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Dissecting the Structural Plasticity and Dynamics of Cytochrome P450 2B4 by Molecular Dynamics Simulations
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.ORCID iD: 0000-0003-4167-6413
East China University of Science and Technology.
East China University of Science and Technology.
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(English)Manuscript (preprint) (Other academic)
Abstract [en]

The plasticity of cytochrome P450 enzymes (P450s) is known to contribute significantly to their catalytic capacity of metabolizing various substrates. Although numerous studies have been performed, factors governing the plasticity and dynamics of P450s are still not fully understood. In this study, taking CYP2B4 as an example, we dissect the protein plasticity and dynamics in different environments. CYP2B4 is featured by a high degree of plasticity that exhibits open, closed, and intermediate states. By analyzing the CYP2B4 crystal structures, we identified the structural features for the closed, open and intermediate states. Interestingly, formation of the dimer structure was found in the open and intermediate structures. The subsequent MD simulations of the open structure in water confirmed the importance of the dimer form in stabilizing the open conformations. MD simulations of the closed and open structures in the membrane environment and the free energies for opening the F-G cassette obtained from the umbrella sampling calculations indicate that the membrane environment is important for stabilizing the F-G cassette. The dynamical network analysis indicates that Asp105 on the B-C loop plays an important role in transiting the structure from the open to intermediate. Our results thus unveil the mechanism of dimer formation and open-to-intermediate transition for CYP2B4 in the water and membrane environments.

Keywords [en]
P450, Conformational plasticity, Molecular dynamics, CYP2B4, Umbrella sampling
National Category
Theoretical Chemistry Other Biological Topics
Identifiers
URN: urn:nbn:se:kth:diva-273358OAI: oai:DiVA.org:kth-273358DiVA, id: diva2:1430332
Note

QC 20200518

Available from: 2020-05-14 Created: 2020-05-14 Last updated: 2020-05-18Bibliographically approved
In thesis
1. Theoretical Studies of Drug-Metabolizing Cytochrome P450 Enzymes
Open this publication in new window or tab >>Theoretical Studies of Drug-Metabolizing Cytochrome P450 Enzymes
2020 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

The family of cytochrome P450 enzymes (P450s) belongs to one of the most important enzyme families in the human body. P450s are involved in the synthesis of endogenous compounds and metabolism of exogenous substances. In mammalian species, drug metabolizing P450s are anchored in the bilayer lipid membrane, which allows the enzymes to interact with other proteins and ligand molecules. A wealth of knowledge about the structures, functions, and mechanisms of P450s have been obtained from both experimental and theoretical studies. However, the mechanisms behind some experimental results, such as the regio- and stereoselectivity and structural flexibility are still elusive.

In this thesis, I present the work done in my doctoral studies, which was focused on the catalytic selectivity and structural flexibility of P450s. Multiple theoretical modeling approaches, such as homology modeling, molecular docking, molecular dynamics, quantum mechanics, and quantum mechanics/molecular mechanics, were applied in the studies. In papers I and II, the regio- and stereoselectivity of CYP4F2, CYP3A4, and CYP19A1 catalyzed C–H hydroxylation of different substrates were studied. The results indicate that the ligand reactivity and accessibility can be decisive for the regio- and stereoselectivity. However, which of them is more important is system-dependent. The quantum mechanics/molecular mechanics calculation results imply that the distribution of spin natural orbitals could be used for discriminating the roles of the reactivity and accessibility. In papers III and IV, the conformational dynamics of the open and closed structures of CYP2B4 and the ligand cooperativity phenomenon of midazolam metabolized by CYP3A4 were investigated using molecular dynamics simulations. From the simulation results, we identified the key residues for the conformational dynamics for the open-to-intermediate transition and found that the ligand cooperativity is also caused by the large flexibility of P450. The results also indicated that the homotropic cooperativity mainly occurs in the large and flexible productive site, rather than in the remote allosteric site.

Abstract [sv]

Familjen av cytokrom P450-enzymer (P450) tillhör en av de viktigaste enzymfamiljerna i människokroppen. P450 är involverade i syntesen av endogena föreningar och metabolism av exogena substanser. Hos däggdjursarter är läkemedelsmetaboliserande P450s bundna till lipidmembranet i cellerna, vilket påverkar P450s förmåga att interagera med andra proteiner och ligandmolekyler. En mängd kunskap om P450:s struktur, funktion och mekanism har erhållits från både experimentella och teoretiska studier. Däremot är mekanismerna bakom vissa experimentella resultat, såsom regio- och stereoselektivitet och strukturell flexibilitet fortfarande svårfångade.

 

I denna avhandling presenterar jag det arbete som gjorts under mina doktorandstudier, som fokuserade på den katalytiska selektiviteten och strukturella flexibiliteten hos P450. Flera teoretiska modelleringsmetoder, såsom homologimodellering, molekylär dockning, molekyldynamik, kvantmekanik och kvantmekanik/molekylmekanik har använts i studierna. I artikel I och II studerades regio- och stereoselektiviteten för CYP4F2, CYP3A4 och CYP19A1 C-H hydroxylering av olika substrat. Resultaten indikerar att ligandreaktiviteten och tillgängligheten kan vara avgörande för regio- och stereoselektiviteten. Vilken av dem som är viktigare är emellertid systemberoende. Resultaten av beräkningen med kvantmekanik/molekylmekanik innebär att fördelningen av naturliga spin orbitaler kan användas för att urskilja rollen för substratets reaktivitet och tillgänglighet. I artiklarna III och IV undersöktes konformationsdynamiken för de öppna och slutna strukturerna av CYP2B4 och ligandkooperativitetsfenomenet för midazolam metaboliserat genom CYP3A4 med hjälp av molekyldynamiksimuleringar. Från simuleringsresultaten identifierade vi nyckelaminosyrorna för konformationens dynamik för den öppen-till-intermediär-övergången och fann att ligandens kooperativitet också orsakas av den stora flexibiliteten hos P450. Resultaten indikerade även att den homotropa kooperativiteten huvudsakligen inträffar på det stora och flexibla produktiva sätet, snarare än på det avlägsna allosteriska sätet.

Place, publisher, year, edition, pages
Stockholm, Sweden: KTH Royal Institute of Technology, 2020. p. 75
Series
TRITA-CBH-FOU ; 2020:29
Keywords
Cytochrome P450 enzymes, molecular dynamics, quantum chemistry, structural flexibililty, ONIOM
National Category
Natural Sciences
Research subject
Theoretical Chemistry and Biology
Identifiers
urn:nbn:se:kth:diva-273361 (URN)978-91-7873-546-4 (ISBN)
Public defence
2020-06-10, https://kth-se.zoom.us/webinar/register/WN_cYqhoHWeSuCidzUAeMPKYg, 10:00 (English)
Opponent
Supervisors
Note

QC 2020-05-20

Available from: 2020-05-20 Created: 2020-05-14 Last updated: 2020-05-28Bibliographically approved

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Li, JunhaoZhou, YangTu, Yaoquan

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