Energetic and Kinetic Origins of CALB Interfacial Activation Revealed by PaCS-MD/MSM
[Image: see text] 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...
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ftpubmed:oai:pubmedcentral.nih.gov:10476181 2023-10-09T21:46:49+02:00 Energetic and Kinetic Origins of CALB Interfacial Activation Revealed by PaCS-MD/MSM Wijaya, Tegar N. Kitao, Akio 2023-08-10 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10476181/ http://www.ncbi.nlm.nih.gov/pubmed/37562019 https://doi.org/10.1021/acs.jpcb.3c02041 en eng American Chemical Society http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10476181/ http://www.ncbi.nlm.nih.gov/pubmed/37562019 http://dx.doi.org/10.1021/acs.jpcb.3c02041 © 2023 The Authors. Published by American Chemical Society https://creativecommons.org/licenses/by/4.0/Permits the broadest form of re-use including for commercial purposes, provided that author attribution and integrity are maintained (https://creativecommons.org/licenses/by/4.0/). J Phys Chem B Text 2023 ftpubmed https://doi.org/10.1021/acs.jpcb.3c02041 2023-09-10T00:52:19Z [Image: see text] 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 most stable in the water system, but the stable conformation in the interface system shifts to the semiopen state. These effects could explain the energetics and kinetics origin of the previously reported interfacial activation of CALB. These findings could help expand the application of CALB toward a wide variety of substrates. Text Antarc* Antarctica PubMed Central (PMC) The Journal of Physical Chemistry B 127 34 7431 7441 |
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PubMed Central (PMC) |
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English |
description |
[Image: see text] 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 most stable in the water system, but the stable conformation in the interface system shifts to the semiopen state. These effects could explain the energetics and kinetics origin of the previously reported interfacial activation of CALB. These findings could help expand the application of CALB toward a wide variety of substrates. |
format |
Text |
author |
Wijaya, Tegar N. Kitao, Akio |
spellingShingle |
Wijaya, Tegar N. Kitao, Akio Energetic and Kinetic Origins of CALB Interfacial Activation Revealed by PaCS-MD/MSM |
author_facet |
Wijaya, Tegar N. Kitao, Akio |
author_sort |
Wijaya, Tegar N. |
title |
Energetic and Kinetic Origins of CALB Interfacial Activation Revealed by PaCS-MD/MSM |
title_short |
Energetic and Kinetic Origins of CALB Interfacial Activation Revealed by PaCS-MD/MSM |
title_full |
Energetic and Kinetic Origins of CALB Interfacial Activation Revealed by PaCS-MD/MSM |
title_fullStr |
Energetic and Kinetic Origins of CALB Interfacial Activation Revealed by PaCS-MD/MSM |
title_full_unstemmed |
Energetic and Kinetic Origins of CALB Interfacial Activation Revealed by PaCS-MD/MSM |
title_sort |
energetic and kinetic origins of calb interfacial activation revealed by pacs-md/msm |
publisher |
American Chemical Society |
publishDate |
2023 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10476181/ http://www.ncbi.nlm.nih.gov/pubmed/37562019 https://doi.org/10.1021/acs.jpcb.3c02041 |
genre |
Antarc* Antarctica |
genre_facet |
Antarc* Antarctica |
op_source |
J Phys Chem B |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10476181/ http://www.ncbi.nlm.nih.gov/pubmed/37562019 http://dx.doi.org/10.1021/acs.jpcb.3c02041 |
op_rights |
© 2023 The Authors. Published by American Chemical Society https://creativecommons.org/licenses/by/4.0/Permits the broadest form of re-use including for commercial purposes, provided that author attribution and integrity are maintained (https://creativecommons.org/licenses/by/4.0/). |
op_doi |
https://doi.org/10.1021/acs.jpcb.3c02041 |
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The Journal of Physical Chemistry B |
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127 |
container_issue |
34 |
container_start_page |
7431 |
op_container_end_page |
7441 |
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1779309356750209024 |