Energetic and Kinetic Origin of CALB Interfacial Activation Revealed by PaCS-MD/MSM
Conformational dynamics of Candida antarctica Lipase B (CALB) was investigated by molecular dynamics (MD) simulation, parallel cascade selection MD (PaCS-MD), the Markov state model (MSM), and mainly focused on the lid-opening motion closely related to substrate binding. All-atom MD simulation of CA...
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| Format: | Other/Unknown Material |
| Language: | unknown |
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American Chemical Society (ACS)
2023
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| Online Access: | http://dx.doi.org/10.26434/chemrxiv-2023-17v42 https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6421264e647e3dca999010ac/original/energetic-and-kinetic-origin-of-calb-interfacial-activation-revealed-by-pa-cs-md-msm.pdf |
| Summary: | Conformational dynamics of Candida antarctica Lipase B (CALB) was investigated by molecular dynamics (MD) simulation, parallel cascade selection MD (PaCS-MD), 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 that around the interface constructed by 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, semi-open, and open states. The closed state is the most stable in the water system but the stable conformation in the interface system shifts to the semi-open state. In the interface system, the transition probability to the open state is higher than in the water system. These effects could explain the energetics and kinetics origin of previously reported interfacial activation of CALB. We also suggest two types of mechanisms for substrate binding in which small and hydrophilic substrates bind without interfacial activation while large and bulky substrates bind via interfacial activation. These findings could help expand the application of CALB towards a wide variety of substrates. |
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