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Robust Prediction of Relative Binding Energies for Protein-Protein Complex Mutations Using Free Energy Perturbation Calculations.

التفاصيل البيبلوغرافية
العنوان: Robust Prediction of Relative Binding Energies for Protein-Protein Complex Mutations Using Free Energy Perturbation Calculations.
المؤلفون: Sampson JM; Schrödinger, Inc., Life Sciences Software, New York, NY, USA., Cannon DA; Schrödinger, GmbH, Life Sciences Software, Mannheim, Germany., Duan J; Schrödinger, GmbH, Life Sciences Software, Mannheim, Germany., Epstein JCK; Schrödinger, Inc., Life Sciences Software, New York, NY, USA., Sergeeva AP; Columbia University, Department of Systems Biology, New York, NY, USA., Katsamba PS; Columbia University, Zuckerman Mind Brain Behavior Institute, New York, NY, USA., Mannepalli SM; Columbia University, Zuckerman Mind Brain Behavior Institute, New York, NY, USA., Bahna FA; Columbia University, Zuckerman Mind Brain Behavior Institute, New York, NY, USA., Adihou H; AstraZeneca, Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, Gothenburg, Sweden; Max Planck Institute of Molecular Physiology, AstraZeneca-MPI Satellite Unit, Dortmund, Germany., Guéret SM; AstraZeneca, Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, Gothenburg, Sweden; Max Planck Institute of Molecular Physiology, AstraZeneca-MPI Satellite Unit, Dortmund, Germany., Gopalakrishnan R; AstraZeneca, Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, Gothenburg, Sweden; Max Planck Institute of Molecular Physiology, AstraZeneca-MPI Satellite Unit, Dortmund, Germany., Geschwindner S; AstraZeneca, Mechanistic and Structural Biology, Discovery Sciences, R&D, Gothenburg, Sweden., Rees DG; AstraZeneca, Biologics Engineering, R&D, Cambridge, UK., Sigurdardottir A; AstraZeneca, Biologics Engineering, R&D, Cambridge, UK., Wilkinson T; AstraZeneca, Biologics Engineering, R&D, Cambridge, UK., Dodd RB; AstraZeneca, Biologics Engineering, R&D, Cambridge, UK., De Maria L; AstraZeneca, Medicinal Chemistry, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, Gothenburg, Sweden., Mobarec JC; AstraZeneca, Mechanistic and Structural Biology, Discovery Sciences, R&D, Cambridge, UK., Shapiro L; Columbia University, Zuckerman Mind Brain Behavior Institute, New York, NY, USA; Columbia University, Department of Biochemistry and Molecular Biophysics, New York, NY, USA., Honig B; Columbia University, Department of Systems Biology, New York, NY, USA; Columbia University, Zuckerman Mind Brain Behavior Institute, New York, NY, USA; Columbia University, Department of Biochemistry and Molecular Biophysics, New York, NY, USA; Columbia University, Department of Medicine, New York, NY, USA., Buchanan A; AstraZeneca, Biologics Engineering, R&D, Cambridge, UK., Friesner RA; Columbia University, Department of Chemistry, New York, NY, USA. Electronic address: raf8@columbia.edu., Wang L; Schrödinger, Inc., Life Sciences Software, New York, NY, USA. Electronic address: lingle.wang@schrodinger.com.
المصدر: Journal of molecular biology [J Mol Biol] 2024 Aug 15; Vol. 436 (16), pp. 168640. Date of Electronic Publication: 2024 Jun 04.
نوع المنشور: Journal Article
اللغة: English
بيانات الدورية: Publisher: Elsevier Country of Publication: Netherlands NLM ID: 2985088R Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1089-8638 (Electronic) Linking ISSN: 00222836 NLM ISO Abbreviation: J Mol Biol Subsets: MEDLINE
أسماء مطبوعة: Publication: Amsterdam : Elsevier
Original Publication: 1959- : London : Academic Press
مواضيع طبية MeSH: Thermodynamics* , Protein Binding* , Proteins*/metabolism , Proteins*/chemistry , Proteins*/genetics, Mutation ; Point Mutation ; Protein Conformation ; Computational Biology/methods ; Models, Molecular
مستخلص: Computational free energy-based methods have the potential to significantly improve throughput and decrease costs of protein design efforts. Such methods must reach a high level of reliability, accuracy, and automation to be effectively deployed in practical industrial settings in a way that impacts protein design projects. Here, we present a benchmark study for the calculation of relative changes in protein-protein binding affinity for single point mutations across a variety of systems from the literature, using free energy perturbation (FEP+) calculations. We describe a method for robust treatment of alternate protonation states for titratable amino acids, which yields improved correlation with and reduced error compared to experimental binding free energies. Following careful analysis of the largest outlier cases in our dataset, we assess limitations of the default FEP+ protocols and introduce an automated script which identifies probable outlier cases that may require additional scrutiny and calculates an empirical correction for a subset of charge-related outliers. Through a series of three additional case study systems, we discuss how Protein FEP+ can be applied to real-world protein design projects, and suggest areas of further study.
Competing Interests: Declaration of competing interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: ‘J.M.S., D.A.C., J.C.K.E., and L.W. are employees of Schrödinger; B.H. is a consultant for and is on the Scientific Advisory Board of Schrödinger, Inc.; R.A.F. has a significant financial stake in, is a consultant for, and is on the Scientific Advisory Board of Schrödinger, Inc. H.A., S.M.G., R.G., S.G., L.D.M., J.C.M., R.B.D., D.G.R., A.S., T.W., and A.B. are employees of AstraZeneca’.
(Copyright © 2024 Elsevier Ltd. All rights reserved.)
التعليقات: Update of: bioRxiv. 2024 Apr 24:2024.04.22.590325. doi: 10.1101/2024.04.22.590325. (PMID: 38712280)
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معلومات مُعتمدة: INV-016167 United States GATES Bill & Melinda Gates Foundation; R35 GM139585 United States GM NIGMS NIH HHS
فهرسة مساهمة: Keywords: binding affinity prediction; free energy methods; in silico mutational screening; protein binding interface optimization; protein-protein interactions
المشرفين على المادة: 0 (Proteins)
تواريخ الأحداث: Date Created: 20240606 Date Completed: 20240802 Latest Revision: 20240923
رمز التحديث: 20240923
مُعرف محوري في PubMed: PMC11339910
DOI: 10.1016/j.jmb.2024.168640
PMID: 38844044
قاعدة البيانات: MEDLINE
الوصف
تدمد:1089-8638
DOI:10.1016/j.jmb.2024.168640