PMID: 11902900Mar 21, 2002Paper

Quantum mechanics/molecular mechanics studies of triosephosphate isomerase-catalyzed reactions: effect of geometry and tunneling on proton-transfer rate constants

Journal of the American Chemical Society
Qiang Cui, M Karplus

Abstract

The role of tunneling for two proton-transfer steps in the reactions catalyzed by triosephosphate isomerase (TIM) has been studied. One step is the rate-limiting proton transfer from Calpha in the substrate to Glu 165, and the other is an intrasubstrate proton transfer proposed for the isomerization of the enediolate intermediate. The latter, which is not important in the wild-type enzyme but is a useful model system because of its simplicity, has also been examined in the gas phase and in solution. Variational transition-state theory with semiclassical ground-state tunneling was used for the calculation with potential energy surface determined by an AM1 method specifically parametrized for the TIM system. The effect of tunneling on the reaction rate was found to be less than a factor of 10 at room temperature; the tunneling becomes more important at lower temperature, as expected. The imaginary frequency (barrier) mode and modes that have large contributions to the reaction path curvature are localized on the atoms in the active site, within 4 A of the substrate. This suggests that only a small number of atoms that are close to the substrate and their motions (e.g., donor-acceptor vibration) directly determine the magnitude of...Continue Reading

References

Mar 10, 1989·Science·Y ChaJ P Klinman
Jan 1, 1984·Proceedings of the National Academy of Sciences of the United States of America·A Warshel
Jan 1, 1995·Methods in Enzymology·W W Cleland
Nov 14, 1997·Proceedings of the National Academy of Sciences of the United States of America·D Antoniou, S D Schwartz
Sep 15, 1988·Physical Review A: General Physics·A D Becke
Aug 12, 1985·Physical Review Letters·P HanggiU Weiss
May 10, 2000·Proceedings of the National Academy of Sciences of the United States of America·P G BolhuisD Chandler
Dec 6, 2000·Proceedings of the National Academy of Sciences of the United States of America·D ZhongA H Zewail
Jul 18, 2001·Journal of the American Chemical Society·Q Cui, M Karplus
Aug 3, 1990·Science·D G Truhlar, M S Gordon
Oct 1, 1995·Annual Review of Physical Chemistry·J M Bowman, G C Schatz
Apr 30, 1998·The Journal of Physical Chemistry. B·A D MacKerellM Karplus

❮ Previous
Next ❯

Citations

Apr 20, 2004·Current Opinion in Structural Biology·Sharon Hammes-Schiffer
May 11, 2006·Chemical Reviews·Mats H M OlssonArieh Warshel
Oct 1, 2009·Journal of the American Chemical Society·Wing-Yin Tsang, John P Richard
Jan 13, 2006·The Journal of Physical Chemistry. a·P H KönigQ Cui
Jun 28, 2011·Physical Chemistry Chemical Physics : PCCP·Ville R I Kaila, Gerhard Hummer
Sep 21, 2011·Proceedings of the National Academy of Sciences of the United States of America·Nicholas BoekelheideThomas F Miller
Apr 29, 2009·The Journal of Biological Chemistry·Osbourne QuayeGiovanni Gadda
Jul 29, 2006·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Sara NuñezNeil A Burton
Jul 29, 2006·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Mats H M OlssonArieh Warshel
Mar 31, 2005·Annual Review of Physical Chemistry·Richard A Friesner, Victor Guallar
Jun 12, 2013·Annual Review of Biochemistry·Judith P Klinman, Amnon Kohen
Jan 2, 2003·Proceedings of the National Academy of Sciences of the United States of America·Gerwald JoglLiang Tong
May 5, 2005·Proceedings of the National Academy of Sciences of the United States of America·M Karplus, J Kuriyan
Dec 14, 2005·Proceedings of the National Academy of Sciences of the United States of America·Xiaohua Zhang, Thomas C Bruice
Aug 24, 2010·Current Opinion in Chemical Biology·Vishal C NashineStephen J Benkovic
Dec 1, 2004·Drug Discovery Today. Technologies·Richard A Friesner
Sep 27, 2005·Trends in Biochemical Sciences·Derren J Heyes, C Neil Hunter
Jul 12, 2005·Journal of Molecular Graphics & Modelling·Guohui Li, Qiang Cui
Mar 6, 2004·Journal of Molecular Biology·Victor GuallarRichard A Friesner
Dec 10, 2002·Annual Review of Biophysics and Biomolecular Structure·R M DanielJ C Smith
Aug 27, 2016·Molecular Simulation·Xiya LuQiang Cui
Jul 8, 2017·Journal of the American Chemical Society·Yashraj S KulkarniShina C L Kamerlin
Nov 23, 2017·Chemical Society Reviews·Junwei Lucas Bao, Donald G Truhlar
Mar 29, 2016·Mass Spectrometry Reviews·Tianfang WangJohn H Bowie
Dec 30, 2014·Theoretical Biology & Medical Modelling·Jack A TuszynskiRabab M Abou El-Magd
May 7, 2010·Physical Chemistry Chemical Physics : PCCP·Ricardo A Mata
Oct 28, 2019·Biochemical Society Transactions·Cátia MoreiraShina Caroline Lynn Kamerlin
May 16, 2009·Journal of Computational Chemistry·B R BrooksM Karplus
May 23, 2014·Physical Chemistry Chemical Physics : PCCP·Qiang Cui, Marcus Elstner
Sep 19, 2003·The Journal of Biological Chemistry·Keisuke HamadaMasashi Miyano
Jan 11, 2003·The Journal of Biological Chemistry·Inari Kursula, Rik K Wierenga
Jun 15, 2011·Chembiochem : a European Journal of Chemical Biology·Moumita SamantaPadmanabhan Balaram
Nov 9, 2007·PLoS Neglected Tropical Diseases·Vanesa Olivares-IllanaArmando Gómez-Puyou
Mar 7, 2019·Frontiers in Bioengineering and Biotechnology·Michael D Toney

❮ 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.