The type IA topoisomerase catalytic cycle: A normal mode analysis and molecular dynamics simulation

Proteins
Bing XiongAlbert M Berghuis

Abstract

Type IA topoisomerases alter the topological state of DNA to relax the supercoils introduced during the DNA replication and transcription process, giving them critical roles in many cellular functions. To manipulate the DNA, type IA topoisomerases first cleave one DNA strand and form a covalent linkage between a catalytic tyrosine residue and the 5'-phosphoryl of the DNA. This is followed by a movement of domain III of the topoisomerase to accommodate the second DNA strand in the center channel of the topoisomerase. Domain III is then closed for religation of the cleaved DNA and subsequently reopened to release the passing strand. Although numerous biophysical and biochemical studies have examined this catalytic cycle, fundamental questions remain such as how domain III opens and closes during this process. We have used computational simulation methods, namely normal mode analysis and molecular dynamics, to investigate the catalytic cycle of Escherichia coli topoisomerase III as a representative of the type IA topoisomerases. It was found that domain II is intrinsically flexible and may empower the enzyme to perform its function by triggering domain III opening and closing. A molecular dynamics simulation and MM-PBSA analysis s...Continue Reading

References

Oct 3, 1999·Nature Structural Biology·H FeinbergA Mondragón
Oct 3, 1999·Nature Structural Biology·H FeinbergA Mondragón
Nov 27, 1999·Structure·A Mondragón, R DiGate
Sep 6, 2000·Journal of Molecular Biology·J MaM Karplus
Jun 8, 2001·Annual Review of Biochemistry·J J Champoux
Feb 14, 2002·Proceedings of the National Academy of Sciences of the United States of America·Yufeng ShenJianpeng Ma
May 15, 2002·Trends in Pharmacological Sciences·James J Champoux
Jun 4, 2002·Nature Reviews. Molecular Cell Biology·James C Wang
Jun 8, 2002·BMC Biochemistry·Adriana Ahumada, Yuk-Ching Tse-Dinh
Jun 19, 2002·Accounts of Chemical Research·Martin Karplus
Aug 9, 2002·Proceedings of the National Academy of Sciences of the United States of America·N H DekkerV Croquette
Aug 29, 2002·Nature Structural Biology·Martin Karplus, J Andrew McCammon
Sep 11, 2002·Proceedings of the National Academy of Sciences of the United States of America·James J Champoux
May 14, 2004·Annual Review of Biophysics and Biomolecular Structure·Kevin D Corbett, James M Berger
Jun 18, 2004·Journal of Molecular Biology·Qiang CuiMartin Karplus
Jun 25, 2004·The Journal of Biological Chemistry·Bokun ChengYuk-Ching Tse-Dinh
Apr 20, 2005·Current Opinion in Structural Biology·John Mongan, David A Case
Aug 17, 2005·Current Medicinal Chemistry. Anti-cancer Agents·E L Baldwin, N Osheroff
Feb 24, 2006·Journal of Molecular Biology·Paras Jain, Valakunja Nagaraja
Mar 15, 2006·Biophysical Journal·Indira H Shrivastava, Ivet Bahar
May 2, 2006·Journal of Molecular Biology·Michel DuguetClaire Bouthier de La Tour
Jun 23, 2006·Medicinal Chemistry·Gregory I Giles, Ram P Sharma
Dec 5, 2006·Biochimie·Thierry Viard, Claire Bouthier de la Tour
Jan 5, 2007·Annual Review of Biophysics and Biomolecular Structure·Michael K Gilson, Huan-Xiang Zhou

❮ Previous
Next ❯

Citations

Feb 11, 2014·Nature Structural & Molecular Biology·Nicolas BocquetNicolas H Thomä
Aug 13, 2013·Journal of Molecular Graphics & Modelling·Neslihan UcuncuogluLevent Sari
Jan 11, 2017·Journal of Medicinal Chemistry·Giovanni CapranicoGiovanni Chillemi
Nov 28, 2018·Nature Structural & Molecular Biology·Maria MillsKeir C Neuman
Apr 12, 2020·The Journal of Biological Chemistry·Anna H Bizard, Ian D Hickson
Jan 11, 2016·Advanced Materials·Melissabye GunnooDamien Thompson
Dec 29, 2020·Structure·Rohan Bythell-Douglas, Andrew J Deans

❮ 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.