1
|
Bosy M, Scroggs MW, Betcke T, Burman E, Cooper CD. Coupling finite and boundary element methods to solve the Poisson-Boltzmann equation for electrostatics in molecular solvation. J Comput Chem 2024; 45:787-797. [PMID: 38126925 DOI: 10.1002/jcc.27262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 10/03/2023] [Accepted: 11/05/2023] [Indexed: 12/23/2023]
Abstract
The Poisson-Boltzmann equation is widely used to model electrostatics in molecular systems. Available software packages solve it using finite difference, finite element, and boundary element methods, where the latter is attractive due to the accurate representation of the molecular surface and partial charges, and exact enforcement of the boundary conditions at infinity. However, the boundary element method is limited to linear equations and piecewise constant variations of the material properties. In this work, we present a scheme that couples finite and boundary elements for the linearised Poisson-Boltzmann equation, where the finite element method is applied in a confined solute region and the boundary element method in the external solvent region. As a proof-of-concept exercise, we use the simplest methods available: Johnson-Nédélec coupling with mass matrix and diagonal preconditioning, implemented using the Bempp-cl and FEniCSx libraries via their Python interfaces. We showcase our implementation by computing the polar component of the solvation free energy of a set of molecules using a constant and a Gaussian-varying permittivity. As validation, we compare against well-established finite difference solvers for an extensive binding energy data set, and with the finite difference code APBS (to 0.5%) for Gaussian permittivities. We also show scaling results from protein G B1 (955 atoms) up to immunoglobulin G (20,148 atoms). For small problems, the coupled method was efficient, outperforming a purely boundary integral approach. For Gaussian-varying permittivities, which are beyond the applicability of boundary elements alone, we were able to run medium to large-sized problems on a single workstation. The development of better preconditioning techniques and the use of distributed memory parallelism for larger systems remains an area for future work. We hope this work will serve as inspiration for future developments that consider space-varying field parameters, and mixed linear-nonlinear schemes for molecular electrostatics with implicit solvent models.
Collapse
Affiliation(s)
- Michał Bosy
- School of Computer Science and Mathematics, Kingston University London, Kingston upon Thames, UK
| | | | - Timo Betcke
- Department of Mathematics, University College London, London, UK
| | - Erik Burman
- Department of Mathematics, University College London, London, UK
| | - Christopher D Cooper
- Department of Mechanical Engineering and Centro Científico Tecnológico de Valparaíso, Universidad Técnica Federico Santa María, Valparaíso, Chile
| |
Collapse
|
2
|
Chen J, Xu Y, Yang X, Cang Z, Geng W, Wei GW. Poisson-Boltzmann-based machine learning model for electrostatic analysis. Biophys J 2024:S0006-3495(24)00107-3. [PMID: 38356263 DOI: 10.1016/j.bpj.2024.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 01/26/2024] [Accepted: 02/09/2024] [Indexed: 02/16/2024] Open
Abstract
Electrostatics is of paramount importance to chemistry, physics, biology, and medicine. The Poisson-Boltzmann (PB) theory is a primary model for electrostatic analysis. However, it is highly challenging to compute accurate PB electrostatic solvation free energies for macromolecules due to the nonlinearity, dielectric jumps, charge singularity, and geometric complexity associated with the PB equation. The present work introduces a PB-based machine learning (PBML) model for biomolecular electrostatic analysis. Trained with the second-order accurate MIBPB solver, the proposed PBML model is found to be more accurate and faster than several eminent PB solvers in electrostatic analysis. The proposed PBML model can provide highly accurate PB electrostatic solvation free energy of new biomolecules or new conformations generated by molecular dynamics with much reduced computational cost.
Collapse
Affiliation(s)
- Jiahui Chen
- Department of Mathematics, University of Arkansas, Fayetteville, Arkansas
| | | | - Xin Yang
- Department of Mathematics, Southern Methodist University, Dallas, Texas
| | - Zixuan Cang
- Department of Mathematics, North Carolina State University, Raleigh, North Carolina
| | - Weihua Geng
- Department of Mathematics, Southern Methodist University, Dallas, Texas.
| | - Guo-Wei Wei
- Department of Mathematics, Michigan State University, East Lansing, Michigan; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan.
| |
Collapse
|
3
|
Case D, Aktulga HM, Belfon K, Cerutti DS, Cisneros GA, Cruzeiro VD, Forouzesh N, Giese TJ, Götz AW, Gohlke H, Izadi S, Kasavajhala K, Kaymak MC, King E, Kurtzman T, Lee TS, Li P, Liu J, Luchko T, Luo R, Manathunga M, Machado MR, Nguyen HM, O’Hearn KA, Onufriev AV, Pan F, Pantano S, Qi R, Rahnamoun A, Risheh A, Schott-Verdugo S, Shajan A, Swails J, Wang J, Wei H, Wu X, Wu Y, Zhang S, Zhao S, Zhu Q, Cheatham TE, Roe DR, Roitberg A, Simmerling C, York DM, Nagan MC, Merz KM. AmberTools. J Chem Inf Model 2023; 63:6183-6191. [PMID: 37805934 PMCID: PMC10598796 DOI: 10.1021/acs.jcim.3c01153] [Citation(s) in RCA: 92] [Impact Index Per Article: 92.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Indexed: 10/10/2023]
Abstract
AmberTools is a free and open-source collection of programs used to set up, run, and analyze molecular simulations. The newer features contained within AmberTools23 are briefly described in this Application note.
Collapse
Affiliation(s)
- David
A. Case
- Department
of Chemistry and Chemical Biology, Rutgers
University, Piscataway 08854, New Jersey, United States
| | - Hasan Metin Aktulga
- Department
of Computer Science and Engineering, Michigan
State University, East Lansing 48824-1322, Michigan, United States
| | - Kellon Belfon
- FOG
Pharmaceuticals Inc., Cambridge 02140, Massachusetts, United States
| | - David S. Cerutti
- Psivant, 451 D Street, Suite 205, Boston 02210, Massachusetts, United States
| | - G. Andrés Cisneros
- Department
of Physics, Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson 75801, Texas, United States
| | - Vinícius
Wilian D. Cruzeiro
- Department
of Chemistry and The PULSE Institute, Stanford
University, Stanford 94305, California, United States
| | - Negin Forouzesh
- Department
of Computer Science, California State University, Los Angeles 90032, California, United States
| | - Timothy J. Giese
- Laboratory
for Biomolecular Simulation Research, Institute for Quantitative Biomedicine
and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway 08854, New Jersey, United States
| | - Andreas W. Götz
- San
Diego Supercomputer Center, University of
California San Diego, La Jolla 92093-0505, California, United States
| | - Holger Gohlke
- Institute
for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
- Institute
of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, Jülich 52425, Germany
| | - Saeed Izadi
- Pharmaceutical
Development, Genentech, Inc., South San Francisco 94080, California, United
States
| | - Koushik Kasavajhala
- Laufer
Center for Physical and Quantitative Biology, Department of Chemistry, Stony Brook University, Stony Brook 11794, New York, United States
| | - Mehmet C. Kaymak
- Department
of Computer Science and Engineering, Michigan
State University, East Lansing 48824-1322, Michigan, United States
| | - Edward King
- Departments
of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering,
Materials Science and Engineering, and Biomedical Engineering, Graduate
Program in Chemical and Materials Physics, University of California, Irvine 92697, California, United States
| | - Tom Kurtzman
- Ph.D.
Programs in Chemistry, Biochemistry, and Biology, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York 10016, New York, United States
- Department
of Chemistry, Lehman College, 250 Bedford Park Blvd West, Bronx 10468, New York, United States
| | - Tai-Sung Lee
- Laboratory
for Biomolecular Simulation Research, Institute for Quantitative Biomedicine
and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway 08854, New Jersey, United States
| | - Pengfei Li
- Department
of Chemistry and Biochemistry, Loyola University
Chicago, Chicago 60660, Illinois, United States
| | - Jian Liu
- Beijing
National Laboratory for Molecular Sciences, Institute of Theoretical
and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Tyler Luchko
- Department
of Physics and Astronomy, California State
University, Northridge, Northridge 91330, California, United States
| | - Ray Luo
- Departments
of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering,
Materials Science and Engineering, and Biomedical Engineering, Graduate
Program in Chemical and Materials Physics, University of California, Irvine 92697, California, United States
| | - Madushanka Manathunga
- Department
of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing 48824-1322, Michigan, United States
| | | | - Hai Minh Nguyen
- Department
of Chemistry and Chemical Biology, Rutgers
University, Piscataway 08854, New Jersey, United States
| | - Kurt A. O’Hearn
- Department
of Computer Science and Engineering, Michigan
State University, East Lansing 48824-1322, Michigan, United States
| | - Alexey V. Onufriev
- Departments
of Computer Science and Physics, Virginia
Tech, Blacksburg 24061, Virginia, United
States
| | - Feng Pan
- Department
of Statistics, Florida State University, Tallahassee 32304, Florida, United States
| | - Sergio Pantano
- Institut Pasteur de Montevideo, Montevideo 11400, Uruguay
| | - Ruxi Qi
- Cryo-EM
Center, Southern University of Science and
Technology, Shenzhen 518055, China
| | - Ali Rahnamoun
- Department
of Computer Science and Engineering, Michigan
State University, East Lansing 48824-1322, Michigan, United States
| | - Ali Risheh
- Department
of Computer Science, California State University, Los Angeles 90032, California, United States
| | - Stephan Schott-Verdugo
- Institute
of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, Jülich 52425, Germany
| | - Akhil Shajan
- Department
of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing 48824-1322, Michigan, United States
| | - Jason Swails
- Entos, 4470 W Sunset
Blvd, Suite 107, Los Angeles 90027, California, United States
| | - Junmei Wang
- Department
of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh 15261, Pennsylvania, United States
| | - Haixin Wei
- Departments
of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering,
Materials Science and Engineering, and Biomedical Engineering, Graduate
Program in Chemical and Materials Physics, University of California, Irvine 92697, California, United States
| | - Xiongwu Wu
- Laboratory
of Computational Biology, NHLBI, NIH, Bethesda 20892, Maryland, United States
| | - Yongxian Wu
- Departments
of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering,
Materials Science and Engineering, and Biomedical Engineering, Graduate
Program in Chemical and Materials Physics, University of California, Irvine 92697, California, United States
| | - Shi Zhang
- Laboratory
for Biomolecular Simulation Research, Institute for Quantitative Biomedicine
and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway 08854, New Jersey, United States
| | - Shiji Zhao
- Departments
of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering,
Materials Science and Engineering, and Biomedical Engineering, Graduate
Program in Chemical and Materials Physics, University of California, Irvine 92697, California, United States
- Nurix Therapeutics, Inc., San Francisco 94158, California, United States
| | - Qiang Zhu
- Departments
of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering,
Materials Science and Engineering, and Biomedical Engineering, Graduate
Program in Chemical and Materials Physics, University of California, Irvine 92697, California, United States
| | - Thomas E. Cheatham
- Department
of Medicinal Chemistry, The University of
Utah, 30 South 2000 East, Salt Lake City 84112, Utah, United
States
| | - Daniel R. Roe
- Laboratory
of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda 20892, Maryland, United States
| | - Adrian Roitberg
- Department
of Chemistry, The University of Florida, 440 Leigh Hall, Gainesville 32611-7200, Florida, United States
| | - Carlos Simmerling
- Laufer
Center for Physical and Quantitative Biology, Department of Chemistry, Stony Brook University, Stony Brook 11794, New York, United States
| | - Darrin M. York
- Laboratory
for Biomolecular Simulation Research, Institute for Quantitative Biomedicine
and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway 08854, New Jersey, United States
| | - Maria C. Nagan
- Department
of Chemistry, Stony Brook University, Stony Brook 11794, New York, United States
| | - Kenneth M. Merz
- Department
of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing 48824-1322, Michigan, United States
| |
Collapse
|
4
|
Huang Z, Zhao S, Cieplak P, Duan Y, Luo R, Wei H. Optimal Scheme to Achieve Energy Conservation in Induced Dipole Models. J Chem Theory Comput 2023; 19:5047-5057. [PMID: 37441805 PMCID: PMC10434752 DOI: 10.1021/acs.jctc.3c00226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/15/2023]
Abstract
Induced dipole models have proven to be effective tools for simulating electronic polarization effects in biochemical processes, yet their potential has been constrained by energy conservation issue, particularly when historical data is utilized for dipole prediction. This study identifies error outliers as the primary factor causing this failure of energy conservation and proposes a comprehensive scheme to overcome this limitation. Leveraging maximum relative errors as a convergence metric, our data demonstrates that energy conservation can be upheld even when using historical information for dipole predictions. Our study introduces the multi-order extrapolation method to quicken induction iteration and optimize the use of historical data, while also developing the preconditioned conjugate gradient with local iterations to refine the iteration process and effectively remove error outliers. This scheme further incorporates a "peek" step via Jacobi under-relaxation for optimal performance. Simulation evidence suggests that our proposed scheme can achieve energy convergence akin to that of point-charge models within a limited number of iterations, thus promising significant improvements in efficiency and accuracy.
Collapse
Affiliation(s)
- Zhen Huang
- Chemical and Materials Physics Graduate Program, University of California, Irvine. Irvine, California 92697, United States
- Departments of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering, University of California, Irvine. Irvine, California 92697, United States
| | - Shiji Zhao
- Departments of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering, University of California, Irvine. Irvine, California 92697, United States
- Nurix Therapeutics, Inc., 1700 Owens St. Suite 205, San Francisco, CA 94158, United States
| | - Piotr Cieplak
- SBP Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Yong Duan
- UC Davis Genome Center and Department of Biomedical Engineering, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Ray Luo
- Chemical and Materials Physics Graduate Program, University of California, Irvine. Irvine, California 92697, United States
- Departments of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering, University of California, Irvine. Irvine, California 92697, United States
| | - Haixin Wei
- Departments of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering, University of California, Irvine. Irvine, California 92697, United States
- Department of Chemistry & Biochemistry, University of California, San Diego. 9500 Gilman Drive, La Jolla, California 92093, United States
| |
Collapse
|
5
|
Liu X, Zheng L, Qin C, Zhang JZH, Sun Z. Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host-guest binding: I. Standard procedure. J Comput Aided Mol Des 2022; 36:735-752. [PMID: 36136209 DOI: 10.1007/s10822-022-00475-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 09/06/2022] [Indexed: 10/14/2022]
Abstract
Despite the massive application of end-point free energy methods in protein-ligand and protein-protein interactions, computational understandings about their performance in relatively simple and prototypical host-guest systems are limited. In this work, we present a comprehensive benchmark calculation with standard end-point free energy techniques in a recent host-guest dataset containing 13 host-guest pairs involving the carboxylated-pillar[6]arene host. We first assess the charge schemes for solutes by comparing the charge-produced electrostatics with many ab initio references, in order to obtain a preliminary albeit detailed view of the charge quality. Then, we focus on four modelling details of end-point free energy calculations, including the docking procedure for the generation of initial condition, the charge scheme for host and guest molecules, the water model used in explicit-solvent sampling, and the end-point methods for free energy estimation. The binding thermodynamics obtained with different modelling schemes are compared with experimental references, and some practical guidelines on maximizing the performance of end-point methods in practical host-guest systems are summarized. Further, we compare our simulation outcome with predictions in the grand challenge and discuss further developments to improve the prediction quality of end-point free energy methods. Overall, unlike the widely acknowledged applicability in protein-ligand binding, the standard end-point calculations cannot produce useful outcomes in host-guest binding and thus are not recommended unless alterations are performed.
Collapse
Affiliation(s)
- Xiao Liu
- School of Mathematics, Physics and Statistics, Shanghai University of Engineering Science, Shanghai, 201620, China.
| | - Lei Zheng
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, 200062, China
| | - Chu Qin
- School of Mathematics, Physics and Statistics, Shanghai University of Engineering Science, Shanghai, 201620, China
| | - John Z H Zhang
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, 200062, China.,School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China.,Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, China.,Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Zhaoxi Sun
- College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China.
| |
Collapse
|
6
|
Ekesan Ş, McCarthy E, Case DA, York DM. RNA Electrostatics: How Ribozymes Engineer Active Sites to Enable Catalysis. J Phys Chem B 2022; 126:5982-5990. [PMID: 35862934 PMCID: PMC9496635 DOI: 10.1021/acs.jpcb.2c03727] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Electrostatic interactions are fundamental to RNA structure and function, and intimately influenced by solvation and the ion atmosphere. RNA enzymes, or ribozymes, are catalytic RNAs that are able to enhance reaction rates over a million-fold, despite having only a limited repertoire of building blocks and available set of chemical functional groups. Ribozyme active sites usually occur at junctions where negatively charged helices come together, and in many cases leverage this strained electrostatic environment to recruit metal ions in solution that can assist in catalysis. Similar strategies have been implicated in related artificially engineered DNA enzymes. Herein, we apply Poisson-Boltzmann, 3D-RISM, and molecular simulations to study a set of metal-dependent small self-cleaving ribozymes (hammerhead, pistol, and Varkud satellite) as well as an artificially engineered DNAzyme (8-17) to examine electrostatic features and their relation to the recruitment of monovalent and divalent metal ions important for activity. We examine several fundamental roles for these ions that include: (1) structural integrity of the catalytically active state, (2) pKa tuning of residues involved in acid-base catalysis, and (3) direct electrostatic stabilization of the transition state via Lewis acid catalysis. Taken together, these examples demonstrate how RNA electrostatics orchestrates the site-specific and territorial binding of metal ions to play important roles in catalysis.
Collapse
Affiliation(s)
- Şölen Ekesan
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Erika McCarthy
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - David A. Case
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Darrin M. York
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| |
Collapse
|
7
|
López R, Díaz N, Francisco E, Martín-Pendás A, Suárez D. QM/MM Energy Decomposition Using the Interacting Quantum Atoms Approach. J Chem Inf Model 2022; 62:1510-1524. [PMID: 35212531 PMCID: PMC8965874 DOI: 10.1021/acs.jcim.1c01372] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The interacting quantum atoms (IQA) method decomposes the quantum mechanical (QM) energy of a molecular system in terms of one- and two-center (atomic) contributions within the context of the quantum theory of atoms in molecules. Here, we demonstrate that IQA, enhanced with molecular mechanics (MM) and Poisson-Boltzmann surface-area (PBSA) solvation methods, is naturally extended to the realm of hybrid QM/MM methodologies, yielding intra- and inter-residue energy terms that characterize all kinds of covalent and noncovalent bonding interactions. To test the robustness of this approach, both metal-water interactions and QM/MM boundary artifacts are characterized in terms of the IQA descriptors derived from QM regions of varying size in Zn(II)- and Mg(II)-water clusters. In addition, we analyze a homologous series of inhibitors in complex with a matrix metalloproteinase (MMP-12) by carrying out QM/MM-PBSA calculations on their crystallographic structures followed by IQA energy decomposition. Overall, these applications not only show the advantages of the IQA QM/MM approach but also address some of the challenges lying ahead for expanding the QM/MM methodology.
Collapse
Affiliation(s)
- Roberto López
- Departamento de Química y Física Aplicadas, Universidad de León, Facultad de Biología, Campus de Vegazana s/n, 24071 León (Castilla y León), Spain
| | - Natalia Díaz
- Departamento de Química Física y Analítica, Universidad de Oviedo, Facultad de Química, Julián Clavería 8, 33006 Oviedo (Asturias), Spain
| | - Evelio Francisco
- Departamento de Química Física y Analítica, Universidad de Oviedo, Facultad de Química, Julián Clavería 8, 33006 Oviedo (Asturias), Spain
| | - Angel Martín-Pendás
- Departamento de Química Física y Analítica, Universidad de Oviedo, Facultad de Química, Julián Clavería 8, 33006 Oviedo (Asturias), Spain
| | - Dimas Suárez
- Departamento de Química Física y Analítica, Universidad de Oviedo, Facultad de Química, Julián Clavería 8, 33006 Oviedo (Asturias), Spain
| |
Collapse
|
8
|
Adendorff MR, Tang GQ, Millar D, Bathe M, Bricker W. Computational investigation of the impact of core sequence on immobile DNA four-way junction structure and dynamics. Nucleic Acids Res 2022; 50:717-730. [PMID: 34935970 PMCID: PMC8789063 DOI: 10.1093/nar/gkab1246] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 11/28/2021] [Accepted: 12/06/2021] [Indexed: 12/19/2022] Open
Abstract
Immobile four-way junctions (4WJs) are core structural motifs employed in the design of programmed DNA assemblies. Understanding the impact of sequence on their equilibrium structure and flexibility is important to informing the design of complex DNA architectures. While core junction sequence is known to impact the preferences for the two possible isomeric states that junctions reside in, previous investigations have not quantified these preferences based on molecular-level interactions. Here, we use all-atom molecular dynamics simulations to investigate base-pair level structure and dynamics of four-way junctions, using the canonical Seeman J1 junction as a reference. Comparison of J1 with equivalent single-crossover topologies and isolated nicked duplexes reveal conformational impact of the double-crossover motif. We additionally contrast J1 with a second junction core sequence termed J24, with equal thermodynamic preference for each isomeric configuration. Analyses of the base-pair degrees of freedom for each system, free energy calculations, and reduced-coordinate sampling of the 4WJ isomers reveal the significant impact base sequence has on local structure, isomer bias, and global junction dynamics.
Collapse
Affiliation(s)
- Matthew R Adendorff
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Guo Qing Tang
- Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - David P Millar
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - William P Bricker
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Chemical and Biological Engineering, University of New Mexico, Albuquerque, NM 87131, USA
| |
Collapse
|
9
|
Valdés-Tresanco MS, Valdés-Tresanco ME, Valiente PA, Moreno E. gmx_MMPBSA: A New Tool to Perform End-State Free Energy Calculations with GROMACS. J Chem Theory Comput 2021; 17:6281-6291. [PMID: 34586825 DOI: 10.1021/acs.jctc.1c00645] [Citation(s) in RCA: 609] [Impact Index Per Article: 203.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecular mechanics/Poisson-Boltzmann (Generalized-Born) surface area is one of the most popular methods to estimate binding free energies. This method has been proven to balance accuracy and computational efficiency, especially when dealing with large systems. As a result of its popularity, several programs have been developed for performing MM/PB(GB)SA calculations within the GROMACS community. These programs, however, present several limitations. Here we present gmx_MMPBSA, a new tool to perform end-state free energy calculations from GROMACS molecular dynamics trajectories. gmx_MMPBSA provides the user with several options, including binding free energy calculations with different solvation models (PB, GB, or 3D-RISM), stability calculations, computational alanine scanning, entropy corrections, and binding free energy decomposition. Noteworthy, several promising methodologies to calculate relative binding free energies such as alanine scanning with variable dielectric constant and interaction entropy have also been implemented in gmx_MMPBSA. Two additional tools-gmx_MMPBSA_test and gmx_MMPBSA_ana-have been integrated within gmx_MMPBSA to improve its usability. Multiple illustrating examples can be accessed through gmx_MMPBSA_test, while gmx_MMPBSA_ana provides fast, easy, and efficient access to different graphics plotted from gmx_MMPBSA output files. The latest version (v1.4.3, 26/05/2021) is available free of charge (documentation, test files, and tutorials included) at https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA.
Collapse
Affiliation(s)
| | - Mario E Valdés-Tresanco
- Centre for Molecular Simulations and Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Pedro A Valiente
- Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada.,Center of Protein Studies, Faculty of Biology, University of Havana, 25 & J, 10400, La Habana, Cuba
| | - Ernesto Moreno
- Faculty of Basic Sciences, University of Medellin, Medellin 050026, Colombia
| |
Collapse
|
10
|
Wei H, Zhao Z, Luo R. Machine-Learned Molecular Surface and Its Application to Implicit Solvent Simulations. J Chem Theory Comput 2021; 17:6214-6224. [PMID: 34516109 DOI: 10.1021/acs.jctc.1c00492] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Implicit solvent models, such as Poisson-Boltzmann models, play important roles in computational studies of biomolecules. A vital step in almost all implicit solvent models is to determine the solvent-solute interface, and the solvent excluded surface (SES) is the most widely used interface definition in these models. However, classical algorithms used for computing SES are geometry-based, so that they are neither suitable for parallel implementations nor convenient for obtaining surface derivatives. To address the limitations, we explored a machine learning strategy to obtain a level set formulation for the SES. The training process was conducted in three steps, eventually leading to a model with over 95% agreement with the classical SES. Visualization of tested molecular surfaces shows that the machine-learned SES overlaps with the classical SES in almost all situations. Further analyses show that the machine-learned SES is incredibly stable in terms of rotational variation of tested molecules. Our timing analysis shows that the machine-learned SES is roughly 2.5 times as efficient as the classical SES routine implemented in Amber/PBSA on a tested central processing unit (CPU) platform. We expect further performance gain on massively parallel platforms such as graphics processing units (GPUs) given the ease in converting the machine-learned SES to a parallel procedure. We also implemented the machine-learned SES into the Amber/PBSA program to study its performance on reaction field energy calculation. The analysis shows that the two sets of reaction field energies are highly consistent with a 1% deviation on average. Given its level set formulation, we expect the machine-learned SES to be applied in molecular simulations that require either surface derivatives or high efficiency on parallel computing platforms.
Collapse
Affiliation(s)
- Haixin Wei
- Departments of Materials Science and Engineering, Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, and Biomedical Engineering, Graduate Program in Chemical and Materials Physics, University of California, Irvine, California 92697, United States
| | - Zekai Zhao
- Departments of Materials Science and Engineering, Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, and Biomedical Engineering, Graduate Program in Chemical and Materials Physics, University of California, Irvine, California 92697, United States
| | - Ray Luo
- Departments of Materials Science and Engineering, Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, and Biomedical Engineering, Graduate Program in Chemical and Materials Physics, University of California, Irvine, California 92697, United States
| |
Collapse
|
11
|
King E, Aitchison E, Li H, Luo R. Recent Developments in Free Energy Calculations for Drug Discovery. Front Mol Biosci 2021; 8:712085. [PMID: 34458321 PMCID: PMC8387144 DOI: 10.3389/fmolb.2021.712085] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 07/27/2021] [Indexed: 01/11/2023] Open
Abstract
The grand challenge in structure-based drug design is achieving accurate prediction of binding free energies. Molecular dynamics (MD) simulations enable modeling of conformational changes critical to the binding process, leading to calculation of thermodynamic quantities involved in estimation of binding affinities. With recent advancements in computing capability and predictive accuracy, MD based virtual screening has progressed from the domain of theoretical attempts to real application in drug development. Approaches including the Molecular Mechanics Poisson Boltzmann Surface Area (MM-PBSA), Linear Interaction Energy (LIE), and alchemical methods have been broadly applied to model molecular recognition for drug discovery and lead optimization. Here we review the varied methodology of these approaches, developments enhancing simulation efficiency and reliability, remaining challenges hindering predictive performance, and applications to problems in the fields of medicine and biochemistry.
Collapse
Affiliation(s)
- Edward King
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States
| | - Erick Aitchison
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States
| | - Han Li
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, CA, United States
| | - Ray Luo
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, CA, United States
- Department of Materials Science and Engineering, University of California, Irvine, CA, United States
- Department of Biomedical Engineering, University of California, Irvine, CA, United States
| |
Collapse
|
12
|
King E, Qi R, Li H, Luo R, Aitchison E. Estimating the Roles of Protonation and Electronic Polarization in Absolute Binding Affinity Simulations. J Chem Theory Comput 2021; 17:2541-2555. [PMID: 33764050 DOI: 10.1021/acs.jctc.0c01305] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Accurate prediction of binding free energies is critical to streamlining the drug development and protein design process. With the advent of GPU acceleration, absolute alchemical methods, which simulate the removal of ligand electrostatics and van der Waals interactions with the protein, have become routinely accessible and provide a physically rigorous approach that enables full consideration of flexibility and solvent interaction. However, standard explicit solvent simulations are unable to model protonation or electronic polarization changes upon ligand transfer from water to the protein interior, leading to inaccurate prediction of binding affinities for charged molecules. Here, we perform extensive simulation totaling ∼540 μs to benchmark the impact of modeling conditions on predictive accuracy for absolute alchemical simulations. Binding to urokinase plasminogen activator (UPA), a protein frequently overexpressed in metastatic tumors, is evaluated for a set of 10 inhibitors with extended flexibility, highly charged character, and titratable properties. We demonstrate that the alchemical simulations can be adapted to utilize the MBAR/PBSA method to improve the accuracy upon incorporating electronic polarization, highlighting the importance of polarization in alchemical simulations of binding affinities. Comparison of binding energy prediction at various protonation states indicates that proper electrostatic setup is also crucial in binding affinity prediction of charged systems, prompting us to propose an alternative binding mode with protonated ligand phenol and Hid-46 at the binding site, a testable hypothesis for future experimental validation.
Collapse
Affiliation(s)
| | - Ruxi Qi
- Cryo-EM Center, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | | | | | | |
Collapse
|
13
|
Díaz N, Suárez D. Understanding the Conformational Properties of Fluorinated Polypeptides: Molecular Modelling of Unguisin A. J Chem Inf Model 2020; 61:223-237. [PMID: 33325701 DOI: 10.1021/acs.jcim.0c00746] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In this work, we investigate the conformational properties of unguisin A, a natural macrocyclic heptapeptide that incorporates a γ-aminobutyric acid (Gaba), and four of its difluorinated stereoisomers at the Gaba residue. According to nuclear magnetic resonance (NMR) experiments, their secondary structure depends dramatically on the stereochemistry of the fluorinated carbon atoms. However, many molecular details of the structure and flexibility of these systems remain unknown, so that a rationale of the conformational changes induced by the fluorine atoms in the macrocycle is still missing. To fill this gap, we apply enhanced molecular dynamics (MD) techniques to explore the peptide conformational space in dimethyl sulfoxide solution followed by 4-8 μs of conventional MD simulations that provide extensive equilibrium sampling. The simulations, which compare reasonably well with the NMR-based observations, show that the secondary structure of the macrocycle is altered substantially upon fluorination, except for the (S,S) diastereomer. It also turns out that the conformations of the fluorinated peptides are visited during the enhanced MD simulation of natural unguisin A, suggesting thus that conformations accessible to the unsubstituted macrocyclic peptide may be selected by fluorination. Therefore, computational characterization of the macrocyclic peptides could be helpful in the rational design of stereoselective fluorinated peptides with fine-tuned conformation and activity.
Collapse
Affiliation(s)
- Natalia Díaz
- Departamento de Química Física y Analítica, Universidad de Oviedo, Avda. Julián Clavería 8, 33006 Oviedo, Asturias, Spain
| | - Dimas Suárez
- Departamento de Química Física y Analítica, Universidad de Oviedo, Avda. Julián Clavería 8, 33006 Oviedo, Asturias, Spain
| |
Collapse
|
14
|
Li C, McGowan M, Alexov E, Zhao S. A Newton-like iterative method implemented in the DelPhi for solving the nonlinear Poisson-Boltzmann equation. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2020; 17:6259-6277. [PMID: 33378855 PMCID: PMC9883664 DOI: 10.3934/mbe.2020331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
DelPhi is a popular scientific program which numerically solves the Poisson-Boltzmann equation (PBE) for electrostatic potentials and energies of biomolecules immersed in water via finite difference method. It is well known for its accuracy, reliability, flexibility, and efficiency. In this work, a new edition of DelPhi that uses a novel Newton-like method to solve the nonlinear PBE, in addition to the already implemented Successive Over Relaxation (SOR) algorithm, is introduced. Our tests on various examples have shown that this new method is superior to the SOR method in terms of stability when solving the nonlinear PBE, being able to converge even for problems involving very strong nonlinearity.
Collapse
Affiliation(s)
- Chuan Li
- Department of Mathematics, West Chester University of Pennsylvania, West Chester, Pennsylvania, 19383, USA
| | - Mark McGowan
- Department of Mathematics, University of Alabama, Tuscaloosa, AL 35487, USA
| | - Emil Alexov
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina, 29634, USA
| | - Shan Zhao
- Department of Mathematics, University of Alabama, Tuscaloosa, AL 35487, USA
| |
Collapse
|
15
|
Gaurav K, Adhikary T, Satpati P. dUMP/F-dUMP Binding to Thymidylate Synthase: Human Versus Mycobacterium tuberculosis. ACS OMEGA 2020; 5:17182-17192. [PMID: 32715203 PMCID: PMC7376888 DOI: 10.1021/acsomega.0c01224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 06/18/2020] [Indexed: 06/11/2023]
Abstract
Thymidylate synthase is an enzyme that catalyzes deoxythymidine monophosphate (dTMP) synthesis from substrate deoxyuridine monophosphate (dUMP). Thymidylate synthase of Mycobacterium tuberculosis (MtbThyX) is structurally distinct from its human analogue human thymidylate synthase (hThyA), thus drawing attention as an attractive drug target for combating tuberculosis. Fluorodeoxyuridylate (F-dUMP) is a successful inhibitor of both MtbThyX and hThyA, thus limited by poor selectivity. Understanding the dynamics and energetics associated with substrate/inhibitor binding to thymidylate synthase in atomic details remains a fundamental unsolved problem, which is necessary for a new selective inhibitor design. Structural studies of MtbThyX and hThyA bound substrate/inhibitor complexes not only revealed the extensive specific interaction network between protein and ligands but also opened up the possibility of directly computing the energetics of the substrate versus inhibitor recognition. Using experimentally determined structures as a template, we report extensive computer simulations (∼4.5 μs) that allow us to quantitatively estimate ligand selectivity (dUMP vs F-dUMP) by MtbThyX and hThyA. We show that MtbThyX prefers deprotonated dUMP (enolate form) as the substrate, whereas hThyA binds to the keto form of dUMP. Computed energetics clearly show that MtbThyX is less selective between dUMP and F-dUMP, favoring the latter, relative to hThyA. The simulations reveal the role of tyrosine at position 135 (Y135) of hThyA in amplifying the selectivity. The protonation state of the pyrimidine base of the ligand (i.e., keto or enolate) seems to have no role in MtbThyX ligand selectivity. A molecular gate (consists of Y108, K165, H203, and a water molecule) restricts water accessibility and offers a desolvated dry ligand-binding pocket for MtbThyX. The ligand-binding pocket of hThyA is relatively wet and exposed to bulk water.
Collapse
|
16
|
Vargas RE, Duong VT, Han H, Ta AP, Chen Y, Zhao S, Yang B, Seo G, Chuc K, Oh S, El Ali A, Razorenova OV, Chen J, Luo R, Li X, Wang W. Elucidation of WW domain ligand binding specificities in the Hippo pathway reveals STXBP4 as YAP inhibitor. EMBO J 2020; 39:e102406. [PMID: 31782549 PMCID: PMC6939200 DOI: 10.15252/embj.2019102406] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Revised: 11/06/2019] [Accepted: 11/11/2019] [Indexed: 12/20/2022] Open
Abstract
The Hippo pathway, which plays a critical role in organ size control and cancer, features numerous WW domain-based protein-protein interactions. However, ~100 WW domains and 2,000 PY motif-containing peptide ligands are found in the human proteome, raising a "WW-PY" binding specificity issue in the Hippo pathway. In this study, we have established the WW domain binding specificity for Hippo pathway components and uncovered a unique amino acid sequence required for it. By using this criterion, we have identified a WW domain-containing protein, STXBP4, as a negative regulator of YAP. Mechanistically, STXBP4 assembles a protein complex comprising α-catenin and a group of Hippo PY motif-containing components/regulators to inhibit YAP, a process that is regulated by actin cytoskeleton tension. Interestingly, STXBP4 is a potential tumor suppressor for human kidney cancer, whose downregulation is correlated with YAP activation in clear cell renal cell carcinoma. Taken together, our study not only elucidates the WW domain binding specificity for the Hippo pathway, but also reveals STXBP4 as a player in actin cytoskeleton tension-mediated Hippo pathway regulation.
Collapse
MESH Headings
- Adaptor Proteins, Signal Transducing/antagonists & inhibitors
- Adaptor Proteins, Signal Transducing/genetics
- Adaptor Proteins, Signal Transducing/metabolism
- Animals
- Apoptosis
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Carcinoma, Renal Cell/genetics
- Carcinoma, Renal Cell/metabolism
- Carcinoma, Renal Cell/pathology
- Cell Proliferation
- Female
- Gene Expression Regulation, Neoplastic
- Hippo Signaling Pathway
- Humans
- Kidney Neoplasms/genetics
- Kidney Neoplasms/metabolism
- Kidney Neoplasms/pathology
- Mice
- Mice, Inbred BALB C
- Mice, Nude
- Prognosis
- Protein Binding
- Protein Serine-Threonine Kinases/genetics
- Protein Serine-Threonine Kinases/metabolism
- Signal Transduction
- Survival Rate
- Transcription Factors/antagonists & inhibitors
- Transcription Factors/genetics
- Transcription Factors/metabolism
- Transcription, Genetic
- Tumor Cells, Cultured
- Vesicular Transport Proteins/genetics
- Vesicular Transport Proteins/metabolism
- WW Domains
- Xenograft Model Antitumor Assays
- YAP-Signaling Proteins
Collapse
Affiliation(s)
- Rebecca E Vargas
- Department of Developmental and Cell BiologyUniversity of California, IrvineIrvineCAUSA
| | - Vy Thuy Duong
- Department of ChemistryUniversity of California, IrvineIrvineCAUSA
| | - Han Han
- Department of Developmental and Cell BiologyUniversity of California, IrvineIrvineCAUSA
| | - Albert Paul Ta
- Department of Developmental and Cell BiologyUniversity of California, IrvineIrvineCAUSA
| | - Yuxuan Chen
- Department of Developmental and Cell BiologyUniversity of California, IrvineIrvineCAUSA
| | - Shiji Zhao
- Department of Developmental and Cell BiologyUniversity of California, IrvineIrvineCAUSA
| | - Bing Yang
- Department of Developmental and Cell BiologyUniversity of California, IrvineIrvineCAUSA
| | - Gayoung Seo
- Department of Developmental and Cell BiologyUniversity of California, IrvineIrvineCAUSA
| | - Kimberly Chuc
- Department of Developmental and Cell BiologyUniversity of California, IrvineIrvineCAUSA
| | - Sunwoo Oh
- Department of Developmental and Cell BiologyUniversity of California, IrvineIrvineCAUSA
| | - Amal El Ali
- Department of Molecular Biology and BiochemistryUniversity of California, IrvineIrvineCAUSA
| | - Olga V Razorenova
- Department of Molecular Biology and BiochemistryUniversity of California, IrvineIrvineCAUSA
| | - Junjie Chen
- Department of Experimental Radiation OncologyThe University of Texas MD Anderson Cancer CenterHoustonTXUSA
| | - Ray Luo
- Department of Molecular Biology and BiochemistryUniversity of California, IrvineIrvineCAUSA
- Department of Chemical and Biomolecular EngineeringUniversity of California, IrvineIrvineCAUSA
- Department of Materials Science and EngineeringUniversity of California, IrvineIrvineCAUSA
- Department of Biomedical EngineeringUniversity of California, IrvineIrvineCAUSA
| | - Xu Li
- School of Life SciencesWestlake UniversityHangzhouZhejiangChina
| | - Wenqi Wang
- Department of Developmental and Cell BiologyUniversity of California, IrvineIrvineCAUSA
| |
Collapse
|
17
|
Wei H, Luo A, Qiu T, Luo R, Qi R. Improved Poisson-Boltzmann Methods for High-Performance Computing. J Chem Theory Comput 2019; 15:6190-6202. [PMID: 31525962 DOI: 10.1021/acs.jctc.9b00602] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Implicit solvent models based on the Poisson-Boltzmann equation (PBE) have been widely used to study electrostatic interactions in biophysical processes. These models often treat the solvent and solute regions as high and low dielectric continua, leading to a large jump in dielectrics across the molecular surface which is difficult to handle. Higher order interface schemes are often needed to seek higher accuracy for PBE applications. However, these methods are usually very liberal in the use of grid points nearby the molecular surface, making them difficult to use on high-performance computing platforms. Alternatively, the harmonic average (HA) method has been used to approximate dielectric interface conditions near the molecular surface with surprisingly good convergence and is well suited for high-performance computing. By adopting a 7-point stencil, the HA method is advantageous in generating simple 7-banded coefficient matrices, which greatly facilitate linear system solution with dense data parallelism, on high-performance computing platforms such as a graphics processing unit (GPU). However, the HA method is limited due to its lower accuracy. Therefore, it would be of great interest for high-performance applications to develop more accurate methods while retaining the simplicity and effectiveness of the 7-point stencil discretization scheme. In this study, we have developed two new algorithms based on the spirit of the HA method by introducing more physical interface relations and imposing the discretized Poisson's equation to the second order, respectively. Our testing shows that, for typical biomolecules, the new methods significantly improve the numerical accuracy to that comparable to the second-order solvers and with ∼65% overall efficiency gain on widely available high-performance GPU platforms.
Collapse
|
18
|
Wang E, Sun H, Wang J, Wang Z, Liu H, Zhang JZH, Hou T. End-Point Binding Free Energy Calculation with MM/PBSA and MM/GBSA: Strategies and Applications in Drug Design. Chem Rev 2019; 119:9478-9508. [DOI: 10.1021/acs.chemrev.9b00055] [Citation(s) in RCA: 578] [Impact Index Per Article: 115.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Ercheng Wang
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Huiyong Sun
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Junmei Wang
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Zhe Wang
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Hui Liu
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - John Z. H. Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, Shanghai Key Laboratory of Green Chemistry & Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
- NYU−ECNU Center for Computational Chemistry, NYU Shanghai, Shanghai 200122, China
- Department of Chemistry, New York University, New York, New York 10003, United States
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
| | - Tingjun Hou
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| |
Collapse
|
19
|
Greene D, Qi R, Nguyen R, Qiu T, Luo R. Heterogeneous Dielectric Implicit Membrane Model for the Calculation of MMPBSA Binding Free Energies. J Chem Inf Model 2019; 59:3041-3056. [PMID: 31145610 PMCID: PMC7197397 DOI: 10.1021/acs.jcim.9b00363] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Membrane-bound protein receptors are a primary biological drug target, but the computational analysis of membrane proteins has been limited. In order to improve molecular mechanics Poisson-Boltzmann surface area (MMPBSA) binding free energy calculations for membrane protein-ligand systems, we have optimized a new heterogeneous dielectric implicit membrane model, with respect to free energy simulations in explicit membrane and explicit water, and implemented it into the Amber software suite. This new model supersedes our previous uniform, single dielectric implicit membrane model by allowing the dielectric constant to vary with depth within the membrane. We calculated MMPBSA binding free energies for the human purinergic platelet receptor (P2Y12R) and two of the muscarinic acetylcholine receptors (M2R and M3R) bound to various antagonist ligands using both membrane models, and we found that the heterogeneous dielectric membrane model has a stronger correlation with experimental binding affinities compared to the older model under otherwise identical conditions. This improved membrane model increases the utility of MMPBSA calculations for the rational design and improvement of future drug candidates.
Collapse
|
20
|
Wei H, Luo R, Qi R. An efficient second-order poisson-boltzmann method. J Comput Chem 2019; 40:1257-1269. [PMID: 30776135 PMCID: PMC6422926 DOI: 10.1002/jcc.25783] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 11/29/2018] [Accepted: 01/06/2019] [Indexed: 11/08/2022]
Abstract
Immersed interface method (IIM) is a promising high-accuracy numerical scheme for the Poisson-Boltzmann model that has been widely used to study electrostatic interactions in biomolecules. However, the IIM suffers from instability and slow convergence for typical applications. In this study, we introduced both analytical interface and surface regulation into IIM to address these issues. The analytical interface setup leads to better accuracy and its convergence closely follows a quadratic manner as predicted by theory. The surface regulation further speeds up the convergence for nontrivial biomolecules. In addition, uncertainties of the numerical energies for tested systems are also reduced by about half. More interestingly, the analytical setup significantly improves the linear solver efficiency and stability by generating more precise and better-conditioned linear systems. Finally, we implemented the bottleneck linear system solver on GPUs to further improve the efficiency of the method, so it can be widely used for practical biomolecular applications. © 2019 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Haixin Wei
- Department of Chemical Engineering and Materials Science, University of California, Irvine, California, 92697
| | - Ray Luo
- Department of Chemical Engineering and Materials Science, University of California, Irvine, California, 92697.,Department of Molecular Biology and Biochemistry, University of California, Irvine, California, 92697.,Department of Biomedical Engineering, University of California, Irvine, California, 92697
| | - Ruxi Qi
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California, 92697
| |
Collapse
|
21
|
Suárez D, Díaz N. Affinity Calculations of Cyclodextrin Host-Guest Complexes: Assessment of Strengths and Weaknesses of End-Point Free Energy Methods. J Chem Inf Model 2019; 59:421-440. [PMID: 30566348 DOI: 10.1021/acs.jcim.8b00805] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The end-point methods like MM/PBSA or MM/GBSA estimate the free energy of a biomolecule by combining its molecular mechanics energy with solvation free energy and entropy terms. On the one hand, their performance largely depends on the particular system of interest, and despite numerous attempts to improve their reliability that have resulted in many variants, there is still no clear alternative to improve their accuracy. On the other hand, the relatively small cyclodextrin host-guest complexes, for which high-quality binding calorimetric data are usually available, are becoming reference models for testing the accuracy of free energy methods. In this work, we further assess the performance of various MM/PBSA-like approaches as applied to cyclodextrin complexes. To this end, we select a set of complexes between β-cyclodextrin and 57 small organic molecules that has been previously studied with the binding energy distribution analysis method in combination with an implicit solvent model ( Wickstrom, L.; He, P.; Gallicchio, E.; Levy, R. M. J. Chem. Theory Comput. 2013 , 9 , 3136 - 3150 ). For each complex, a conventional 1.0 μs molecular dynamics simulation in explicit solvent is performed. Then we employ semiempirical quantum chemical calculations, several variants of the MM-PB(GB)SA methods, entropy estimations, etc., to assess the reliability of the end-point affinity calculations. The best end-point protocol in this study, which combines DFTB3 energies with entropy corrections, yields estimations of the binding free energies that still have substantial errors (RMSE = 2.2 kcal/mol), but it exhibits a good prediction capacity in terms of ligand ranking ( R2 = 0.66) that is close to or even better than that of rigorous free energy methodologies. Our results can be helpful to discriminate between the intrinsic limitations of the end-point methods and other sources of error, such as the underlying energy and continuum solvation methods.
Collapse
Affiliation(s)
- Dimas Suárez
- Departamento de Química Física y Analítica , Universidad de Oviedo , Avda. Julián Clavería 8 , Oviedo , Asturias 33006 , Spain
| | - Natalia Díaz
- Departamento de Química Física y Analítica , Universidad de Oviedo , Avda. Julián Clavería 8 , Oviedo , Asturias 33006 , Spain
| |
Collapse
|
22
|
Qi R, Luo R. Robustness and Efficiency of Poisson-Boltzmann Modeling on Graphics Processing Units. J Chem Inf Model 2018; 59:409-420. [PMID: 30550277 DOI: 10.1021/acs.jcim.8b00761] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Poisson-Boltzmann equation (PBE) based continuum electrostatics models have been widely used in modeling electrostatic interactions in biochemical processes, particularly in estimating protein-ligand binding affinities. Fast convergence of PBE solvers is crucial in binding affinity computations as numerous snapshots need to be processed. Efforts have been reported to develop PBE solvers on graphics processing units (GPUs) for efficient modeling of biomolecules, though only relatively simple successive over-relaxation and conjugate gradient methods were implemented. However, neither convergence nor scaling properties of the two methods are optimal for large biomolecules. On the other hand, geometric multigrid (MG) has been shown to be an optimal solver on CPUs, though no MG have been reported for biomolecular applications on GPUs. This is not a surprise as it is a more complex method and depends on simpler but limited iterative methods such as Gauss-Seidel in its core relaxation procedure. The robustness and efficiency of MG on GPUs are also unclear. Here we present an implementation and a thorough analysis of MG on GPUs. Our analysis shows that robustness is a more pronounced issue than efficiency for both MG and other tested solvers when the single precision is used for complex biomolecules. We further show how to balance robustness and efficiency utilizing MG's overall efficiency and conjugate gradient's robustness, pointing to a hybrid GPU solver with a good balance of efficiency and accuracy. The new PBE solver will significantly improve the computational throughput for a range of biomolecular applications on the GPU platforms.
Collapse
|
23
|
Chen W, Ren X, Chang CEA. Discovery of CDK8/CycC Ligands with a New Virtual Screening Tool. ChemMedChem 2018; 14:107-118. [PMID: 30403831 DOI: 10.1002/cmdc.201800559] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Revised: 11/02/2018] [Indexed: 12/15/2022]
Abstract
Selective inhibition of cyclin-dependent kinase 8 and cyclin C (CDK8/CycC) has been suggested as a promising strategy for decreasing mitogenic signals in cancer cells with reduced toxicity toward normal cells. We developed a novel virtual screening protocol for drug development and applied it to the discovery of new CDK8/CycC type II ligands, which is likely to achieve long residence time and specificity. We first analyzed the binding thermodynamics of 11 published pyrazolourea ligands using molecular dynamics simulations and a free-energy calculation method, VM2, and extracted the key binding information to assist virtual screening. The urea moiety was found to be the critical structural contributor of the reference ligands. Starting with the urea moiety, we conducted substructure-based searches with our newly developed superposition and single-point energy evaluation method, followed by free-energy calculations, and singled out three purchasable compounds for bioassay testing. The ranking from the experimental results is completely consistent with the predicted rankings. A potent drug-like compound was found to have a Kd value of 42.5 nm, which is similar to those of the most potent reference ligands; this provided a good starting point for further improvement. This study shows that our novel virtual screening protocol is an accurate and efficient tool for drug development.
Collapse
Affiliation(s)
- Wei Chen
- Department of Chemistry, University of California, Riverside, CA, 92521, USA.,ChemConsulting LLC, Frederick, MD, 21704, USA.,NanChang Lead Biotech LLC, NanChang, JiangXi, 330096, China
| | - Xiaodong Ren
- Department of Chemistry, University of California, Riverside, CA, 92521, USA
| | - Chia-En A Chang
- Department of Chemistry, University of California, Riverside, CA, 92521, USA
| |
Collapse
|
24
|
Labat F, Civalleri B, Dovesi R. Implicit Solvation Using a Generalized Finite-Difference Approach in CRYSTAL: Implementation and Results for Molecules, Polymers, and Surfaces. J Chem Theory Comput 2018; 14:5969-5983. [PMID: 30347161 DOI: 10.1021/acs.jctc.8b00762] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present the implementation of an implicit solvation model in the CRYSTAL code. The solvation energy is separated into two components: the electrostatic contribution arising from a self-consistent reaction field treatment obtained within a generalized finite-difference Poisson model, augmented by a nonelectrostatic contribution proportional to the solvent-accessible surface area of the solute. A discontinuous dielectric boundary is used, along with a solvent-excluded surface built from interlocking atom-centered spheres on which apparent surface point charges are mapped. The procedure is general and can be performed at both the Hartree-Fock and density functional theory levels, with pure or hybrid functionals, for systems periodic in 0, 1, and 2 directions, that is, for isolated molecules and extended polymers and surfaces. The Poisson equation resolution and apparent surface charge formalism is first validated on model analytical test cases. The good agreement obtained on solvation free energies is further confirmed by calculations performed on a large test set of 501 neutral molecules, for which a mean unsigned error of 1.3 kcal/mol is obtained when compared to the available experimental data. Importantly, the self-consistent reaction field procedure converges well for all molecules tested. This is further verified for all polymers and surfaces considered. In particular, for periodic systems, results obtained on an infinite glycine chain and on the wettability parameters of SiO2 surfaces are in good agreement with previously published data. The size extensivity of the energetic terms involved in the electrostatic contribution to the solvation energy is also well verified. These encouraging results constitute a first step to take into account complex environments in the CRYSTAL code, potentially allowing for a more accurate modeling of complex processes for both periodic and nonperiodic systems.
Collapse
Affiliation(s)
- Frédéric Labat
- PSL Research University, Chimie Paristech-CNRS , Institut de Recherche de Chimie de Paris , 11 rue P. et M. Curie , 75005 Paris , France
| | - Bartolomeo Civalleri
- Dipartimento di Chimica IFM , Università di Torino and NIS - Nanostructured Interfaces and Surfaces - Centre of Excellence , Via P. Giuria 7 , 10125 Torino , Italy
| | - Roberto Dovesi
- Dipartimento di Chimica IFM , Università di Torino and NIS - Nanostructured Interfaces and Surfaces - Centre of Excellence , Via P. Giuria 7 , 10125 Torino , Italy
| |
Collapse
|
25
|
Xiao L, Luo R. Exploring a multi-scale method for molecular simulation in continuum solvent model: Explicit simulation of continuum solvent as an incompressible fluid. J Chem Phys 2018; 147:214112. [PMID: 29221408 DOI: 10.1063/1.5016052] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We explored a multi-scale algorithm for the Poisson-Boltzmann continuum solvent model for more robust simulations of biomolecules. In this method, the continuum solvent/solute interface is explicitly simulated with a numerical fluid dynamics procedure, which is tightly coupled to the solute molecular dynamics simulation. There are multiple benefits to adopt such a strategy as presented below. At this stage of the development, only nonelectrostatic interactions, i.e., van der Waals and hydrophobic interactions, are included in the algorithm to assess the quality of the solvent-solute interface generated by the new method. Nevertheless, numerical challenges exist in accurately interpolating the highly nonlinear van der Waals term when solving the finite-difference fluid dynamics equations. We were able to bypass the challenge rigorously by merging the van der Waals potential and pressure together when solving the fluid dynamics equations and by considering its contribution in the free-boundary condition analytically. The multi-scale simulation method was first validated by reproducing the solute-solvent interface of a single atom with analytical solution. Next, we performed the relaxation simulation of a restrained symmetrical monomer and observed a symmetrical solvent interface at equilibrium with detailed surface features resembling those found on the solvent excluded surface. Four typical small molecular complexes were then tested, both volume and force balancing analyses showing that these simple complexes can reach equilibrium within the simulation time window. Finally, we studied the quality of the multi-scale solute-solvent interfaces for the four tested dimer complexes and found that they agree well with the boundaries as sampled in the explicit water simulations.
Collapse
Affiliation(s)
- Li Xiao
- Departments of Biomedical Engineering, University of California, Irvine, California 92697, USA
| | - Ray Luo
- Departments of Biomedical Engineering, University of California, Irvine, California 92697, USA
| |
Collapse
|
26
|
Greene D, Po T, Pan J, Tabibian T, Luo R. Computational Analysis for the Rational Design of Anti-Amyloid Beta (Aβ) Antibodies. J Phys Chem B 2018; 122:4521-4536. [PMID: 29617557 DOI: 10.1021/acs.jpcb.8b01837] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Alzheimer's disease (AD) is a neurodegenerative disorder that lacks effective treatment options. Anti-amyloid beta (Aβ) antibodies are the leading drug candidates to treat AD, but the results of clinical trials have been disappointing. Introducing rational mutations into anti-Aβ antibodies to increase their effectiveness is a way forward, but the path to take is unclear. In this study, we demonstrate the use of computational fragment-based docking and MMPBSA binding free energy calculations in the analysis of anti-Aβ antibodies for rational drug design efforts. Our fragment-based docking method successfully predicts the emergence of the common EFRH epitope. MD simulations coupled with MMPBSA binding free energy calculations are used to analyze scenarios described in prior studies, and we computationally introduce rational mutations into PFA1 to predict mutations that can improve its binding affinity toward the pE3-Aβ3-8 form of Aβ. Two out of our four proposed mutations are predicted to stabilize binding. Our study demonstrates that a computational approach may lead to an improved drug candidate for AD in the future.
Collapse
|
27
|
Li Q, Chen HF. Synergistic regulation mechanism of iperoxo and LY2119620 for muscarinic acetylcholine M2 receptor. RSC Adv 2018; 8:13067-13074. [PMID: 35542505 PMCID: PMC9079678 DOI: 10.1039/c8ra01545g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 03/30/2018] [Indexed: 11/21/2022] Open
Abstract
Muscarinic acetylcholine receptors are GPCRs that regulate the activity of a diverse array of central and peripheral functions in the human body, including the parasympathetic actions of acetylcholine. The M2 muscarinic receptor subtype plays a key role in modulating cardiac function and many important central processes. The orthosteric agonist and allosteric modulator can bind the pocket of M2. However, the detailed relationship between orthosteric agonist and allosteric modulator of M2 is still unclear. In this study, we intend to elucidate the residue-level regulation mechanism and pathway via a combined approach of dynamical correlation network and molecular dynamics simulation. Specifically computational residue-level fluctuation correlation data was analyzed to reveal detailed dynamics signatures in the regulation process. A hypothesis of "synergistic regulation" is proposed to reveal the cooperation affection between the orthosteric agonist and allosteric modulator, which is subsequently validated by perturbation and mutation analyses. Two possible synergistic regulation pathways of 2CU-I178-Y403-W400-F396-L114-Y440-Nb9 and IXO-V111-F396-L114-Y440-Nb9 were identified by the shortest path algorithm and were confirmed by the mutation of junction node. Furthermore, the efficiency of information transfer of bound M2 is significant higher than any single binding system. Our study shows that targeting the synergistic regulation pathways may better regulate the calcium channel of M2. The knowledge gained in this study may help develop drugs for diseases of the central nervous system and metabolic disorders.
Collapse
Affiliation(s)
- Quan Li
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, College of Life Sciences and Biotechnology, Shanghai Jiaotong University Shanghai 200240 China +86-21-34204348 +86-21-34204348
| | - Hai-Feng Chen
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, College of Life Sciences and Biotechnology, Shanghai Jiaotong University Shanghai 200240 China +86-21-34204348 +86-21-34204348
- Shanghai Center for Bioinformation Technology Shanghai 200235 China
| |
Collapse
|
28
|
Kongsune P, Hannongbua S. The role of conserved QXG and binding affinity of S23G & S26G receptors on avian H5, swine H1 and human H1 of influenza A virus hemagglutinin. J Mol Graph Model 2018; 82:12-19. [PMID: 29625417 DOI: 10.1016/j.jmgm.2018.03.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 03/05/2018] [Accepted: 03/28/2018] [Indexed: 10/17/2022]
Abstract
Outbreaks of avian, human and swine influenza are a serious concern for public health. In the reproductive cycle of the influenza virus, hemagglutinin (HA) is the primary protein responsible for binding to glycan receptor sites on the host cell surface. MD simulations of avian H5, swine H1 and human H1 complexed with S23G and S26G receptors were performed to study the role of key residues on the receptor conformational behaviors, hydrogen bond formation, binding free energy and residue-wise energy contribution. The obtained results indicated that the relative energies of swH1_S23G and swH1_S26G were found to be close to each other (3.1 kcal/mol) while the relative energies of AvH5 and HuH1 were found to be significantly different (11.1 ± 6.8 and 29.0 ± 8.2 kcal/mol for AvH5 and HuH1, respectively).
Collapse
Affiliation(s)
- Panita Kongsune
- Department of Chemistry, Faculty of Science, Thaksin University, Phattalung, 93210, Thailand.
| | - Supot Hannongbua
- Computational Chemistry Unit Cell, Department of Chemistry, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Bangkok, 10330, Thailand
| |
Collapse
|
29
|
Kesherwani M, Velmurugan D. Molecular insights into substrate binding mechanism of undecaprenyl pyrophosphate with membrane integrated phosphatidyl glycerophosphate phosphatase B (PgpB) using molecular dynamics simulation approach. J Biomol Struct Dyn 2018. [PMID: 29528805 DOI: 10.1080/07391102.2018.1449666] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Undecaprenyl phosphate (C55-P) acts as carrier lipid in the synthesis of peptidoglycan, which is de novo synthesized from dephosphorylation of undecaprenyl pyrophosphate (C55-PP). The phosphatidylglycerol phosphate phosphatase B (PgpB) catalyzes the dephosphorylation of C55-PP and forms C55-P. As no structural study has been made regarding the binding of C55-PP to PgpB, in the current study, in silico molecular docking, followed by 150 ns molecular dynamics simulation of the putative binding complex in membrane/solvent environment has been performed to understand conformational dynamics. Results are compared with simulated apo form and PE inhibitor-bound form. Analysis of correlated residual fluctuation network in apo form, C55-PP bound and PE inhibitor-bound form suggests that difference in dynamic coupling between TM domain and α2 and α3 helix of periplasmic domain provides ligand binding to facilitate catalysis or to show inhibitory activity. Distance distribution in catalytic residual pair, H207-R104; H207-R201 and H207-D211 which stabilizes phosphate-enzyme intermediate shows a narrow peak in 2.4-3.6 Å in substrate-bound compared to apo form. Binding interactions and binding free energy analyses complement the partial inhibition of PE where PE has less binding free energy compared to the C55-PP substrate as well as the difference in binding interaction with catalytic pocket. Thus, the present study provides how substrate binding couples the movement in TM domain and periplasmic domain which might help in the understanding of active site communication in PgpB. C55-PP phosphatase interactions with a catalytic pocket of PgpB provide new insight for designing drugs against bacterial infection.
Collapse
Affiliation(s)
- Manish Kesherwani
- a Centre for Advanced Study in Crystallography and Biophysics , University of Madras, Guindy Campus , Chennai , India
| | - Devadasan Velmurugan
- a Centre for Advanced Study in Crystallography and Biophysics , University of Madras, Guindy Campus , Chennai , India
| |
Collapse
|
30
|
Okiyama Y, Nakano T, Watanabe C, Fukuzawa K, Mochizuki Y, Tanaka S. Fragment Molecular Orbital Calculations with Implicit Solvent Based on the Poisson–Boltzmann Equation: Implementation and DNA Study. J Phys Chem B 2018; 122:4457-4471. [DOI: 10.1021/acs.jpcb.8b01172] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Yoshio Okiyama
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
| | - Tatsuya Nakano
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
- Division of Medicinal Safety Science, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa 210-9501, Japan
| | - Chiduru Watanabe
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
| | - Kaori Fukuzawa
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
- Faculty of Pharmaceutical Sciences, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo 142-8501, Japan
| | - Yuji Mochizuki
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
- Department of Chemistry and Research Center for Smart Molecules, Faculty of Science, Rikkyo University, 3-34-1 Nishi-ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
| | - Shigenori Tanaka
- Graduate School of System Informatics, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe, Hyogo 657-8501, Japan
| |
Collapse
|
31
|
Wang C, Greene D, Xiao L, Qi R, Luo R. Recent Developments and Applications of the MMPBSA Method. Front Mol Biosci 2018; 4:87. [PMID: 29367919 PMCID: PMC5768160 DOI: 10.3389/fmolb.2017.00087] [Citation(s) in RCA: 325] [Impact Index Per Article: 54.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 11/30/2017] [Indexed: 12/23/2022] Open
Abstract
The Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) approach has been widely applied as an efficient and reliable free energy simulation method to model molecular recognition, such as for protein-ligand binding interactions. In this review, we focus on recent developments and applications of the MMPBSA method. The methodology review covers solvation terms, the entropy term, extensions to membrane proteins and high-speed screening, and new automation toolkits. Recent applications in various important biomedical and chemical fields are also reviewed. We conclude with a few future directions aimed at making MMPBSA a more robust and efficient method.
Collapse
Affiliation(s)
- Changhao Wang
- Chemical and Materials Physics Graduate Program, University of California, Irvine, Irvine, CA, United States
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
- Department of Physics and Astronomy, University of California, Irvine, Irvine, CA, United States
| | - D'Artagnan Greene
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
| | - Li Xiao
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, United States
| | - Ruxi Qi
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
| | - Ray Luo
- Chemical and Materials Physics Graduate Program, University of California, Irvine, Irvine, CA, United States
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, United States
- Department of Chemical Engineering and Materials Science, University of California, Irvine, Irvine, CA, United States
| |
Collapse
|
32
|
Wang C, Ren P, Luo R. Ionic Solution: What Goes Right and Wrong with Continuum Solvation Modeling. J Phys Chem B 2017; 121:11169-11179. [PMID: 29164898 DOI: 10.1021/acs.jpcb.7b09616] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Solvent-mediated electrostatic interactions were well recognized to be important in the structure and function of molecular systems. Ionic interaction is an important component in electrostatic interactions, especially in highly charged molecules, such as nucleic acids. Here, we focus on the quality of the widely used Poisson-Boltzmann surface area (PBSA) continuum models in modeling ionic interactions by comparing with both explicit solvent simulations and the experiment. In this work, the molality-dependent chemical potentials for sodium chloride (NaCl) electrolyte were first simulated in the SPC/E explicit solvent. Our high-quality simulation agrees well with both the previous study and the experiment. Given the free-energy simulations in SPC/E as the benchmark, we used the same sets of snapshots collected in the SPC/E solvent model for PBSA free-energy calculations in the hope to achieve the maximum consistency between the two solvent models. Our comparative analysis shows that the molality-dependent chemical potentials of NaCl were reproduced well with both linear PB and nonlinear PB methods, although nonlinear PB agrees better with SPC/E and the experiment. Our free-energy simulations also show that the presence of salt increases the hydrophobic effect in a nonlinear fashion, in qualitative agreement with previous theoretical studies of Onsager and Samaras. However, the lack of molality-dependency in the nonelectrostatics continuum models dramatically reduces the overall quality of PBSA methods in modeling salt-dependent energetics. These analyses point to further improvements needed for more robust modeling of solvent-mediated interactions by the continuum solvation frameworks.
Collapse
Affiliation(s)
| | - Pengyu Ren
- Department of Biomedical Engineering, University of Texas , Austin, Texas 78712, United States
| | | |
Collapse
|
33
|
Abi-Ghanem J, Rabin C, Porrini M, Dausse E, Toulmé JJ, Gabelica V. Electrostatics Explains the Position-Dependent Effect of G⋅U Wobble Base Pairs on the Affinity of RNA Kissing Complexes. Chemphyschem 2017; 18:2782-2790. [PMID: 28762245 DOI: 10.1002/cphc.201700337] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 06/29/2017] [Indexed: 01/03/2023]
Abstract
In the RNA realm, non-Watson-Crick base pairs are abundant and can affect both the RNA 3D structure and its function. Here, we investigated the formation of RNA kissing complexes in which the loop-loop interaction is modulated by non-Watson-Crick pairs. Mass spectrometry, surface plasmon resonance, and UV-melting experiments show that the G⋅U wobble base pair favors kissing complex formation only when placed at specific positions. We tried to rationalize this effect by molecular modeling, including molecular mechanics Poisson-Boltzmann surface area (MMPBSA) thermodynamics calculations and PBSA calculations of the electrostatic potential surfaces. Modeling reveals that the G⋅U stabilization is due to a specific electrostatic environment defined by the base pairs of the entire loop-loop region. The loop is not symmetric, and therefore the identity and position of each base pair matters. Predicting and visualizing the electrostatic environment created by a given sequence can help to design specific kissing complexes with high affinity, for potential therapeutic, nanotechnology or analytical applications.
Collapse
Affiliation(s)
- Josephine Abi-Ghanem
- Univ. Bordeaux, INSERM, CNRS, Laboratoire Acides Nucléiques, Régulations Naturelle et Artificielle, ARNA, U1212, UMR5320, IECB, 2 rue Robert Escarpit, 33607, Pessac, France
| | - Clémence Rabin
- Univ. Bordeaux, INSERM, CNRS, Laboratoire Acides Nucléiques, Régulations Naturelle et Artificielle, ARNA, U1212, UMR5320, IECB, 2 rue Robert Escarpit, 33607, Pessac, France
| | - Massimiliano Porrini
- Univ. Bordeaux, INSERM, CNRS, Laboratoire Acides Nucléiques, Régulations Naturelle et Artificielle, ARNA, U1212, UMR5320, IECB, 2 rue Robert Escarpit, 33607, Pessac, France
| | - Eric Dausse
- Univ. Bordeaux, INSERM, CNRS, Laboratoire Acides Nucléiques, Régulations Naturelle et Artificielle, ARNA, U1212, UMR5320, 146 rue Léo Saignat, 33076, Bordeaux, France
| | - Jean-Jacques Toulmé
- Univ. Bordeaux, INSERM, CNRS, Laboratoire Acides Nucléiques, Régulations Naturelle et Artificielle, ARNA, U1212, UMR5320, 146 rue Léo Saignat, 33076, Bordeaux, France
| | - Valérie Gabelica
- Univ. Bordeaux, INSERM, CNRS, Laboratoire Acides Nucléiques, Régulations Naturelle et Artificielle, ARNA, U1212, UMR5320, IECB, 2 rue Robert Escarpit, 33607, Pessac, France
| |
Collapse
|
34
|
Suárez D, Díaz N. Ligand Strain and Entropic Effects on the Binding of Macrocyclic and Linear Inhibitors: Molecular Modeling of Penicillopepsin Complexes. J Chem Inf Model 2017; 57:2045-2055. [PMID: 28737392 DOI: 10.1021/acs.jcim.7b00355] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Using extensive molecular dynamics simulations, we investigate the structure and dynamics of the complexes formed between penicillopepsin and two peptidomimetic inhibitors: a linear compound, isovaleryl(P4)-valine(P3)-asparagine(P2)-leucine(P1)-phosphonate-phenylalanine(P1'), and its macrocylic analog that includes a methylene bridge between the Asn(P2) and Phe(P1') side chains. The macrocyclic inhibitor, which has a 420-fold stronger affinity than that of the acyclic one, has been considered to lower the entropic penalty for binding. To better understand this binding preference, the solution structure of the inhibitors is studied by molecular dynamics simulations. Subsequently, we assess the influence of the enzyme/inhibitor contacts, the enzyme-induced inhibitor strain, the variation of the ligand configurational entropy and the enzyme reorganization by combining molecular-mechanics Poisson-Boltzmann surface area and normal mode calculations with conformational entropy calculations. We find that there is no relevant entropic stabilization on the binding of the cyclic inhibitor with respect to the acyclic analog because the methylene bridge does not reduce appreciably the conformational flexibility of the free inhibitor. The most important factors explaining the stronger affinity of the macrocyclic inhibitor are the conformational filtering and the lower ligand strain induced by the methylene bridge.
Collapse
Affiliation(s)
- Dimas Suárez
- Departamento de Química Física y Analítica, Universidad de Oviedo , Avda. Julián Claveria 8, 33006 Oviedo, Spain
| | - Natalia Díaz
- Departamento de Química Física y Analítica, Universidad de Oviedo , Avda. Julián Claveria 8, 33006 Oviedo, Spain
| |
Collapse
|
35
|
Xiao L, Diao J, Greene D, Wang J, Luo R. A Continuum Poisson-Boltzmann Model for Membrane Channel Proteins. J Chem Theory Comput 2017; 13:3398-3412. [PMID: 28564540 PMCID: PMC5728381 DOI: 10.1021/acs.jctc.7b00382] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Membrane proteins constitute a large portion of the human proteome and perform a variety of important functions as membrane receptors, transport proteins, enzymes, signaling proteins, and more. Computational studies of membrane proteins are usually much more complicated than those of globular proteins. Here, we propose a new continuum model for Poisson-Boltzmann calculations of membrane channel proteins. Major improvements over the existing continuum slab model are as follows: (1) The location and thickness of the slab model are fine-tuned based on explicit-solvent MD simulations. (2) The highly different accessibilities in the membrane and water regions are addressed with a two-step, two-probe grid-labeling procedure. (3) The water pores/channels are automatically identified. The new continuum membrane model is optimized (by adjusting the membrane probe, as well as the slab thickness and center) to best reproduce the distributions of buried water molecules in the membrane region as sampled in explicit water simulations. Our optimization also shows that the widely adopted water probe of 1.4 Å for globular proteins is a very reasonable default value for membrane protein simulations. It gives the best compromise in reproducing the explicit water distributions in membrane channel proteins, at least in the water accessible pore/channel regions. Finally, we validate the new membrane model by carrying out binding affinity calculations for a potassium channel, and we observe good agreement with the experimental results.
Collapse
Affiliation(s)
| | | | | | - Junmei Wang
- Department of Pharmaceutical Sciences, University of Pittsburgh , Pittsburgh, Pennsylvania 15261, United States
| | | |
Collapse
|
36
|
Qi R, Botello-Smith WM, Luo R. Acceleration of Linear Finite-Difference Poisson-Boltzmann Methods on Graphics Processing Units. J Chem Theory Comput 2017; 13:3378-3387. [PMID: 28553983 DOI: 10.1021/acs.jctc.7b00336] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Electrostatic interactions play crucial roles in biophysical processes such as protein folding and molecular recognition. Poisson-Boltzmann equation (PBE)-based models have emerged as widely used in modeling these important processes. Though great efforts have been put into developing efficient PBE numerical models, challenges still remain due to the high dimensionality of typical biomolecular systems. In this study, we implemented and analyzed commonly used linear PBE solvers for the ever-improving graphics processing units (GPU) for biomolecular simulations, including both standard and preconditioned conjugate gradient (CG) solvers with several alternative preconditioners. Our implementation utilizes the standard Nvidia CUDA libraries cuSPARSE, cuBLAS, and CUSP. Extensive tests show that good numerical accuracy can be achieved given that the single precision is often used for numerical applications on GPU platforms. The optimal GPU performance was observed with the Jacobi-preconditioned CG solver, with a significant speedup over standard CG solver on CPU in our diversified test cases. Our analysis further shows that different matrix storage formats also considerably affect the efficiency of different linear PBE solvers on GPU, with the diagonal format best suited for our standard finite-difference linear systems. Further efficiency may be possible with matrix-free operations and integrated grid stencil setup specifically tailored for the banded matrices in PBE-specific linear systems.
Collapse
Affiliation(s)
- Ruxi Qi
- Department of Molecular Biology and Biochemistry University of California , Irvine, California 92697-3900, United States
| | - Wesley M Botello-Smith
- Department of Molecular Biology and Biochemistry University of California , Irvine, California 92697-3900, United States
| | - Ray Luo
- Department of Molecular Biology and Biochemistry University of California , Irvine, California 92697-3900, United States
| |
Collapse
|
37
|
Wang C, Xiao L, Luo R. Numerical interpretation of molecular surface field in dielectric modeling of solvation. J Comput Chem 2017; 38:1057-1070. [PMID: 28318096 PMCID: PMC5464005 DOI: 10.1002/jcc.24782] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 01/10/2017] [Accepted: 02/20/2017] [Indexed: 11/07/2022]
Abstract
Continuum solvent models, particularly those based on the Poisson-Boltzmann equation (PBE), are widely used in the studies of biomolecular structures and functions. Existing PBE developments have been mainly focused on how to obtain more accurate and/or more efficient numerical potentials and energies. However to adopt the PBE models for molecular dynamics simulations, a difficulty is how to interpret dielectric boundary forces accurately and efficiently for robust dynamics simulations. This study documents the implementation and analysis of a range of standard fitting schemes, including both one-sided and two-sided methods with both first-order and second-order Taylor expansions, to calculate molecular surface electric fields to facilitate the numerical calculation of dielectric boundary forces. These efforts prompted us to develop an efficient approximated one-dimensional method, which is to fit the surface field one dimension at a time, for biomolecular applications without much compromise in accuracy. We also developed a surface-to-atom force partition scheme given a level set representation of analytical molecular surfaces to facilitate their applications to molecular simulations. Testing of these fitting methods in the dielectric boundary force calculations shows that the second-order methods, including the one-dimensional method, consistently perform among the best in the molecular test cases. Finally, the timing analysis shows the approximated one-dimensional method is far more efficient than standard second-order methods in the PBE force calculations. © 2017 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Changhao Wang
- Chemical and Materials Physics Graduate Program, University of California, Irvine, California, 92697
- Department of Physics and Astronomy, University of California, Irvine, California, 92697
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California, 92697
| | - Li Xiao
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California, 92697
- Department of Biomedical Engineering, University of California, Irvine, California, 92697
| | - Ray Luo
- Chemical and Materials Physics Graduate Program, University of California, Irvine, California, 92697
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California, 92697
- Department of Biomedical Engineering, University of California, Irvine, California, 92697
- Department of Chemical Engineering and Materials Science, University of California, Irvine, California, 92697
| |
Collapse
|
38
|
Nguyen DD, Wang B, Wei GW. Accurate, robust, and reliable calculations of Poisson-Boltzmann binding energies. J Comput Chem 2017; 38:941-948. [PMID: 28211071 PMCID: PMC5844473 DOI: 10.1002/jcc.24757] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 11/28/2016] [Accepted: 01/22/2017] [Indexed: 12/18/2022]
Abstract
Poisson-Boltzmann (PB) model is one of the most popular implicit solvent models in biophysical modeling and computation. The ability of providing accurate and reliable PB estimation of electrostatic solvation free energy, ΔGel, and binding free energy, ΔΔGel, is important to computational biophysics and biochemistry. In this work, we investigate the grid dependence of our PB solver (MIBPB) with solvent excluded surfaces for estimating both electrostatic solvation free energies and electrostatic binding free energies. It is found that the relative absolute error of ΔGel obtained at the grid spacing of 1.0 Å compared to ΔGel at 0.2 Å averaged over 153 molecules is less than 0.2%. Our results indicate that the use of grid spacing 0.6 Å ensures accuracy and reliability in ΔΔGel calculation. In fact, the grid spacing of 1.1 Å appears to deliver adequate accuracy for high throughput screening. © 2017 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Duc D Nguyen
- Department of Mathematics, Michigan State University, Michigan, 48824
| | - Bao Wang
- Department of Mathematics, Michigan State University, Michigan, 48824
| | - Guo-Wei Wei
- Department of Mathematics, Michigan State University, Michigan, 48824
- Department of Electrical and Computer Engineering, Michigan State University, Michigan, 48824
- Department of Biochemistry and Molecular Biology, Michigan State University, Michigan, 48824
| |
Collapse
|
39
|
Molavi Tabrizi A, Goossens S, Mehdizadeh Rahimi A, Cooper CD, Knepley MG, Bardhan JP. Extending the Solvation-Layer Interface Condition Continum Electrostatic Model to a Linearized Poisson–Boltzmann Solvent. J Chem Theory Comput 2017; 13:2897-2914. [DOI: 10.1021/acs.jctc.6b00832] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Amirhossein Molavi Tabrizi
- Department
of Mechanical and Industrial Engineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Spencer Goossens
- Department
of Mechanical and Industrial Engineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Ali Mehdizadeh Rahimi
- Department
of Mechanical and Industrial Engineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Christopher D. Cooper
- Departamento
de Ingeniería Mecánica and Centro Científico
Tecnológico de Valparaíso (CCTVal), Universidad Técnica Federico Santa María, Valparaiso, Chile
| | - Matthew G. Knepley
- Department
of Computational and Applied Mathematics, Rice University, Houston, Texas 77005, United States
| | - Jaydeep P. Bardhan
- Department
of Mechanical and Industrial Engineering, Northeastern University, Boston, Massachusetts 02115, United States
| |
Collapse
|
40
|
Molavi Tabrizi A, Goossens S, Mehdizadeh Rahimi A, Knepley M, Bardhan JP. Predicting solvation free energies and thermodynamics in polar solvents and mixtures using a solvation-layer interface condition. J Chem Phys 2017. [DOI: 10.1063/1.4977037] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Amirhossein Molavi Tabrizi
- Department of Mechanical and Industrial Engineering, Northeastern University, Boston, Massachusetts 02115, USA
| | - Spencer Goossens
- Department of Mechanical and Industrial Engineering, Northeastern University, Boston, Massachusetts 02115, USA
| | - Ali Mehdizadeh Rahimi
- Department of Mechanical and Industrial Engineering, Northeastern University, Boston, Massachusetts 02115, USA
| | - Matthew Knepley
- Department of Computational and Applied Mathematics, Rice University, Houston, Texas 77005, USA
| | - Jaydeep P. Bardhan
- Department of Mechanical and Industrial Engineering, Northeastern University, Boston, Massachusetts 02115, USA
| |
Collapse
|
41
|
Qian T, Wo J, Zhang Y, Song Q, Feng G, Luo R, Lin S, Wu G, Chen HF. Crystal Structure of StnA for the Biosynthesis of Antitumor Drug Streptonigrin Reveals a Unique Substrate Binding Mode. Sci Rep 2017; 7:40254. [PMID: 28074848 PMCID: PMC5225493 DOI: 10.1038/srep40254] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 12/02/2016] [Indexed: 01/16/2023] Open
Abstract
Streptonigrin methylesterase A (StnA) is one of the tailoring enzymes that modify the aminoquinone skeleton in the biosynthesis pathway of Streptomyces species. Although StnA has no significant sequence homology with the reported α/β-fold hydrolases, it shows typical hydrolytic activity in vivo and in vitro. In order to reveal its functional characteristics, the crystal structures of the selenomethionine substituted StnA (SeMet-StnA) and the complex (S185A mutant) with its substrate were resolved to the resolution of 2.71 Å and 2.90 Å, respectively. The overall structure of StnA can be described as an α-helix cap domain on top of a common α/β hydrolase domain. The substrate methyl ester of 10'-demethoxystreptonigrin binds in a hydrophobic pocket that mainly consists of cap domain residues and is close to the catalytic triad Ser185-His349-Asp308. The transition state is stabilized by an oxyanion hole formed by the backbone amides of Ala102 and Leu186. The substrate binding appears to be dominated by interactions with several specific hydrophobic contacts and hydrogen bonds in the cap domain. The molecular dynamics simulation and site-directed mutagenesis confirmed the important roles of the key interacting residues in the cap domain. Structural alignment and phylogenetic tree analysis indicate that StnA represents a new subfamily of lipolytic enzymes with the specific binding pocket located at the cap domain instead of the interface between the two domains.
Collapse
Affiliation(s)
- Tianle Qian
- State Key Laboratory of Microbial metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Jing Wo
- State Key Laboratory of Microbial metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Yan Zhang
- State Key Laboratory of Microbial metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai, 200025, China
| | - Quanwei Song
- State Key Laboratory of Microbial metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
- Key laboratory of Pesticide and Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University, 152 Luoyu Road, Wuhan 430079, China
| | - Guoqiang Feng
- Key laboratory of Pesticide and Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University, 152 Luoyu Road, Wuhan 430079, China
| | - Ray Luo
- Departments of Molecular Biology and Biochemistry, Chemical Engineering and Materials Science, and Biomedical Engineering, University of California, Irvine, California 92697-3900, USA
| | - Shuangjin Lin
- State Key Laboratory of Microbial metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Geng Wu
- State Key Laboratory of Microbial metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Hai-Feng Chen
- State Key Laboratory of Microbial metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
- Shanghai Center for Bioinformation Technology, 1278 Keyuan Road, Shanghai, 200235, China
| |
Collapse
|
42
|
Hajzer V, Fišera R, Latika A, Durmis J, Kollár J, Frecer V, Tučeková Z, Miertuš S, Kostolanský F, Varečková E, Šebesta R. Stereoisomers of oseltamivir – synthesis, in silico prediction and biological evaluation. Org Biomol Chem 2017; 15:1828-1841. [DOI: 10.1039/c6ob02673g] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Three diastereoisomers of oseltamivir were synthesized, their properties predicted by quantum-chemical calculations and their antiviral activities evaluated.
Collapse
Affiliation(s)
| | | | | | | | - Jakub Kollár
- Comenius University in Bratislava
- Faculty of Pharmacy
- Department of Pharmaceutical Analysis and Nuclear Pharmacy
- SK-83232 Bratislava
- Slovakia
| | - Vladimír Frecer
- Comenius University in Bratislava
- Faculty of Pharmacy
- Department of Physical Chemistry of Drugs
- SK-83232 Bratislava
- Slovakia
| | - Zuzana Tučeková
- University of SS. Cyril and Methodius
- Faculty of Natural Sciences
- Department of Biotechnologies
- SK-91701 Trnava
- Slovakia
| | - Stanislav Miertuš
- ICARST n.o
- SK-84104 Bratislava
- Slovakia
- University of SS. Cyril and Methodius
- Faculty of Natural Sciences
| | - František Kostolanský
- Biomedical Research Center
- Institute of Virology
- Slovak Academy of Sciences
- Department of Orthomyxovirus Research
- SK-84505 Bratislava
| | - Eva Varečková
- Biomedical Research Center
- Institute of Virology
- Slovak Academy of Sciences
- Department of Orthomyxovirus Research
- SK-84505 Bratislava
| | - Radovan Šebesta
- Comenius University in Bratislava
- Faculty of Natural Sciences
- Department of Organic Chemistry
- SK-84215 Bratislava
- Slovakia
| |
Collapse
|
43
|
Greene D, Botello-Smith WM, Follmer A, Xiao L, Lambros E, Luo R. Modeling Membrane Protein-Ligand Binding Interactions: The Human Purinergic Platelet Receptor. J Phys Chem B 2016; 120:12293-12304. [PMID: 27934233 PMCID: PMC5460638 DOI: 10.1021/acs.jpcb.6b09535] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Membrane proteins, due to their roles as cell receptors and signaling mediators, make prime candidates for drug targets. The computational analysis of protein-ligand binding affinities has been widely employed as a tool in rational drug design efforts. Although efficient implicit solvent-based methods for modeling globular protein-ligand binding have been around for many years, the extension of such methods to membrane protein-ligand binding is still in its infancy. In this study, we extended the widely used Amber/MMPBSA method to model membrane protein-ligand systems, and we used it to analyze protein-ligand binding for the human purinergic platelet receptor (P2Y12R), a prominent drug target in the inhibition of platelet aggregation for the prevention of myocardial infarction and stroke. The binding affinities, computed by the Amber/MMPBSA method using standard parameters, correlate well with experiment. A detailed investigation of these parameters was conducted to assess their impact on the accuracy of the method. These analyses show the importance of properly treating the nonpolar solvation interactions and the electrostatic polarization in the binding of nucleotide agonists and non-nucleotide antagonists to P2Y12R. On the basis of the crystal structures and the experimental conditions in the binding assay, we further hypothesized that the nucleotide agonists lose their bound magnesium ion upon binding to P2Y12R, and our computational study supports this hypothesis. Ultimately, this work illustrates the value of computational analysis in the interpretation of experimental binding reactions.
Collapse
Affiliation(s)
- D'Artagnan Greene
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697
| | - Wesley M. Botello-Smith
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697
- Chemical and Materials Physics Graduate Program, University of California, Irvine, CA 92697
- Department of Chemistry, University of California, Irvine, CA 92697
| | - Alec Follmer
- Department of Chemistry, University of California, Irvine, CA 92697
| | - Li Xiao
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697
- Department of Biomedical Engineering, University of California, Irvine, CA 92697
| | - Eleftherios Lambros
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697
| | - Ray Luo
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697
- Chemical and Materials Physics Graduate Program, University of California, Irvine, CA 92697
- Department of Biomedical Engineering, University of California, Irvine, CA 92697
- Department of Chemical Engineering and Materials Science, University of California, Irvine, CA 92697
| |
Collapse
|
44
|
Jetsadawisut W, Nutho B, Meeprasert A, Rungrotmongkol T, Kungwan N, Wolschann P, Hannongbua S. Susceptibility of inhibitors against 3C protease of coxsackievirus A16 and enterovirus A71 causing hand, foot and mouth disease: A molecular dynamics study. Biophys Chem 2016; 219:9-16. [PMID: 27668727 DOI: 10.1016/j.bpc.2016.09.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 09/16/2016] [Accepted: 09/17/2016] [Indexed: 10/21/2022]
Abstract
Hand foot and mouth disease (HFMD) epidemic has occurred in many countries. Coxsackievirus A16 (CV-A16) and Enterovirus A71 (EV-A71) are the main causes of HFMD. Up to now, there are no anti-HFMD drugs available. Rupintrivir, a broad-spectrum inhibitor, is a drug candidate for HFMD treatment, while other HFMD inhibitors designed from several studies have a relatively low efficiency. Therefore, in this work we aim to study the binding mechanisms of rupintrivir and a peptidic α,β-unsaturated ethyl ester (SG85) against both CV-A16 and EV-A71 3C proteases (3Cpro) using all-atoms molecular dynamics simulation. The obtained results indicate that SG85 shows a stronger binding affinity than rupintrivir against CV-A16. Both inhibitors exhibit a comparable affinity against EV-A71 3Cpro. The molecular information of the binding of the two inhibitors to the proteases will be elucidated. Thus, it is implied that these two compounds may be used as leads for further anti-HFMD drug design and development.
Collapse
Affiliation(s)
- W Jetsadawisut
- Computational Chemistry Unit Cell, Department of Chemistry, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Patumwan, Bangkok 10330, Thailand
| | - B Nutho
- Program in Biotechnology, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Bangkok 10330, Thailand
| | - A Meeprasert
- Structural and Computational Biology Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Bangkok 10330, Thailand
| | - T Rungrotmongkol
- Structural and Computational Biology Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Bangkok 10330, Thailand; Ph.D. Program in Bioinformatics and Computational Biology, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Patumwan, Bangkok 10330, Thailand.
| | - N Kungwan
- Department of Chemistry, Faculty of Science, Chiang Mai University, 239 Huay Kaew Road, Muang District, Chiang Mai 50200, Thailand
| | - P Wolschann
- Computational Chemistry Unit Cell, Department of Chemistry, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Patumwan, Bangkok 10330, Thailand; Department of Pharmaceutical Technology and Biopharmaceutics, University of Vienna, Vienna 1090, Austria; Institute of Theoretical Chemistry, University of Vienna, Vienna 1090, Austria
| | - S Hannongbua
- Computational Chemistry Unit Cell, Department of Chemistry, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Patumwan, Bangkok 10330, Thailand.
| |
Collapse
|
45
|
Wang C, Nguyen PH, Pham K, Huynh D, Le TBN, Wang H, Ren P, Luo R. Calculating protein-ligand binding affinities with MMPBSA: Method and error analysis. J Comput Chem 2016; 37:2436-46. [PMID: 27510546 PMCID: PMC5018451 DOI: 10.1002/jcc.24467] [Citation(s) in RCA: 156] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 07/13/2016] [Indexed: 11/07/2022]
Abstract
Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) methods have become widely adopted in estimating protein-ligand binding affinities due to their efficiency and high correlation with experiment. Here different computational alternatives were investigated to assess their impact to the agreement of MMPBSA calculations with experiment. Seven receptor families with both high-quality crystal structures and binding affinities were selected. First the performance of nonpolar solvation models was studied and it was found that the modern approach that separately models hydrophobic and dispersion interactions dramatically reduces RMSD's of computed relative binding affinities. The numerical setup of the Poisson-Boltzmann methods was analyzed next. The data shows that the impact of grid spacing to the quality of MMPBSA calculations is small: the numerical error at the grid spacing of 0.5 Å is already small enough to be negligible. The impact of different atomic radius sets and different molecular surface definitions was further analyzed and weak influences were found on the agreement with experiment. The influence of solute dielectric constant was also analyzed: a higher dielectric constant generally improves the overall agreement with experiment, especially for highly charged binding pockets. The data also showed that the converged simulations caused slight reduction in the agreement with experiment. Finally the direction of estimating absolute binding free energies was briefly explored. Upon correction of the binding-induced rearrangement free energy and the binding entropy lost, the errors in absolute binding affinities were also reduced dramatically when the modern nonpolar solvent model was used, although further developments were apparently necessary to further improve the MMPBSA methods. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Changhao Wang
- Chemical and Materials Physics Graduate Program, Irvine, California, 92697
- Department of Molecular Biology and Biochemistry, Irvine, California, 92697
- Department of Physics and Astronomy, University of California, Irvine, California, 92697
| | - Peter H Nguyen
- Department of Molecular Biology and Biochemistry, Irvine, California, 92697
| | - Kevin Pham
- Department of Molecular Biology and Biochemistry, Irvine, California, 92697
| | - Danielle Huynh
- Department of Molecular Biology and Biochemistry, Irvine, California, 92697
| | | | - Hongli Wang
- Department of Molecular Biology and Biochemistry, Irvine, California, 92697
| | - Pengyu Ren
- Department of Biomedical Engineering, University of Texas, Austin, Texas, 78712
| | - Ray Luo
- Chemical and Materials Physics Graduate Program, Irvine, California, 92697.
- Department of Molecular Biology and Biochemistry, Irvine, California, 92697.
- Department of Chemical Engineering and Materials Science, Irvine, California, 92697.
- Department of Biomedical Engineering, University of California, Irvine, California, 92697.
| |
Collapse
|
46
|
Dynamics Correlation Network for Allosteric Switching of PreQ1 Riboswitch. Sci Rep 2016; 6:31005. [PMID: 27484311 PMCID: PMC4971525 DOI: 10.1038/srep31005] [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: 04/13/2016] [Accepted: 07/11/2016] [Indexed: 02/06/2023] Open
Abstract
Riboswitches are a class of metabolism control elements mostly found in bacteria. Due to their fundamental importance in bacteria gene regulation, riboswitches have been proposed as antibacterial drug targets. Prequeuosine (preQ1) is the last free precursor in the biosynthetic pathway of queuosine that is crucial for translation efficiency and fidelity. However, the regulation mechanism for the preQ1 riboswitch remains unclear. Here we constructed fluctuation correlation network based on all-atom molecular dynamics simulations to reveal the regulation mechanism. The results suggest that the correlation network in the bound riboswitch is distinctly different from that in the apo riboswitch. The community network indicates that the information freely transfers from the binding site of preQ1 to the expression platform of the P3 helix in the bound riboswitch and the P3 helix is a bottleneck in the apo riboswitch. Thus, a hypothesis of “preQ1-binding induced allosteric switching” is proposed to link riboswitch and translation regulation. The community networks of mutants support this hypothesis. Finally, a possible allosteric pathway of A50-A51-A52-U10-A11-G12-G56 was also identified based on the shortest path algorithm and confirmed by mutations and network perturbation. The novel fluctuation network analysis method can be used as a general strategy in studies of riboswitch structure-function relationship.
Collapse
|
47
|
Yang J, Liu H, Liu X, Gu C, Luo R, Chen HF. Synergistic Allosteric Mechanism of Fructose-1,6-bisphosphate and Serine for Pyruvate Kinase M2 via Dynamics Fluctuation Network Analysis. J Chem Inf Model 2016; 56:1184-1192. [PMID: 27227511 DOI: 10.1021/acs.jcim.6b00115] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Pyruvate kinase M2 (PKM2) plays a key role in tumor metabolism and regulates the rate-limiting final step of glycolysis. In tumor cells, there are two allosteric effectors for PKM2: fructose-1,6-bisphosphate (FBP) and serine. However, the relationship between FBP and serine for allosteric regulation of PKM2 is unknown. Here we constructed residue/residue fluctuation correlation network based on all-atom molecular dynamics simulations to reveal the regulation mechanism. The results suggest that the correlation network in bound PKM2 is distinctly different from that in the free state, FBP/PKM2, or Ser/PKM2. The community network analysis indicates that the information can freely transfer from the allosteric sites of FBP and serine to the substrate site in bound PKM2, while there exists a bottleneck for information transfer in the network of the free state. Furthermore, the binding free energy between the substrate and PKM2 for bound PKM2 is significantly lower than either of FBP/PKM2 or Ser/PKM2. Thus, a hypothesis of "synergistic allosteric mechanism" is proposed for the allosteric regulation of FBP and serine. This hypothesis was further confirmed by the perturbational and mutational analyses of community networks and binding free energies. Finally, two possible synergistic allosteric pathways of FBP-K433-T459-R461-A109-V71-R73-MG2-OXL and Ser-I47-C49-R73-MG2-OXL were identified based on the shortest path algorithm and were confirmed by the network perturbation analysis. Interestingly, no similar pathways could be found in the free state. The process targeting on the allosteric pathways can better regulate the glycolysis of PKM2 and significantly inhibit the progression of tumor.
Collapse
Affiliation(s)
- Jingxu Yang
- State Key Laboratory of Microbial metabolism, Department of Bioinformatics and Biostatistics, College of Life Sciences and Biotechnology, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Hao Liu
- State Key Laboratory of Microbial metabolism, Department of Bioinformatics and Biostatistics, College of Life Sciences and Biotechnology, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Xiaorui Liu
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200030, China.,Institute of Embryo-Fetal Original Adult Disease Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200030, China
| | - Chengbo Gu
- State Key Laboratory of Microbial metabolism, Department of Bioinformatics and Biostatistics, College of Life Sciences and Biotechnology, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Ray Luo
- Departments of Molecular Biology and Biochemistry, Chemical Engineering and Materials Science, Biomedical Engineering, University of California, Irvine, California 92697-3900, USA
| | - Hai-Feng Chen
- State Key Laboratory of Microbial metabolism, Department of Bioinformatics and Biostatistics, College of Life Sciences and Biotechnology, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai, 200240, China.,Shanghai Center for Bioinformation Technology, 1278 Keyuan Road, Shanghai, 200235, China
| |
Collapse
|
48
|
Xiao L, Wang C, Ye X, Luo R. Charge Central Interpretation of the Full Nonlinear PB Equation: Implications for Accurate and Scalable Modeling of Solvation Interactions. J Phys Chem B 2016; 120:8707-21. [PMID: 27146097 DOI: 10.1021/acs.jpcb.6b04439] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Continuum solvation modeling based upon the Poisson-Boltzmann equation (PBE) is widely used in structural and functional analysis of biomolecules. In this work, we propose a charge-central interpretation of the full nonlinear PBE electrostatic interactions. The validity of the charge-central view or simply charge view, as formulated as a vacuum Poisson equation with effective charges, was first demonstrated by reproducing both electrostatic potentials and energies from the original solvated full nonlinear PBE. There are at least two benefits when the charge-central framework is applied. First the convergence analyses show that the use of polarization charges allows a much faster converging numerical procedure for electrostatic energy and forces calculation for the full nonlinear PBE. Second, the formulation of the solvated electrostatic interactions as effective charges in vacuum allows scalable algorithms to be deployed for large biomolecular systems. Here, we exploited the charge-view interpretation and developed a particle-particle particle-mesh (P3M) strategy for the full nonlinear PBE systems. We also studied the accuracy and convergence of solvation forces with the charge-view and the P3M methods. It is interesting to note that the convergence of both the charge-view and the P3M methods is more rapid than the original full nonlinear PBE method. Given the developments and validations documented here, we are working to adapt the P3M treatment of the full nonlinear PBE model to molecular dynamics simulations.
Collapse
Affiliation(s)
| | | | - Xiang Ye
- Department of Physics, Shanghai Normal University , Shanghai 200234, China
| | | |
Collapse
|
49
|
Synergistic Modification Induced Specific Recognition between Histone and TRIM24 via Fluctuation Correlation Network Analysis. Sci Rep 2016; 6:24587. [PMID: 27079666 PMCID: PMC4832343 DOI: 10.1038/srep24587] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 03/31/2016] [Indexed: 01/19/2023] Open
Abstract
Histone modification plays a key role in gene regulation and gene expression. TRIM24 as a histone reader can recognize histone modification. However the specific recognition mechanism between TRIM24 and histone modification is unsolved. Here, systems biology method of dynamics correlation network based on molecular dynamics simulation was used to answer the question. Our network analysis shows that the dynamics correlation network of H3K23ac is distinctly different from that of wild type and other modifications. A hypothesis of “synergistic modification induced recognition” is then proposed to link histone modification and TRIM24 binding. These observations were further confirmed from community analysis of networks with mutation and network perturbation. Finally, a possible recognition pathway is also identified based on the shortest path search for H3K23ac. Significant difference of recognition pathway was found among different systems due to methylation and acetylation modifications. The analysis presented here and other studies show that the dynamic network-based analysis might be a useful general strategy to study the biology of protein post-translational modification and associated recognition.
Collapse
|
50
|
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.
Collapse
|