Molecular dynamics simulations of membrane proteins

Biophysics Reviews
Turgut Baştuğ, Serdar Kuyucak

Abstract

Membrane proteins control the traffic across cell membranes and thereby play an essential role in cell function from transport of various solutes to immune response via molecular recognition. Because it is very difficult to determine the structures of membrane proteins experimentally, computational methods have been increasingly used to study their structure and function. Here we focus on two classes of membrane proteins-ion channels and transporters-which are responsible for the generation of action potentials in nerves, muscles, and other excitable cells. We describe how computational methods have been used to construct models for these proteins and to study the transport mechanism. The main computational tool is the molecular dynamics (MD) simulation, which can be used for everything from refinement of protein structures to free energy calculations of transport processes. We illustrate with specific examples from gramicidin and potassium channels and aspartate transporters how the function of these membrane proteins can be investigated using MD simulations.

References

Jan 1, 1989·Annual Review of Biophysics and Biophysical Chemistry·D L Beveridge, F M DiCapua
Mar 1, 1971·Proceedings of the National Academy of Sciences of the United States of America·D W Urry
Jan 1, 1994·Annual Review of Biophysics and Biomolecular Structure·B Roux, M Karplus
Feb 1, 1996·Journal of Molecular Graphics·W HumphreyK Schulten
Oct 17, 1996·Nature·N Zerangue, M P Kavanaugh
Nov 5, 1999·Biophysical Journal·T W AllenS H Chung
Nov 5, 1999·Biophysical Journal·S H ChungS Kuyucak
Apr 29, 2000·Nature·J Aqvist, V Luzhkov
Nov 2, 2001·Nature·S Bernèche, B Roux
Feb 21, 2002·Quarterly Reviews of Biophysics·D P TielemanM S Sansom
Mar 21, 2002·Nature Reviews. Cancer·Michael M GottesmanSusan E Bates
Jun 25, 2002·Biophysical Journal·Shin-Ho ChungSerdar Kuyucak
Jul 19, 2002·Biophysical Journal·Indira H ShrivastavaMark S P Sansom
Aug 31, 2002·Biophysical Journal·Scott EdwardsShin-Ho Chung
Apr 2, 2003·Biophysical Journal·Toby W AllenShin-Ho Chung
Jul 3, 2003·Proceedings of the National Academy of Sciences of the United States of America·Simon Bernèche, Benoît Roux
Jun 11, 2004·Annual Review of Biochemistry·Amy L Davidson, Jue Chen
May 5, 2005·Annual Review of Biophysics and Biomolecular Structure·Benoît Roux
Jul 9, 2005·Science·Stephen B LongRoderick Mackinnon
Oct 14, 2005·Journal of Computational Chemistry·James C PhillipsKlaus Schulten
Sep 1, 2006·Nature·Roger J P Dawson, Kaspar P Locher
Jan 12, 2007·Biochemistry and Cell Biology = Biochimie Et Biologie Cellulaire·Eliud O OlooD Peter Tieleman
Mar 17, 2007·The Journal of Chemical Physics·Turgut Baştuğ, Serdar Kuyucak
Dec 14, 2007·Nature·J Preben MorthPoul Nissen
Jun 3, 2008·Biophysical Journal·Zhijian Huang, Emad Tajkhorshid
Aug 6, 2008·The Journal of Biological Chemistry·Indira H ShrivastavaIvet Bahar
Aug 14, 2008·The Journal of Physical Chemistry. B·Denis Bucher, Serdar Kuyucak
Sep 16, 2008·Biophysical Journal·Po-Chao Wen, Emad Tajkhorshid
Mar 17, 2010·Proceedings of the National Academy of Sciences of the United States of America·Morten Ø JensenDavid E Shaw
Jun 17, 2010·Physiology·Yi WangEmad Tajkhorshid

❮ Previous
Next ❯

Citations

Apr 2, 2015·IET Nanobiotechnology·Samaneh DavoudiMahdi Zaeifi Yamchi
Jan 22, 2014·Physical Chemistry Chemical Physics : PCCP·Yinglong MiaoJ Andrew McCammon
Mar 27, 2013·Marine Drugs·M Harunur RashidSerdar Kuyucak
Nov 19, 2014·Future Medicinal Chemistry·Serdar Kuyucak, Raymond S Norton
Mar 8, 2016·Biochimica Et Biophysica Acta·Matti Javanainen, Hector Martinez-Seara

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.