Energetic and Kinetic Origins of CALB Interfacial Activation Revealed by PaCS-MD/MSM.

ABSTRACT: The conformational dynamics of Candida antarctica lipase B (CALB) was investigated by molecular dynamics (MD) simulation, parallel cascade selection MD (PaCS-MD), and the Markov state model (MSM) and mainly focused on the lid-opening motion closely related to substrate binding. All-atom MD simulation of CALB was conducted in water and on the interface of water and tricaprylin. CALB initially situated in water and separated by layers of water from the interface is spontaneously adsorbed onto the tricaprylin surface during MD simulation. The opening and closing motions of the lid are simulated by PaCS-MD, and subsequent MSM analysis provided the free-energy landscape and time scale of the conformational transitions among the closed, semiopen, and open states. The closed state is the m

SUBMITTER: Wijaya TN 

PROVIDER: S-EPMC10476181 | biostudies-literature | 2023 Aug

REPOSITORIES: biostudies-literature