Peer Review #2 of "PBxplore: a tool to analyze local protein structure and deformability with Protein Blocks (v0.1)"

ABSTRACTProteins are highly dynamic macromolecules. A classical way to analyze their inner flexibility is to perform molecular dynamics simulations. In this context, we present the advantage to use small structural prototypes, namely the Protein Blocks (PBs). PBs give a good approximation of the local structure of the protein backbone. More importantly, by reducing the conformational complexity of protein structures, they allow analyzes of local protein deformability which cannot be done with other methods and had been used efficiently in different applications. PBxplore is a suite of tools to analyze the dynamics and deformability of protein structures using PBs. It is able to process large amount of data such as those produced by molecular dynamics simulations. It produces various outputs with text and graphics, such as frequencies, entropy and information logo. PBxplore is available at https://github.com/pierrepo/PBxplore and is released under the open-source MIT license.

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

PeerJ ◽

10.7717/peerj.4013 ◽

2017 ◽

Vol 5 ◽

pp. e4013 ◽

Cited By ~ 12

Author(s):

Jonathan Barnoud ◽

Hubert Santuz ◽

Pierrick Craveur ◽

Agnel Praveen Joseph ◽

Vincent Jallu ◽

...

Keyword(s):

Molecular Dynamics ◽

Protein Structure ◽

Molecular Dynamics Simulations ◽

Open Source ◽

Local Structure ◽

Protein Structures ◽

Local Protein Structure ◽

Dynamics Simulations ◽

Protein Blocks ◽

Local Protein

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.

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LOCUSTRA: Accurate Prediction of Local Protein Structure Using a Two-Layer Support Vector Machine Approach

Journal of Chemical Information and Modeling ◽

10.1021/ci800178a ◽

2008 ◽

Vol 48 (9) ◽

pp. 1903-1908 ◽

Cited By ~ 30

Author(s):

Olav Zimmermann ◽

Ulrich H. E. Hansmann

Keyword(s):

Support Vector Machine ◽

Protein Structure ◽

Accurate Prediction ◽

Support Vector ◽

Local Protein Structure ◽

Local Protein

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Determination of Local Protein Structure by Spin Label Difference 2D NMR: The Region Neighboring Asp61 of Subunit c of the F1Fo ATP Synthase

Biochemistry ◽

10.1021/bi00005a020 ◽

1995 ◽

Vol 34 (5) ◽

pp. 1635-1645 ◽

Cited By ~ 60

Author(s):

Mark E. Girvin ◽

Robert H. Fillingame

Keyword(s):

Protein Structure ◽

Atp Synthase ◽

Spin Label ◽

2D Nmr ◽

Subunit C ◽

F1fo Atp Synthase ◽

Local Protein Structure ◽

Local Protein

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Crystal Structures of [Fe]-Hydrogenase from Methanolacinia paynteri Suggest a Path of the FeGP-Cofactor Incorporation Process

Inorganics ◽

10.3390/inorganics8090050 ◽

2020 ◽

Vol 8 (9) ◽

pp. 50

Author(s):

Gangfeng Huang ◽

Francisco Javier Arriaza-Gallardo ◽

Tristan Wagner ◽

Seigo Shima

Keyword(s):

Crystal Structure ◽

Protein Structure ◽

Guanosine Monophosphate ◽

Amino Group ◽

Prosthetic Group ◽

Closed Conformation ◽

Open Conformation ◽

Local Protein Structure ◽

Local Protein

[Fe]-hydrogenase (Hmd) catalyzes the reversible heterolytic cleavage of H2, and hydride transfer to methenyl-tetrahydromethanopterin (methenyl-H4MPT+). The iron-guanylylpyridinol (FeGP) cofactor, the prosthetic group of Hmd, can be extracted from the holoenzyme and inserted back into the protein. Here, we report the crystal structure of an asymmetric homodimer of Hmd from Methanolacinia paynteri (pHmd), which was composed of one monomer in the open conformation with the FeGP cofactor (holo-form) and a second monomer in the closed conformation without the cofactor (apo-form). In addition, we report the symmetric pHmd-homodimer structure in complex with guanosine monophosphate (GMP) or guanylylpyridinol (GP), in which each ligand was bound to the protein, where the GMP moiety of the FeGP-cofactor is bound in the holo-form. Binding of GMP and GP modified the local protein structure but did not induce the open conformation. The amino-group of the Lys150 appears to interact with the 2-hydroxy group of pyridinol ring in the pHmd–GP complex, which is not the case in the structure of the pHmd–FeGP complex. Lys150Ala mutation decreased the reconstitution rate of the active enzyme with the FeGP cofactor at the physiological pH. These results suggest that Lys150 might be involved in the FeGP-cofactor incorporation into the Hmd protein in vivo.

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