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Hatch HW, Bergonzo C, Blanco MA, Yuan G, Grudinin S, Lund M, Curtis JE, Grishaev AV, Liu Y, Shen VK. Anisotropic coarse-grain Monte Carlo simulations of lysozyme, lactoferrin, and NISTmAb by precomputing atomistic models. J Chem Phys 2024; 161:094113. [PMID: 39234967 DOI: 10.1063/5.0224809] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Accepted: 08/16/2024] [Indexed: 09/06/2024] Open
Abstract
We develop a multiscale coarse-grain model of the NIST Monoclonal Antibody Reference Material 8671 (NISTmAb) to enable systematic computational investigations of high-concentration physical instabilities such as phase separation, clustering, and aggregation. Our multiscale coarse-graining strategy captures atomic-resolution interactions with a computational approach that is orders of magnitude more efficient than atomistic models, assuming the biomolecule can be decomposed into one or more rigid bodies with known, fixed structures. This method reduces interactions between tens of thousands of atoms to a single anisotropic interaction site. The anisotropic interaction between unique pairs of rigid bodies is precomputed over a discrete set of relative orientations and stored, allowing interactions between arbitrarily oriented rigid bodies to be interpolated from the precomputed table during coarse-grained Monte Carlo simulations. We present this approach for lysozyme and lactoferrin as a single rigid body and for the NISTmAb as three rigid bodies bound by a flexible hinge with an implicit solvent model. This coarse-graining strategy predicts experimentally measured radius of gyration and second osmotic virial coefficient data, enabling routine Monte Carlo simulation of medically relevant concentrations of interacting proteins while retaining atomistic detail. All methodologies used in this work are available in the open-source software Free Energy and Advanced Sampling Simulation Toolkit.
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Affiliation(s)
- Harold W Hatch
- Chemical Informatics Research Group, Chemical Sciences Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899-8380, USA
| | - Christina Bergonzo
- Institute for Bioscience and Biotechnology Research, Rockville, Maryland 20850, USA
- Biomolecular Structure and Function Group, Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899-8380, USA
| | - Marco A Blanco
- Discovery Pharmaceutical Sciences, Merck Research Laboratories, Merck & Co., Inc., West Point, Pennsylvania 19486, USA
| | - Guangcui Yuan
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| | - Sergei Grudinin
- CNRS, Grenoble INP, LJK, Université Grenoble Alpes, 38000 Grenoble, France
| | - Mikael Lund
- Division of Computational Chemistry, Lund University, Lund, Sweden
| | - Joseph E Curtis
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| | - Alexander V Grishaev
- Institute for Bioscience and Biotechnology Research, Rockville, Maryland 20850, USA
- Biomolecular Structure and Function Group, Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899-8380, USA
| | - Yun Liu
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
- Center for Neutron Science, Department of Chemical and Biomolecular Engineering, College of Engineering, University of Delaware, Newark, Delaware 19711, USA
| | - Vincent K Shen
- Chemical Informatics Research Group, Chemical Sciences Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899-8380, USA
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Entropy and Entropic Forces to Model Biological Fluids. ENTROPY 2021; 23:e23091166. [PMID: 34573791 PMCID: PMC8465225 DOI: 10.3390/e23091166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/08/2021] [Accepted: 08/17/2021] [Indexed: 11/16/2022]
Abstract
Living cells are complex systems characterized by fluids crowded by hundreds of different elements, including, in particular, a high density of polymers. They are an excellent and challenging laboratory to study exotic emerging physical phenomena, where entropic forces emerge from the organization processes of many-body interactions. The competition between microscopic and entropic forces may generate complex behaviors, such as phase transitions, which living cells may use to accomplish their functions. In the era of big data, where biological information abounds, but general principles and precise understanding of the microscopic interactions is scarce, entropy methods may offer significant information. In this work, we developed a model where a complex thermodynamic equilibrium resulted from the competition between an effective electrostatic short-range interaction and the entropic forces emerging in a fluid crowded by different sized polymers. The target audience for this article are interdisciplinary researchers in complex systems, particularly in thermodynamics and biophysics modeling.
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Hyltegren K, Polimeni M, Skepö M, Lund M. Integrating All-Atom and Coarse-Grained Simulations-Toward Understanding of IDPs at Surfaces. J Chem Theory Comput 2020; 16:1843-1853. [PMID: 32036660 DOI: 10.1021/acs.jctc.9b01041] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present a scheme for transferring conformational degrees of freedom from all-atom (AA) simulations of an intrinsically disordered protein (IDP) to coarse-grained (CG) Monte Carlo (MC) simulations using conformational swap moves. AA simulations of a single histatin 5 peptide in water were used to obtain a structural ensemble, which is reweighted in a CGMC simulation in the presence of a negatively charged surface. For efficient sampling, the AA trajectory was condensed using two approaches: RMSD clustering (based on the root-mean-square difference in atom positions) and a "naı̈ve" truncation, where only every 100th frame of the trajectory was included in the library. The results show that even libraries with few structures well reproduce the radius of gyration and interaction free energy as functions of the distance from the surface. We further observe that the surface slightly promotes the secondary structure of histatin 5 and more so if using explicit surface charges rather than smeared charges.
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Affiliation(s)
- Kristin Hyltegren
- Division of Theoretical Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Marco Polimeni
- Division of Theoretical Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Marie Skepö
- Division of Theoretical Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden.,LINXS-Lund Institute of Advanced Neutron and X-ray Science, Scheelevägen 19, SE-223 70 Lund, Sweden
| | - Mikael Lund
- Division of Theoretical Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden.,LINXS-Lund Institute of Advanced Neutron and X-ray Science, Scheelevägen 19, SE-223 70 Lund, Sweden
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Gotlib IY, Victorov AI. Association kinetics and equilibrium in solutions of cross-associating chains that contain inactive spacers. POLYMER 2020. [DOI: 10.1016/j.polymer.2019.122085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Brylski O, Ebbinghaus S, Mueller JW. Melting Down Protein Stability: PAPS Synthase 2 in Patients and in a Cellular Environment. Front Mol Biosci 2019; 6:31. [PMID: 31131283 PMCID: PMC6509946 DOI: 10.3389/fmolb.2019.00031] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 04/15/2019] [Indexed: 12/17/2022] Open
Abstract
Within the crowded and complex environment of the cell, a protein experiences stabilizing excluded-volume effects and destabilizing quinary interactions with other proteins. Which of these prevail, needs to be determined on a case-by-case basis. PAPS synthases are dimeric and bifunctional enzymes, providing activated sulfate in the form of 3′-phosphoadenosine-5′-phosphosulfate (PAPS) for sulfation reactions. The human PAPS synthases PAPSS1 and PAPSS2 differ significantly in their protein stability as PAPSS2 is a naturally fragile protein. PAPS synthases bind a series of nucleotide ligands and some of them markedly stabilize these proteins. PAPS synthases are of biomedical relevance as destabilizing point mutations give rise to several pathologies. Genetic defects in PAPSS2 have been linked to bone and cartilage malformations as well as a steroid sulfation defect. All this makes PAPS synthases ideal to study protein unfolding, ligand binding, and the stabilizing and destabilizing factors in their cellular environment. This review provides an overview on current concepts of protein folding and stability and links this with our current understanding of the different disease mechanisms of PAPSS2-related pathologies with perspectives for future research and application.
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Affiliation(s)
- Oliver Brylski
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Braunschweig, Germany
| | - Simon Ebbinghaus
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Braunschweig, Germany
| | - Jonathan W Mueller
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, United Kingdom.,Centre for Endocrinology, Diabetes and Metabolism, Birmingham Health Partners, Birmingham, United Kingdom
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Sarupria S. Editorial: “Introduction to the special issue on advanced molecular simulations: Methods and applications”. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2018. [DOI: 10.1142/s0219633618020017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Sapna Sarupria
- Department of Chemical & Biomolecular Engineering, Clemson University, Clemson, SC 29634, USA
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