Nitric oxide reactivity with globins as investigated through computer simulation

Methods in Enzymology
Marcelo A MartiDarío A Estrin

Abstract

This chapter reviews the application of classical and quantum-mechanical atomistic simulation tools used in the investigation of several relevant issues in nitric oxide reactivity with globins and presents different simulation strategies based on classical force fields: standard molecular dynamics, essential dynamics, umbrella sampling, multiple steering molecular dynamics, and a novel technique for exploring the protein energy landscape. It also presents hybrid quantum-classical schemes as a tool to obtain relevant information regarding binding energies and chemical reactivity of globins. As illustrative examples, investigations of the structural flexibility, ligand migration profiles, oxygen affinity, and reactivity toward nitric oxide of truncated hemoglobin N of Mycobacterium tuberculosis are presented.

References

Oct 18, 1990·Nature·M Karplus, G A Petsko
Dec 1, 1993·Proteins·A AmadeiH J Berendsen
Jun 4, 1996·Biochemistry·R F EichJ S Olson
Oct 28, 1996·Physical Review Letters·J P PerdewM Ernzerhof
Oct 6, 2000·The Journal of Biological Chemistry·E E ScottJ S Olson
Mar 29, 2001·Proceedings of the National Academy of Sciences of the United States of America·G Hummer, A Szabo
Apr 18, 2002·Proceedings of the National Academy of Sciences of the United States of America·Hugues OuelletMichel Guertin
Jul 5, 2002·Journal of Molecular Biology·Matthew P JacobsonBarry Honig
Dec 13, 2002·Proceedings of the National Academy of Sciences of the United States of America·Stefan Franzen
Jun 26, 2004·Science·Mary A DwyerHomme W Hellinga
Jul 9, 2004·Journal of the American Chemical Society·Victor Guallar, Richard A Friesner
Jul 23, 2004·The Journal of Chemical Physics·Sanghyun Park, Klaus Schulten
Sep 29, 2004·Journal of Biological Inorganic Chemistry : JBIC : a Publication of the Society of Biological Inorganic Chemistry·L Mattias BlombergPer E M Siegbahn
Mar 24, 2005·Journal of the American Chemical Society·Alejandro CrespoDarío A Estrin
Mar 31, 2005·Annual Review of Physical Chemistry·Richard A Friesner, Victor Guallar
May 12, 2005·Journal of the American Chemical Society·Alejandro CrespoAdrian E Roitberg
May 26, 2005·Journal of the American Chemical Society·Marcelo A MartíDario A Estrin
Sep 1, 2005·Journal of Biological Inorganic Chemistry : JBIC : a Publication of the Society of Biological Inorganic Chemistry·M Laura FernándezDarío A Estrin
Jan 28, 2006·Journal of Inorganic Biochemistry·Paul R GardnerJohn S Olson
Jan 31, 2006·Journal of Inorganic Biochemistry·Marcelo A MartiDario A Estrin
Jun 17, 2006·Journal of Inorganic Biochemistry·Daniel M CopelandGeorge B Richter-Addo
Sep 21, 2006·Journal of the American Chemical Society·Luciana CapeceDarío A Estrin
Apr 30, 1998·The Journal of Physical Chemistry. B·A D MacKerellM Karplus

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Citations

Nov 16, 2011·Biochemistry·Luciana CapeceSyun-Ru Yeh
Dec 27, 2011·The Journal of Physical Chemistry. B·Luciana CapeceMarcelo A Marti
Jun 9, 2016·Journal of Chemical Theory and Computation·Claudia L RamírezLuciana Capece
Jan 1, 2012·Scientifica·Paul R Gardner
Nov 16, 2010·Journal of Biological Inorganic Chemistry : JBIC : a Publication of the Society of Biological Inorganic Chemistry·Barry D HowesGiulietta Smulevich
Mar 3, 2020·Inorganic Chemistry·Nicolás O FogliaDarío A Estrin
Apr 22, 2021·Journal of Inorganic Biochemistry·Laia Julió PlanaLuciana Capece
Apr 24, 2021·Journal of Inorganic Biochemistry·Jaime E Martinez GrundmanJuliette T J Lecomte
Jan 15, 2014·The Journal of Physical Chemistry. B·Juan P BustamanteCristiano Viappiani
Jun 20, 2018·Inorganic Chemistry·Fernando M BoubetaSara E Bari
Dec 6, 2018·Journal of Chemical Information and Modeling·Laia Julió PlanaLuciana Capece

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