D, Atilgan C. Screened Nonbonded interactions in native proteins manipulate optimal paths for robust residue communication. Biophysical Journal. 2007;92(9):3052–3062. doi: 10.1529/biophysj.106.099440. - DOI - PMC - PubMed
    1. Barnoud J, Santuz H, De Brevern AG, Poulain P. 2017. PBxplore (v1.3.8): a program to explore protein structures with Protein Blocks. Zenodo.
    1. Bassi S. A primer on python for life science researchers. PLOS Computational Biology. 2007;3(11):e199. doi: 10.1371/journal.pcbi.0030199. - DOI - PMC - PubMed
    1. Bernstein FC, Koetzle TF, Williams GJ, Meyer EF, Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M. The Protein Data Bank: a computer-based archival file for macromolecular structures. Journal of Molecular Biology. 1977;112(3):535–542. - PubMed