Toward quantitative simulations of carbon monoxide escape pathways in myoglobin

The Journal of Physical Chemistry. B
Ron Elber, Q H Gibson

Abstract

Straightforward molecular dynamics trajectories have been computed to explore the diffusion of carbon monoxide through myoglobin. The classical equations of motion were integrated for 2 ns and the resulting pathways analyzed. Two types of runs were examined. Type i: Myoglobin and a ligand embedded in a periodic box with 9996 water molecules; the water molecules are rigid but the bonds of the protein are flexible. Type ii: Myoglobin with a solvation shell (153 water molecules) in which all bond lengths are fixed. In trajectories of type i, the diffusing ligand visits a significant part of the protein matrix and was not constrained to the proximity of the heme pocket before escaping. The maximum time of the trajectories was 2 ns. It was shorter if the ligand escaped earlier. Two ligands (from a total of 88) escape to the solvent from nonclassical gates (non-E-helix gates). In trajectories of type ii, the overall fluctuations of the protein are smaller and the ligand explores significantly smaller internal space. The escape rate from type ii trajectories (11 of 400) is comparable to type i and is not dramatically different from experiment (1 of 100). Interestingly, the two simulations with comparable rates sampled different pathwa...Continue Reading

References

Aug 15, 1979·Journal of Molecular Biology·D A Case, M Karplus
Oct 5, 1980·Journal of Molecular Biology·S E Phillips
Jan 27, 1995·Journal of Molecular Biology·M L QuillinH Li
Jan 9, 1996·Proceedings of the National Academy of Sciences of the United States of America·P J Steinbach, B R Brooks
Oct 8, 1997·Biochemistry·E E Scott, Q H Gibson
Oct 6, 2000·The Journal of Biological Chemistry·E E ScottJ S Olson
Dec 18, 2001·The Journal of Biological Chemistry·Federica DraghiJohn S Olson
Jun 21, 2003·Science·Friedrich SchottePhilip A Anfinrud
Oct 19, 2004·Proceedings of the National Academy of Sciences of the United States of America·Gerhard HummerPhilip A Anfinrud
Dec 17, 2004·Proceedings of the National Academy of Sciences of the United States of America·Yuhong WangAhmed H Zewail
Mar 21, 2006·Proceedings of the National Academy of Sciences of the United States of America·Dominique BourgeoisMaurizio Brunori
Jun 6, 2006·Biophysical Journal·Jordi CohenKlaus Schulten
Jun 23, 2006·Acta Crystallographica. Section D, Biological Crystallography·Roman ArandaGeorge N Phillips
Apr 21, 2007·Biophysical Journal·Ilya J FinkelsteinM D Fayer
Jul 12, 2007·The Journal of Physical Chemistry. B·Dmitry A Kondrashov, William R Montfort

❮ Previous
Next ❯

Citations

Nov 9, 2012·Journal of Biological Inorganic Chemistry : JBIC : a Publication of the Society of Biological Inorganic Chemistry·Anthony BocahutEwen Lescop
Feb 24, 2012·The Journal of Physical Chemistry. B·Grazia CottoneRon Elber
Jan 5, 2011·The Journal of Biological Chemistry·Ivan BirukouJohn S Olson
Aug 4, 2012·The Journal of Biological Chemistry·Mallory D SalterJohn S Olson
Nov 8, 2013·The Journal of Physical Chemistry. B·Shuji Kaieda, Bertil Halle
Mar 5, 2016·Journal of Chemical Theory and Computation·Maria S ShadrinaGilles H Peslherbe
Feb 7, 2014·Scientific Reports·Yingying JiangIsaac C Sanchez
Jul 29, 2008·Biophysical Journal·Edward LymanGregory A Voth
Feb 8, 2013·Biochimica Et Biophysica Acta·M Fátima Lucas, Víctor Guallar
Mar 6, 2012·Biophysical Journal·M Fátima Lucas, Víctor Guallar
Feb 11, 2015·Journal of the American Chemical Society·Tang-Qing YuCameron F Abrams
Apr 26, 2013·The Journal of Physical Chemistry. B·Masayoshi TakayanagiMasataka Nagaoka
Dec 31, 2009·Journal of the American Chemical Society·Luca MaraglianoEric Vanden-Eijnden
Mar 19, 2013·Journal of Chemical Theory and Computation·Mauro Lapelosa, Cameron F Abrams
May 11, 2011·Journal of the American Chemical Society·Anthony BocahutSophie Sacquin-Mora
Jun 17, 2019·The Journal of Chemical Physics·Jakub Rydzewski, Omar Valsson
Mar 24, 2018·The Journal of Chemical Physics·J Rydzewski, W Nowak
Nov 19, 2009·The Journal of Physical Chemistry. B·Anthony BocahutSophie Sacquin-Mora
Sep 19, 2009·The Journal of Physical Chemistry. B·Liang XuXicheng Wang
Apr 5, 2012·The Journal of Physical Chemistry Letters·Michael L DrummondThomas R Cundari

❮ 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.