دورية أكاديمية
أعرض في EDS

Modeling membrane geometries implicitly in Rosetta.

التفاصيل البيبلوغرافية
العنوان: Modeling membrane geometries implicitly in Rosetta.
المؤلفون: Woods H; Center of Structural Biology, Vanderbilt University, Nashville, Tennessee, USA.; Chemical and Physical Biology Program, Vanderbilt University, Nashville, Tennessee, USA., Leman JK; Center for Computational Biology, Flatiron Institute, New York, New York, USA., Meiler J; Center of Structural Biology, Vanderbilt University, Nashville, Tennessee, USA.; Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA.; Institute for Drug Discovery, Leipzig University Medical School, Leipzig, Germany.
المصدر: Protein science : a publication of the Protein Society [Protein Sci] 2024 Mar; Vol. 33 (3), pp. e4908.
نوع المنشور: Journal Article
اللغة: English
بيانات الدورية: Publisher: Cold Spring Harbor Laboratory Press Country of Publication: United States NLM ID: 9211750 Publication Model: Print Cited Medium: Internet ISSN: 1469-896X (Electronic) Linking ISSN: 09618368 NLM ISO Abbreviation: Protein Sci Subsets: MEDLINE
أسماء مطبوعة: Publication: 2001- : Woodbury, NY : Cold Spring Harbor Laboratory Press
Original Publication: New York, N.Y. : Cambridge University Press, c1992-
مواضيع طبية MeSH: Membrane Proteins*/chemistry , Liposomes*, Lipid Bilayers/chemistry ; Models, Molecular ; Micelles
مستخلص: Interactions between membrane proteins (MPs) and lipid bilayers are critical for many cellular functions. In the Rosetta molecular modeling suite, the implicit membrane energy function is based on a "slab" model, which represent the membrane as a flat bilayer. However, in nature membranes often have a curvature that is important for function and/or stability. Even more prevalent, in structural biology research MPs are reconstituted in model membrane systems such as micelles, bicelles, nanodiscs, or liposomes. Thus, we have modified the existing membrane energy potentials within the RosettaMP framework to allow users to model MPs in different membrane geometries. We show that these modifications can be utilized in core applications within Rosetta such as structure refinement, protein-protein docking, and protein design. For MP structures found in curved membranes, refining these structures in curved, implicit membranes produces higher quality models with structures closer to experimentally determined structures. For MP systems embedded in multiple membranes, representing both membranes results in more favorable scores compared to only representing one of the membranes. Modeling MPs in geometries mimicking the membrane model system used in structure determination can improve model quality and model discrimination.
(© 2024 The Authors. Protein Science published by Wiley Periodicals LLC on behalf of The Protein Society.)
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معلومات مُعتمدة: R01GM129261 United States NH NIH HHS
فهرسة مساهمة: Keywords: Rosetta; implicit membrane; membrane proteins; protein structure
المشرفين على المادة: 0 (Membrane Proteins)
0 (Liposomes)
0 (Lipid Bilayers)
0 (Micelles)
تواريخ الأحداث: Date Created: 20240215 Date Completed: 20240216 Latest Revision: 20240217
رمز التحديث: 20240217
مُعرف محوري في PubMed: PMC10868433
DOI: 10.1002/pro.4908
PMID: 38358133
قاعدة البيانات: MEDLINE
الوصف
تدمد:1469-896X
DOI:10.1002/pro.4908