title: Flap Dynamics in Aspartic Proteases: A Computational Perspective.
abstract: Recent advances in biochemistry and drug design have placed proteases as one of the critical target groups for developing novel small-molecule inhibitors. Among all proteases, aspartic proteases have gained significant attention due to their role in HIV/AIDS, malaria, Alzheimer's disease, etc. The binding cleft is covered by one or two β-hairpins (flaps) which need to be opened before a ligand can bind. After binding, the flaps close to retain the ligand in the active site. Development of computational tools has improved our understanding of flap dynamics and its role in ligand recognition. In the past decade, several computational approaches, for example molecular dynamics (MD) simulations, coarse-grained simulations, replica-exchange molecular dynamics (REMD) and metadynamics, have been used to understand flap dynamics and conformational motions associated with flap movements. This review is intended to summarize the computational progress towards understanding the flap dynamics of proteases and to be a reference for future studies in this field.
authors.affiliation: Centre for Analysis and Synthesis, Department of Chemistry, Lund University, PO Box 124, SE-221 00, Lund, Sweden.
authors.forename: Mukul
authors.initials: M
authors.lastname: Mahanti
authors.affiliation: Division of Biophysical Chemistry, Department of Chemistry, Lund University, PO Box 124, SE-22100, Lund, Sweden.
authors.forename: Soumendranath
authors.initials: S
authors.lastname: Bhakat
authors.affiliation: Centre for Analysis and Synthesis, Department of Chemistry, Lund University, PO Box 124, SE-221 00, Lund, Sweden.
authors.forename: Ulf J
authors.initials: UJ
authors.lastname: Nilsson
authors.affiliation: Division of Biophysical Chemistry, Department of Chemistry, Lund University, PO Box 124, SE-22100, Lund, Sweden.
authors.forename: Pär
authors.initials: P
authors.lastname: Söderhjelm
mesh_terms: D057055:Aspartic Acid Proteases / Q000737:chemistry*; D020134:Catalytic Domain; D016333:HIV Protease / Q000737:chemistry; D056004:Molecular Dynamics Simulation; D011487:Protein Conformation
chemical_list: D057055:Aspartic Acid Proteases; D016333:HIV Protease
keywords: HIV protease, plasmepsin; Protease; aspartic protease; beta amino secretase; flap; molecular modelling