Nanosecond molecular dynamics of HIV protease-inhibitor complexes: Insight into the differential binding potency of diastereoisomers.

LEPŠÍK, Martin, Zdeněk KŘÍŽ a Zdeněk HAVLAS. Nanosecond molecular dynamics of HIV protease-inhibitor complexes: Insight into the differential binding potency of diastereoisomers. Online. In Materials in Structure Chemistry, Biology, Physics and Technology. Praha: Krystalografická společnost, 2003. s. 23-23. ISBN 1211 - 5894. [citováno 2024-04-23]

Základní údaje

• Originální název: Nanosecond molecular dynamics of HIV protease-inhibitor complexes: Insight into the differential binding potency of diastereoisomers.
• Název anglicky: Nanosecond molecular dynamics of HIV protease-inhibitor complexes: Insight into the differential binding potency of diastereoisomers.
• Autoři: LEPŠÍK, Martin (203 Česká republika), Zdeněk KŘÍŽ (203 Česká republika, garant) a Zdeněk HAVLAS (203 Česká republika)
• Vydání: Praha, Materials in Structure Chemistry, Biology, Physics and Technology, od s. 23-23, 1 s. 2003.
• Nakladatel: Krystalografická společnost

Další údaje

• Originální jazyk: čeština
• Typ výsledku: Stať ve sborníku
• Obor: 10403 Physical chemistry
• Stát vydavatele: Česká republika
• Utajení: není předmětem státního či obchodního tajemství
• WWW: URL
• Kód RIV: RIV/00216224:14310/03:00009541
• Organizační jednotka: Přírodovědecká fakulta
• ISBN: 1211 - 5894
• Klíčová slova anglicky: HIV Protease; molecular dynamics
• Štítky: HIV Protease, molecular dynamics

Anotace

The inhibitory potency of four nanomolar diastereomeric inhibitors of HIV-1 protease [1] was studied by molecular dynamics simulations and MM-GBSA/PBSA analysis. As a starting point we used the crystal structures of protease-inhibitor complexes [2, 3]. Having added hydrogens, we surrounded the complexes with a box of explicit water molecules and added counterions to neutralize the box. Using AMBER 7 program package [4], we minimized, heated and equilibrated the system after which we ran 2-nanosecond-long production dynamics. Periodic boundary conditions were used and long-range electrostatics was treated by particle mesh Ewald (PME) technique. An analysis of the molecular dynamical trajectories was performed and their quality assessed. The protease-inhibitor binding energies were calculated with MM-GBSA/PBSA approach. The effect of the length of the simulation, method to calculate solvation energy, and other factors upon the results was determined.

Anotace anglicky

The inhibitory potency of four nanomolar diastereomeric inhibitors of HIV-1 protease [1] was studied by molecular dynamics simulations and MM-GBSA/PBSA analysis. As a starting point we used the crystal structures of protease-inhibitor complexes [2, 3]. Having added hydrogens, we surrounded the complexes with a box of explicit water molecules and added counterions to neutralize the box. Using AMBER 7 program package [4], we minimized, heated and equilibrated the system after which we ran 2-nanosecond-long production dynamics. Periodic boundary conditions were used and long-range electrostatics was treated by particle mesh Ewald (PME) technique. An analysis of the molecular dynamical trajectories was performed and their quality assessed. The protease-inhibitor binding energies were calculated with MM-GBSA/PBSA approach. The effect of the length of the simulation, method to calculate solvation energy, and other factors upon the results was determined.

Návaznosti

• LN00A016, projekt VaV: Název: BIOMOLEKULÁRNÍ CENTRUM

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Biomolekulární centrum