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Wilson E, Vant J, Layton J, Boyd R, Lee H, Turilli M, Hernández B, Wilkinson S, Jha S, Gupta C, Sarkar D, Singharoy A. Large-Scale Molecular Dynamics Simulations of Cellular Compartments. Methods Mol Biol 2021; 2302:335-356. [PMID: 33877636 DOI: 10.1007/978-1-0716-1394-8_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
Molecular dynamics or MD simulation is gradually maturing into a tool for constructing in vivo models of living cells in atomistic details. The feasibility of such models is bolstered by integrating the simulations with data from microscopic, tomographic and spectroscopic experiments on exascale supercomputers, facilitated by the use of deep learning technologies. Over time, MD simulation has evolved from tens of thousands of atoms to over 100 million atoms comprising an entire cell organelle, a photosynthetic chromatophore vesicle from a purple bacterium. In this chapter, we present a step-by-step outline for preparing, executing and analyzing such large-scale MD simulations of biological systems that are essential to life processes. All scripts are provided via GitHub.
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Affiliation(s)
- Eric Wilson
- The School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
| | - John Vant
- The School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
| | - Jacob Layton
- The School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
| | - Ryan Boyd
- The School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
| | - Hyungro Lee
- RADICAL, ECE, Rutgers University, Piscataway, NJ, USA
| | | | | | | | - Shantenu Jha
- RADICAL, ECE, Rutgers University, Piscataway, NJ, USA.,Brookhaven National Laboratory, Upton, NY, USA
| | - Chitrak Gupta
- The School of Molecular Sciences, Arizona State University, Tempe, AZ, USA.
| | - Daipayan Sarkar
- The School of Molecular Sciences, Arizona State University, Tempe, AZ, USA. .,Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.
| | - Abhishek Singharoy
- The School of Molecular Sciences, Arizona State University, Tempe, AZ, USA.
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2
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Wu K, Xu S, Wan B, Xiu P, Zhou X. A novel multiscale scheme to accelerate atomistic simulations of bio-macromolecules by adaptively driving coarse-grained coordinates. J Chem Phys 2020; 152:114115. [PMID: 32199430 DOI: 10.1063/1.5135309] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
All-atom molecular dynamics (MD) simulations of bio-macromolecules can yield relatively accurate results while suffering from the limitation of insufficient conformational sampling. On the other hand, the coarse-grained (CG) MD simulations efficiently accelerate conformational changes in biomolecules but lose atomistic details and accuracy. Here, we propose a novel multiscale simulation method called the adaptively driving multiscale simulation (ADMS)-it efficiently accelerates biomolecular dynamics by adaptively driving virtual CG atoms on the fly while maintaining the atomistic details and focusing on important conformations of the original system with irrelevant conformations rarely sampled. Herein, the "adaptive driving" is based on the short-time-averaging response of the system (i.e., an approximate free energy surface of the original system), without requiring the construction of the CG force field. We apply the ADMS to two peptides (deca-alanine and Ace-GGPGGG-Nme) and one small protein (HP35) as illustrations. The simulations show that the ADMS not only efficiently captures important conformational states of biomolecules and drives fast interstate transitions but also yields, although it might be in part, reliable protein folding pathways. Remarkably, a ∼100-ns explicit-solvent ADMS trajectory of HP35 with three CG atoms realizes folding and unfolding repeatedly and captures the important states comparable to those from a 398-µs standard all-atom MD simulation.
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Affiliation(s)
- Kai Wu
- Department of Engineering Mechanics, Zhejiang University, Hangzhou 310027, China
| | - Shun Xu
- Computer Network Information Center, Chinese Academy of Sciences, Beijing 100190, China
| | - Biao Wan
- Beijing Computational Science Research Center, Beijing 1100193, China
| | - Peng Xiu
- Department of Engineering Mechanics, Zhejiang University, Hangzhou 310027, China
| | - Xin Zhou
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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3
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Xie L, Shen L, Chen ZN, Yang M. Efficient free energy calculations by combining two complementary tempering sampling methods. J Chem Phys 2017; 146:024103. [PMID: 28088161 DOI: 10.1063/1.4973607] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Affiliation(s)
- Liangxu Xie
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Lin Shen
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Zhe-Ning Chen
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Yangqiao West Road 155, Fuzhou, Fujian 350002, China
| | - Mingjun Yang
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
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4
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Abi Mansour A, Ortoleva PJ. Reverse Coarse-Graining for Equation-Free Modeling: Application to Multiscale Molecular Dynamics. J Chem Theory Comput 2016; 12:5541-5548. [PMID: 27631340 DOI: 10.1021/acs.jctc.6b00348] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Constructing atom-resolved states from low-resolution data is of practical importance in many areas of science and engineering. This problem is addressed in this article in the context of multiscale factorization methods for molecular dynamics. These methods capture the crosstalk between atomic and coarse-grained scales arising in macromolecular systems. This crosstalk is accounted for by Trotter factorization, which is used to separate the all-atom from the coarse-grained phases of the computation. In this approach, short molecular dynamics runs are used to advance in time the coarse-grained variables, which in turn guide the all-atom state. To achieve this coevolution, an all-atom microstate consistent with the updated coarse-grained variables must be recovered. This recovery is cast here as a nonlinear optimization problem that is solved with a quasi-Newton method. The approach yields a Boltzmann-relevant microstate whose coarse-grained representation and some of its fine-scale features are preserved. Embedding this algorithm in multiscale factorization is shown to be accurate and scalable for simulating proteins and their assemblies.
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Affiliation(s)
- Andrew Abi Mansour
- Department of Chemistry and Center for Theoretical and Computational Nanoscience, Indiana University , Bloomington, Indiana 47405, United States
| | - Peter J Ortoleva
- Department of Chemistry and Center for Theoretical and Computational Nanoscience, Indiana University , Bloomington, Indiana 47405, United States
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5
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Mansour AA, Sereda YV, Yang J, Ortoleva PJ. Prospective on multiscale simulation of virus-like particles: Application to computer-aided vaccine design. Vaccine 2015; 33:5890-6. [DOI: 10.1016/j.vaccine.2015.05.099] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 05/25/2015] [Accepted: 05/28/2015] [Indexed: 10/23/2022]
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6
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Yang M, Yang L, Gao Y, Hu H. Combine umbrella sampling with integrated tempering method for efficient and accurate calculation of free energy changes of complex energy surface. J Chem Phys 2015; 141:044108. [PMID: 25084882 DOI: 10.1063/1.4887340] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Umbrella sampling is an efficient method for the calculation of free energy changes of a system along well-defined reaction coordinates. However, when there exist multiple parallel channels along the reaction coordinate or hidden barriers in directions perpendicular to the reaction coordinate, it is difficult for conventional umbrella sampling to reach convergent sampling within limited simulation time. Here, we propose an approach to combine umbrella sampling with the integrated tempering sampling method. The umbrella sampling method is applied to chemically more relevant degrees of freedom that possess significant barriers. The integrated tempering sampling method is used to facilitate the sampling of other degrees of freedom which may possess statistically non-negligible barriers. The combined method is applied to two model systems, butane and ACE-NME molecules, and shows significantly improved sampling efficiencies as compared to standalone conventional umbrella sampling or integrated tempering sampling approaches. Further analyses suggest that the enhanced performance of the new method come from the complemented advantages of umbrella sampling with a well-defined reaction coordinate and integrated tempering sampling in orthogonal space. Therefore, the combined approach could be useful in the simulation of biomolecular processes, which often involves sampling of complex rugged energy landscapes.
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Affiliation(s)
- Mingjun Yang
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Lijiang Yang
- College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yiqin Gao
- College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Hao Hu
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
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7
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Zhang L, Lua LHL, Middelberg APJ, Sun Y, Connors NK. Biomolecular engineering of virus-like particles aided by computational chemistry methods. Chem Soc Rev 2015; 44:8608-18. [DOI: 10.1039/c5cs00526d] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Multi-scale investigation of VLP self-assembly aided by computational methods is facilitating the design, redesign, and modification of functionalized VLPs.
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Affiliation(s)
- Lin Zhang
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education
- School of Chemical Engineering and Technology
- Tianjin University
- Tianjin 300072, People's Republic of China
| | - Linda H. L. Lua
- Protein Expression Facility
- The University of Queensland
- Brisbane, Australia
| | - Anton P. J. Middelberg
- Australian Institute for Bioengineering and Nanotechnology
- The University of Queensland
- Brisbane, Australia
| | - Yan Sun
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education
- School of Chemical Engineering and Technology
- Tianjin University
- Tianjin 300072, People's Republic of China
| | - Natalie K. Connors
- Australian Institute for Bioengineering and Nanotechnology
- The University of Queensland
- Brisbane, Australia
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8
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Yang J, Singharoy A, Sereda Y, Ortoleva P. Quasiequivalence of multiscale coevolution and ensemble MD simulations: A demonstration with lactoferrin. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2014.10.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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9
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Sereda YV, Ortoleva PJ. A multiscale variational approach to the kinetics of viscous classical liquids: The coarse-grained mean field approximation. J Chem Phys 2014; 140:134104. [DOI: 10.1063/1.4869860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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10
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Sereda YV, Espinosa-Duran JM, Ortoleva PJ. Energy transfer between a nanosystem and its host fluid: a multiscale factorization approach. J Chem Phys 2014; 140:074102. [PMID: 24559333 DOI: 10.1063/1.4864200] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Energy transfer between a macromolecule or supramolecular assembly and a host medium is considered from the perspective of Newton's equations and Lie-Trotter factorization. The development starts by demonstrating that the energy of the molecule evolves slowly relative to the time scale of atomic collisions-vibrations. The energy is envisioned to be a coarse-grained variable that coevolves with the rapidly fluctuating atomistic degrees of freedom. Lie-Trotter factorization is shown to be a natural framework for expressing this coevolution. A mathematical formalism and workflow for efficient multiscale simulation of energy transfer is presented. Lactoferrin and human papilloma virus capsid-like structure are used for validation.
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Affiliation(s)
- Yuriy V Sereda
- Center for Cell and Virus Theory, Department of Chemistry, Indiana University, 800 E. Kirkwood Ave, Bloomington, Indiana 47405, USA
| | - John M Espinosa-Duran
- Center for Cell and Virus Theory, Department of Chemistry, Indiana University, 800 E. Kirkwood Ave, Bloomington, Indiana 47405, USA
| | - Peter J Ortoleva
- Center for Cell and Virus Theory, Department of Chemistry, Indiana University, 800 E. Kirkwood Ave, Bloomington, Indiana 47405, USA
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11
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Abi Mansour A, Ortoleva PJ. Multiscale Factorization Method for Simulating Mesoscopic Systems with Atomic Precision. J Chem Theory Comput 2014; 10:518-523. [PMID: 24803852 PMCID: PMC3985745 DOI: 10.1021/ct400615a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Indexed: 01/05/2023]
Abstract
Mesoscopic N-atom systems derive their structural and dynamical properties from processes coupled across multiple scales in space and time. A multiscale method for simulating these systems in the friction dominated regime from the underlying N-atom formulation is presented. The method integrates notions of multiscale analysis, Trotter factorization, and a hypothesis that the momenta conjugate to coarse-grained variables constitute a stationary process on the time scale of coarse-grained dynamics. The method is demonstrated for lactoferrin, nudaurelia capensis omega virus, and human papillomavirus to assess its accuracy.
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Affiliation(s)
- Andrew Abi Mansour
- Department of Chemistry, Indiana
University, Bloomington, Indiana 47405, United
States
| | - Peter J. Ortoleva
- Department of Chemistry, Indiana
University, Bloomington, Indiana 47405, United
States
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12
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Joshi H, Lewis K, Singharoy A, Ortoleva PJ. Epitope engineering and molecular metrics of immunogenicity: a computational approach to VLP-based vaccine design. Vaccine 2013; 31:4841-7. [PMID: 23933338 DOI: 10.1016/j.vaccine.2013.07.075] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Revised: 07/25/2013] [Accepted: 07/30/2013] [Indexed: 01/05/2023]
Abstract
Developing antiviral vaccines is increasingly challenging due to associated time and cost of production as well as emerging drug-resistant strains. A computer-aided vaccine design strategy is presented that could greatly accelerate the discovery process and yield vaccines with high immunogenicity and thermal stability. Our strategy is based on foreign viral epitopes engineered onto well-established virus-like particles (VLPs) and demonstrates that such constructs present similar affinity for antibodies as does a native virus. This binding affinity serves as one molecular metric of immunogenicity. As a demonstration, we engineered a preS1 epitope of hepatitis B virus (HBV) onto the EF loop of human papillomavirus VLP (HPV-VLP). HBV-associated HzKR127 antibody displayed binding affinity for this structure at distances and strengths similar to those for the complex of the antibody with the full HBV (PDBID: 2EH8). This antibody binding affinity assessment, along with other molecular immunogenicity metrics, could be a key component of a computer-aided vaccine design strategy.
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Affiliation(s)
- Harshad Joshi
- Center for Cell and Virus Theory, Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
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13
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Affiliation(s)
- Marissa G. Saunders
- Department of Chemistry, Institute for Biophysical Dynamics, James Franck Institute, and Computation Institute, University of Chicago, Chicago, Illinois 60637;
| | - Gregory A. Voth
- Department of Chemistry, Institute for Biophysical Dynamics, James Franck Institute, and Computation Institute, University of Chicago, Chicago, Illinois 60637;
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14
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Quick R, Singharoy A, Ortoleva P. Quasiperiodic oscillation and possible Second Law violation in a nanosystem. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2013.03.083] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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15
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Ortoleva P, Singharoy A, Pankavich S. Hierarchical Multiscale Modeling of Macromolecules and their Assemblies. SOFT MATTER 2013; 9:4319-4335. [PMID: 23671457 PMCID: PMC3650908 DOI: 10.1039/c3sm50176k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Soft materials (e.g., enveloped viruses, liposomes, membranes and supercooled liquids) simultaneously deform or display collective behaviors, while undergoing atomic scale vibrations and collisions. While the multiple space-time character of such systems often makes traditional molecular dynamics simulation impractical, a multiscale approach has been presented that allows for long-time simulation with atomic detail based on the co-evolution of slowly-varying order parameters (OPs) with the quasi-equilibrium probability density of atomic configurations. However, this approach breaks down when the structural change is extreme, or when nearest-neighbor connectivity of atoms is not maintained. In the current study, a self-consistent approach is presented wherein OPs and a reference structure co-evolve slowly to yield long-time simulation for dynamical soft-matter phenomena such as structural transitions and self-assembly. The development begins with the Liouville equation for N classical atoms and an ansatz on the form of the associated N-atom probability density. Multiscale techniques are used to derive Langevin equations for the coupled OP-configurational dynamics. The net result is a set of equations for the coupled stochastic dynamics of the OPs and centers of mass of the subsystems that constitute a soft material body. The theory is based on an all-atom methodology and an interatomic force field, and therefore enables calibration-free simulations of soft matter, such as macromolecular assemblies.
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Affiliation(s)
- P Ortoleva
- Center for Cell and Virus Theory, Department of Chemistry, Indiana University, Bloomington, IN 47405
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16
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Sereda YV, Ortoleva PJ. Variational methods for time-dependent classical many-particle systems. PHYSICA A 2013; 392:628-638. [PMID: 23459064 PMCID: PMC3580877 DOI: 10.1016/j.physa.2012.10.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
A variational method for the classical Liouville equation is introduced that facilitates the development of theories for non-equilibrium classical systems. The method is based on the introduction of a complex-valued auxiliary quantity Ψ that is related to the classical position-momentum probability density ρ via ρ = Ψ*Ψ. A functional of Ψ is developed whose extrema imply that ρ satisfies the Liouville equation. Multiscale methods are used to develop trial functions to be optimized by the variational principle. The present variational principle with multiscale trial functions can capture both the microscopic and the coarse-grained descriptions, thereby yielding theories that account for the two way exchange of information across multiple scales in space and time. Equations of the Smoluchowski form for the coarse-grained state probability density are obtained. Constraints on the initial state of the N-particle probability density for which the aforementioned equation is closed and conserves probability are presented. The methodology has applicability to a wide range of systems including macromolecular assemblies, ionic liquids, and nanoparticles.
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Affiliation(s)
- Yuriy V. Sereda
- Department of Chemistry, Indiana University, 800 E. Kirkwood Ave., Bloomington, Indiana 47405, USA
| | - Peter J. Ortoleva
- Department of Chemistry, Indiana University, 800 E. Kirkwood Ave., Bloomington, Indiana 47405, USA
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17
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Singharoy A, Joshi H, Ortoleva PJ. Multiscale macromolecular simulation: role of evolving ensembles. J Chem Inf Model 2012; 52:2638-49. [PMID: 22978601 DOI: 10.1021/ci3002952] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Multiscale analysis provides an algorithm for the efficient simulation of macromolecular assemblies. This algorithm involves the coevolution of a quasiequilibrium probability density of atomic configurations and the Langevin dynamics of spatial coarse-grained variables denoted order parameters (OPs) characterizing nanoscale system features. In practice, implementation of the probability density involves the generation of constant OP ensembles of atomic configurations. Such ensembles are used to construct thermal forces and diffusion factors that mediate the stochastic OP dynamics. Generation of all-atom ensembles at every Langevin time step is computationally expensive. Here, multiscale computation for macromolecular systems is made more efficient by a method that self-consistently folds in ensembles of all-atom configurations constructed in an earlier step, history, of the Langevin evolution. This procedure accounts for the temporal evolution of these ensembles, accurately providing thermal forces and diffusions. It is shown that efficiency and accuracy of the OP-based simulations is increased via the integration of this historical information. Accuracy improves with the square root of the number of historical timesteps included in the calculation. As a result, CPU usage can be decreased by a factor of 3-8 without loss of accuracy. The algorithm is implemented into our existing force-field based multiscale simulation platform and demonstrated via the structural dynamics of viral capsomers.
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Affiliation(s)
- A Singharoy
- Center for Cell and Virus Theory, Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
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18
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Sereda YV, Singharoy AB, Jarrold MF, Ortoleva PJ. Discovering free energy basins for macromolecular systems via guided multiscale simulation. J Phys Chem B 2012; 116:8534-44. [PMID: 22423635 PMCID: PMC3408247 DOI: 10.1021/jp2126174] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
An approach for the automated discovery of low free energy states of macromolecular systems is presented. The method does not involve delineating the entire free energy landscape but proceeds in a sequential free energy minimizing state discovery; i.e., it first discovers one low free energy state and then automatically seeks a distinct neighboring one. These states and the associated ensembles of atomistic configurations are characterized by coarse-grained variables capturing the large-scale structure of the system. A key facet of our approach is the identification of such coarse-grained variables. Evolution of these variables is governed by Langevin dynamics driven by thermal-average forces and mediated by diffusivities, both of which are constructed by an ensemble of short molecular dynamics runs. In the present approach, the thermal-average forces are modified to account for the entropy changes following from our knowledge of the free energy basins already discovered. Such forces guide the system away from the known free energy minima, over free energy barriers, and to a new one. The theory is demonstrated for lactoferrin, known to have multiple energy-minimizing structures. The approach is validated using experimental structures and traditional molecular dynamics. The method can be generalized to enable the interpretation of nanocharacterization data (e.g., ion mobility-mass spectrometry, atomic force microscopy, chemical labeling, and nanopore measurements).
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Affiliation(s)
- Yuriy V. Sereda
- Center for Cell and Virus Theory, Department of Chemistry, Indiana University, 800 E. Kirkwood Ave, Bloomington, IN 47405
| | - Abhishek B. Singharoy
- Center for Cell and Virus Theory, Department of Chemistry, Indiana University, 800 E. Kirkwood Ave, Bloomington, IN 47405
| | - Martin F. Jarrold
- Center for Cell and Virus Theory, Department of Chemistry, Indiana University, 800 E. Kirkwood Ave, Bloomington, IN 47405
| | - Peter J. Ortoleva
- Center for Cell and Virus Theory, Department of Chemistry, Indiana University, 800 E. Kirkwood Ave, Bloomington, IN 47405
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19
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Singharoy A, Joshi H, Miao Y, Ortoleva PJ. Space warping order parameters and symmetry: application to multiscale simulation of macromolecular assemblies. J Phys Chem B 2012; 116:8423-34. [PMID: 22356532 PMCID: PMC4937887 DOI: 10.1021/jp2119247] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Coarse-grained features of macromolecular assemblies are understood via a set of order parameters (OPs) constructed in terms of their all-atom configuration. OPs are shown to be slowly changing in time and capture the large-scale spatial features of macromolecular assemblies. The relationship of these variables to the classic notion of OPs based on symmetry breaking phase transitions is discussed. OPs based on space warping transformations are analyzed in detail as they naturally provide a connection between overall structure of an assembly and all-atom configuration. These OPs serve as the basis of a multiscale analysis that yields Langevin equations for OP dynamics. In this context, the characteristics of OPs and PCA modes are compared. The OPs enable efficient all-atom multiscale simulations of the dynamics of macromolecular assemblies in response to changes in microenvironmental conditions, as demonstrated on the structural transitions of cowpea chlorotic mottle virus capsid (CCMV) and RNA of the satellite tobacco mosaic virus (STMV).
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Affiliation(s)
- Abhishek Singharoy
- Center for Cell and Virus Theory, Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Harshad Joshi
- Center for Cell and Virus Theory, Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | | | - Peter J. Ortoleva
- Center for Cell and Virus Theory, Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
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20
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Yukalov VI, Yukalova EP. Statistics of Multiscale Fluctuations in Macromolecular Systems. J Phys Chem B 2012; 116:8435-48. [DOI: 10.1021/jp212052r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Vyacheslav I. Yukalov
- Bogolubov
Laboratory of Theoretical Physics, and ‡Laboratory of Information Technologies, Joint Institute for Nuclear Research, Dubna 141980, Russia
| | - Elizaveta P. Yukalova
- Bogolubov
Laboratory of Theoretical Physics, and ‡Laboratory of Information Technologies, Joint Institute for Nuclear Research, Dubna 141980, Russia
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21
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Singharoy A, Sereda Y, Ortoleva PJ. Hierarchical Order Parameters for Macromolecular Assembly Simulations I: Construction and Dynamical Properties of Order Parameters. J Chem Theory Comput 2012; 8:1379-1392. [PMID: 22661911 PMCID: PMC3361912 DOI: 10.1021/ct200574x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Macromolecular assemblies often display a hierarchical organization of macromolecules or their sub-assemblies. To model this, we have formulated a space warping method that enables capturing overall macromolecular structure and dynamics via a set of coarse-grained order parameters (OPs). This article is the first of two describing the construction and computational implementation of an additional class of OPs that has built into them the hierarchical architecture of macromolecular assemblies. To accomplish this, first, the system is divided into subsystems, each of which is described via a representative set of OPs. Then, a global set of variables is constructed from these subsystem-centered OPs to capture overall system organization. Dynamical properties of the resulting OPs are compared to those of our previous nonhierarchical ones, and implied conceptual and computational advantages are discussed for a 100ns, 2 million atom solvated Human Papillomavirus-like particle simulation. In the second article, the hierarchical OPs are shown to enable a multiscale analysis that starts with the N-atom Liouville equation and yields rigorous Langevin equations of stochastic OP dynamics. The latter is demonstrated via a force-field based simulation algorithm that probes key structural transition pathways, simultaneously accounting for all-atom details and overall structure.
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Affiliation(s)
- Abhishek Singharoy
- Center for Cell and Virus Theory, Department of Chemistry, Indiana University, Bloomington, IN 47405
| | - Yuriy Sereda
- Center for Cell and Virus Theory, Department of Chemistry, Indiana University, Bloomington, IN 47405
| | - Peter J. Ortoleva
- Center for Cell and Virus Theory, Department of Chemistry, Indiana University, Bloomington, IN 47405
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Shreif Z, Ortoleva P. Scaling behavior of quantum nanosystems: emergence of quasi-particles, collective modes, and mixed exchange symmetry states. J Chem Phys 2012; 134:104106. [PMID: 21405155 DOI: 10.1063/1.3560450] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Examples of quantum nanosystems are graphene nanoribbons, molecular wires, and superconducting nanoparticles. The objective of the multiscale theory presented here is to provide a new perspective on the coupling of processes across scales in space and time underlying the dynamics of these systems. The long range objective for this multiscale approach is to serve as an efficient computational algorithm. Long space-time dynamics is derived using a perturbation expansion in the ratio ɛ of the nearest-neighbor distance to a nanometer-scale characteristic length and a theorem on the equivalence of long time-averages and expectation values. This dynamics is shown to satisfy a coarse-grained wave equation (CGWE) which takes a Schrödinger-like form with modified masses and interactions. The scaling of space and time is determined by the orders of magnitude of various contributions to the N-body potential. If the spatial scale of the coarse-graining is too large, the CGWE would imply an unbounded growth of gradients; if it is too short, the system's size would display uncontrolled growth inappropriate for the bound states of interest, i.e., collective motion or migration within a stable nanoassembly. The balance of these two extremes removes arbitrariness in the choice of the scaling of space-time. Since the long-scale dynamics of each Fermion involves its interaction with many others, we hypothesize that the solutions of the CGWE have mean-field character to good approximation, i.e., can be factorized into single-particle functions. This leads to a coarse-grained mean-field approximation that is distinct in character from traditional Hartree-Fock theory. A variational principle is used to derive equations for the single-particle functions. This theme is developed and used to derive an equation for low-lying disturbances from the ground state corresponding to long wavelength density disturbances or long-scale migration. An algorithm for the efficient simulation of quantum nanosystems is suggested.
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Affiliation(s)
- Zeina Shreif
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
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Saunders MG, Voth GA. Coarse-graining of multiprotein assemblies. Curr Opin Struct Biol 2012; 22:144-50. [PMID: 22277168 DOI: 10.1016/j.sbi.2012.01.003] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2011] [Revised: 01/02/2012] [Accepted: 01/04/2012] [Indexed: 11/24/2022]
Abstract
Multiscale models are important tools to elucidate how small changes in local subunit conformations may propagate to affect the properties of macromolecular complexes. We review recent advances in coarse-graining methods for poly-protein assemblies, systems that are composed of many copies of relatively few components, with a particular focus on viral capsids and cytoskeletal filaments. These methods are grouped into two broad categories-mapping methods, which use information from one scale of representation to parameterize a lower resolution model, and bridging methods, which repeatedly connect different scales during simulation-and we provide examples of both classes at different levels of complexity. Collectively, these models illustrate the numerous approaches to information transfer between scales and demonstrate that the complexity required of the model depends in general on the nature of the information sought.
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Affiliation(s)
- Marissa G Saunders
- Department of Chemistry, Institute for Biophysical Dynamics, James Franck Institute, and Computation Institute, University of Chicago, Chicago, IL 60637, United States
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Singharoy A, Joshi H, Cheluvaraja S, Miao Y, Brown D, Ortoleva P. Simulating microbial systems: addressing model uncertainty/incompleteness via multiscale and entropy methods. Methods Mol Biol 2012; 881:433-67. [PMID: 22639222 DOI: 10.1007/978-1-61779-827-6_15] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Most systems of interest in the natural and engineering sciences are multiscale in character. Typically available models are incomplete or uncertain. Thus, a probabilistic approach is required. We present a deductive multiscale approach to address such problems, focusing on virus and cell systems to demonstrate the ideas. There is usually an underlying physical model, all factors in which (e.g., particle masses, charges, and force constants) are known. For example, the underlying model can be cast in terms of a collection of N-atoms evolving via Newton's equations. When the number of atoms is 10(6) or more, these physical models cannot be simulated directly. However, one may only be interested in a coarse-grained description, e.g., in terms of molecular populations or overall system size, shape, position, and orientation. The premise of this chapter is that the coarse-grained equations should be derived from the underlying model so that a deductive calibration-free methodology is achieved. We consider a reduction in resolution from a description for the state of N-atoms to one in terms of coarse-grained variables. This implies a degree of uncertainty in the underlying microstates. We present a methodology for modeling microbial systems that integrates equations for coarse-grained variables with a probabilistic description of the underlying fine-scale ones. The implementation of our strategy as a general computational platform (SimEntropics™) for microbial modeling and prospects for developments and applications are discussed.
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Affiliation(s)
- A Singharoy
- Department of Chemistry, Center for Cell and Virus Theory, Indiana University, Bloomington, IN, USA
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Joshi H, Cheluvaraja S, Somogyi E, Brown DR, Ortoleva P. A molecular dynamics study of loop fluctuation in human papillomavirus type 16 virus-like particles: a possible indicator of immunogenicity. Vaccine 2011; 29:9423-30. [PMID: 22027487 DOI: 10.1016/j.vaccine.2011.10.039] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2011] [Revised: 08/15/2011] [Accepted: 10/17/2011] [Indexed: 12/28/2022]
Abstract
Immunogenicity varies between the human papillomavirus (HPV) L1 monomer assemblies of various sizes (e.g., monomers, pentamers or whole capsids). The hypothesis that this can be attributed to the intensity of fluctuations of important loops containing neutralizing epitopes for the various assemblies is proposed for HPV L1 assemblies. Molecular dynamics simulations were utilized to begin testing this hypothesis. Fluctuations of loops that contain critical neutralizing epitopes (especially FG loop) were quantified via root-mean-square fluctuation and features in the frequency spectrum of dynamic changes in loop conformation. If this fluctuation-immunogenicity hypothesis is a universal aspect of immunogenicity (i.e., immune system recognition of an epitope within a loop is more reliable when it is presented via a more stable delivery structure), then fluctuation measures can serve as one predictor of immunogenicity as part of a computer-aided vaccine design strategy.
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Affiliation(s)
- Harshad Joshi
- Chemistry Department, Indiana University, Bloomington, IN 47405, USA
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Joshi H, Singharoy A, Sereda YV, Cheluvaraja SC, Ortoleva PJ. Multiscale simulation of microbe structure and dynamics. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2011; 107:200-17. [PMID: 21802438 PMCID: PMC3383072 DOI: 10.1016/j.pbiomolbio.2011.07.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Accepted: 07/01/2011] [Indexed: 10/18/2022]
Abstract
A multiscale mathematical and computational approach is developed that captures the hierarchical organization of a microbe. It is found that a natural perspective for understanding a microbe is in terms of a hierarchy of variables at various levels of resolution. This hierarchy starts with the N -atom description and terminates with order parameters characterizing a whole microbe. This conceptual framework is used to guide the analysis of the Liouville equation for the probability density of the positions and momenta of the N atoms constituting the microbe and its environment. Using multiscale mathematical techniques, we derive equations for the co-evolution of the order parameters and the probability density of the N-atom state. This approach yields a rigorous way to transfer information between variables on different space-time scales. It elucidates the interplay between equilibrium and far-from-equilibrium processes underlying microbial behavior. It also provides framework for using coarse-grained nanocharacterization data to guide microbial simulation. It enables a methodical search for free-energy minimizing structures, many of which are typically supported by the set of macromolecules and membranes constituting a given microbe. This suite of capabilities provides a natural framework for arriving at a fundamental understanding of microbial behavior, the analysis of nanocharacterization data, and the computer-aided design of nanostructures for biotechnical and medical purposes. Selected features of the methodology are demonstrated using our multiscale bionanosystem simulator DeductiveMultiscaleSimulator. Systems used to demonstrate the approach are structural transitions in the cowpea chlorotic mosaic virus, RNA of satellite tobacco mosaic virus, virus-like particles related to human papillomavirus, and iron-binding protein lactoferrin.
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Affiliation(s)
- Harshad Joshi
- Center for Cell and Virus Theory, Department of Chemistry, Indiana University, Bloomington, IN 47405 U. S. A
| | - Abhishek Singharoy
- Center for Cell and Virus Theory, Department of Chemistry, Indiana University, Bloomington, IN 47405 U. S. A
| | - Yuriy V. Sereda
- Center for Cell and Virus Theory, Department of Chemistry, Indiana University, Bloomington, IN 47405 U. S. A
| | - Srinath C. Cheluvaraja
- Center for Cell and Virus Theory, Department of Chemistry, Indiana University, Bloomington, IN 47405 U. S. A
| | - Peter J. Ortoleva
- Center for Cell and Virus Theory, Department of Chemistry, Indiana University, Bloomington, IN 47405 U. S. A
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