Methanethiol Binding Strengths and Deprotonation Energies in Zn(II)-Imidazole Complexes from M05-2X and MP2 Theories: Coordination Number and Geometry Influences Relevant to Zinc Enzymes

The Journal of Physical Chemistry. B
Douglas P Linder, Kenton R Rodgers

Abstract

Zn(II) is used in nature as a biocatalyst in hundreds of enzymes, and the structure and dynamics of its catalytic activity are subjects of considerable interest. Many of the Zn(II)-based enzymes are classified as hydrolytic enzymes, in which the Lewis acidic Zn(II) center facilitates proton transfer(s) to a Lewis base, from proton donors such as water or thiol. This report presents the results of a quantum computational study quantifying the dynamic relationship between the zinc coordination number (CN), its coordination geometry, and the thermodynamic driving force behind these proton transfers originating from a charge-neutral methylthiol ligand. Specifically, density functional theory (DFT) and second-order perturbation theory (MP2) calculations have been performed on a series of [(imidazole)nZn-S(H)CH3](2+) and [(imidazole)nZn-SCH3](+) complexes with the CN varied from 1 to 6, n = 0-5. As the number of imidazole ligands coordinated to zinc increases, the S-H proton dissociation energy also increases, (i.e., -S(H)CH3 becomes less acidic), and the Zn-S bond energy decreases. Furthermore, at a constant CN, the S-H proton dissociation energy decreases as the S-Zn-(ImH)n angles increase about their equilibrium position. The zinc...Continue Reading

References

Jun 1, 1994·Proteins·J C SpurlinoT A Pulvino
Oct 1, 1995·Protein Science : a Publication of the Protein Society·J W BeckerJ D Hermes
Jan 5, 1999·Bioorganic & Medicinal Chemistry Letters·M G NatchusB De
Jul 18, 2001·Journal of the American Chemical Society·L P KotraS Mobashery
Nov 1, 2001·Annual Review of Cell and Developmental Biology·M D Sternlicht, Z Werb
Dec 26, 2001·Chemical Reviews·M WhittakerA J Gearing
Mar 23, 2002·Circulation Research·Francis G Spinale
Mar 30, 2002·Science·Lisa M CoussensLynn M Matrisian
Sep 5, 2002·Nature Reviews. Cancer·Christopher Mark Overall, Carlos López-Otín
Oct 24, 2002·Journal of the American Chemical Society·Franklin J MoyRobert Powers
Oct 29, 2002·Inorganic Chemistry·Vladimir Pelmenschikov, Per E M Siegbahn
Jan 24, 2004·Heart Failure Reviews·Merry L Lindsey
Feb 26, 2004·Journal of the American Chemical Society·Yen-lin Lin, Carmay Lim
May 11, 2004·Inorganic Chemistry·Faith E Jacobsen, Seth M Cohen
Sep 9, 2004·Chemical Society Reviews·Mijoon LeeShahriar Mobashery
Apr 30, 2005·Inorganic Chemistry·Monika SommerhalterAmy C Rosenzweig
Jan 7, 2006·Journal of Proteome Research·Claudia AndreiniAntonio Rosato
Feb 26, 2008·Proceedings of the National Academy of Sciences of the United States of America·Markos KoutmosMartha L Ludwig
Jan 14, 2009·Biometals : an International Journal on the Role of Metal Ions in Biology, Biochemistry, and Medicine·David S Auld
Sep 5, 2009·Chemical Reviews·Wolfgang Maret, Yuan Li
Sep 23, 2009·Dalton Transactions : an International Journal of Inorganic Chemistry·Sérgio Filipe SousaMaria João Ramos
Mar 6, 2010·The Journal of Biological Chemistry·Cynthia TallantF Xavier Gomis-Rüth
Sep 26, 2013·Inorganic Chemistry·Mikko LaitaojaJanne Jänis
Oct 1, 2013·Journal of Medicinal Chemistry·Joshua A Day, Seth M Cohen
Feb 11, 2014·Biochemistry·Melissa L Zastrow, Vincent L Pecoraro
Mar 19, 2014·Journal of the American Chemical Society·David P MartinSeth M Cohen
Nov 22, 2014·Nature Reviews. Molecular Cell Biology·Caroline BonnansZena Werb
Feb 7, 2015·Arteriosclerosis, Thrombosis, and Vascular Biology·Mengcheng ShenZamaneh Kassiri
May 12, 2015·Frontiers in Bioscience (Landmark Edition)·Jillian M Cathcart, Jian Cao

❮ Previous
Next ❯

Citations

Jul 14, 2018·Journal of Enzyme Inhibition and Medicinal Chemistry·Mehdi BouchouitAbdelmalek Bouraiou
Sep 22, 2018·Physical Chemistry Chemical Physics : PCCP·Douglas P LinderKenton R Rodgers
Jun 28, 2019·The Journal of Physical Chemistry. a·Rahma DahmaniMajdi Hochlaf

❮ 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.