Dissipative electro-elastic network model of protein electrostatics

Physical Biology
Daniel R MartinDmitry V Matyushov

Abstract

We propose a dissipative electro-elastic network model to describe the dynamics and statistics of electrostatic fluctuations at active sites of proteins. The model combines the harmonic network of residue beads with overdamped dynamics of the normal modes of the network characterized by two friction coefficients. The electrostatic component is introduced to the model through atomic charges of the protein force field. The overall effect of the electrostatic fluctuations of the network is recorded through the frequency-dependent response functions of the electrostatic potential and electric field at the protein active site. We also consider the dynamics of displacements of individual residues in the network and the dynamics of distances between pairs of residues. The model is tested against loss spectra of residue displacements and the electrostatic potential and electric field at the heme's iron from all-atom molecular dynamics simulations of three hydrated globular proteins.

References

Mar 17, 1995·Science·P G WolynesD Thirumalai
Feb 1, 1996·Journal of Molecular Graphics·W HumphreyK Schulten
Feb 13, 2001·Biophysical Journal·A R AtilganI Bahar
Apr 5, 2001·Protein Engineering·F Tama, Y H Sanejouand
Jan 31, 2002·Proceedings of the National Academy of Sciences of the United States of America·Bertil Halle
Mar 7, 2002·Proceedings of the National Academy of Sciences of the United States of America·Jane S Richardson, David C Richardson
Jun 13, 2002·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·K AchterholdF G Parak
Jul 20, 2002·Biophysical Chemistry·Markus MeuwlyMartin Karplus
Mar 8, 2003·Quarterly Reviews of Biophysics·Frank GabelGiuseppe Zaccai
Jul 25, 2003·Proceedings of the National Academy of Sciences of the United States of America·Florence TamaCharles L Brooks
Jul 21, 2004·Journal of Computational Chemistry·Felix AutenriethZaida Luthey-Schulten
Sep 28, 2004·Proceedings of the National Academy of Sciences of the United States of America·P W FenimoreR D Young
May 19, 2005·Journal of the American Chemical Society·Daniele AndreattaMark A Berg
Aug 2, 2005·Biophysical Journal·Mingyang Lu, Jianpeng Ma
Oct 14, 2005·Journal of Computational Chemistry·James C PhillipsKlaus Schulten
Dec 20, 2005·Accounts of Chemical Research·Wei MinX Sunney Xie
Dec 20, 2005·Biophysical Journal·Paula Petrone, Vijay S Pande
Dec 31, 2005·Physical Review Letters·Dengming Ming, Michael E Wall
May 13, 2006·Annual Review of Biophysics and Biomolecular Structure·Florence Tama, Charles L Brooks
Jun 28, 2006·The Journal of Physical Chemistry. B·Marie SkepöThomas Arnebrant
Oct 20, 2006·Biochimica Et Biophysica Acta·Arieh WarshelWilliam W Parson
Mar 16, 2007·Physical Review Letters·F PontiggiaH Orland
Aug 2, 2007·Journal of the American Chemical Society·Michael S LawrenceDavid R Liu
Oct 30, 2007·Methods in Cell Biology·Feng DongNathan A Baker
Nov 16, 2007·Proceedings of the National Academy of Sciences of the United States of America·Luyuan ZhangDongping Zhong
Dec 14, 2007·Nature·Katherine Henzler-Wildman, Dorothee Kern
Dec 21, 2007·Proceedings of the National Academy of Sciences of the United States of America·Simon EbbinghausMartina Havenith
Mar 4, 2008·The Journal of Physical Chemistry. B·Benjamin T MillerBernard R Brooks
Apr 25, 2008·The Journal of Chemical Physics·David N LeBard, Dmitry V Matyushov
Jul 29, 2008·Biophysical Journal·Edward LymanGregory A Voth
Oct 4, 2008·Proceedings of the National Academy of Sciences of the United States of America·Mingyang Lu, Jianpeng Ma
Jan 1, 2009·The Journal of Physical Chemistry. B·Yong Zhang, John E Straub
Jan 24, 2009·The Journal of Biological Chemistry·C Nick PaceJ Martin Scholtz
Jan 27, 2009·Biophysical Journal·Demian RiccardiGeorge N Phillips
Mar 3, 2009·Proceedings of the National Academy of Sciences of the United States of America·Hans FrauenfelderRobert D Young
Jul 7, 2009·Biochimica Et Biophysica Acta·Wolfgang Doster
Jul 18, 2009·The Journal of Physical Chemistry. B·Sebnem G Essiz, Rob D Coalson
Aug 21, 2009·The Journal of Physical Chemistry. B·David N Lebard, Dmitry V Matyushov
Mar 3, 2010·Annual Review of Biophysics·Ivet BaharEran Eyal

❮ Previous
Next ❯

Citations

Aug 13, 2013·PloS One·Bryant GipsonLydia E Kavraki
Nov 7, 2012·The Journal of Chemical Physics·Daniel R Martin, Dmitry V Matyushov
Mar 5, 2013·Protein Science : a Publication of the Protein Society·Min Hyeok KimMoon Ki Kim
Feb 23, 2021·Frontiers in Molecular Biosciences·Robert L JerniganAndrzej Kloczkowski

❮ 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.