دورية أكاديمية
Simulation of Reversible Protein-Protein Binding and Calculation of Binding Free Energies Using Perturbed Distance Restraints.
| العنوان: | Simulation of Reversible Protein-Protein Binding and Calculation of Binding Free Energies Using Perturbed Distance Restraints. |
|---|---|
| المؤلفون: | Perthold JW; Institute for Molecular Modeling and Simulation, Department for Material Sciences and Process Engineering, University of Natural Resources and Life Sciences (BOKU) Vienna , Muthgasse 18, 1190 Vienna, Austria., Oostenbrink C; Institute for Molecular Modeling and Simulation, Department for Material Sciences and Process Engineering, University of Natural Resources and Life Sciences (BOKU) Vienna , Muthgasse 18, 1190 Vienna, Austria. |
| المصدر: | Journal of chemical theory and computation [J Chem Theory Comput] 2017 Nov 14; Vol. 13 (11), pp. 5697-5708. Date of Electronic Publication: 2017 Oct 03. |
| نوع المنشور: | Journal Article |
| اللغة: | English |
| بيانات الدورية: | Publisher: American Chemical Society Country of Publication: United States NLM ID: 101232704 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1549-9626 (Electronic) Linking ISSN: 15499618 NLM ISO Abbreviation: J Chem Theory Comput Subsets: MEDLINE |
| أسماء مطبوعة: | Original Publication: Washington, D.C. : American Chemical Society, c2005- |
| مواضيع طبية MeSH: | Molecular Dynamics Simulation*, DNA Polymerase I/*chemistry , Ubiquitin/*chemistry, Humans ; Protein Binding ; Thermodynamics |
| مستخلص: | Virtually all biological processes depend on the interaction between proteins at some point. The correct prediction of biomolecular binding free-energies has many interesting applications in both basic and applied pharmaceutical research. While recent advances in the field of molecular dynamics (MD) simulations have proven the feasibility of the calculation of protein-protein binding free energies, the large conformational freedom of proteins and complex free energy landscapes of binding processes make such calculations a difficult task. Moreover, convergence and reversibility of resulting free-energy values remain poorly described. In this work, an easy-to-use, yet robust approach for the calculation of standard-state protein-protein binding free energies using perturbed distance restraints is described. In the binding process the conformations of the proteins were restrained, as suggested earlier. Two approaches to avoid end-state problems upon release of the conformational restraints were compared. The method was evaluated by practical application to a small model complex of ubiquitin and the very flexible ubiquitin-binding domain of human DNA polymerase ι (UBM2). All computed free energy differences were closely monitored for convergence, and the calculated binding free energies had a mean unsigned deviation of only 1.4 or 2.5 kJ·mol -1 from experimental values. Statistical error estimates were in the order of thermal noise. We conclude that the presented method has promising potential for broad applicability to quantitatively describe protein-protein and various other kinds of complex formation. |
| References: | J Mol Biol. 2003 Jul 18;330(4):891-913. (PMID: 12850155) Mol Cell. 2010 Feb 12;37(3):408-17. (PMID: 20159559) J Chem Theory Comput. 2017 Jan 10;13(1):42-54. (PMID: 27933808) J Proteome Res. 2010 May 7;9(5):2216-25. (PMID: 20329755) J Phys Chem B. 2006 Apr 27;110(16):8488-98. (PMID: 16623536) J Chem Theory Comput. 2009 Sep 8;5(9):2531-43. (PMID: 26616630) J Comput Chem. 2013 Oct 15;34(27):2360-71. (PMID: 24038118) J Comput Chem. 2004 Jan 30;25(2):238-50. (PMID: 14648622) Biopolymers. 1983 Dec;22(12):2577-637. (PMID: 6667333) J Phys Chem B. 2010 Feb 4;114(4):1652-60. (PMID: 20055378) J Chem Phys. 2007 Jan 7;126(1):014101. (PMID: 17212484) Biophys J. 2003 Apr;84(4):2223-33. (PMID: 12668431) J Chem Theory Comput. 2013 Sep 10;9(9):null. (PMID: 24223529) Biochemistry. 2010 Nov 30;49(47):10198-207. (PMID: 21049971) J Chem Theory Comput. 2012 Oct 9;8(10):3705-23. (PMID: 26593015) Biophys J. 2011 Jan 19;100(2):469-77. (PMID: 21244843) Biochemistry. 2013 Feb 26;52(8):1466-76. (PMID: 23374097) Angew Chem Int Ed Engl. 2006 Jun 19;45(25):4064-92. (PMID: 16761306) Bioinformatics. 2014 Feb 1;30(3):326-34. (PMID: 24273239) J Chem Theory Comput. 2012 Oct 9;8(10):3820-9. (PMID: 26593023) PLoS One. 2016 May 11;11(5):e0155251. (PMID: 27166787) Biophys J. 2008 Oct;95(8):3575-90. (PMID: 18621828) J Chem Theory Comput. 2015 Sep 8;11(9):4427-4438. (PMID: 26366131) J Chem Theory Comput. 2013 Aug 13;9(8):null. (PMID: 24179453) J Chem Theory Comput. 2011 Oct 11;7(10):3379-90. (PMID: 26598168) J Chem Theory Comput. 2009 Apr 14;5(4):909-18. (PMID: 26609600) J Chem Phys. 2004 Feb 8;120(6):2618-28. (PMID: 15268405) Proc Natl Acad Sci U S A. 2013 Dec 3;110(49):E4708-13. (PMID: 24248370) J Comput Aided Mol Des. 2015 May;29(5):397-411. (PMID: 25808134) |
| معلومات مُعتمدة: | I 1999 Austria FWF_ Austrian Science Fund FWF |
| المشرفين على المادة: | 0 (Ubiquitin) EC 2.7.7.7 (DNA Polymerase I) |
| تواريخ الأحداث: | Date Created: 20170913 Date Completed: 20181127 Latest Revision: 20220129 |
| رمز التحديث: | 20231215 |
| مُعرف محوري في PubMed: | PMC5688412 |
| DOI: | 10.1021/acs.jctc.7b00706 |
| PMID: | 28898077 |
| قاعدة البيانات: | MEDLINE |
Find this issue from the American Chemical Society | تدمد: | 1549-9626 |
|---|---|
| DOI: | 10.1021/acs.jctc.7b00706 |