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Xi C, Zheng F, Gao G, Song Z, Zhang B, Dong C, Du XW, Wang LW. Ion Solvation Free Energy Calculation Based on Ab Initio Molecular Dynamics Using a Hybrid Solvent Model. J Chem Theory Comput 2022; 18:6878-6891. [PMID: 36253911 DOI: 10.1021/acs.jctc.1c01298] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Free energy calculation of small molecules or ion species in aqueous solvent is one of the most important problems in electrochemistry study. Although there are many previous approaches to calculate such free energies, they are based on ab initio methods and suffer from various limitations and approximations. In the current work, we developed a hybrid approach based on ab initio molecular dynamics (AIMD) simulations to calculate the ion solvation energy. In this approach, a small water cluster surrounding the central ion is used, and implicit solvent model is applied outside the water cluster. A dynamic potential well is used during AIMD to keep the water cluster together. Quasi-harmonic approximation is used to calculate the entropy contribution, while the total energy average is used to calculate the enthalpy term. The obtained solvation voltages of the bulk metal agree with experiments within 0.3 eV, and the simulation results for the solvation energies of gaseous ions are close to the experimental observations. Besides the free energies, radial pair distribution functions and coordination numbers of hydrated cations are also obtained. The remaining challenges of this method are also discussed.
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Affiliation(s)
- Cong Xi
- Materials Science Division, Lawrence Berkeley National Laboratory, Berkeley, California94720, United States.,Institute of New Energy Materials, School of Materials Science and Engineering, Tianjin University, Tianjin30072, People's Republic of China
| | - Fan Zheng
- Materials Science Division, Lawrence Berkeley National Laboratory, Berkeley, California94720, United States
| | - Guoping Gao
- Materials Science Division, Lawrence Berkeley National Laboratory, Berkeley, California94720, United States
| | - Zhigang Song
- Materials Science Division, Lawrence Berkeley National Laboratory, Berkeley, California94720, United States
| | - Buyu Zhang
- Materials Science Division, Lawrence Berkeley National Laboratory, Berkeley, California94720, United States
| | - Cunku Dong
- Institute of New Energy Materials, School of Materials Science and Engineering, Tianjin University, Tianjin30072, People's Republic of China
| | - Xi-Wen Du
- Institute of New Energy Materials, School of Materials Science and Engineering, Tianjin University, Tianjin30072, People's Republic of China
| | - Lin-Wang Wang
- Materials Science Division, Lawrence Berkeley National Laboratory, Berkeley, California94720, United States
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2
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Buyukdagli S. Explicit solvent theory of salt-induced dielectric decrement. Phys Chem Chem Phys 2022; 24:13976-13987. [DOI: 10.1039/d2cp00853j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Within the framework of an electrolyte model composed of structured solvent molecules and salt ions coupled by electrostatic and hard-core interactions, we characterize the physical mechanism behind salt-induced dielectric decrement.
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3
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Pascal S, David S, Andraud C, Maury O. Near-infrared dyes for two-photon absorption in the short-wavelength infrared: strategies towards optical power limiting. Chem Soc Rev 2021; 50:6613-6658. [DOI: 10.1039/d0cs01221a] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The recent advances in the field of two-photon absorbing chromophores in the short-wavelength infrared spectral range (SWIR 1100–2500 nm) are summarized, highlighting the development of optical power limiting devices in this spectral range.
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Affiliation(s)
- Simon Pascal
- Univ. Lyon
- ENS Lyon
- CNRS UMR 5182
- Laboratoire de Chimie
- 69364 Lyon
| | - Sylvain David
- Univ. Lyon
- ENS Lyon
- CNRS UMR 5182
- Laboratoire de Chimie
- 69364 Lyon
| | - Chantal Andraud
- Univ. Lyon
- ENS Lyon
- CNRS UMR 5182
- Laboratoire de Chimie
- 69364 Lyon
| | - Olivier Maury
- Univ. Lyon
- ENS Lyon
- CNRS UMR 5182
- Laboratoire de Chimie
- 69364 Lyon
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4
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Amin AN, Lin YH, Das S, Chan HS. Analytical Theory for Sequence-Specific Binary Fuzzy Complexes of Charged Intrinsically Disordered Proteins. J Phys Chem B 2020; 124:6709-6720. [PMID: 32639157 DOI: 10.1021/acs.jpcb.0c04575] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Intrinsically disordered proteins (IDPs) are important for biological functions. In contrast to folded proteins, molecular recognition among certain IDPs is "fuzzy" in that their binding and/or phase separation are stochastically governed by the interacting IDPs' amino acid sequences, while their assembled conformations remain largely disordered. To help elucidate a basic aspect of this fascinating yet poorly understood phenomenon, the binding of a homo or heterodimeric pair of polyampholytic IDPs is modeled statistical mechanically using cluster expansion. We find that the binding affinities of binary fuzzy complexes in the model correlate strongly with a newly derived simple "joint sequence charge decoration" parameter readily calculable from the pair of IDPs' sequence charge patterns. Predictions by our analytical theory are in essential agreement with coarse-grained explicit-chain simulations. This computationally efficient theoretical framework is expected to be broadly applicable to rationalizing and predicting sequence-specific IDP-IDP polyelectrostatic interactions.
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Affiliation(s)
- Alan N Amin
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Yi-Hsuan Lin
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada.,Molecular Medicine, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
| | - Suman Das
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Hue Sun Chan
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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5
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Xin X, Niu X, Liu W, Wang D. Hybrid Solvation Model with First Solvation Shell for Calculation of Solvation Free Energy. Chemphyschem 2020; 21:762-769. [PMID: 32154979 DOI: 10.1002/cphc.202000039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/15/2020] [Indexed: 02/03/2023]
Abstract
We present a hybrid solvation model with first solvation shell to calculate solvation free energies. This hybrid model combines the quantum mechanics and molecular mechanics methods with the analytical expression based on the Born solvation model to calculate solvation free energies. Based on calculated free energies of solvation and reaction profiles in gas phase, we set up a unified scheme to predict reaction profiles in solution. The predicted solvation free energies and reaction barriers are compared with experimental results for twenty bimolecular nucleophilic substitution reactions. These comparisons show that our hybrid solvation model can predict reliable solvation free energies and reaction barriers for chemical reactions of small molecules in aqueous solution.
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Affiliation(s)
- Xin Xin
- College of Physics and Electronics, Shandong Normal University, Jinan, Shandong, 250014, China
| | - Xiao Niu
- College of Physics and Electronics, Shandong Normal University, Jinan, Shandong, 250014, China
| | - Wanqi Liu
- College of Physics and Electronics, Shandong Normal University, Jinan, Shandong, 250014, China
| | - Dunyou Wang
- College of Physics and Electronics, Shandong Normal University, Jinan, Shandong, 250014, China
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6
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Das Mahanta D, Islam SI, Choudhury S, Das DK, Mitra RK, Barman A. Contrasting hydration dynamics in DME and DMSO aqueous solutions: A combined optical pump-probe and GHz-THz dielectric relaxation investigation. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.111194] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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7
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Das Mahanta D, Rana D, Patra A, Mukherjee B, Mitra RK. Heterogeneous structure and solvation dynamics of DME/water binary mixtures: A combined spectroscopic and simulation investigation. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.04.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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8
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Liu L, Nakamura I. Solvation Energy of Ions in Polymers: Effects of Chain Length and Connectivity on Saturated Dipoles near Ions. J Phys Chem B 2017; 121:3142-3150. [DOI: 10.1021/acs.jpcb.7b00671] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lijun Liu
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
| | - Issei Nakamura
- Department of Physics, Michigan Technological University, Houghton, Michigan 49931, United States
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9
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Shelton DP. Orientation correlation and local field in liquid nitrobenzene. J Chem Phys 2016; 144:234506. [PMID: 27334178 DOI: 10.1063/1.4953794] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- David P. Shelton
- Department of Physics and Astronomy, University of Nevada, Las Vegas, Nevada 89154-4002, USA
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10
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Affiliation(s)
- Dmitry V. Matyushov
- Department of Physics and Department of Chemistry and Biochemistry, Arizona State University, P.O. Box 871504, Tempe, Arizona 85287, USA
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11
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Duan X, Nakamura I. A new lattice Monte Carlo simulation for dielectric saturation in ion-containing liquids. SOFT MATTER 2015; 11:3566-3571. [PMID: 25807274 DOI: 10.1039/c5sm00336a] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We develop a new, rapid method for the lattice Monte Carlo simulation of ion-containing liquids that accounts for the effects of the reorganization of solvent dipoles under external electrostatic fields. Our results are in reasonable agreement with the analytical solutions to the dielectric continuum theory of Booth for single ions, ion pairs, and ionic cross-links. We also illustrate the substantial disparity between the dielectric functions for like and unlike charges on the nanometer scale. Our simulation rationalizes the experimental data for the dependence of the bulk dielectric value of water on ion concentrations in terms of saturated dipoles near ions.
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Affiliation(s)
- Xiaozheng Duan
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China.
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12
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Walsh PS, Buchanan EG, Gord JR, Zwier TS. Binding water to a PEG-linked flexible bichromophore: IR spectra of diphenoxyethane-(H2O)n clusters, n = 2-4. J Chem Phys 2015; 142:154303. [PMID: 25903886 DOI: 10.1063/1.4917305] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Affiliation(s)
- Patrick S. Walsh
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, USA
| | - Evan G. Buchanan
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, USA
| | - Joseph R. Gord
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, USA
| | - Timothy S. Zwier
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, USA
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13
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14
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Persson RAX, Voulgarakis NK, Chu JW. Dynamic mesoscale model of dipolar fluids via fluctuating hydrodynamics. J Chem Phys 2014; 141:174105. [DOI: 10.1063/1.4900498] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
- Rasmus A. X. Persson
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu 30068, Taiwan
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 30068, Taiwan
| | | | - Jhih-Wei Chu
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu 30068, Taiwan
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 30068, Taiwan
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15
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Bardhan JP, Knepley MG. Communication: modeling charge-sign asymmetric solvation free energies with nonlinear boundary conditions. J Chem Phys 2014; 141:131103. [PMID: 25296776 PMCID: PMC4193973 DOI: 10.1063/1.4897324] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 09/25/2014] [Indexed: 01/28/2023] Open
Abstract
We show that charge-sign-dependent asymmetric hydration can be modeled accurately using linear Poisson theory after replacing the standard electric-displacement boundary condition with a simple nonlinear boundary condition. Using a single multiplicative scaling factor to determine atomic radii from molecular dynamics Lennard-Jones parameters, the new model accurately reproduces MD free-energy calculations of hydration asymmetries for: (i) monatomic ions, (ii) titratable amino acids in both their protonated and unprotonated states, and (iii) the Mobley "bracelet" and "rod" test problems [D. L. Mobley, A. E. Barber II, C. J. Fennell, and K. A. Dill, "Charge asymmetries in hydration of polar solutes," J. Phys. Chem. B 112, 2405-2414 (2008)]. Remarkably, the model also justifies the use of linear response expressions for charging free energies. Our boundary-element method implementation demonstrates the ease with which other continuum-electrostatic solvers can be extended to include asymmetry.
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Affiliation(s)
- Jaydeep P Bardhan
- Department of Mechanical and Industrial Engineering, Northeastern University, Boston, Massachusetts 02115, USA
| | - Matthew G Knepley
- Computation Institute, The University of Chicago, Chicago, Illinois 60637, USA
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16
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Koehl P, Poitevin F, Orland H, Delarue M. Modified Poisson–Boltzmann equations for characterizing biomolecular solvation. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2014. [DOI: 10.1142/s021963361440001x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Methods for computing electrostatic interactions often account implicitly for the solvent, due to the much smaller number of degrees of freedom involved. In the Poisson–Boltzmann (PB) approach the electrostatic potential is obtained by solving the Poisson–Boltzmann equation (PBE), where the solvent region is modeled as a homogeneous medium with a high dielectric constant. PB however is not exempt of problems. It does not take into account for example the sizes of the ions in the atmosphere surrounding the solute, nor does it take into account the inhomogeneous dielectric response of water due to the presence of a highly charged surface. In this paper we review two major modifications of PB that circumvent these problems, namely the size-modified PB (SMPB) equation and the Dipolar Poisson–Boltzmann Langevin (DPBL) model. In SMPB, steric effects between ions are accounted for with a lattice gas model. In DPBL, the solvent region is no longer modeled as a homogeneous dielectric media but rather as an assembly of self-orienting interacting dipoles of variable density. This model results in a dielectric profile that transits smoothly from the solute to the solvent region as well as in a variable solvent density that depends on the charges of the solute. We show successful applications of the DPBL formalism to computing the solvation free energies of isolated ions in water. Further developments of more accurately modified PB models are discussed.
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Affiliation(s)
- Patrice Koehl
- Department of Computer Science and Genome Center, University of California, Davis, CA 95616, USA
| | - Frederic Poitevin
- Unité de Dynamique Structurale des Macromolécules, UMR 3528 du CNRS, Institut Pasteur, 75015 Paris, France
| | - Henri Orland
- Service de Physique Théorique, CEA-Saclay, 91191 Gif/Yvette Cedex, France
| | - Marc Delarue
- Unité de Dynamique Structurale des Macromolécules, UMR 3528 du CNRS, Institut Pasteur, 75015 Paris, France
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17
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A novel implicit solvent model for simulating the molecular dynamics of RNA. Biophys J 2014; 105:1248-57. [PMID: 24010668 DOI: 10.1016/j.bpj.2013.07.033] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Revised: 06/21/2013] [Accepted: 07/23/2013] [Indexed: 11/24/2022] Open
Abstract
Although molecular dynamics simulations can be accelerated by more than an order of magnitude by implicitly describing the influence of the solvent with a continuum model, most currently available implicit solvent simulations cannot robustly simulate the structure and dynamics of nucleic acids. The difficulties become exacerbated especially for RNAs, suggesting the presence of serious physical flaws in the prior continuum models for the influence of the solvent and counter ions on the nucleic acids. We present a novel, to our knowledge, implicit solvent model for simulating nucleic acids by combining the Langevin-Debye model and the Poisson-Boltzmann equation to provide a better estimate of the electrostatic screening of both the water and counter ions. Tests of the model involve comparisons of implicit and explicit solvent simulations for three RNA targets with 20, 29, and 75 nucleotides. The model provides reasonable agreement with explicit solvent simulations, and directions for future improvement are noted.
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18
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Bardhan JP. Gradient Models in Molecular Biophysics: Progress, Challenges, Opportunities. JOURNAL OF THE MECHANICAL BEHAVIOR OF MATERIALS 2013; 22:169-184. [PMID: 25505358 PMCID: PMC4259120 DOI: 10.1515/jmbm-2013-0024] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
In the interest of developing a bridge between researchers modeling materials and those modeling biological molecules, we survey recent progress in developing nonlocal-dielectric continuum models for studying the behavior of proteins and nucleic acids. As in other areas of science, continuum models are essential tools when atomistic simulations (e.g. molecular dynamics) are too expensive. Because biological molecules are essentially all nanoscale systems, the standard continuum model, involving local dielectric response, has basically always been dubious at best. The advanced continuum theories discussed here aim to remedy these shortcomings by adding features such as nonlocal dielectric response, and nonlinearities resulting from dielectric saturation. We begin by describing the central role of electrostatic interactions in biology at the molecular scale, and motivate the development of computationally tractable continuum models using applications in science and engineering. For context, we highlight some of the most important challenges that remain and survey the diverse theoretical formalisms for their treatment, highlighting the rigorous statistical mechanics that support the use and improvement of continuum models. We then address the development and implementation of nonlocal dielectric models, an approach pioneered by Dogonadze, Kornyshev, and their collaborators almost forty years ago. The simplest of these models is just a scalar form of gradient elasticity, and here we use ideas from gradient-based modeling to extend the electrostatic model to include additional length scales. The paper concludes with a discussion of open questions for model development, highlighting the many opportunities for the materials community to leverage its physical, mathematical, and computational expertise to help solve one of the most challenging questions in molecular biology and biophysics.
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19
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Theoretical investigation of two-photon absorption and fluorescence properties of cypridina luciferin-based derivatives: 2,3,5-trisubstituted pyrazine compounds. J PHYS ORG CHEM 2013. [DOI: 10.1002/poc.3177] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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20
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Liu Y, Zhao S, Wu J. A Site Density Functional Theory for Water: Application to Solvation of Amino Acid Side Chains. J Chem Theory Comput 2013; 9:1896-908. [DOI: 10.1021/ct3010936] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yu Liu
- Departments of Chemical and
Environmental Engineering and Mathematics, University of California,
Riverside, California 92521, United States
| | - Shuangliang Zhao
- State Key Laboratory of Chemical
Engineering, East China University of Science and Technology, Shanghai,
200238, P. R. China
| | - Jianzhong Wu
- Departments of Chemical and
Environmental Engineering and Mathematics, University of California,
Riverside, California 92521, United States
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21
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Bergendahl LT, Paterson MJ. Influence of electronic effects on one- and two-photon absorption in porphyrin isomers. RSC Adv 2013. [DOI: 10.1039/c3ra40790j] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
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23
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Baxa MC, Haddadian EJ, Jha AK, Freed KF, Sosnick TR. Context and force field dependence of the loss of protein backbone entropy upon folding using realistic denatured and native state ensembles. J Am Chem Soc 2012; 134:15929-36. [PMID: 22928488 DOI: 10.1021/ja3064028] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The loss of conformational entropy is the largest unfavorable quantity affecting a protein's stability. We calculate the reduction in the number of backbone conformations upon folding using the distribution of backbone dihedral angles (ϕ,ψ) obtained from an experimentally validated denatured state model, along with all-atom simulations for both the denatured and native states. The average loss of entropy per residue is TΔS(BB)(U-N) = 0.7, 0.9, or 1.1 kcal·mol(-1) at T = 298 K, depending on the force field used, with a 0.6 kcal·mol(-1) dispersion across the sequence. The average equates to a decrease of a factor of 3-7 in the number of conformations available per residue (f = Ω(Denatured)/Ω(Native)) or to a total of f(tot) = 3(n)-7(n) for an n residue protein. Our value is smaller than most previous estimates where f = 7-20, that is, our computed TΔS(BB)(U-N) is smaller by 10-100 kcal mol(-1) for n = 100. The differences emerge from our use of realistic native and denatured state ensembles as well as from the inclusion of accurate local sequence preferences, neighbor effects, and correlated motions (vibrations), in contrast to some previous studies that invoke gross assumptions about the entropy in either or both states. We find that the loss of entropy primarily depends on the local environment and less on properties of the native state, with the exception of α-helical residues in some force fields.
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Affiliation(s)
- Michael C Baxa
- Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, United States
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24
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Kumar R, Sumpter BG, Kilbey SM. Charge regulation and local dielectric function in planar polyelectrolyte brushes. J Chem Phys 2012; 136:234901. [DOI: 10.1063/1.4729158] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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25
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Xu Z, Cai W. Fast Analytical Methods for Macroscopic Electrostatic Models in Biomolecular Simulations. SIAM REVIEW. SOCIETY FOR INDUSTRIAL AND APPLIED MATHEMATICS 2011; 53:683-720. [PMID: 23745011 PMCID: PMC3671632 DOI: 10.1137/090774288] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We review recent developments of fast analytical methods for macroscopic electrostatic calculations in biological applications, including the Poisson-Boltzmann (PB) and the generalized Born models for electrostatic solvation energy. The focus is on analytical approaches for hybrid solvation models, especially the image charge method for a spherical cavity, and also the generalized Born theory as an approximation to the PB model. This review places much emphasis on the mathematical details behind these methods.
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Affiliation(s)
- Zhenli Xu
- Department of Mathematics and Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China, and Department of Mathematics and Statistics, University of North Carolina, Charlotte, NC 28223 ()
| | - Wei Cai
- Department of Mathematics and Statistics, University of North Carolina, Charlotte, NC 28223 (), and Beijing International Center for Mathematical Research, Beijing, People's Republic of China, 100871
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26
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Wang R, Wang ZG. Effects of ion solvation on phase equilibrium and interfacial tension of liquid mixtures. J Chem Phys 2011; 135:014707. [DOI: 10.1063/1.3607969] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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27
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Wang LF, Meng XW, Tang FQ. Density functional theory study of electronic absorption spectra and intermolecular interactions of porphyrin–borate complexes. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.theochem.2010.06.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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28
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Baird NJ, Gong H, Zaheer SS, Freed KF, Pan T, Sosnick TR. Extended structures in RNA folding intermediates are due to nonnative interactions rather than electrostatic repulsion. J Mol Biol 2010; 397:1298-306. [PMID: 20188108 DOI: 10.1016/j.jmb.2010.02.025] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2009] [Revised: 02/11/2010] [Accepted: 02/13/2010] [Indexed: 11/28/2022]
Abstract
RNA folding occurs via a series of transitions between metastable intermediate states for Mg(2+) concentrations below those needed to fold the native structure. In general, these folding intermediates are considerably less compact than their respective native states. Our previous work demonstrates that the major equilibrium intermediate of the 154-residue specificity domain (S-domain) of the Bacillus subtilis RNase P RNA is more extended than its native structure. We now investigate two models with falsifiable predictions regarding the origins of the extended intermediate structures in the S-domains of the B. subtilis and the Escherichia coli RNase P RNA that belong to different classes of P RNA and have distinct native structures. The first model explores the contribution of electrostatic repulsion, while the second model probes specific interactions in the core of the folding intermediate. Using small-angle X-ray scattering and Langevin dynamics simulations, we show that electrostatics plays only a minor role, whereas specific interactions largely account for the extended nature of the intermediate. Structural contacts in the core, including a nonnative base pair, help to stabilize the intermediate conformation. We conclude that RNA folding intermediates adopt extended conformations due to short-range, nonnative interactions rather than generic electrostatic repulsion of helical domains. These principles apply to other ribozymes and riboswitches that undergo functionally relevant conformational changes.
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Affiliation(s)
- Nathan J Baird
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
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Zhang YH, Zhao W, Jiang P, Zhang LJ, Zhang T, Wang J. Structural parameters and vibrational spectra of a series of zinc meso-phenylporphyrins: a DFT and experimental study. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2010; 75:880-890. [PMID: 20042362 DOI: 10.1016/j.saa.2009.12.027] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2009] [Revised: 10/14/2009] [Accepted: 12/07/2009] [Indexed: 05/28/2023]
Abstract
The influences of meso-phenyl substitution on the geometric structure and vibrational spectra have been studied by DFT calculation (B3LYP/6-31G(d)) and experiment on a series of zinc porphyrins (ZnTPP: zinc 5,10,15,20-tetraphenylporphyrin; ZnTrPP: zinc 5,10,15-triphenylporphryin; ZnDPP: zinc 5,15-dipenylporphyirn; ZnMPP: zinc 5-monophenylporphyrin; ZnP: zinc porphine). Calculation indicates that meso-phenyl substitution gives rise to slight out-of-plane distortion but significant in-plane distortion, especially for the configuration around C(m) atom, to zinc porphyrin. The assignment of experimental vibrational spectra was proposed mainly on the basis of calculation. Different shifting tendency upon meso-phenyl substitution is observed for different structure-sensitive bands, such as the shifting of nu(2), nu(3), nu(6), and nu(8) modes toward higher frequencies and nu(4) and nu(28) modes toward lower frequencies, upon meso-phenyl substitution. This is attributed primarily to in-plane nuclear reorganization effect (IPNR), though the contribution from out-of-plane distortion cannot be excluded completely. Analysis on vibrational structure reveals that asymmetric meso-phenyl substitution, especially the 5,15-diphenyl substitution of ZnDPP, brings about asymmetric vibrational displacement, or even splitting of vibrational structure to normal modes involving mainly the motion of meso-C(m). This is ascribed to the reduction of symmetry of porphyrin skeleton caused by asymmetric meso-phenyl substitution.
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Affiliation(s)
- Ying-Hui Zhang
- Department of Chemistry, Nankai University, Weijin Road 94, Tianjin 300071, People's Republic of China.
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30
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Wang ZG. Fluctuation in electrolyte solutions: the self energy. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2010; 81:021501. [PMID: 20365565 DOI: 10.1103/physreve.81.021501] [Citation(s) in RCA: 147] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2009] [Indexed: 05/16/2023]
Abstract
We address the issue of the self energy of the mobile ions in electrolyte solutions within a general Gaussian renormalized fluctuation theory using a field-theoretic approach. We introduce the Born radii of the ions in the form of a charge distribution allowing for different Born radii between the cations and anions. The model thus automatically yields a theory free of divergences and accounts for the solvation of the ions at the level of continuous dielectric media. In an inhomogeneous dielectric medium, the self energy is in general position dependent and differences in the self energy between cations and anions can give rise to local charge separation in a macroscopically neutral system. Treating the Born radius a as a smallness parameter, we show that the self energy can be split into an O(a(-1)) nonuniversal contribution and an O(a0) universal contribution that depends only on the ion concentration, valency, and the spatially varying dielectric constant. For a weakly inhomogeneous dielectric medium, the nonuniversal part of the self energy is shown to have the form of the Born energy with the local dielectric constant. This self energy is incorporated into the Poisson-Boltzmann equation as a simple means of including this local fluctuation effect in a mean-field theory. We illustrate the phenomenon of charge separation by considering cations and anions of difference sizes and valencies in a periodic dielectric medium.
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Affiliation(s)
- Zhen-Gang Wang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA.
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31
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Stenuit G, Castellarin-Cudia C, Plekan O, Feyer V, Prince KC, Goldoni A, Umari P. Valence electronic properties of porphyrin derivatives. Phys Chem Chem Phys 2010; 12:10812-7. [DOI: 10.1039/c004332j] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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32
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Abstract
For three molecules with weak or negligible charge overlap, we prove that the three-body interaction energy obtained from quantum perturbation theory (to leading order) fits a dielectric model with a nonlocal electronic screening function. The electronic charge cloud of each molecule acts as a dielectric medium for the interaction of the remaining two with the nonlocal dielectric function epsilon(r,r') obtained by O. S. Jenkins and K. L. C. Hunt [J. Chem. Phys. 119, 8250 (2003)], by considering the charge redistribution induced in a single molecule by an external perturbation. The dielectric function depends parametrically on the coordinates of the nuclei, within the Born-Oppenheimer approximation. We also prove that the force on each nucleus in molecule A depends on intramolecular dielectric screening within A. The potential from the charge distribution of B, screened by C acting as a dielectric medium, is further screened linearly within A; and similarly, with the roles of B and C reversed. In addition, the potential due to the unperturbed charge distribution of B and the potential due to the unperturbed charge distribution of C, acting simultaneously, are screened nonlinearly within A. The results show that nonlocal dielectric theory holds on the molecular level, provided that the overlap of the electronic charge distributions is weak.
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Affiliation(s)
- A Mandal
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
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33
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Qin P, Xu Z, Cai W, Jacobs D. Image Charge Methods for a Three-Dielectric-Layer Hybrid Solvation Model of Biomolecules. COMMUNICATIONS IN COMPUTATIONAL PHYSICS 2009; 6:955-977. [PMID: 20556225 PMCID: PMC2885744 DOI: 10.4208/cicp.2009.v6.p955] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
This paper introduces a three dielectric layer hybrid solvation model for treating electrostatic interactions of biomolecules in solvents using the Poisson-Boltzmann equation. In this model, an interior spherical cavity will contain the solute and some explicit solvent molecules, and an intermediate buffer layer and an exterior layer contain the bulk solvent. A special dielectric permittivity profile is used to achieve a continuous dielectric transition from the interior cavity to the exterior layer. The selection of this special profile using a harmonic interpolation allows an analytical solution of the model by generalizing the classical Kirkwood series expansion. Discrete image charges are used to speed up calculations for the electrostatic potential within the interior and buffer layer regions. Semi-analytical and least squares methods are used to construct an accurate discrete image approximation for the reaction field due to solvent with or without salt effects. In particular, the image charges obtained by the least squares method provide accurate approximations to the reaction field independent of the ionic concentration of the solvent. Numerical results are presented to validate the accuracy and effectiveness of the image charge methods.
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Affiliation(s)
- Peihua Qin
- Institute of Computational Mathematics, Chinese Academy of Sciences; Graduate University of Chinese Academy of Sciences, Beijing 100190, China
| | - Zhenli Xu
- Department of Mathematics and Statistics, University of North Carolina at Charlotte, Charlotte, NC 28223-0001, USA
| | - Wei Cai
- Department of Mathematics and Statistics, University of North Carolina at Charlotte, Charlotte, NC 28223-0001, USA
| | - Donald Jacobs
- Department of Physics and Optical Science, University of North Carolina at Charlotte, Charlotte, NC 28223-0001, USA
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34
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Botek E, Champagne B. Remarkable two-photon absorption in open-shell singlet systems. J Chem Phys 2009; 131:114316. [DOI: 10.1063/1.3225202] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
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35
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Koehl P, Orland H, Delarue M. Computing ion solvation free energies using the dipolar Poisson model. J Phys Chem B 2009; 113:5694-7. [PMID: 19385689 DOI: 10.1021/jp9010907] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A new continuum model is presented for computing the solvation free energies of cations in water. It combines in a single formalism based on statistical thermodynamics the Poisson model for electrostatics with the Langevin dipole model to account for nonuniform water dipole distribution around the ions. An excellent match between experimental and computed solvation free energies is obtained for 10 monovalent and divalent ions.
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36
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Fulton RL. The nonlinear dielectric behavior of water: Comparisons of various approaches to the nonlinear dielectric increment. J Chem Phys 2009; 130:204503. [DOI: 10.1063/1.3139211] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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37
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Gong H, Freed KF. Langevin-Debye model for nonlinear electrostatic screening of solvated ions. PHYSICAL REVIEW LETTERS 2009; 102:057603. [PMID: 19257555 DOI: 10.1103/physrevlett.102.057603] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2008] [Revised: 01/06/2009] [Indexed: 05/27/2023]
Abstract
Ion-ion interactions are central to numerous phenomena in geology, biology, and material science, but current understanding is based on linear theories of limited physical applicability. Using the Langevin-Debye model, we investigate how nonlinear dielectric saturation alters screening of electrostatic interactions between solvated charges and show that charge screening in liquids strongly depends on the charge magnitudes but negligibly on the ion radii. Qualitatively different universal screening functions are predicted for ions with charges of the same or opposite signs.
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Affiliation(s)
- Haipeng Gong
- The James Franck Institute, University of Chicago, Chicago, Illinois 60637, USA
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38
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Ma YP, He SG, Ding XL, Wang ZC, Xue W, Shi Q. Theoretical study of intermolecular interactions in meso-tetraphenylporphyrin diacid dimer (H4TPPCl2)2. Phys Chem Chem Phys 2009; 11:2543-52. [DOI: 10.1039/b815010a] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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39
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Baxa MC, Freed KF, Sosnick TR. Quantifying the structural requirements of the folding transition state of protein A and other systems. J Mol Biol 2008; 381:1362-81. [PMID: 18625237 PMCID: PMC2742318 DOI: 10.1016/j.jmb.2008.06.067] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2008] [Revised: 06/18/2008] [Accepted: 06/23/2008] [Indexed: 11/22/2022]
Abstract
The B-domain of protein A is a small three-helix bundle that has been the subject of considerable experimental and theoretical investigation. Nevertheless, a unified view of the structure of the transition-state ensemble (TSE) is still lacking. To characterize the TSE of this surprisingly challenging protein, we apply a combination of psi analysis (which probes the role of specific side-chain to side-chain contacts) and kinetic H/D amide isotope effects (which measures hydrogen-bond content), building upon previous studies using mutational phi analysis (which probes the energetic influence of side-chain substitutions). The second helix is folded in the TSE, while helix formation appears just at the carboxy and amino termini of the first and third helices, respectively. The experimental data suggest a homogenous yet plastic TS with a native-like topology. This study generalizes our earlier conclusion, based on two larger alpha/beta proteins, that the TSEs of most small proteins achieve approximately 70% of their native state's relative contact order. This high percentage limits the degree of possible TS heterogeneity and requires a reevaluation of the structural content of the TSE of other proteins, especially when they are characterized as small or polarized.
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Affiliation(s)
- Michael C. Baxa
- Department of Physics, University of Chicago, 929 E. 57th St., Chicago, IL 60637
- Institute for Biophysical Dynamics, University of Chicago, 929 E. 57th St., Chicago, IL 60637
| | - Karl F. Freed
- James Franck Institute and Department of Chemistry, University of Chicago, 929 E. 57th St., Chicago, IL 60637
| | - Tobin R. Sosnick
- Institute for Biophysical Dynamics, University of Chicago, 929 E. 57th St., Chicago, IL 60637
- Department of Biochemistry and Molecular Biology, University of Chicago, 929 E. 57th St., Chicago, IL 60637
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40
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Influence of nonlinear electrostatics on transfer energies between liquid phases: charge burial is far less expensive than Born model. Proc Natl Acad Sci U S A 2008; 105:11146-51. [PMID: 18678891 DOI: 10.1073/pnas.0804506105] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The widely used Born model describes the electrostatic response of continuous media using static dielectric constants. However, when applied to a liquid environment, a comparison of Born model predictions with experimental values (e.g., transfer free energies and pK(a) shifts) found that agreement is only achieved by using physically unrealistic dielectric constants for proteins, lipids, etc., and/or equally unrealistic atomic radii. This leads to questions concerning the physical origins for this failure of the Born model. We partially resolve this question by applying the Langevin-Debye (LD) model of a continuous distribution of point, polarizable dipoles, a model that contains an added dependence of the electrostatic response on the solvent's optical dielectric constant and both gas- and liquid-phase dipole moments, features absent in the Born model to which the LD model reduces for weak fields. The LD model is applied to simple representations of three biologically relevant systems: (i) globular proteins, (ii) lipid bilayers, and (iii) membrane proteins. The linear Born treatment greatly overestimates both the self-energy and the transfer free energy from water to hydrophobic environments (e.g., a protein interior). By using the experimental dielectric constant, the energy cost of charge burial in either globular or membrane proteins of the Born model is reduced by almost 50% with the nonlinear theory as is the pK(a) shift, and the shifts agree well with experimental trends.
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41
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Kent A, Jha AK, Fitzgerald JE, Freed KF. Benchmarking implicit solvent folding simulations of the amyloid beta(10-35) fragment. J Phys Chem B 2008; 112:6175-86. [PMID: 18348560 PMCID: PMC2719849 DOI: 10.1021/jp077099h] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A pathogenetic feature of Alzhemier disease is the aggregation of monomeric beta-amyloid proteins (Abeta) to form oligomers. Usually these oligomers of long peptides aggregate on time scales of microseconds or longer, making computational studies using atomistic molecular dynamics models prohibitively expensive and making it essential to develop computational models that are cheaper and at the same time faithful to physical features of the process. We benchmark the ability of our implicit solvent model to describe equilibrium and dynamic properties of monomeric Abeta(10-35) using all-atom Langevin dynamics (LD) simulations, since Alphabeta(10-35) is the only fragment whose monomeric properties have been measured. The accuracy of the implicit solvent model is tested by comparing its predictions with experiment and with those from a new explicit water MD simulation, (performed using CHARMM and the TIP3P water model) which is approximately 200 times slower than the implicit water simulations. The dependence on force field is investigated by running multiple trajectories for Alphabeta(10-35) using the CHARMM, OPLS-aal, and GS-AMBER94 force fields, whereas the convergence to equilibrium is tested for each force field by beginning separate trajectories from the native NMR structure, a completely stretched structure, and from unfolded initial structures. The NMR order parameter, S2, is computed for each trajectory and is compared with experimental data to assess the best choice for treating aggregates of Alphabeta. The computed order parameters vary significantly with force field. Explicit and implicit solvent simulations using the CHARMM force fields display excellent agreement with each other and once again support the accuracy of the implicit solvent model. Alphabeta(10-35) exhibits great flexibility, consistent with experiment data for the monomer in solution, while maintaining a general strand-loop-strand motif with a solvent-exposed hydrophobic patch that is believed to be important for aggregation. Finally, equilibration of the peptide structure requires an implicit solvent LD simulation as long as 30 ns.
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Affiliation(s)
- Andrew Kent
- Department of Chemistry, The University of Chicago, Chicago, IL 60637
- The James Franck Institute, The University of Chicago, Chicago, IL 60637
| | - Abhishek K Jha
- Department of Chemistry, The University of Chicago, Chicago, IL 60637
- Institute of Biophysical Dynamics, The University of Chicago, Chicago, IL 60637
- The James Franck Institute, The University of Chicago, Chicago, IL 60637
| | - James E Fitzgerald
- Institute of Biophysical Dynamics, The University of Chicago, Chicago, IL 60637
- Department of Mathematics, The University of Chicago, Chicago, IL 60637
- Department of Physics, The University of Chicago, Chicago, IL 60637
| | - Karl F Freed
- Department of Chemistry, The University of Chicago, Chicago, IL 60637
- The James Franck Institute, The University of Chicago, Chicago, IL 60637
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