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Maffeo C, Chou HY, Aksimentiev A. Single-molecule biophysics experiments in silico: Toward a physical model of a replisome. iScience 2022; 25:104264. [PMID: 35521518 PMCID: PMC9062759 DOI: 10.1016/j.isci.2022.104264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 03/23/2022] [Accepted: 04/12/2022] [Indexed: 11/25/2022] Open
Abstract
The interpretation of single-molecule experiments is frequently aided by computational modeling of biomolecular dynamics. The growth of computing power and ongoing validation of computational models suggest that it soon may be possible to replace some experiments outright with computational mimics. Here, we offer a blueprint for performing single-molecule studies in silico using a DNA-binding protein as a test bed. We demonstrate how atomistic simulations, typically limited to sub-millisecond durations and zeptoliter volumes, can guide development of a coarse-grained model for use in simulations that mimic single-molecule experiments. We apply the model to recapitulate, in silico, force-extension characterization of protein binding to single-stranded DNA and protein and DNA replacement assays, providing a detailed portrait of the underlying mechanics. Finally, we use the model to simulate the trombone loop of a replication fork, a large complex of proteins and DNA. Coarse-grained model derived from all-atom simulation recapitulates experiments Model reproduces the elastic response to force and exchange dynamics Model reveals structure of intermediate states usually inaccessible to experiment Model applied to viral replisome with trombone loop containing tens of SSB proteins
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Affiliation(s)
- Christopher Maffeo
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 W Green St, Urbana, 61801 IL, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405 N Matthews Avenue, Urbana, 61801 IL, USA
| | - Han-Yi Chou
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 W Green St, Urbana, 61801 IL, USA
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 W Green St, Urbana, 61801 IL, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405 N Matthews Avenue, Urbana, 61801 IL, USA
- Corresponding author
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Arnaudon A, De Castro AL, Holm DD. Noise and Dissipation on Coadjoint Orbits. JOURNAL OF NONLINEAR SCIENCE 2017; 28:91-145. [PMID: 29367809 PMCID: PMC5756579 DOI: 10.1007/s00332-017-9404-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Accepted: 06/12/2017] [Indexed: 06/01/2023]
Abstract
We derive and study stochastic dissipative dynamics on coadjoint orbits by incorporating noise and dissipation into mechanical systems arising from the theory of reduction by symmetry, including a semidirect product extension. Random attractors are found for this general class of systems when the Lie algebra is semi-simple, provided the top Lyapunov exponent is positive. We study in details two canonical examples, the free rigid body and the heavy top, whose stochastic integrable reductions are found and numerical simulations of their random attractors are shown.
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Affiliation(s)
- Alexis Arnaudon
- Department of Mathematics, Imperial College, London, SW7 2AZ UK
| | - Alex L. De Castro
- Department of Mathematics, Imperial College, London, SW7 2AZ UK
- Departamento de Matemática, PUC-Rio, Rio de Janeiro, 22451-900 Brazil
| | - Darryl D. Holm
- Department of Mathematics, Imperial College, London, SW7 2AZ UK
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Szklarczyk OM, González-Segredo N, Kukura P, Oppenheim A, Choquet D, Sandoghdar V, Helenius A, Sbalzarini IF, Ewers H. Receptor concentration and diffusivity control multivalent binding of Sv40 to membrane bilayers. PLoS Comput Biol 2013; 9:e1003310. [PMID: 24244125 PMCID: PMC3828148 DOI: 10.1371/journal.pcbi.1003310] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 08/20/2013] [Indexed: 11/19/2022] Open
Abstract
Incoming Simian Virus 40 particles bind to their cellular receptor, the glycolipid GM1, in the plasma membrane and thereby induce membrane deformation beneath the virion leading to endocytosis and infection. Efficient membrane deformation depends on receptor lipid structure and the organization of binding sites on the internalizing particle. To determine the role of receptor diffusion, concentration and the number of receptors required for stable binding in this interaction, we analyze the binding of SV40 to GM1 in supported membrane bilayers by computational modeling based on experimental data. We measure the diffusion rates of SV40 virions in solution by fluorescence correlation spectroscopy and of the receptor in bilayers by single molecule tracking. Quartz-crystal microbalance with dissipation (QCM-D) is used to measure binding of SV40 virus-like particles to bilayers containing the viral receptor GM1. We develop a phenomenological stochastic dynamics model calibrated against this data, and use it to investigate the early events of virus attachment to lipid membranes. Our results indicate that SV40 requires at least 4 attached receptors to achieve stable binding. We moreover find that receptor diffusion is essential for the establishment of stable binding over the physiological range of receptor concentrations and that receptor concentration controls the mode of viral motion on the target membrane. Our results provide quantitative insight into the initial events of virus-host interaction at the nanoscopic level.
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Affiliation(s)
- Oliwia M. Szklarczyk
- MOSAIC Group, Institute of Theoretical Computer Science and Swiss Institute of Bioinformatics, ETH Zurich, Zurich, Switzerland
- Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Nélido González-Segredo
- MOSAIC Group, Institute of Theoretical Computer Science and Swiss Institute of Bioinformatics, ETH Zurich, Zurich, Switzerland
| | - Philipp Kukura
- Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Ariella Oppenheim
- Department of Haematology, Hebrew University Faculty of Medicine, Jerusalem, Israel
| | - Daniel Choquet
- 4UMR 5297 CNRS, Universite de Bordeaux, Bordeaux, France
| | - Vahid Sandoghdar
- Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Ari Helenius
- Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Ivo F. Sbalzarini
- MOSAIC Group, Institute of Theoretical Computer Science and Swiss Institute of Bioinformatics, ETH Zurich, Zurich, Switzerland
| | - Helge Ewers
- Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
- Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
- * E-mail:
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Gordon D, Chen R, Chung SH. Computational methods of studying the binding of toxins from venomous animals to biological ion channels: theory and applications. Physiol Rev 2013; 93:767-802. [PMID: 23589832 PMCID: PMC3768100 DOI: 10.1152/physrev.00035.2012] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The discovery of new drugs that selectively block or modulate ion channels has great potential to provide new treatments for a host of conditions. One promising avenue revolves around modifying or mimicking certain naturally occurring ion channel modulator toxins. This strategy appears to offer the prospect of designing drugs that are both potent and specific. The use of computational modeling is crucial to this endeavor, as it has the potential to provide lower cost alternatives for exploring the effects of new compounds on ion channels. In addition, computational modeling can provide structural information and theoretical understanding that is not easily derivable from experimental results. In this review, we look at the theory and computational methods that are applicable to the study of ion channel modulators. The first section provides an introduction to various theoretical concepts, including force-fields and the statistical mechanics of binding. We then look at various computational techniques available to the researcher, including molecular dynamics, brownian dynamics, and molecular docking systems. The latter section of the review explores applications of these techniques, concentrating on pore blocker and gating modifier toxins of potassium and sodium channels. After first discussing the structural features of these channels, and their modes of block, we provide an in-depth review of past computational work that has been carried out. Finally, we discuss prospects for future developments in the field.
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Affiliation(s)
- Dan Gordon
- Research School of Biology, The Australian National University, Acton, ACT 0200, Australia.
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Gordon D, Chung SH. Extension of Brownian dynamics for studying blockers of ion channels. J Phys Chem B 2012; 116:14285-94. [PMID: 23157405 DOI: 10.1021/jp309751e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We present new Brownian dynamics techniques for studying blockers of ion channels. By treating the channel as a fixed body, simulating the blocker molecules using rigid bodies, and using an implicit water force field with explicit ions, we are able to carry out fast simulations that can be used to investigate the dynamics of block and unblock, deduce binding modes, and calculate binding affinities. We test our program using the NavAb bacterial sodium channel, whose structure was recently solved (Payandeh et al. Nature, 2011, 475, 353-358) in conjunction with the μ-conotoxin PIIIA blocker. We derive an ohmic current-voltage relationship for channel permeation, calculate potentials of mean force for blocker unbinding, and deduce multiple binding modes for the blocker. Our results are shown to be compatible with other computational and experimental results. Finally, we discuss future improvements such as the inclusion of flexible side chains. After these improvements are carried out, we anticipate our program will be an extremely useful new tool that could be used to help develop new drugs to treat a range of ion-channel related diseases.
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Affiliation(s)
- Dan Gordon
- Research School of Biology, Building 46, The Australian National University, Canberra, ACT 0200 Australia.
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Gordon D, Chen R, Ho J, Coote ML, Chung SH. Rigid Body Brownian Dynamics as a Tool for Studying Ion Channel Blockers. J Phys Chem B 2012; 116:1933-41. [DOI: 10.1021/jp210105f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Dan Gordon
- Research School of Biology, Australian National University, Canberra, Australia
| | - Rong Chen
- Research School of Biology, Australian National University, Canberra, Australia
| | - Junming Ho
- Research School of Chemistry, Australian National University, Canberra, Australia
| | - Michelle L. Coote
- Research School of Chemistry, Australian National University, Canberra, Australia
| | - Shin-Ho Chung
- Research School of Biology, Australian National University, Canberra, Australia
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