NDLI: Insights from simulations into the mechanism of human topoisomerase I: explanation for a seeming controversy in experiments.

Please wait, while we are loading the content...

Year: 2017 Volume: 73

Year: 2017 Volume: 72

Year: 2017 Volume: 71

Year: 2016 Volume: 73

Year: 2016 Volume: 71

Year: 2016 Volume: 70

Year: 2016 Volume: 69

Year: 2016 Volume: 68

Year: 2016 Volume: 67

Year: 2016 Volume: 66

Year: 2016 Volume: 65

Year: 2016 Volume: 64

Year: 2016 Volume: 63

Year: 2015 Volume: 62

Year: 2015 Volume: 61

Year: 2015 Volume: 60

Year: 2015 Volume: 59

Year: 2015 Volume: 58

Year: 2015 Volume: 57

Year: 2015 Volume: 56

Year: 2015 Volume: 55

Year: 2014 Volume: 54

Year: 2014 Volume: 53

Year: 2014 Volume: 51

Year: 2014 Volume: 50

Year: 2014 Volume: 49

Year: 2014 Volume: 48

Year: 2014 Volume: 47

Year: 2013 Volume: 46

Year: 2013 Volume: 45

Year: 2013 Volume: 44

In silico bioremediation of polycyclic aromatic hydrocarbon: a frontier in environmental chemistry.

Theoretical study on the proton shuttle mechanism of saccharopine dehydrogenase.

TDDFT studies on electronic structures, chiroptical properties and solvent effect on the CD spectra of diphosphonate-functionalized polyoxomolybdates.

Molecular dynamics simulation of single-walled silicon carbide nanotubes immersed in water.

Quantum polarized ligand docking investigation to understand the significance of protonation states in histone deacetylase inhibitors.

Conserved water mediated H-bonding dynamics of Ser117 and Thr119 residues in human transthyretin-thyroxin complexation: inhibitor modeling study through docking and molecular dynamics simulation.

MD and QM/MM study on catalytic mechanism of a FAD-dependent enzyme ORF36: for nitro sugar biosynthesis.

Homology modeling, ligand docking and in silico mutagenesis of neurospora Hsp80 (90): insight into intrinsic ATPase activity.

Is the conformational flexibility of piperazine derivatives important to inhibit HIV-1 replication?

Complex between human RNase HI and the phosphonate-DNA/RNA duplex: molecular dynamics study.

AutoGrow 3.0: an improved algorithm for chemically tractable, semi-automated protein inhibitor design.

Prediction of boiling points of organic compounds by QSPR tools.

Investigation of simple and water assisted tautomerism in a derivative of 1,3,4-oxadiazole: a DFT study.

Hybrid density functional based study on the band structure of trioctahedral mica and its dependence on the variation of Fe(2+) content.

Study of the interaction of Huperzia saururus Lycopodium alkaloids with the acetylcholinesterase enzyme.

Interactions of acetylcholine binding site residues contributing to nicotinic acetylcholine receptor gating: role of residues Y93, Y190, K145 and D200.

Molecular modeling revealed that ligand dissociation from thyroid hormone receptors is affected by receptor heterodimerization.

Homology modeling study toward identifying structural properties in the HA2 B-loop that would influence the HA1 receptor-binding site.

Modeling of multifunctional donor-bridge-acceptor 4,6-di(thiophen-2-yl)pyrimidine derivatives: a first principles study.

The emerging role of cloud computing in molecular modelling.

Similarity-based virtual screening for microtubule stabilizers reveals novel antimitotic scaffold.

Characterization and comparison of pore landscapes in crystalline porous materials.

Structural and functional insights on folate receptor (FR ) by homology modeling, ligand docking and molecular dynamics.

In silico design: extended molecular dynamic simulations of a new series of dually acting inhibitors against EGFR and HER2.

Molecular dynamics simulations of isoleucine-release pathway in GAF domain of N-CodY from Bacillus Subtilis.

Structure based design towards the identification of novel binding sites and inhibitors for the chikungunya virus envelope proteins.

Crystal structure, stability and spectroscopic properties of methane and CO2 hydrates.

Structural requirements of 3-carboxyl-4(1H)-quinolones as potential antimalarials from 2D and 3D QSAR analysis.

A combined molecular docking-based and pharmacophore-based target prediction strategy with a probabilistic fusion method for target ranking.

Insights from simulations into the mechanism of human topoisomerase I: explanation for a seeming controversy in experiments.

Potent inhibitors precise to S1' loop of MMP-13, a crucial target for osteoarthritis.

Theoretical study on photophysical properties of Pt(II) triarylborons with a 2,2-bpy core derivatives.

Year: 2013 Volume: 43

Year: 2013 Volume: 42

Year: 2013 Volume: 41

Year: 2013 Volume: 40

Year: 2013 Volume: 39

Year: 2012 Volume: 38

Year: 2012 Volume: 37

Year: 2012 Volume: 36

Year: 2012 Volume: 35

Year: 2012 Volume: 34

Year: 2012 Volume: 33

Year: 2012 Volume: 32

Year: 2011 Volume: 31

Year: 2011 Volume: 30

Year: 2011 Volume: 29

Year: 2010 Volume: 29

Year: 2010 Volume: 28

Year: 2009 Volume: 28

Year: 2009 Volume: 27

Year: 2008 Volume: 27

Year: 2008 Volume: 26

Year: 2007 Volume: 26

Year: 2006 Volume: 25

Year: 2001 Volume: 19

Insights from simulations into the mechanism of human topoisomerase I: explanation for a seeming controversy in experiments.

Content Provider	World Health Organization (WHO)-Global Index Medicus
Author	Ucuncuoglu, Neslihan Andricioaei, Ioan Sari, Levent
Description	Country affiliation: Turkey Author Affiliation: Ucuncuoglu N ( Department of Physics, Fatih University, Istanbul 34500, Turkey.)
Abstract	Human topoisomerase-I is a vital enzyme involved in cellular regulation of DNA supercoiling. We extend our previous work on wild type enzyme [13] to study how different enzyme mutants with various parts of the protein clamped by disulfide mutations affect DNA rotation. Three different mutants have been simulated; they are clamped enzyme-DNA systems in which the disulfide bridge is formed by replacing His367 and Ala499, Gly365 and Ser534, and, respectively, Leu429 and Lys436 with Cys pairs. The first of these mutants, a 'distally clamped' enzyme, mimics the experimental study of Carey et al. [11], which reports DNA rotation within the clamped enzyme. The second one, a 'proximal clamp', mimics the study of Woo et al. [12], who do not observe DNA rotation. The third is a newly suggested mutant that clamps the hinge for protein opening; we use it to test a hypothesis on negative supercoil relaxation. Our simulations show that the helical domain 5 totally melts in relaxation of positive supercoils when the enzyme is proximally clamped, while it preserves its structure very well within the distally clamped one. Moreover, a distally clamped protein permits DNA rotations in both directions, while the proximal clamp allows rotations only for negatively supercoiled DNA. These observations reconcile the two seemingly contradictory experimental findings, suggesting that subtle changes in the location of the disulfide bridge alter the mechanism significantly.
File Format	HTM / HTML
ISSN	10933263
Volume Number	44
e-ISSN	18734243
Journal	Journal of Molecular Graphics and Modelling
Language	English
Publisher	Elsevier
Publisher Date	2013-07-01
Publisher Place	United States
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Discipline Molecular Biology Dna Topoisomerases, Type I Chemistry Dna Models, Molecular Metabolism Humans Molecular Docking Simulation Molecular Dynamics Simulation Nucleic Acid Conformation Protein Binding Protein Conformation Quantitative Structure-activity Relationship Journal Article Research Support, Non-u.s. Gov't
Content Type	Text
Resource Type	Article
Subject	Computer Graphics and Computer-Aided Design Spectroscopy Materials Chemistry Physical and Theoretical Chemistry

Central Library (ISO-9001:2015 Certified)
Indian Institute of Technology Kharagpur
Kharagpur, West Bengal, India | PIN - 721302

See location in the Map
03222 282435
Mail: support@ndl.gov.in

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in