Structural and dynamical properties of a full-length HIV-1 integrase: molecular dynamics simulations

Journal of Biomolecular Structure & Dynamics
Atchara WijitkosoomSupot Hannongbua

Abstract

The structural and dynamical properties of the complete full-length structure of HIV-1 integrase were investigated using Molecular Dynamics approach. Simulations were carried out for the three systems, core domain only (CORE), full-length structure without (FULL) and with a Mg2+ (FULL+ION) in its active site, aimed to investigate the difference in the molecular properties of the full-length models due to their different construction procedures as well as the effects of the two ends, C- and N-terminal, on those properties in the core domain. The full-length structure was prepared from the two experimental structures of two-domain fragment. The following properties were observed to differ significantly from the previous reports: (i) relative topology formed by an angle between the three domains; (ii) the cavity size defined by the catalytic triad, Asp64, Asp116, and Glu152; (iii) distances and solvation of the Mg2+; and (iv) conformation of the catalytic residues. In addition, the presence of the two terminal domains decreases the mobility of the central core domain significantly.

References

Jun 30, 1992·Biochemical and Biophysical Research Communications·M Schauer, A Billich
Sep 1, 1995·Trends in Biochemical Sciences·R A Sayle, E J Milner-White
Aug 8, 1995·Biochemistry·P J LodiA M Gronenborn
Feb 1, 1996·Journal of Molecular Graphics·R KoradiK Wüthrich
Jul 1, 1997·Nature Structural Biology·M CaiA M Gronenborn
Aug 5, 1998·Proceedings of the National Academy of Sciences of the United States of America·Y GoldgurD R Davies
Jun 4, 1999·Biophysical Journal·R D LinsJ A McCammon
Nov 11, 1999·Proceedings of the National Academy of Sciences of the United States of America·Y GoldgurD R Davies
Feb 12, 2000·Journal of Molecular Biology·Z N YangC C Hyde
Jul 13, 2000·Proceedings of the National Academy of Sciences of the United States of America·J C ChenR M Stroud
Oct 4, 2000·Proceedings of the National Academy of Sciences of the United States of America·A S EspesethD J Hazuda
Nov 7, 2000·Journal of Medicinal Chemistry·C A SotrifferJ A McCammon
Sep 19, 2002·Journal of the American Chemical Society·Carlos SimmerlingAdrian E Roitberg
Feb 13, 2003·Biopolymers·Alexei A PodtelezhnikovJ Andrew McCammon
Oct 16, 2003·Biochemical and Biophysical Research Communications·Laura De LucaAlba Chimirri
Aug 3, 2005·Journal of Computer-aided Molecular Design·Rajeshri G KarkiMarc C Nicklaus
Sep 17, 2005·Biochemical and Biophysical Research Communications·Laura De LucaAlba Chimirri

❮ Previous
Next ❯

Citations

Dec 3, 2008·Journal of Molecular Modeling·Devendra K DhakedEvans C Coutinho
May 2, 2012·Journal of Biomolecular Structure & Dynamics·Sangeetha BalasubramanianAmutha Ramaswamy

❮ 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.