Molecular dynamics simulations of ligand-induced flap closing in HIV-1 protease approach X-ray resolution: establishing the role of bound water in the flap closing …

G Singh, S Senapati - Biochemistry, 2008 - ACS Publications
The necessity of understanding the detailed mechanism of flap dynamics in designing HIV-1
protease inhibitors is immense. Crystal structures have provided us with a static overview of …

Conformational motions of hiv-1 protease identified using reversible digitally filtered molecular dynamics

AP Wiley, SL Williams, JW Essex - Journal of Chemical Theory …, 2009 - ACS Publications
HIV-1 protease performs a vital step in the propagation of the HIV virus and is therefore an
important drug target in the treatment of AIDS. It consists of a homodimer, with access to the …

Structural and dynamical aspects of HIV-1 protease and its role in drug resistance

BR Meher, S Patel - Advances in Protein Chemistry and Structural Biology, 2013 - Elsevier
Acquired immunodeficiency syndrome (AIDS) caused by the retrovirus human
immunodeficiency virus (HIV) has become a major epidemic afflicting mankind. The Joint …

Energy Flow Perspective on the Mechanism of the Conformational Dynamics in Biomolecules

S Wu - 2022 - search.proquest.com
Most functional processes of proteins involve significant conformational changes. In those
activated processes, the system needs to cross an energy barrier. A comprehensive …

Clarifying allosteric control of flap conformations in the 1TW7 crystal structure of HIV‐1 protease

KW Lexa, KL Damm, JJ Quintero… - Proteins: Structure …, 2009 - Wiley Online Library
HIV-1 protease (HIVp) inhibitors are essential for current AIDS treatments, and new
compounds are still a very active area of research. The conformational behavior of the flap …

[PDF][PDF] Atomistic simulations of the HIV-1 protease folding inhibition

G Verkhivker, G Tiana, C Camilloni, D Provasi… - Biophysical journal, 2008 - cell.com
Biochemical experiments have recently revealed that the p-S8 peptide, with an amino-acid
sequence identical to the conserved fragment 83–93 (S8) of the HIV-1 protease, can inhibit …

[HTML][HTML] Crystal structure of an FIV/HIV chimeric protease complexed with the broad-based inhibitor, TL-3

H Heaslet, YC Lin, K Tam, BE Torbett, JH Elder… - Retrovirology, 2007 - Springer
We have obtained the 1.7 Å crystal structure of FIV protease (PR) in which 12 critical
residues around the active site have been substituted with the structurally equivalent …

Exploring the flap dynamics of the South African HIV subtype C protease in presence of FDA‐approved inhibitors: MD study

SI Maphumulo, AK Halder, T Govender… - Chemical biology & …, 2018 - Wiley Online Library
HIV‐1 protease (HIV PR) is considered as one of the most attractive targets for the treatment
of HIV and the impact of flap dynamics of HIV PR on the binding affinities of protease …

[PDF][PDF] Mutation Effects on 3D-Structural Reorganization Using HIV-1 Protease as a Case Study.

BR Meher, M Vaishnavi, MVS Kumar, S Patel… - 2019 - brmeher.com
Acquired immunodeficiency syndrome (AIDS) spread by the human immunodeficiency virus
(HIV) has become an epidemic worldwide (Sanou et al., 2012). In 2016, it is assessed that …

Reconstruction of the binding pathway of an anti-HIV drug, Indinavir, in complex with the HTLV-1 protease by Unaggregated Unbiased Molecular Dynamics simulation

F Sohraby, H Aryapour - bioRxiv, 2021 - biorxiv.org
Retroviruses are a growing concern for the health of human beings, and one of the
dangerous members of this family is the Human T-cell Leukemia Virus 1 (HTLV-1) virus. It …