Literature DB >> 30048836

Microscopic view of lipids and their diverse biological functions.

Po-Chao Wen1, Paween Mahinthichaichan1, Noah Trebesch1, Tao Jiang1, Zhiyu Zhao1, Eric Shinn1, Yuhang Wang1, Mrinal Shekhar1, Karan Kapoor1, Chun Kit Chan1, Emad Tajkhorshid2.   

Abstract

Biological membranes and their diverse lipid constituents play key roles in a broad spectrum of cellular and physiological processes. Characterization of membrane-associated phenomena at a microscopic level is therefore essential to our fundamental understanding of such processes. Due to the semi-fluid and dynamic nature of lipid bilayers, and their complex compositions, detailed characterization of biological membranes at an atomic scale has been refractory to experimental approaches. Computational modeling and simulation offer a highly complementary toolset with sufficient spatial and temporal resolutions to fill this gap. Here, we review recent molecular dynamics studies focusing on the diversity of lipid composition of biological membranes, or aiming at the characterization of lipid-protein interaction, with the overall goal of dissecting how lipids impact biological roles of the cellular membranes.
Copyright © 2018 Elsevier Ltd. All rights reserved.

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Year:  2018        PMID: 30048836      PMCID: PMC6221948          DOI: 10.1016/j.sbi.2018.07.003

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


  60 in total

1.  CHARMM-GUI Martini Maker for modeling and simulation of complex bacterial membranes with lipopolysaccharides.

Authors:  Pin-Chia Hsu; Bart M H Bruininks; Damien Jefferies; Paulo Cesar Telles de Souza; Jumin Lee; Dhilon S Patel; Siewert J Marrink; Yifei Qi; Syma Khalid; Wonpil Im
Journal:  J Comput Chem       Date:  2017-08-03       Impact factor: 3.376

2.  Atomistic insight into lipid translocation by a TMEM16 scramblase.

Authors:  Neville P Bethel; Michael Grabe
Journal:  Proc Natl Acad Sci U S A       Date:  2016-11-21       Impact factor: 11.205

3.  Molecular Simulations of Mixed Lipid Bilayers with Sphingomyelin, Glycerophospholipids, and Cholesterol.

Authors:  Indrani Bera; Jeffery B Klauda
Journal:  J Phys Chem B       Date:  2017-05-12       Impact factor: 2.991

4.  Curvature-undulation coupling as a basis for curvature sensing and generation in bilayer membranes.

Authors:  Ryan P Bradley; Ravi Radhakrishnan
Journal:  Proc Natl Acad Sci U S A       Date:  2016-08-16       Impact factor: 11.205

5.  Through the Lipopolysaccharide Glass: A Potent Antimicrobial Peptide Induces Phase Changes in Membranes.

Authors:  Damien Jefferies; Pin-Chia Hsu; Syma Khalid
Journal:  Biochemistry       Date:  2017-03-07       Impact factor: 3.162

6.  Effect of Lipid Charge on Membrane Immersion of Cytochrome P450 3A4.

Authors:  Veronika Navrátilová; Markéta Paloncýová; Karel Berka; Michal Otyepka
Journal:  J Phys Chem B       Date:  2016-10-19       Impact factor: 2.991

Review 7.  Force Field Development for Lipid Membrane Simulations.

Authors:  Alexander P Lyubartsev; Alexander L Rabinovich
Journal:  Biochim Biophys Acta       Date:  2016-01-04

8.  Free Energy Landscape of Lipid Interactions with Regulatory Binding Sites on the Transmembrane Domain of the EGF Receptor.

Authors:  George Hedger; David Shorthouse; Heidi Koldsø; Mark S P Sansom
Journal:  J Phys Chem B       Date:  2016-05-09       Impact factor: 2.991

9.  Bilayer-Mediated Structural Transitions Control Mechanosensitivity of the TREK-2 K2P Channel.

Authors:  Prafulla Aryal; Viwan Jarerattanachat; Michael V Clausen; Marcus Schewe; Conor McClenaghan; Liam Argent; Linus J Conrad; Yin Y Dong; Ashley C W Pike; Elisabeth P Carpenter; Thomas Baukrowitz; Mark S P Sansom; Stephen J Tucker
Journal:  Structure       Date:  2017-04-06       Impact factor: 5.006

10.  Spontaneous inward opening of the dopamine transporter is triggered by PIP2-regulated dynamics of the N-terminus.

Authors:  George Khelashvili; Nathaniel Stanley; Michelle A Sahai; Jaime Medina; Michael V LeVine; Lei Shi; Gianni De Fabritiis; Harel Weinstein
Journal:  ACS Chem Neurosci       Date:  2015-08-17       Impact factor: 4.418

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  10 in total

1.  Characterization of Lipid-Protein Interactions and Lipid-Mediated Modulation of Membrane Protein Function through Molecular Simulation.

Authors:  Melanie P Muller; Tao Jiang; Chang Sun; Muyun Lihan; Shashank Pant; Paween Mahinthichaichan; Anda Trifan; Emad Tajkhorshid
Journal:  Chem Rev       Date:  2019-04-12       Impact factor: 60.622

Review 2.  Computational Dissection of Membrane Transport at a Microscopic Level.

Authors:  Tao Jiang; Po-Chao Wen; Noah Trebesch; Zhiyu Zhao; Shashank Pant; Karan Kapoor; Mrinal Shekhar; Emad Tajkhorshid
Journal:  Trends Biochem Sci       Date:  2019-12-05       Impact factor: 13.807

3.  Integrating hydrogen-deuterium exchange mass spectrometry with molecular dynamics simulations to probe lipid-modulated conformational changes in membrane proteins.

Authors:  Chloe Martens; Mrinal Shekhar; Andy M Lau; Emad Tajkhorshid; Argyris Politis
Journal:  Nat Protoc       Date:  2019-10-11       Impact factor: 13.491

4.  Targeting lipid-protein interaction to treat Syk-mediated acute myeloid leukemia.

Authors:  Indira Singaram; Ashutosh Sharma; Shashank Pant; Muyun Lihan; Mi-Jeong Park; Melissa Pergande; Pawanthi Buwaneka; Yusi Hu; Nadim Mahmud; You-Me Kim; Stephanie Cologna; Vladimir Gevorgyan; Irum Khan; Emad Tajkhorshid; Wonhwa Cho
Journal:  Nat Chem Biol       Date:  2022-10-13       Impact factor: 16.174

5.  Probing cholesterol binding and translocation in P-glycoprotein.

Authors:  Sundar Thangapandian; Karan Kapoor; Emad Tajkhorshid
Journal:  Biochim Biophys Acta Biomembr       Date:  2019-10-30       Impact factor: 3.747

Review 6.  Computational Modeling of Realistic Cell Membranes.

Authors:  Siewert J Marrink; Valentina Corradi; Paulo C T Souza; Helgi I Ingólfsson; D Peter Tieleman; Mark S P Sansom
Journal:  Chem Rev       Date:  2019-01-09       Impact factor: 72.087

Review 7.  The energetics of protein-lipid interactions as viewed by molecular simulations.

Authors:  Robin A Corey; Phillip J Stansfeld; Mark S P Sansom
Journal:  Biochem Soc Trans       Date:  2020-02-28       Impact factor: 4.919

8.  Phosphatidylinositol 4-kinase III beta regulates cell shape, migration, and focal adhesion number.

Authors:  Patricia Bilodeau; Daniel Jacobsen; Denise Law-Vinh; Jonathan M Lee
Journal:  Mol Biol Cell       Date:  2020-06-17       Impact factor: 4.138

9.  Non-covalent double bond sensors for gas-phase infrared spectroscopy of unsaturated fatty acids.

Authors:  Carla Kirschbaum; Kim Greis; Maike Lettow; Sandy Gewinner; Wieland Schöllkopf; Gerard Meijer; Gert von Helden; Kevin Pagel
Journal:  Anal Bioanal Chem       Date:  2021-05-06       Impact factor: 4.142

Review 10.  Every Detail Matters. That Is, How the Interaction between Gα Proteins and Membrane Affects Their Function.

Authors:  Agnieszka Polit; Paweł Mystek; Ewa Błasiak
Journal:  Membranes (Basel)       Date:  2021-03-20
  10 in total

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