1
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Chen HH, Pang XH, Dai JL, Jiang JG. Functional Characterization of a CruP-Like Isomerase in Dunaliella. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:10005-10013. [PMID: 38626461 DOI: 10.1021/acs.jafc.4c01912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2024]
Abstract
Dunaliella bardawil is a marine unicellular green algal that produces large amounts of β-carotene and is a model organism for studying the carotenoid synthesis pathway. However, there are still many mysteries about the enzymes of the D. bardawil lycopene synthesis pathway that have not been revealed. Here, we have identified a CruP-like lycopene isomerase, named DbLyISO, and successfully cloned its gene from D. bardawil. DbLyISO showed a high homology with CruPs. We constructed a 3D model of DbLyISO and performed molecular docking with lycopene, as well as molecular dynamics testing, to identify the functional characteristics of DbLyISO. Functional activity of DbLyISO was also performed by overexpressing gene in both E. coli and D. bardawil. Results revealed that DbLyISO acted at the C-5 and C-13 positions of lycopene, catalyzing its cis-trans isomerization to produce a more stable trans structure. These results provide new ideas for the development of a carotenoid series from engineered bacteria, algae, and plants.
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Affiliation(s)
- Hao-Hong Chen
- College of Food Science and Bioengineering, South China University of Technology, Guangzhou 510640, China
- Department of Bioengineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Xiao-Hui Pang
- College of Food Science and Bioengineering, South China University of Technology, Guangzhou 510640, China
| | - Ju-Liang Dai
- College of Food Science and Bioengineering, South China University of Technology, Guangzhou 510640, China
| | - Jian-Guo Jiang
- College of Food Science and Bioengineering, South China University of Technology, Guangzhou 510640, China
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2
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Bini M, Tozzini V, Brancolini G. Deconstructing Electrostatics of Functionalized Metal Nanoparticles from Molecular Dynamics Simulations. J Phys Chem B 2023; 127:8226-8241. [PMID: 37714525 PMCID: PMC10544014 DOI: 10.1021/acs.jpcb.3c03481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 08/31/2023] [Indexed: 09/17/2023]
Abstract
Gold nanoparticles (NPs) with different surface functionalizations can selectively interact with specific proteins, allowing a wide range of possible applications in biotechnology and biomedicine. To prevent their tendency to aggregate and to modulate their interaction with charged biomolecules or substrates (e.g., for biosensing applications), they can be functionalized with charged groups, introducing a mutual interaction which can be modulated by changing the ionic strength of the solvent. In silico modeling of these systems is often addressed with low-resolution models, which must account for these effects in the, often implicit, solvent representation. Here, we present a systematic conformational dynamic characterization of ligand-coated gold nanoparticles with different sizes, charges, and functionalizations by means of atomistic molecular dynamics simulations. Based on these, we deconstruct their electrostatic properties and propose a general representation of their average-long-range interactions extendable to different sizes, charges, and ionic strengths. This study clarifies in detail the role of the different features of the NP (charge, size, structure) and of the ionic strength in determining the details of the interparticle interaction and represents the first step toward a general strategy for the parametrization of NP coarse-grained models able to account for varying ionic strengths.
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3
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Chollet I, Lagardère L, Piquemal JP. ANKH: A Generalized O( N) Interpolated Ewald Strategy for Molecular Dynamics Simulations. J Chem Theory Comput 2023; 19:2887-2905. [PMID: 37134146 DOI: 10.1021/acs.jctc.3c00015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
To evaluate electrostatics interactions, molecular dynamics (MD) simulations rely on Particle Mesh Ewald (PME), an O(Nlog(N)) algorithm that uses Fast Fourier Transforms (FFTs) or, alternatively, on O(N) Fast Multipole Methods (FMM) approaches. However, the FFTs low scalability remains a strong bottleneck for large-scale PME simulations on supercomputers. On the opposite, FFT-free FMM techniques are able to deal efficiently with such systems but they fail to reach PME performances for small- to medium-size systems, limiting their real-life applicability. We propose ANKH, a strategy grounded on interpolated Ewald summations and designed to remain efficient/scalable for any size of systems. The method is generalized for distributed point multipoles, and so for induced dipoles, which makes it suitable for high performance simulations using new generation polarizable force fields toward exascale computing.
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Affiliation(s)
- Igor Chollet
- LAGA, Université Sorbonne Paris Nord, UMR 7539, Villetaneuse, France and LCT, Sorbonne Université, UMR 7616, Paris, 75006, France
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4
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Consta S. Atomistic Modeling of Jet Formation in Charged Droplets. J Phys Chem B 2022; 126:8350-8357. [PMID: 36201739 DOI: 10.1021/acs.jpcb.2c05849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The first atomistic simulations that reveal the mechanism of Rayleigh fission are presented. It is demonstrated that simple ion or macroion ejection takes place through droplet deformation from a spherical into a distinct "tear" shape that contains a conical protrusion. We assert that the latter state is a free-energy minimum along an order parameter that measures the degree of droplet asphericity. The charged droplet's long-time evolution proceeds by alternating between the two minima above and below the critical value that are reached through solvent evaporation and ion ejection, respectively. For the first time, this mechanism allows one to explain the nature of the progeny droplets and the percentage of charge lost during fission. The cone half angle is estimated and found to be in good agreement with the value predicted from the solution of the electrostatic equation for the dielectric liquid. It is found that the conical deformation is independent of the effect of electrohydrodynamic forces reported in experiments. Contrary to the experimental observations of two diametrically opposite jets for droplets suspended in the electric field, we find that a single jet is formed at the Rayleigh limit. The study provides insight into the mechanism of capture of a macroion in jets appearing in electrospray ionization mass spectrometry (ESI-MS) experiments and may explain the tolerance of the ESI-MS spectrum to salt contamination of the sample.
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Affiliation(s)
- Styliani Consta
- Department of Chemistry, The University of Western Ontario, London, Ontario, CanadaN6A 5B7.,Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EWUnited Kingdom
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5
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George A, Mondal S, Purnaprajna M, Athri P. Review of Electrostatic Force Calculation Methods and Their Acceleration in Molecular Dynamics Packages Using Graphics Processors. ACS OMEGA 2022; 7:32877-32896. [PMID: 36157750 PMCID: PMC9494432 DOI: 10.1021/acsomega.2c03189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 08/26/2022] [Indexed: 06/16/2023]
Abstract
Molecular dynamics (MD) simulations probe the conformational repertoire of macromolecular systems using Newtonian dynamic equations. The time scales of MD simulations allow the exploration of biologically relevant phenomena and can elucidate spatial and temporal properties of the building blocks of life, such as deoxyribonucleic acid (DNA) and protein, across microsecond (μs) time scales using femtosecond (fs) time steps. A principal bottleneck toward extending MD calculations to larger time scales is the long-range electrostatic force measuring component of the naive nonbonded force computation algorithm, which scales with a complexity of (N, number of atoms). In this review, we present various methods to determine electrostatic interactions in often-used open-source MD packages as well as the implementation details that facilitate acceleration of the electrostatic interaction calculation.
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Affiliation(s)
- Anu George
- Department
of Computer Science and Engineering, Amrita
School of Engineering, Bengaluru 560035, Amrita Vishwa Vidyapeetham, India
| | | | - Madhura Purnaprajna
- Department
of Computer Science and Engineering, PES
University, Bengaluru 560085, India
| | - Prashanth Athri
- Department
of Computer Science and Engineering, Amrita
School of Engineering, Bengaluru 560035, Amrita Vishwa Vidyapeetham, India
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6
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Jones D, Allen JE, Yang Y, Drew Bennett WF, Gokhale M, Moshiri N, Rosing TS. Accelerators for Classical Molecular Dynamics Simulations of Biomolecules. J Chem Theory Comput 2022; 18:4047-4069. [PMID: 35710099 PMCID: PMC9281402 DOI: 10.1021/acs.jctc.1c01214] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Atomistic Molecular Dynamics (MD) simulations provide researchers the ability to model biomolecular structures such as proteins and their interactions with drug-like small molecules with greater spatiotemporal resolution than is otherwise possible using experimental methods. MD simulations are notoriously expensive computational endeavors that have traditionally required massive investment in specialized hardware to access biologically relevant spatiotemporal scales. Our goal is to summarize the fundamental algorithms that are employed in the literature to then highlight the challenges that have affected accelerator implementations in practice. We consider three broad categories of accelerators: Graphics Processing Units (GPUs), Field-Programmable Gate Arrays (FPGAs), and Application Specific Integrated Circuits (ASICs). These categories are comparatively studied to facilitate discussion of their relative trade-offs and to gain context for the current state of the art. We conclude by providing insights into the potential of emerging hardware platforms and algorithms for MD.
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Affiliation(s)
- Derek Jones
- Department of Computer Science and Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States.,Global Security Computing Applications Division, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
| | - Jonathan E Allen
- Global Security Computing Applications Division, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
| | - Yue Yang
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
| | - William F Drew Bennett
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
| | - Maya Gokhale
- Center for Applied Scientific Computing, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
| | - Niema Moshiri
- Department of Computer Science and Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Tajana S Rosing
- Department of Computer Science and Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
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7
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Wieczór M, Genna V, Aranda J, Badia RM, Gelpí JL, Gapsys V, de Groot BL, Lindahl E, Municoy M, Hospital A, Orozco M. Pre-exascale HPC approaches for molecular dynamics simulations. Covid-19 research: A use case. WILEY INTERDISCIPLINARY REVIEWS. COMPUTATIONAL MOLECULAR SCIENCE 2022; 13:e1622. [PMID: 35935573 PMCID: PMC9347456 DOI: 10.1002/wcms.1622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 04/25/2022] [Accepted: 04/28/2022] [Indexed: 06/15/2023]
Abstract
Exascale computing has been a dream for ages and is close to becoming a reality that will impact how molecular simulations are being performed, as well as the quantity and quality of the information derived for them. We review how the biomolecular simulations field is anticipating these new architectures, making emphasis on recent work from groups in the BioExcel Center of Excellence for High Performance Computing. We exemplified the power of these simulation strategies with the work done by the HPC simulation community to fight Covid-19 pandemics. This article is categorized under:Data Science > Computer Algorithms and ProgrammingData Science > Databases and Expert SystemsMolecular and Statistical Mechanics > Molecular Dynamics and Monte-Carlo Methods.
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Affiliation(s)
- Miłosz Wieczór
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and TechnologyBarcelonaSpain
- Department of Physical ChemistryGdansk University of TechnologyGdańskPoland
| | - Vito Genna
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Juan Aranda
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | | | - Josep Lluís Gelpí
- Barcelona Supercomputing CenterBarcelonaSpain
- Department of Biochemistry and BiomedicineUniversity of BarcelonaBarcelonaSpain
| | - Vytautas Gapsys
- Max Planck Institute for Multidisciplinary SciencesComputational Biomolecular Dynamics GroupGoettingenGermany
| | - Bert L. de Groot
- Max Planck Institute for Multidisciplinary SciencesComputational Biomolecular Dynamics GroupGoettingenGermany
| | - Erik Lindahl
- Department of Applied PhysicsSwedish e‐Science Research Center, KTH Royal Institute of TechnologyStockholmSweden
- Department of Biochemistry and Biophysics, Science for Life LaboratoryStockholm UniversityStockholmSweden
| | | | - Adam Hospital
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and TechnologyBarcelonaSpain
- Department of Biochemistry and BiomedicineUniversity of BarcelonaBarcelonaSpain
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8
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Zimmermann MT. Molecular Modeling is an Enabling Approach to Complement and Enhance Channelopathy Research. Compr Physiol 2022; 12:3141-3166. [PMID: 35578963 DOI: 10.1002/cphy.c190047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Hundreds of human membrane proteins form channels that transport necessary ions and compounds, including drugs and metabolites, yet details of their normal function or how function is altered by genetic variants to cause diseases are often unknown. Without this knowledge, researchers are less equipped to develop approaches to diagnose and treat channelopathies. High-resolution computational approaches such as molecular modeling enable researchers to investigate channelopathy protein function, facilitate detailed hypothesis generation, and produce data that is difficult to gather experimentally. Molecular modeling can be tailored to each physiologic context that a protein may act within, some of which may currently be difficult or impossible to assay experimentally. Because many genomic variants are observed in channelopathy proteins from high-throughput sequencing studies, methods with mechanistic value are needed to interpret their effects. The eminent field of structural bioinformatics integrates techniques from multiple disciplines including molecular modeling, computational chemistry, biophysics, and biochemistry, to develop mechanistic hypotheses and enhance the information available for understanding function. Molecular modeling and simulation access 3D and time-dependent information, not currently predictable from sequence. Thus, molecular modeling is valuable for increasing the resolution with which the natural function of protein channels can be investigated, and for interpreting how genomic variants alter them to produce physiologic changes that manifest as channelopathies. © 2022 American Physiological Society. Compr Physiol 12:3141-3166, 2022.
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Affiliation(s)
- Michael T Zimmermann
- Bioinformatics Research and Development Laboratory, Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Clinical and Translational Sciences Institute, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
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9
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Kameda T, Asano K, Togashi Y. Free energy landscape of RNA binding dynamics in start codon recognition by eukaryotic ribosomal pre-initiation complex. PLoS Comput Biol 2021; 17:e1009068. [PMID: 34125830 PMCID: PMC8224888 DOI: 10.1371/journal.pcbi.1009068] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 06/24/2021] [Accepted: 05/12/2021] [Indexed: 12/25/2022] Open
Abstract
Specific interaction between the start codon, 5'-AUG-3', and the anticodon, 5'-CAU-3', ensures accurate initiation of translation. Recent studies show that several near-cognate start codons (e.g. GUG and CUG) can play a role in initiating translation in eukaryotes. However, the mechanism allowing initiation through mismatched base-pairs at the ribosomal decoding site is still unclear at an atomic level. In this work, we propose an extended simulation-based method to evaluate free energy profiles, through computing the distance between each base-pair of the triplet interactions involved in recognition of start codons in eukaryotic translation pre-initiation complex. Our method provides not only the free energy penalty for mismatched start codons relative to the AUG start codon, but also the preferred pathways of transitions between bound and unbound states, which has not been described by previous studies. To verify the method, the binding dynamics of cognate (AUG) and near-cognate start codons (CUG and GUG) were simulated. Evaluated free energy profiles agree with experimentally observed changes in initiation frequencies from respective codons. This work proposes for the first time how a G:U mismatch at the first position of codon (GUG)-anticodon base-pairs destabilizes the accommodation in the initiating eukaryotic ribosome and how initiation at a CUG codon is nearly as strong as, or sometimes stronger than, that at a GUG codon. Our method is expected to be applied to study the affinity changes for various mismatched base-pairs.
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Affiliation(s)
- Takeru Kameda
- Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
- RIKEN Center for Biosystems Dynamics Research (BDR), Wako, Saitama, Japan
| | - Katsura Asano
- Molecular Cellular and Developmental Biology Program, Division of Biology, Kansas State University, Manhattan, Kansas, United States of America
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
- Hiroshima Research Center for Healthy Aging (HiHA), Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| | - Yuichi Togashi
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
- Research Center for the Mathematics on Chromatin Live Dynamics (RcMcD), Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
- RIKEN Center for Biosystems Dynamics Research (BDR), Higashi-Hiroshima, Hiroshima, Japan
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10
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Kaya H, Hardy DJ, Skeel RD. Multilevel summation for periodic electrostatics using B-splines. J Chem Phys 2021; 154:144105. [PMID: 33858159 PMCID: PMC8036131 DOI: 10.1063/5.0040925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 03/23/2021] [Indexed: 11/14/2022] Open
Abstract
Fast methods for calculating two-body interactions have many applications, and for molecular science and cosmology, it is common to employ periodic boundary conditions. However, for the 1/r potential, the energy and forces are ill-defined. Adopted here is the model given by the classic Ewald sum. For the fast calculation of two-body forces, the most celebrated method is the fast multipole method and its tree-code predecessor. However, molecular simulations typically employ mesh-based approximations and the fast Fourier transform. Both types of methods have significant drawbacks, which, in most respects, are overcome by the less well-known multilevel summation method (MSM). Presented here is a realization of the MSM, which can be regarded as a multilevel extension of the (smoothed) particle mesh Ewald (PME) method, but with the Ewald softening replaced by one having a finite range. The two-level (single-grid) version of MSM requires fewer tuning parameters than PME and is marginally faster. Additionally, higher-level versions of MSM scale well to large numbers of processors, whereas PME and other two-level methods do not. Although higher-level versions of MSM are less efficient on a single processor than the two-level version, evidence suggests that they are more efficient than other methods that scale well, such as the fast multipole method and tree codes.
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Affiliation(s)
- Hüseyin Kaya
- Technology Management, Payten, Inc., ITU Advanced Research and Innovation Center, Istanbul 34396, Turkey
| | - David J. Hardy
- Beckman Insitute, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801, USA
| | - Robert D. Skeel
- School of Mathematical and Statistical Sciences, Arizona State University, Tempe, Arizona 85287, USA
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11
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Kwan V, O’Dwyer R, Laur D, Tan J, Consta S. Relation between Ejection Mechanism and Ion Abundance in the Electric Double Layer of Droplets. J Phys Chem A 2021; 125:2954-2966. [DOI: 10.1021/acs.jpca.1c01522] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Victor Kwan
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Ryan O’Dwyer
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - David Laur
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Jiahua Tan
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
- College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Styliani Consta
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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12
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Predescu C, Bergdorf M, Shaw DE. Midtown splines: An optimal charge assignment for electrostatics calculations. J Chem Phys 2020; 153:224117. [PMID: 33317288 DOI: 10.1063/5.0021496] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Transferring particle charges to and from a grid plays a central role in the particle-mesh algorithms widely used to evaluate the electrostatic energy in molecular dynamics (MD) simulations. The computational cost of this transfer process represents a substantial part of the overall time required for simulation and is primarily determined by the size of the support (the set of grid nodes at which the transfer function is evaluated). The accuracy of the resulting approximation depends on the form of the transfer function, of which several have been proposed, as well as the size and shape of its support. Here, we show how to derive the transfer function that yields maximal asymptotic accuracy for a given support in the limit of fine grid resolution, finding that all such functions are splines, and we determine these functions (which we refer to as midtown splines) for a variety of choices of support to find optimally efficient transfer functions at accuracy levels relevant to MD simulations. We describe midtown splines that achieve fourth- and sixth-order accuracy in the grid spacing while requiring a support size of 32 and 88 grid nodes, respectively, compared to the 64 and 216 nodes required by the most widely used transfer functions (B-splines). At accuracy levels typically used in MD simulations, the use of midtown splines thus cuts the time required for charge spreading by roughly a factor of two.
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Affiliation(s)
| | | | - David E Shaw
- D. E. Shaw Research, New York, New York 10036, USA
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13
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Assembly of a patchy protein into variable 2D lattices via tunable multiscale interactions. Nat Commun 2020; 11:3770. [PMID: 32724112 PMCID: PMC7387446 DOI: 10.1038/s41467-020-17562-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 07/07/2020] [Indexed: 12/24/2022] Open
Abstract
Self-assembly of molecular building blocks into higher-order structures is exploited in living systems to create functional complexity and represents a powerful strategy for constructing new materials. As nanoscale building blocks, proteins offer unique advantages, including monodispersity and atomically tunable interactions. Yet, control of protein self-assembly has been limited compared to inorganic or polymeric nanoparticles, which lack such attributes. Here, we report modular self-assembly of an engineered protein into four physicochemically distinct, precisely patterned 2D crystals via control of four classes of interactions spanning Ångström to several-nanometer length scales. We relate the resulting structures to the underlying free-energy landscape by combining in-situ atomic force microscopy observations of assembly with thermodynamic analyses of protein-protein and -surface interactions. Our results demonstrate rich phase behavior obtainable from a single, highly patchy protein when interactions acting over multiple length scales are exploited and predict unusual bulk-scale properties for protein-based materials that ensue from such control. As nanoscale building blocks, proteins offer unique advantages, including monodispersity and atomically tunable interactions, but their self-assembly is limited compared to inorganic or polymeric nanoparticles. Here, the authors show modular self-assembly of an engineered protein into four physicochemically distinct patterned 2D crystals via control of four classes of interactions.
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14
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Phillips JC, Hardy DJ, Maia JDC, Stone JE, Ribeiro JV, Bernardi RC, Buch R, Fiorin G, Hénin J, Jiang W, McGreevy R, Melo MCR, Radak BK, Skeel RD, Singharoy A, Wang Y, Roux B, Aksimentiev A, Luthey-Schulten Z, Kalé LV, Schulten K, Chipot C, Tajkhorshid E. Scalable molecular dynamics on CPU and GPU architectures with NAMD. J Chem Phys 2020; 153:044130. [PMID: 32752662 PMCID: PMC7395834 DOI: 10.1063/5.0014475] [Citation(s) in RCA: 1203] [Impact Index Per Article: 300.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 07/01/2020] [Indexed: 02/06/2023] Open
Abstract
NAMDis a molecular dynamics program designed for high-performance simulations of very large biological objects on CPU- and GPU-based architectures. NAMD offers scalable performance on petascale parallel supercomputers consisting of hundreds of thousands of cores, as well as on inexpensive commodity clusters commonly found in academic environments. It is written in C++ and leans on Charm++ parallel objects for optimal performance on low-latency architectures. NAMD is a versatile, multipurpose code that gathers state-of-the-art algorithms to carry out simulations in apt thermodynamic ensembles, using the widely popular CHARMM, AMBER, OPLS, and GROMOS biomolecular force fields. Here, we review the main features of NAMD that allow both equilibrium and enhanced-sampling molecular dynamics simulations with numerical efficiency. We describe the underlying concepts utilized by NAMD and their implementation, most notably for handling long-range electrostatics; controlling the temperature, pressure, and pH; applying external potentials on tailored grids; leveraging massively parallel resources in multiple-copy simulations; and hybrid quantum-mechanical/molecular-mechanical descriptions. We detail the variety of options offered by NAMD for enhanced-sampling simulations aimed at determining free-energy differences of either alchemical or geometrical transformations and outline their applicability to specific problems. Last, we discuss the roadmap for the development of NAMD and our current efforts toward achieving optimal performance on GPU-based architectures, for pushing back the limitations that have prevented biologically realistic billion-atom objects to be fruitfully simulated, and for making large-scale simulations less expensive and easier to set up, run, and analyze. NAMD is distributed free of charge with its source code at www.ks.uiuc.edu.
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Affiliation(s)
| | - David J. Hardy
- NIH Center for Macromolecular Modeling and
Bioinformatics, Theoretical and Computational Biophysics Group, Beckman Institute for
Advanced Science and Technology, University of Illinois at
Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Julio D. C. Maia
- NIH Center for Macromolecular Modeling and
Bioinformatics, Theoretical and Computational Biophysics Group, Beckman Institute for
Advanced Science and Technology, University of Illinois at
Urbana-Champaign, Urbana, Illinois 61801, USA
| | - John E. Stone
- NIH Center for Macromolecular Modeling and
Bioinformatics, Theoretical and Computational Biophysics Group, Beckman Institute for
Advanced Science and Technology, University of Illinois at
Urbana-Champaign, Urbana, Illinois 61801, USA
| | - João V. Ribeiro
- NIH Center for Macromolecular Modeling and
Bioinformatics, Theoretical and Computational Biophysics Group, Beckman Institute for
Advanced Science and Technology, University of Illinois at
Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Rafael C. Bernardi
- NIH Center for Macromolecular Modeling and
Bioinformatics, Theoretical and Computational Biophysics Group, Beckman Institute for
Advanced Science and Technology, University of Illinois at
Urbana-Champaign, Urbana, Illinois 61801, USA
| | | | - Giacomo Fiorin
- National Heart, Lung and Blood Institute, National
Institutes of Health, Bethesda, Maryland 20814,
USA
| | - Jérôme Hénin
- Laboratoire de Biochimie Théorique UPR 9080, CNRS
and Université de Paris, Paris, France
| | | | - Ryan McGreevy
- NIH Center for Macromolecular Modeling and
Bioinformatics, Theoretical and Computational Biophysics Group, Beckman Institute for
Advanced Science and Technology, University of Illinois at
Urbana-Champaign, Urbana, Illinois 61801, USA
| | | | - Brian K. Radak
- NIH Center for Macromolecular Modeling and
Bioinformatics, Theoretical and Computational Biophysics Group, Beckman Institute for
Advanced Science and Technology, University of Illinois at
Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Robert D. Skeel
- School of Mathematical and Statistical Sciences,
Arizona State University, Tempe, Arizona 85281,
USA
| | - Abhishek Singharoy
- School of Molecular Sciences, Arizona State
University, Tempe, Arizona 85281, USA
| | - Yi Wang
- Department of Physics, The Chinese University of
Hong Kong, Shatin, Hong Kong, China
| | - Benoît Roux
- Department of Biochemistry, University of
Chicago, Chicago, Illinois 60637, USA
| | | | | | | | | | - Christophe Chipot
- Authors to whom correspondence should be addressed:
and . URL: http://www.ks.uiuc.edu
| | - Emad Tajkhorshid
- Authors to whom correspondence should be addressed:
and . URL: http://www.ks.uiuc.edu
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15
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Urano R, Shinoda W, Yoshii N, Okazaki S. Exact long-range Coulombic energy calculation for net charged systems neutralized by uniformly distributed background charge using fast multipole method and its application to efficient free energy calculation. J Chem Phys 2020; 152:244115. [DOI: 10.1063/5.0007957] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Ryo Urano
- Department of Materials Chemistry, Nagoya University, Nagoya 464-8603, Japan
| | - Wataru Shinoda
- Department of Materials Chemistry, Nagoya University, Nagoya 464-8603, Japan
| | - Noriyuki Yoshii
- Department of Materials Chemistry, Nagoya University, Nagoya 464-8603, Japan
- Center for Computational Science, Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan
| | - Susumu Okazaki
- Department of Materials Chemistry, Nagoya University, Nagoya 464-8603, Japan
- Center for Computational Science, Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan
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16
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Shin E, Lim C, Kang UJ, Kim M, Park J, Kim D, Choi W, Hong J, Baig C, Lee DW, Kim BS. Mussel-Inspired Copolyether Loop with Superior Antifouling Behavior. Macromolecules 2020. [DOI: 10.1021/acs.macromol.0c00481] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Eeseul Shin
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea
| | - Chanoong Lim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Uk Jung Kang
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Minseong Kim
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Jinwoo Park
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Dongseok Kim
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea
| | - Woojin Choi
- Department of Chemical & Biomolecular Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Jinkee Hong
- Department of Chemical & Biomolecular Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Chunggi Baig
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Dong Woog Lee
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Byeong-Su Kim
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea
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17
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Yoshii N, Andoh Y, Okazaki S. Fast multipole method for three-dimensional systems with periodic boundary condition in two directions. J Comput Chem 2020; 41:940-948. [PMID: 31930548 DOI: 10.1002/jcc.26141] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 12/01/2019] [Accepted: 12/02/2019] [Indexed: 12/11/2022]
Abstract
We derived a new expression for the electrostatic interaction of three-dimensional charge-neutral systems with two-dimensional periodic boundary conditions (slab geometry) using a fast multipole method (FMM). Contributions from all the image cells are expressed as a sum of real and reciprocal space terms, and a self-interaction term. The reciprocal space contribution consists of two parts: zero and nonzero terms of the absolute value of the reciprocal lattice vector. To test the new expressions, electrostatic interactions were calculated for a randomly placed charge distribution in a cubic box and liquid water produced by molecular dynamics calculation. The accuracy could be controlled by the degree of expansion of the FMM. In the present expression, the computational complexity of the electrostatic interaction of N-particle systems is order N, which is superior to that of the conventional two-dimensional periodic Ewald method for a slab geometry and the particle mesh Ewald method with a large empty space at an interface of the unit cell. © 2020 Wiley Periodicals, Inc.
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Affiliation(s)
- Noriyuki Yoshii
- Center for Computational Science, Graduate School of Engineering, Nagoya University, Nagoya, 464-8603, Japan.,Department of Materials Chemistry, Nagoya University, Nagoya, Japan
| | - Yoshimichi Andoh
- Center for Computational Science, Graduate School of Engineering, Nagoya University, Nagoya, 464-8603, Japan
| | - Susumu Okazaki
- Center for Computational Science, Graduate School of Engineering, Nagoya University, Nagoya, 464-8603, Japan.,Department of Materials Chemistry, Nagoya University, Nagoya, Japan
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18
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Ram Lamichhane T, Prasad Lamichhane H. Structural changes in thyroid hormone receptor-beta by T3 binding and L330S mutational interactions. AIMS BIOPHYSICS 2020. [DOI: 10.3934/biophy.2020003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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19
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Krasny R, Wang L. A treecode based on barycentric Hermite interpolation for electrostatic particle interactions. COMPUTATIONAL AND MATHEMATICAL BIOPHYSICS 2019. [DOI: 10.1515/cmb-2019-0006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Abstract
A particle-cluster treecode based on barycentric Hermite interpolation is presented for fast summation of electrostatic particle interactions in 3D. The interpolation nodes are Chebyshev points of the 2nd kind in each cluster. It is noted that barycentric Hermite interpolation is scale-invariant in a certain sense that promotes the treecode’s efficiency. Numerical results for the Coulomb and screened Coulomb potentials show that the treecode run time scales like O(N log N), where N is the number of particles in the system. The advantage of the barycentric Hermite treecode is demonstrated in comparison with treecodes based on Taylor approximation and barycentric Lagrange interpolation.
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Affiliation(s)
- Robert Krasny
- Department of Mathematics , University of Michigan , Ann Arbor , MI 48109 , USA
| | - Lei Wang
- Department of Mathematical Sciences , University of Wisconsin-Milwaukee , Milwaukee , WI 53211 , USA
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20
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Boateng HA. Periodic Coulomb Tree Method: An Alternative to Parallel Particle Mesh Ewald. J Chem Theory Comput 2019; 16:7-17. [PMID: 31747267 DOI: 10.1021/acs.jctc.9b00648] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Particle mesh Ewald (PME) is generally the method of choice for handling electrostatics in simulations with periodic boundary conditions. The excellent efficiency of PME on low processor counts is largely due to the use of the fast Fourier transform (FFT). However, due to the FFT's high communication cost, PME scales poorly in parallel. We develop a periodic Coulomb tree (PCT) method for electrostatic interactions in periodic boundary conditions as an alternative to PME in parallel simulations. We verify the accuracy of PCT by comparison of structural and dynamical properties of three different systems obtained via MD simulations using PME and PCT and provide parallel timing comparisons of the two methods on up to 1024 cores.
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Affiliation(s)
- Henry A Boateng
- Department of Mathematics , San Francisco State University , 1600 Holloway Ave. , San Francisco , California 94132 , United States.,Department of Mathematics , Bates College , 2 Andrews Rd. , Lewiston , Maine 04240 , United States
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21
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Jochum C, AdŽić N, Stiakakis E, Derrien TL, Luo D, Kahl G, Likos CN. Structure and stimuli-responsiveness of all-DNA dendrimers: theory and experiment. NANOSCALE 2019; 11:1604-1617. [PMID: 30311616 DOI: 10.1039/c8nr05814h] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We present a comprehensive theoretical and experimental study of the solution phase properties of a DNA-based family of nanoparticles - dendrimer-like DNA molecules (DL-DNA). These charged DNA dendrimers are novel macromolecular aggregates, which hold high promise in targeted self-assembly of soft matter systems in the bulk and at interfaces. To describe the behaviour of this family of dendrimers (with generations ranging from G1 to G7), we use a theoretical model in which base-pairs of a single DL-DNA molecule are modeled by charged monomers, whose interactions are chosen to mimic the equilibrium properties of DNA correctly. Experimental results on the sizes and conformations of DL-DNA are based on static and dynamic light scattering; and molecular dynamics simulations are employed to model the equilibrium properties of DL-DNA, which compare favorably to the findings from experiments while at the same time providing a host of additional information and insight into the molecular structure of the nanostructures. We also examine the salt-responsiveness of these macromolecules, finding that despite the strong screening of electrostatic interactions brought about by the added salt, the macromolecules shrink only slightly, their size robustness stemming from the high bending rigidity of the DNA-segments. The study of these charged dendrimer systems is an important field of research in the area of soft matter due to their potential role for various interdisciplinary applications, ranging from molecular cages and carriers for drug delivery in a living organism to the development of dendrimer- and dendron-based ultra-thin films in the area of nanotechnology. These findings are essential to determine if DL-DNA is a viable candidate for the experimental realization of cluster crystals in the bulk, a novel form of solid with multiple site occupancy.
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Affiliation(s)
- Clemens Jochum
- Institute for Theoretical Physics, TU Wien, Wiedner Hauptstraße 8-10, A-1040 Vienna, Austria.
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22
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Kar RK, Brender JR, Ghosh A, Bhunia A. Nonproductive Binding Modes as a Prominent Feature of Aβ 40 Fiber Elongation: Insights from Molecular Dynamics Simulation. J Chem Inf Model 2018; 58:1576-1586. [PMID: 30047732 DOI: 10.1021/acs.jcim.8b00169] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The formation of amyloid fibers has been implicated in a number of neurodegenerative diseases. The growth of amyloid fibers is strongly thermodynamically favorable, but kinetic traps exist where the incoming monomer binds in an incompatible conformation that blocks further elongation. Unfortunately, this process is difficult to follow experimentally at the atomic level. It is also too complex to simulate in full detail and to date has been explored either through coarse-grained simulations, which may miss many important interactions, or full atomic simulations, in which the incoming peptide is constrained to be near the ideal fiber geometry. Here we use an alternate approach starting from a docked complex in which the monomer is from an experimental NMR structure of one of the major conformations in the unbound ensemble, a largely unstructured peptide with the central hydrophobic region in a 310 helix. A 1000 ns full atomic simulation in explicit solvent shows the formation of a metastable intermediate by sequential, concerted movements of both the fiber and the monomer. A Markov state model shows that the unfolded monomer is trapped at the end of the fiber in a set of interconverting antiparallel β-hairpin conformations. The simulation here may serve as a model for the binding of other non-β-sheet conformations to amyloid fibers.
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Affiliation(s)
- Rajiv K Kar
- Department of Biophysics , Bose Institute , P-1/12 CIT Scheme VII (M) , Kolkata 700054 , India
| | - Jeffrey R Brender
- Radiation Biology Branch , National Institutes of Health , Bethesda , Maryland 20814 , United States
| | - Anirban Ghosh
- Department of Biophysics , Bose Institute , P-1/12 CIT Scheme VII (M) , Kolkata 700054 , India
| | - Anirban Bhunia
- Department of Biophysics , Bose Institute , P-1/12 CIT Scheme VII (M) , Kolkata 700054 , India
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23
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Edorh SPA, Redon S. Incremental update of electrostatic interactions in adaptively restrained particle simulations. J Comput Chem 2018; 39:1455-1469. [PMID: 29624712 DOI: 10.1002/jcc.25215] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 02/27/2018] [Accepted: 02/28/2018] [Indexed: 11/08/2022]
Abstract
The computation of long-range potentials is one of the demanding tasks in Molecular Dynamics. During the last decades, an inventive panoply of methods was developed to reduce the CPU time of this task. In this work, we propose a fast method dedicated to the computation of the electrostatic potential in adaptively restrained systems. We exploit the fact that, in such systems, only some particles are allowed to move at each timestep. We developed an incremental algorithm derived from a multigrid-based alternative to traditional Fourier-based methods. Our algorithm was implemented inside LAMMPS, a popular molecular dynamics simulation package. We evaluated the method on different systems. We showed that the new algorithm's computational complexity scales with the number of active particles in the simulated system, and is able to outperform the well-established Particle Particle Particle Mesh (P3M) for adaptively restrained simulations. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Semeho Prince A Edorh
- Univ. Grenoble Alpes, Inria, CNRS, Grenoble INP (Institue of Engineering Univ. Grenobl Alpes), LJK, Grenoble, 38000, France
| | - Stéphane Redon
- Univ. Grenoble Alpes, Inria, CNRS, Grenoble INP (Institue of Engineering Univ. Grenobl Alpes), LJK, Grenoble, 38000, France
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24
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Salih R, Matthai CC. Computer simulations of the diffusion of Na + and Cl - ions across POPC lipid bilayer membranes. J Chem Phys 2018; 146:105101. [PMID: 28298128 DOI: 10.1063/1.4977703] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We have carried out molecular dynamics simulations using NAMD to study the diffusivity of Na and Cl ions across a POPC lipid bilayer membrane. We show that an imbalance of positively and negatively charged ions on either side of the membrane leads to the diffusion of ions and water molecules. We considered the cases of both weak and very strong charge imbalance across the membrane. The diffusion coefficients of the ions have been determined from the mean square displacements of the particles as a function of time. We find that for strong electrochemical gradients, both the Na and Cl ions diffuse rapidly through pores in the membrane with diffusion coefficients up to ten times larger than in water. Rather surprisingly, we found that although the Na ions are the first to begin the permeation process due to the lower potential barrier that they experience compared to the Cl ions, the latter complete the permeation across the barrier more quickly due to their faster diffusion rates.
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Affiliation(s)
- Rangeen Salih
- Department of Physics and Astronomy, Cardiff University, Cardiff, United Kingdom
| | - C C Matthai
- Department of Physics and Astronomy, Cardiff University, Cardiff, United Kingdom
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25
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Schaettle K, Ruiz Pestana L, Head-Gordon T, Lammers LN. A structural coarse-grained model for clays using simple iterative Boltzmann inversion. J Chem Phys 2018; 148:222809. [DOI: 10.1063/1.5011817] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Karl Schaettle
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California 94720, USA
| | - Luis Ruiz Pestana
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Teresa Head-Gordon
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California 94720, USA
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, USA
- Department of Bioengineering, University of California, Berkeley, Berkeley, California 94720, USA
| | - Laura Nielsen Lammers
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, California 94720, USA
- Earth and Environmental Science Area, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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26
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Boateng HA. Mesh-free hierarchical clustering methods for fast evaluation of electrostatic interactions of point multipoles. J Chem Phys 2018; 147:164104. [PMID: 29096477 DOI: 10.1063/1.4990552] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Electrostatic interactions involving point multipoles are being increasingly implemented to achieve higher accuracy in molecular simulations. A major drawback of multipolar electrostatics is the increased computational cost. Here we develop and compare two Cartesian tree algorithms which employ Taylor approximations and hierarchical clustering to speed up the evaluation of point multipole interactions. We present results from applying the algorithms to compute the free space Coulomb potential and forces of different sets of interacting point multipoles with different densities. The methods achieve high accuracy and speedup of more than an order of magnitude over direct sum calculations and scale well in parallel.
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Affiliation(s)
- H A Boateng
- Department of Mathematics, Bates College, 2 Andrews Rd., Lewiston, Maine 04240, USA
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27
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Chen IJ, Chuang CH, Hsieh YC, Lu YC, Lin WW, Huang CC, Cheng TC, Cheng YA, Cheng KW, Wang YT, Chen FM, Cheng TL, Tzou SC. Selective antibody activation through protease-activated pro-antibodies that mask binding sites with inhibitory domains. Sci Rep 2017; 7:11587. [PMID: 28912497 PMCID: PMC5599682 DOI: 10.1038/s41598-017-11886-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 08/31/2017] [Indexed: 12/16/2022] Open
Abstract
Systemic injection of therapeutic antibodies may cause serious adverse effects due to on-target toxicity to the antigens expressed in normal tissues. To improve the targeting selectivity to the region of disease sites, we developed protease-activated pro-antibodies by masking the binding sites of antibodies with inhibitory domains that can be removed by proteases that are highly expressed at the disease sites. The latency-associated peptide (LAP), C2b or CBa of complement factor 2/B were linked, through a substrate peptide of matrix metalloproteinase-2 (MMP-2), to an anti-epidermal growth factor receptor (EGFR) antibody and an anti-tumor necrosis factor-α (TNF-α) antibody. Results showed that all the inhibitory domains could be removed by MMP-2 to restore the binding activities of the antibodies. LAP substantially reduced (53.8%) the binding activity of the anti-EGFR antibody on EGFR-expressing cells, whereas C2b and CBa were ineffective (21% and 9.3% reduction, respectively). Similarly, LAP also blocked 53.9% of the binding activity of the anti-TNF-α antibody. Finally, molecular dynamic simulation showed that the masking efficiency of LAP, C2b and CBa was 33.7%, 10.3% and −5.4%, respectively, over the binding sites of the antibodies. This strategy may aid in designing new protease-activated pro-antibodies that attain high therapeutic potency yet reduced systemic on-target toxicity.
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Affiliation(s)
- I-Ju Chen
- Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chih-Hung Chuang
- Department of Medical Laboratory Science and Biotechnology, College of Health Sciences, Kaohsiung Medical University, Kaohsiung, Taiwan.,Center for Biomarkers and Biotech Drugs, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Yuan-Chin Hsieh
- Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Yun-Chi Lu
- Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Wen-Wei Lin
- Institute of Biomedical Sciences, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - Chien-Chiao Huang
- Center for Biomarkers and Biotech Drugs, Kaohsiung Medical University, Kaohsiung, Taiwan.,Graduate Institute of Clinical Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.,Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Ta-Chun Cheng
- Center for Biomarkers and Biotech Drugs, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Yi-An Cheng
- Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Kai-Wen Cheng
- Institute of Biomedical Sciences, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - Yeng-Tseng Wang
- Department of Biochemistry, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Fang-Ming Chen
- Department of Surgery, Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Tian-Lu Cheng
- Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan. .,Center for Biomarkers and Biotech Drugs, Kaohsiung Medical University, Kaohsiung, Taiwan. .,Institute of Biomedical Sciences, National Sun Yat-Sen University, Kaohsiung, Taiwan. .,Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan. .,Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.
| | - Shey-Cherng Tzou
- Institute of Molecular Medicine and Bioengineering, Department of Biological Science and Technology, National Chiao Tung University, Hsin-Chu, Taiwan.
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28
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Polticelli F, Leboffe L, Tortosa V, Trezza V, Fanali G, Fasano M, Ascenzi P. Cantharidin inhibits competitively heme-Fe(III) binding to the FA1 site of human serum albumin. J Mol Recognit 2017; 30. [DOI: 10.1002/jmr.2641] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 04/27/2017] [Accepted: 04/27/2017] [Indexed: 12/11/2022]
Affiliation(s)
- Fabio Polticelli
- Department of Sciences; Roma Tre University; Roma Italy
- National Institute of Nuclear Physics, Roma Tre Section; Rome Italy
| | - Loris Leboffe
- Department of Sciences; Roma Tre University; Roma Italy
| | | | | | | | - Mauro Fasano
- Department of Science and High Technology; University of Insubria; Busto Arsizio Varese Italy
- Neuroscience Research Center; University of Insubria; Busto Arsizio Varese Italy
| | - Paolo Ascenzi
- Interdepartmental Laboratory for Electron Microscopy; Roma Tre University; Roma Italy
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29
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Tong J, Wu Z, Briggs MM, Schulten K, McIntosh TJ. The Water Permeability and Pore Entrance Structure of Aquaporin-4 Depend on Lipid Bilayer Thickness. Biophys J 2017; 111:90-9. [PMID: 27410737 DOI: 10.1016/j.bpj.2016.05.039] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 05/13/2016] [Indexed: 12/22/2022] Open
Abstract
Aquaporin-4 (AQP4), the primary water channel in glial cells of the mammalian brain, plays a critical role in water transport in the central nervous system. Previous experiments have shown that the water permeability of AQP4 depends on the cholesterol content in the lipid bilayer, but it was not clear whether changes in permeability were due to direct cholesterol-AQP4 interactions or to indirect effects caused by cholesterol-induced changes in bilayer elasticity or bilayer thickness. To determine the effects resulting only from bilayer thickness, here we use a combination of experiments and simulations to analyze AQP4 in cholesterol-free phospholipid bilayers with similar elastic properties but different hydrocarbon core thicknesses previously determined by x-ray diffraction. The channel (unit) water permeabilities of AQP4 measured by osmotic-gradient experiments were 3.5 ± 0.2 × 10(-13) cm(3)/s (mean ± SE), 3.0 ± 0.3 × 10(-13) cm(3)/s, 2.5 ± 0.2 × 10(-13) cm(3)/s, and 0.9 ± 0.1 × 10(-13) cm(3)/s in bilayers containing (C22:1)(C22:1)PC, (C20:1)(C20:1)PC, (C16:0)(C18:1)PC, and (C13:0)(C13:0)PC, respectively. Channel permeabilities obtained by molecular dynamics (MD) simulations were 3.3 ± 0.1 × 10(-13) cm(3)/s and 2.5 ± 0.1 × 10(-13) cm(3)/s in (C22:1)(C22:1)PC and (C14:0)(C14:0)PC bilayers, respectively. Both the osmotic-gradient and MD-simulation results indicated that AQP4 channel permeability decreased with decreasing bilayer hydrocarbon thickness. The MD simulations also suggested structural modifications in AQP4 in response to changes in bilayer thickness. Although the simulations showed no appreciable changes to the radius of the pore located in the hydrocarbon region of the bilayers, the simulations indicated that there were changes in both pore length and α-helix organization near the cytoplasmic vestibule of the channel. These structural changes, caused by mismatch between the hydrophobic length of AQP4 and the bilayer hydrocarbon thickness, could explain the observed differences in water permeability with changes in bilayer thickness.
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Affiliation(s)
- Jihong Tong
- Department of Cell Biology, Duke University Medical Center, Durham, North Carolina
| | - Zhe Wu
- Center for the Physics of Living Cells and Beckman Institute, University of Illinois Urbana-Champaign, Urbana, Illinois
| | - Margaret M Briggs
- Department of Cell Biology, Duke University Medical Center, Durham, North Carolina
| | - Klaus Schulten
- Center for the Physics of Living Cells and Beckman Institute, University of Illinois Urbana-Champaign, Urbana, Illinois.
| | - Thomas J McIntosh
- Department of Cell Biology, Duke University Medical Center, Durham, North Carolina.
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30
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Iacovelli F, Idili A, Benincasa A, Mariottini D, Ottaviani A, Falconi M, Ricci F, Desideri A. Simulative and Experimental Characterization of a pH-Dependent Clamp-like DNA Triple-Helix Nanoswitch. J Am Chem Soc 2017; 139:5321-5329. [PMID: 28365993 DOI: 10.1021/jacs.6b11470] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Here we couple experimental and simulative techniques to characterize the structural/dynamical behavior of a pH-triggered switching mechanism based on the formation of a parallel DNA triple helix. Fluorescent data demonstrate the ability of this structure to reversibly switch between two states upon pH changes. Two accelerated, half microsecond, MD simulations of the system having protonated or unprotonated cytosines, mimicking the pH 5.0 and 8.0 conditions, highlight the importance of the Hoogsteen interactions in stabilizing the system, finely depicting the time-dependent disruption of the hydrogen bond network. Urea-unfolding experiments and MM/GBSA calculations converge in indicating a stabilization energy at pH 5.0, 2-fold higher than that observed at pH 8.0. These results validate the pH-controlled behavior of the designed structure and suggest that simulative approaches can be successfully coupled with experimental data to characterize responsive DNA-based nanodevices.
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Affiliation(s)
- Federico Iacovelli
- Department of Biology and ‡Department of Chemistry, University of Rome, Tor Vergata , 00173 Rome, Italy
| | - Andrea Idili
- Department of Biology and ‡Department of Chemistry, University of Rome, Tor Vergata , 00173 Rome, Italy
| | - Alessandro Benincasa
- Department of Biology and ‡Department of Chemistry, University of Rome, Tor Vergata , 00173 Rome, Italy
| | - Davide Mariottini
- Department of Biology and ‡Department of Chemistry, University of Rome, Tor Vergata , 00173 Rome, Italy
| | - Alessio Ottaviani
- Department of Biology and ‡Department of Chemistry, University of Rome, Tor Vergata , 00173 Rome, Italy
| | - Mattia Falconi
- Department of Biology and ‡Department of Chemistry, University of Rome, Tor Vergata , 00173 Rome, Italy
| | - Francesco Ricci
- Department of Biology and ‡Department of Chemistry, University of Rome, Tor Vergata , 00173 Rome, Italy
| | - Alessandro Desideri
- Department of Biology and ‡Department of Chemistry, University of Rome, Tor Vergata , 00173 Rome, Italy
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LAMMPS’ PPPM Long-Range Solver for the Second Generation Xeon Phi. LECTURE NOTES IN COMPUTER SCIENCE 2017. [DOI: 10.1007/978-3-319-58667-0_4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Vermaas JV, Hardy DJ, Stone JE, Tajkhorshid E, Kohlmeyer A. TopoGromacs: Automated Topology Conversion from CHARMM to GROMACS within VMD. J Chem Inf Model 2016; 56:1112-6. [PMID: 27196035 DOI: 10.1021/acs.jcim.6b00103] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Molecular dynamics (MD) simulation engines use a variety of different approaches for modeling molecular systems with force fields that govern their dynamics and describe their topology. These different approaches introduce incompatibilities between engines, and previously published software bridges the gaps between many popular MD packages, such as between CHARMM and AMBER or GROMACS and LAMMPS. While there are many structure building tools available that generate topologies and structures in CHARMM format, only recently have mechanisms been developed to convert their results into GROMACS input. We present an approach to convert CHARMM-formatted topology and parameters into a format suitable for simulation with GROMACS by expanding the functionality of TopoTools, a plugin integrated within the widely used molecular visualization and analysis software VMD. The conversion process was diligently tested on a comprehensive set of biological molecules in vacuo. The resulting comparison between energy terms shows that the translation performed was lossless as the energies were unchanged for identical starting configurations. By applying the conversion process to conventional benchmark systems that mimic typical modestly sized MD systems, we explore the effect of the implementation choices made in CHARMM, NAMD, and GROMACS. The newly available automatic conversion capability breaks down barriers between simulation tools and user communities and allows users to easily compare simulation programs and leverage their unique features without the tedium of constructing a topology twice.
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Affiliation(s)
- Josh V Vermaas
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.,Department of Biochemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.,Beckman Insitute, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - David J Hardy
- Beckman Insitute, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - John E Stone
- Beckman Insitute, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Emad Tajkhorshid
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.,Department of Biochemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.,Beckman Insitute, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Axel Kohlmeyer
- Insitute for Computational Molecular Science, Temple University , Philadelphia, Pennsylvania 19122, United States
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Hardy DJ, Wolff MA, Xia J, Schulten K, Skeel RD. Multilevel summation with B-spline interpolation for pairwise interactions in molecular dynamics simulations. J Chem Phys 2016; 144:114112. [PMID: 27004867 DOI: 10.1063/1.4943868] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The multilevel summation method for calculating electrostatic interactions in molecular dynamics simulations constructs an approximation to a pairwise interaction kernel and its gradient, which can be evaluated at a cost that scales linearly with the number of atoms. The method smoothly splits the kernel into a sum of partial kernels of increasing range and decreasing variability with the longer-range parts interpolated from grids of increasing coarseness. Multilevel summation is especially appropriate in the context of dynamics and minimization, because it can produce continuous gradients. This article explores the use of B-splines to increase the accuracy of the multilevel summation method (for nonperiodic boundaries) without incurring additional computation other than a preprocessing step (whose cost also scales linearly). To obtain accurate results efficiently involves technical difficulties, which are overcome by a novel preprocessing algorithm. Numerical experiments demonstrate that the resulting method offers substantial improvements in accuracy and that its performance is competitive with an implementation of the fast multipole method in general and markedly better for Hamiltonian formulations of molecular dynamics. The improvement is great enough to establish multilevel summation as a serious contender for calculating pairwise interactions in molecular dynamics simulations. In particular, the method appears to be uniquely capable for molecular dynamics in two situations, nonperiodic boundary conditions and massively parallel computation, where the fast Fourier transform employed in the particle-mesh Ewald method falls short.
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Affiliation(s)
- David J Hardy
- Beckman Institute, University of Illinois, 405 North Mathews Avenue, Urbana, Illinois 61801, USA
| | - Matthew A Wolff
- Department of Computer Science, Purdue University, 305 North University Street, West Lafayette, Indiana 47907, USA
| | - Jianlin Xia
- Department of Mathematics, Purdue University, 150 North University Street, West Lafayette, Indiana 47907, USA
| | - Klaus Schulten
- Beckman Institute, University of Illinois, 405 North Mathews Avenue, Urbana, Illinois 61801, USA
| | - Robert D Skeel
- Department of Computer Science, Purdue University, 305 North University Street, West Lafayette, Indiana 47907, USA
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Multiscale method for modeling binding phenomena involving large objects: application to kinesin motor domains motion along microtubules. Sci Rep 2016; 6:23249. [PMID: 26988596 PMCID: PMC4796874 DOI: 10.1038/srep23249] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 03/03/2016] [Indexed: 11/30/2022] Open
Abstract
Many biological phenomena involve the binding of proteins to a large object. Because the electrostatic forces that guide binding act over large distances, truncating the size of the system to facilitate computational modeling frequently yields inaccurate results. Our multiscale approach implements a computational focusing method that permits computation of large systems without truncating the electrostatic potential and achieves the high resolution required for modeling macromolecular interactions, all while keeping the computational time reasonable. We tested our approach on the motility of various kinesin motor domains. We found that electrostatics help guide kinesins as they walk: N-kinesins towards the plus-end, and C-kinesins towards the minus-end of microtubules. Our methodology enables computation in similar, large systems including protein binding to DNA, viruses, and membranes.
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SÁENZ-SUÁREZ H, POUTOU-PIÑALES RA, GONZÁLEZ-SANTOS J, BARRETO GE, RIETO-NAVARRERA LP, SÁENZ-MORENO JA, LANDÁZURI P, BARRERA-AVELLANEDA LA. Prediction of glycation sites: new insights from protein structural analysis. Turk J Biol 2016. [DOI: 10.3906/biy-1501-71] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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