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Kalayan J, Curtis RA, Warwicker J, Henchman RH. Thermodynamic Origin of Differential Excipient-Lysozyme Interactions. Front Mol Biosci 2021; 8:689400. [PMID: 34179093 PMCID: PMC8226134 DOI: 10.3389/fmolb.2021.689400] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 05/25/2021] [Indexed: 01/15/2023] Open
Abstract
Understanding the intricate interplay of interactions between proteins, excipients, ions and water is important to achieve the effective purification and stable formulation of protein therapeutics. The free energy of lysozyme interacting with two kinds of polyanionic excipients, citrate and tripolyphosphate, together with sodium chloride and TRIS-buffer, are analysed in multiple-walker metadynamics simulations to understand why tripolyphosphate causes lysozyme to precipitate but citrate does not. The resulting multiscale decomposition of energy and entropy components for water, sodium chloride, excipients and lysozyme reveals that lysozyme is more stabilised by the interaction of tripolyphosphate with basic residues. This is accompanied by more sodium ions being released into solution from tripolyphosphate than for citrate, whilst the latter instead has more water molecules released into solution. Even though lysozyme aggregation is not directly probed in this study, these different mechanisms are suspected to drive the cross-linking between lysozyme molecules with vacant basic residues, ultimately leading to precipitation.
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Affiliation(s)
- Jas Kalayan
- Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom.,Department of Chemistry, The University of Manchester, Manchester, United Kingdom
| | - Robin A Curtis
- Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom.,Departments of Chemical Engineering and Analytical Science, The University of Manchester, Manchester, United Kingdom
| | - Jim Warwicker
- Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom.,Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Richard H Henchman
- Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom.,Department of Chemistry, The University of Manchester, Manchester, United Kingdom.,Faculty of Medicine and Health, Sydney Medical School, The University of Sydney, Sydney, NSW, Australia
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Spiriti J, Wong CF. Qualitative Prediction of Ligand Dissociation Kinetics from Focal Adhesion Kinase Using Steered Molecular Dynamics. Life (Basel) 2021; 11:life11020074. [PMID: 33498237 PMCID: PMC7909260 DOI: 10.3390/life11020074] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 02/05/2023] Open
Abstract
Most early-stage drug discovery projects focus on equilibrium binding affinity to the target alongside selectivity and other pharmaceutical properties. Since many approved drugs have nonequilibrium binding characteristics, there has been increasing interest in optimizing binding kinetics early in the drug discovery process. As focal adhesion kinase (FAK) is an important drug target, we examine whether steered molecular dynamics (SMD) can be useful for identifying drug candidates with the desired drug-binding kinetics. In simulating the dissociation of 14 ligands from FAK, we find an empirical power–law relationship between the simulated time needed for ligand unbinding and the experimental rate constant for dissociation, with a strong correlation depending on the SMD force used. To improve predictions, we further develop regression models connecting experimental dissociation rate with various structural and energetic quantities derived from the simulations. These models can be used to predict dissociation rates from FAK for related compounds.
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Abstract
Troponin is a key regulatory protein in muscle contraction, consisting of three subunits troponin C (TnC), troponin I (TnI), and troponin T (TnT). Calcium association to TnC initiates contraction by causing a series of dynamic and conformational changes that allow the switch peptide of TnI to bind and subsequently cross bridges to form between the thin and thick filament of the sarcomere. Owing to its pivotal role in contraction regulation, troponin has been the focus of numerous computational studies over the last decade. These studies elegantly supplemented a large volume of experimental work and focused on the structure, dynamics and function of the whole troponin complex, individual subunits, and even on segments of the thin filament. Molecular dynamics, Brownian dynamics, and free energy simulations have been used to elucidate the conformational dynamics and underlying free energy landscape of troponin, calcium, and switch peptide binding, as well as the effect of disease mutations, small molecules and post-translational modifications such as phosphorylation. Frequently, simulations have been used to confirm or explain experimental observations. Computer-aided drug discovery tools have been employed to identify novel potential calcium sensitizing agents binding to the TnC-TnI interface. Finally, Markov modeling has contributed to simulating contraction within the sarcomere on the mesoscale. Here we are reviewing and classifying the existing computational work on troponin and its subunits, outline current gaps in simulations elucidating troponin's role in contraction and suggest potential future developments in the field.
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Affiliation(s)
- Jacob D Bowman
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, United States
| | - Steffen Lindert
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, United States
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Hong L, Vani BP, Thiede EH, Rust MJ, Dinner AR. Molecular dynamics simulations of nucleotide release from the circadian clock protein KaiC reveal atomic-resolution functional insights. Proc Natl Acad Sci U S A 2018; 115:E11475-E11484. [PMID: 30442665 PMCID: PMC6298084 DOI: 10.1073/pnas.1812555115] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The cyanobacterial clock proteins KaiA, KaiB, and KaiC form a powerful system to study the biophysical basis of circadian rhythms, because an in vitro mixture of the three proteins is sufficient to generate a robust ∼24-h rhythm in the phosphorylation of KaiC. The nucleotide-bound states of KaiC critically affect both KaiB binding to the N-terminal domain (CI) and the phosphotransfer reactions that (de)phosphorylate the KaiC C-terminal domain (CII). However, the nucleotide exchange pathways associated with transitions among these states are poorly understood. In this study, we integrate recent advances in molecular dynamics methods to elucidate the structure and energetics of the pathway for Mg·ADP release from the CII domain. We find that nucleotide release is coupled to large-scale conformational changes in the KaiC hexamer. Solvating the nucleotide requires widening the subunit interface leading to the active site, which is linked to extension of the A-loop, a structure implicated in KaiA binding. These results provide a molecular hypothesis for how KaiA acts as a nucleotide exchange factor. In turn, structural parallels between the CI and CII domains suggest a mechanism for allosteric coupling between the domains. We relate our results to structures observed for other hexameric ATPases, which perform diverse functions.
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Affiliation(s)
- Lu Hong
- Graduate Program in Biophysical Sciences, The University of Chicago, Chicago, IL 60637
| | - Bodhi P Vani
- Department of Chemistry, The University of Chicago, Chicago, IL 60637
| | - Erik H Thiede
- Department of Chemistry, The University of Chicago, Chicago, IL 60637
| | - Michael J Rust
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL 60637;
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637
- Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL 60637
| | - Aaron R Dinner
- Department of Chemistry, The University of Chicago, Chicago, IL 60637;
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637
- James Franck Institute, The University of Chicago, Chicago, IL 60637
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De Meyer T, Ensing B, Rogge SMJ, De Clerck K, Meijer EJ, Van Speybroeck V. Acidity Constant (pK a ) Calculation of Large Solvated Dye Molecules: Evaluation of Two Advanced Molecular Dynamics Methods. Chemphyschem 2016; 17:3447-3459. [PMID: 27570194 PMCID: PMC5129556 DOI: 10.1002/cphc.201600734] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Indexed: 11/14/2022]
Abstract
pH‐Sensitive dyes are increasingly applied on polymer substrates for the creation of novel sensor materials. Recently, these dye molecules were modified to form a covalent bond with the polymer host. This had a large influence on the pH‐sensitive properties, in particular on the acidity constant (pKa). Obtaining molecular control over the factors that influence the pKa value is mandatory for the future intelligent design of sensor materials. Herein, we show that advanced molecular dynamics (MD) methods have reached the level at which the pKa values of large solvated dye molecules can be predicted with high accuracy. Two MD methods were used in this work: steered or restrained MD and the insertion/deletion scheme. Both were first calibrated on a set of phenol derivatives and afterwards applied to the dye molecule bromothymol blue. Excellent agreement with experimental values was obtained, which opens perspectives for using these methods for designing dye molecules.
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Affiliation(s)
- Thierry De Meyer
- Center for Molecular Modeling, Ghent University, Technologiepark 903, 9052, Zwijnaarde, Belgium.,Department of Textiles, Ghent University, Technologiepark 907, 9052, Zwijnaarde, Belgium
| | - Bernd Ensing
- Amsterdam Center for Multiscale Modeling and Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098XH, Amsterdam, The Netherlands
| | - Sven M J Rogge
- Center for Molecular Modeling, Ghent University, Technologiepark 903, 9052, Zwijnaarde, Belgium
| | - Karen De Clerck
- Department of Textiles, Ghent University, Technologiepark 907, 9052, Zwijnaarde, Belgium
| | - Evert Jan Meijer
- Amsterdam Center for Multiscale Modeling and Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098XH, Amsterdam, The Netherlands
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