Literature DB >> 32036279

Dynamic protein interfaces and conformational landscapes of membrane protein complexes.

Shalmali A Kharche1, Durba Sengupta2.   

Abstract

Dynamic interactions between membrane proteins span a range of spatio-temporal scales and determine several cellular outcomes. Experimental methods in structure determination are able to resolve static protein-protein complexes at the membrane, but lack the resolution required for disordered, flexible domains and dynamic interactions. Computational approaches could bridge the resolution gap and help to unravel molecular details underlying these crucial interactions. Here, we review current approaches to predict dynamic membrane-protein complexes, with a focus on G protein-coupled receptors (GPCRs). Ensemble coarse-grain simulations have captured the conformational heterogeneity of several membrane receptor complexes. In conjunction, the conformational plasticity of protein interfaces especially encompassing unstructured domains is well represented by atomistic simulations. A combined integrative approach will pave the way forward to understand the molecular details of these dynamic complexes.
Copyright © 2020 Elsevier Ltd. All rights reserved.

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Year:  2020        PMID: 32036279     DOI: 10.1016/j.sbi.2020.01.001

Source DB:  PubMed          Journal:  Curr Opin Struct Biol        ISSN: 0959-440X            Impact factor:   6.809


  8 in total

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2.  Harnessing Deep Learning for Optimization of Lennard-Jones Parameters for the Polarizable Classical Drude Oscillator Force Field.

Authors:  Payal Chatterjee; Mert Y Sengul; Anmol Kumar; Alexander D MacKerell
Journal:  J Chem Theory Comput       Date:  2022-04-01       Impact factor: 6.578

3.  Guardians of the Cell: State-of-the-Art of Membrane Proteins from a Computational Point-of-View.

Authors:  Nícia Rosário-Ferreira; Catarina Marques-Pereira; Raquel P Gouveia; Joana Mourão; Irina S Moreira
Journal:  Methods Mol Biol       Date:  2021

4.  All-Atom Molecular Dynamics Elucidating Molecular Mechanisms of Single-Transmembrane Model Peptide Dimerization in a Lipid Bilayer.

Authors:  Hayato Itaya; Kota Kasahara; Qilin Xie; Yoshiaki Yano; Katsumi Matsuzaki; Takuya Takahashi
Journal:  ACS Omega       Date:  2021-04-22

5.  Computational modeling and experimental validation of the EPI-X4/CXCR4 complex allows rational design of small peptide antagonists.

Authors:  Pandian Sokkar; Mirja Harms; Christina Stürzel; Andrea Gilg; Gönül Kizilsavas; Martina Raasholm; Nico Preising; Manfred Wagner; Frank Kirchhoff; Ludger Ständker; Gilbert Weidinger; Benjamin Mayer; Jan Münch; Elsa Sanchez-Garcia
Journal:  Commun Biol       Date:  2021-09-22

6.  Connexins and Pannexins-Similarities and Differences According to the FOD-M Model.

Authors:  Irena Roterman; Katarzyna Stapor; Piotr Fabian; Leszek Konieczny
Journal:  Biomedicines       Date:  2022-06-25

7.  Transient Unfolding and Long-Range Interactions in Viral BCL2 M11 Enable Binding to the BECN1 BH3 Domain.

Authors:  Arvind Ramanathan; Akash Parvatikar; Srinivas C Chennubhotla; Yang Mei; Sangita C Sinha
Journal:  Biomolecules       Date:  2020-09-11

Review 8.  Modeling the Dynamics of Protein-Protein Interfaces, How and Why?

Authors:  Ezgi Karaca; Chantal Prévost; Sophie Sacquin-Mora
Journal:  Molecules       Date:  2022-03-11       Impact factor: 4.411

  8 in total

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