51
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Socher E, Sticht H. Probing the Structure of the Escherichia coli Periplasmic Proteins HdeA and YmgD by Molecular Dynamics Simulations. J Phys Chem B 2016; 120:11845-11855. [PMID: 27787971 DOI: 10.1021/acs.jpcb.6b06091] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
HdeA and YmgD are structurally homologous proteins in the periplasm of Escherichia coli. HdeA has been shown to represent an acid-activated chaperone, whereas the function of YmgD has not yet been characterized. We performed pH-titrating molecular dynamics simulations (pHtMD) to investigate the structural changes of both proteins and to assess whether YmgD may also exhibit an unfolding behavior similar to that of HdeA. The unfolding pathway of HdeA includes partially unfolded dimer structures, which represent a prerequisite for subsequent dissociation. In contrast to the coupled unfolding and dissociation of HdeA, YmgD displays dissociation of the folded subunits, and the subunits do not undergo significant unfolding even at low pH values. The differences in subunit stability between HdeA and YmgD may be explained by the structural features of helix D, which represents the starting point of unfolding in HdeA. In summary, the present study suggests that YmgD either is not an acid-activated chaperone or, at least, does not require unfolding for activation.
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Affiliation(s)
- Eileen Socher
- Division of Bioinformatics, Institute of Biochemistry, Friedrich-Alexander-University Erlangen-Nürnberg (FAU) , Fahrstraße 17, 91054 Erlangen, Germany
| | - Heinrich Sticht
- Division of Bioinformatics, Institute of Biochemistry, Friedrich-Alexander-University Erlangen-Nürnberg (FAU) , Fahrstraße 17, 91054 Erlangen, Germany
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52
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Giard A, Filhol JS, Jolibois F, Cavelier F, Berthomieu D. Prediction of pKa Using DFT: the Nicotianamine Polyacid Example. J Chem Theory Comput 2016; 12:5493-5500. [DOI: 10.1021/acs.jctc.6b00404] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Aude Giard
- Institut Charles
Gerhardt, MACS, UMR 5253 CNRS-ENSCM-UM, 8, rue de l’Ecole Normale, 34296 Montpellier cedex 5, France
| | - Jean-Sébastien Filhol
- Institut Charles
Gerhardt, CTMM, UMR 5253 CNRS-ENSCM-UM, Place Eugène Bataillon, 34296 Montpellier cedex 5, France
| | - Franck Jolibois
- LPCNO, UMR 5215
CNRS-INSA-UPS, 135 avenue de Rangueil 31077 Toulouse Cedex 4, France
| | - Florine Cavelier
- Institut des Biomolécules
Max Mousseron UMR 5247, CNRS -ENSCM-UM Place Eugène Bataillon, 34095 Montpellier cedex 5, France
| | - Dorothée Berthomieu
- Institut Charles
Gerhardt, MACS, UMR 5253 CNRS-ENSCM-UM, 8, rue de l’Ecole Normale, 34296 Montpellier cedex 5, France
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53
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Huang Y, Chen W, Wallace JA, Shen J. All-Atom Continuous Constant pH Molecular Dynamics With Particle Mesh Ewald and Titratable Water. J Chem Theory Comput 2016; 12:5411-5421. [PMID: 27709966 DOI: 10.1021/acs.jctc.6b00552] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Development of a pH stat to properly control solution pH in biomolecular simulations has been a long-standing goal in the community. Toward this goal recent years have witnessed the emergence of the so-called constant pH molecular dynamics methods. However, the accuracy and generality of these methods have been hampered by the use of implicit-solvent models or truncation-based electrostatic schemes. Here we report the implementation of the particle mesh Ewald (PME) scheme into the all-atom continuous constant pH molecular dynamics (CpHMD) method, enabling CpHMD to be performed with a standard MD engine at a fractional added computational cost. We demonstrate the performance using pH replica-exchange CpHMD simulations with titratable water for a stringent test set of proteins, HP36, BBL, HEWL, and SNase. With the sampling time of 10 ns per replica, most pKa's are converged, yielding the average absolute and root-mean-square deviations of 0.61 and 0.77, respectively, from experiment. Linear regression of the calculated vs experimental pKa shifts gives a correlation coefficient of 0.79, a slope of 1, and an intercept near 0. Analysis reveals inadequate sampling of structure relaxation accompanying a protonation-state switch as a major source of the remaining errors, which are reduced as simulation prolongs. These data suggest PME-based CpHMD can be used as a general tool for pH-controlled simulations of macromolecular systems in various environments, enabling atomic insights into pH-dependent phenomena involving not only soluble proteins but also transmembrane proteins, nucleic acids, surfactants, and polysaccharides.
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Affiliation(s)
- Yandong Huang
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy , Baltimore, Maryland 21201, United States
| | - Wei Chen
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy , Baltimore, Maryland 21201, United States
| | - Jason A Wallace
- University of Oklahoma College of Dentistry , Oklahoma City, Oklahoma 73117, United States
| | - Jana Shen
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy , Baltimore, Maryland 21201, United States
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54
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Kim E, Liu Y, Ben-Yoav H, Winkler TE, Yan K, Shi X, Shen J, Kelly DL, Ghodssi R, Bentley WE, Payne GF. Fusing Sensor Paradigms to Acquire Chemical Information: An Integrative Role for Smart Biopolymeric Hydrogels. Adv Healthc Mater 2016; 5:2595-2616. [PMID: 27616350 PMCID: PMC5485850 DOI: 10.1002/adhm.201600516] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 06/26/2016] [Indexed: 12/14/2022]
Abstract
The Information Age transformed our lives but it has had surprisingly little impact on the way chemical information (e.g., from our biological world) is acquired, analyzed and communicated. Sensor systems are poised to change this situation by providing rapid access to chemical information. This access will be enabled by technological advances from various fields: biology enables the synthesis, design and discovery of molecular recognition elements as well as the generation of cell-based signal processors; physics and chemistry are providing nano-components that facilitate the transmission and transduction of signals rich with chemical information; microfabrication is yielding sensors capable of receiving these signals through various modalities; and signal processing analysis enhances the extraction of chemical information. The authors contend that integral to the development of functional sensor systems will be materials that (i) enable the integrative and hierarchical assembly of various sensing components (for chemical recognition and signal transduction) and (ii) facilitate meaningful communication across modalities. It is suggested that stimuli-responsive self-assembling biopolymers can perform such integrative functions, and redox provides modality-spanning communication capabilities. Recent progress toward the development of electrochemical sensors to manage schizophrenia is used to illustrate the opportunities and challenges for enlisting sensors for chemical information processing.
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Affiliation(s)
- Eunkyoung Kim
- Institute for Biosystems and Biotechnology Research, University of Maryland, College Park, MD, 20742, USA
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, 20742, USA
| | - Yi Liu
- Institute for Biosystems and Biotechnology Research, University of Maryland, College Park, MD, 20742, USA
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, 20742, USA
| | - Hadar Ben-Yoav
- Department of Biomedical Engineering, Ben-Gurion University of the Negev, Beer Sheva, 8410501, Israel
| | - Thomas E Winkler
- Institute for Systems Research, University of Maryland, College Park, MD, 20742, USA
- Department of Electrical and Computer Engineering, University of Maryland, College Park, MD, 20742, USA
| | - Kun Yan
- School of Resource and Environmental Science, Hubei Biomass-Resource Chemistry Environmental Biotechnology Key Laboratory, Wuhan University, Wuhan, 430079, China
| | - Xiaowen Shi
- School of Resource and Environmental Science, Hubei Biomass-Resource Chemistry Environmental Biotechnology Key Laboratory, Wuhan University, Wuhan, 430079, China
| | - Jana Shen
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD, 21201, USA
| | - Deanna L Kelly
- Maryland Psychiatric Research Center, University of Maryland School of Medicine, Baltimore, MD, 21228, USA
| | - Reza Ghodssi
- Institute for Systems Research, University of Maryland, College Park, MD, 20742, USA
- Department of Electrical and Computer Engineering, University of Maryland, College Park, MD, 20742, USA
| | - William E Bentley
- Institute for Biosystems and Biotechnology Research, University of Maryland, College Park, MD, 20742, USA
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, 20742, USA
| | - Gregory F Payne
- Institute for Biosystems and Biotechnology Research, University of Maryland, College Park, MD, 20742, USA.
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, 20742, USA.
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55
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Schimka S, Santer S, Mujkić-Ninnemann NM, Bléger D, Hartmann L, Wehle M, Lipowsky R, Santer M. Photosensitive Peptidomimetic for Light-Controlled, Reversible DNA Compaction. Biomacromolecules 2016; 17:1959-68. [DOI: 10.1021/acs.biomac.6b00052] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Selina Schimka
- Institute
of Physics and Astronomy, University of Potsdam, 14476 Potsdam, Germany
- Max Planck Institute
of Colloids and Interfaces, 14424 Potsdam, Germany
| | - Svetlana Santer
- Institute
of Physics and Astronomy, University of Potsdam, 14476 Potsdam, Germany
| | | | - David Bléger
- Humboldt-Universität
zu Berlin, 12489 Berlin, Germany
| | - Laura Hartmann
- Max Planck Institute
of Colloids and Interfaces, 14424 Potsdam, Germany
| | - Marko Wehle
- Theory
and Bio-Systems Group, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany
| | - Reinhard Lipowsky
- Theory
and Bio-Systems Group, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany
| | - Mark Santer
- Theory
and Bio-Systems Group, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany
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56
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Ellis CR, Tsai CC, Hou X, Shen J. Constant pH Molecular Dynamics Reveals pH-Modulated Binding of Two Small-Molecule BACE1 Inhibitors. J Phys Chem Lett 2016; 7:944-9. [PMID: 26905811 PMCID: PMC5713896 DOI: 10.1021/acs.jpclett.6b00137] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Targeting β-secretase (BACE1) with small-molecule inhibitors offers a promising route for treatment of Alzheimer's disease. However, the intricate pH dependence of BACE1 function and inhibitor efficacy has posed major challenges for structure-based drug design. Here we investigate two structurally similar BACE1 inhibitors that have dramatically different inhibitory activity using continuous constant pH molecular dynamics (CpHMD). At high pH, both inhibitors are stably bound to BACE1; however, within the enzyme active pH range, only the iminopyrimidinone-based inhibitor remains bound, while the aminothiazine-based inhibitor becomes partially dissociated following the loss of hydrogen bonding with the active site and change of the 10s loop conformation. The drastically lower activity of the second inhibitor is due to the protonation of a catalytic aspartate and the lack of a propyne tail. This work demonstrates that CpHMD can be used for screening pH-dependent binding profiles of small-molecule inhibitors, providing a new tool for structure-based drug design and optimization.
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Affiliation(s)
- Christopher R. Ellis
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD
| | - Cheng-Chieh Tsai
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD
| | - Xinjun Hou
- Neuroscience Worldwide Medicinal Chemistry, Pfizer Worldwide Research and Development, Cambridge, MA
| | - Jana Shen
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD
- Corresponding Author:
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57
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Donnini S, Ullmann RT, Groenhof G, Grubmüller H. Charge-Neutral Constant pH Molecular Dynamics Simulations Using a Parsimonious Proton Buffer. J Chem Theory Comput 2016; 12:1040-51. [PMID: 26881315 DOI: 10.1021/acs.jctc.5b01160] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In constant pH molecular dynamics simulations, the protonation states of titratable sites can respond to changes of the pH and of their electrostatic environment. Consequently, the number of protons bound to the biomolecule, and therefore the overall charge of the system, fluctuates during the simulation. To avoid artifacts associated with a non-neutral simulation system, we introduce an approach to maintain neutrality of the simulation box in constant pH molecular dynamics simulations, while maintaining an accurate description of all protonation fluctuations. Specifically, we introduce a proton buffer that, like a buffer in experiment, can exchange protons with the biomolecule enabling its charge to fluctuate. To keep the total charge of the system constant, the uptake and release of protons by the buffer are coupled to the titration of the biomolecule with a constraint. We find that, because the fluctuation of the total charge (number of protons) of a typical biomolecule is much smaller than the number of titratable sites of the biomolecule, the number of buffer sites required to maintain overall charge neutrality without compromising the charge fluctuations of the biomolecule, is typically much smaller than the number of titratable sites, implying markedly enhanced simulation and sampling efficiency.
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Affiliation(s)
- Serena Donnini
- Nanoscience Center and Department of Biological and Environmental Sciences, University of Jyväskylä , P. O. Box 35, 40014 Jyväskylä, Finland
| | - R Thomas Ullmann
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry , Am Faßberg 11, 37077 Göttingen, Germany
| | - Gerrit Groenhof
- Nanoscience Center and Department of Chemistry, University of Jyväskylä , P. O. Box 35, 40014 Jyväskylä, Finland
| | - Helmut Grubmüller
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry , Am Faßberg 11, 37077 Göttingen, Germany
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58
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Davis CM, Dyer RB. The Role of Electrostatic Interactions in Folding of β-Proteins. J Am Chem Soc 2016; 138:1456-64. [PMID: 26750867 DOI: 10.1021/jacs.5b13201] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Atomic-level molecular dynamic simulations are capable of fully folding structurally diverse proteins; however, they are limited in their ability to accurately represent electrostatic interactions. Here we have experimentally tested the role of charged residues on stability and folding kinetics of one of the most widely simulated β-proteins, the WW domain. The folding of wild type Pin1 WW domain, which has two positively charged residues in the first turn, was compared to the fast folding mutant FiP35 Pin1, which introduces a negative charge into the first turn. A combination of FTIR spectroscopy and laser-induced temperature-jump coupled with infrared spectroscopy was used to probe changes in the amide I region. The relaxation dynamics of the peptide backbone, β-sheets and β-turns, and negatively charged aspartic acid side chain of FiP35 were measured independently by probing the corresponding bands assigned in the amide I region. Folding is initiated in the turns and the β-sheets form last. While the global folding mechanism is in good agreement with simulation predictions, we observe changes in the protonation state of aspartic acid during folding that have not been captured by simulation methods. The protonation state of aspartic acid is coupled to protein folding; the apparent pKa of aspartic acid in the folded protein is 6.4. The dynamics of the aspartic acid follow the dynamics of the intermediate phase, supporting assignment of this phase to formation of the first hairpin. These results demonstrate the importance of electrostatic interactions in turn stability and formation of extended β-sheet structures.
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Affiliation(s)
- Caitlin M Davis
- Department of Chemistry, Emory University , Atlanta, Georgia 30322, United States
| | - R Brian Dyer
- Department of Chemistry, Emory University , Atlanta, Georgia 30322, United States
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59
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Morrow BH, Eike DM, Murch BP, Koenig PH, Shen JK. Predicting proton titration in cationic micelle and bilayer environments. J Chem Phys 2015; 141:084714. [PMID: 25173037 DOI: 10.1063/1.4893439] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Knowledge of the protonation behavior of pH-sensitive molecules in micelles and bilayers has significant implications in consumer product development and biomedical applications. However, the calculation of pKa's in such environments proves challenging using traditional structure-based calculations. Here we apply all-atom constant pH molecular dynamics with explicit ions and titratable water to calculate the pKa of a fatty acid molecule in a micelle of dodecyl trimethylammonium chloride and liquid as well as gel-phase bilayers of diethyl ester dimethylammonium chloride. Interestingly, the pKa of the fatty acid in the gel bilayer is 5.4, 0.4 units lower than that in the analogous liquid bilayer or micelle, despite the fact that the protonated carboxylic group is significantly more desolvated in the gel bilayer. This work illustrates the capability of all-atom constant pH molecular dynamics in capturing the delicate balance in the free energies of desolvation and Coulombic interactions. It also shows the importance of the explicit treatment of ions in sampling the protonation states. The ability to model dynamics of pH-responsive substrates in a bilayer environment is useful for improving fabric care products as well as our understanding of the side effects of anti-inflammatory drugs.
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Affiliation(s)
- Brian H Morrow
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201, USA
| | - David M Eike
- Computational Chemistry, Modeling and Simulation GCO, Procter and Gamble, Cincinnati, Ohio 45201, USA
| | - Bruce P Murch
- Computational Chemistry, Modeling and Simulation GCO, Procter and Gamble, Cincinnati, Ohio 45201, USA
| | - Peter H Koenig
- Computational Chemistry, Modeling and Simulation GCO, Procter and Gamble, Cincinnati, Ohio 45201, USA
| | - Jana K Shen
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201, USA
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60
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Morrow BH, Payne GF, Shen J. pH-Responsive Self-Assembly of Polysaccharide through a Rugged Energy Landscape. J Am Chem Soc 2015; 137:13024-30. [PMID: 26383701 DOI: 10.1021/jacs.5b07761] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Self-assembling polysaccharides can form complex networks with structures and properties highly dependent on the sequence of triggering cues. Controlling the emergence of such networks provides an opportunity to create soft matter with unique features; however, it requires a detailed understanding of the subtle balance between the attractive and repulsive forces that drives the stimuli-induced self-assembly. Here we employ all-atom molecular dynamics simulations on the order of 100 ns to study the mechanisms of the pH-responsive gelation of the weakly basic aminopolysaccharide chitosan. We find that low pH induces a sharp transition from gel to soluble state, analogous to pH-dependent folding of proteins, while at neutral and high pH self-assembly occurs via a rugged energy landscape, reminiscent of RNA folding. A surprising role of salt is to lubricate the conformational search for the thermodynamically stable states. Although our simulations represent the early events in the self-assembly process of chitosan, which may take seconds or minutes to complete, the atomically detailed insights are consistent with recent experimental observations and provide a basis for understanding how environmental conditions modulate the structure and mechanical properties of the self-assembled polysaccharide systems. The ability to control structure and properties via modification of process conditions will aid in the technological efforts to create complex soft matter with applications ranging from bioelectronics to regenerative medicine.
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Affiliation(s)
- Brian H Morrow
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland , Baltimore, Maryland 21201, United States
| | - Gregory F Payne
- Fischell Department of Bioengineering and Institute for Biosystems and Biotechnology Research, University of Maryland , College Park, Maryland 20742, United States
| | - Jana Shen
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland , Baltimore, Maryland 21201, United States
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61
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Lee J, Miller BT, Damjanović A, Brooks BR. Enhancing constant-pH simulation in explicit solvent with a two-dimensional replica exchange method. J Chem Theory Comput 2015; 11:2560-74. [PMID: 26575555 DOI: 10.1021/ct501101f] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We present a new method for enhanced sampling for constant-pH simulations in explicit water based on a two-dimensional (2D) replica exchange scheme. The new method is a significant extension of our previously developed constant-pH simulation method, which is based on enveloping distribution sampling (EDS) coupled with a one-dimensional (1D) Hamiltonian exchange method (HREM). EDS constructs a hybrid Hamiltonian from multiple discrete end state Hamiltonians that, in this case, represent different protonation states of the system. The ruggedness and heights of the hybrid Hamiltonian's energy barriers can be tuned by the smoothness parameter. Within the context of the 1D EDS-HREM method, exchanges are performed between replicas with different smoothness parameters, allowing frequent protonation-state transitions and sampling of conformations that are favored by the end-state Hamiltonians. In this work, the 1D method is extended to 2D with an additional dimension, external pH. Within the context of the 2D method (2D EDS-HREM), exchanges are performed on a lattice of Hamiltonians with different pH conditions and smoothness parameters. We demonstrate that both the 1D and 2D methods exactly reproduce the thermodynamic properties of the semigrand canonical (SGC) ensemble of a system at a given pH. We have tested our new 2D method on aspartic acid, glutamic acid, lysine, a four residue peptide (sequence KAAE), and snake cardiotoxin. In all cases, the 2D method converges faster and without loss of precision; the only limitation is a loss of flexibility in how CPU time is employed. The results for snake cardiotoxin demonstrate that the 2D method enhances protonation-state transitions, samples a wider conformational space with the same amount of computational resources, and converges significantly faster overall than the original 1D method.
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Affiliation(s)
- Juyong Lee
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - Benjamin T Miller
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - Ana Damjanović
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland 20892, United States.,Department of Biophysics, Johns Hopkins University , Baltimore, Maryland 21218, United States
| | - Bernard R Brooks
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland 20892, United States
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62
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Vila-Viçosa D, Teixeira VH, Baptista AM, Machuqueiro M. Constant-pH MD Simulations of an Oleic Acid Bilayer. J Chem Theory Comput 2015; 11:2367-76. [DOI: 10.1021/acs.jctc.5b00095] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Diogo Vila-Viçosa
- Centro
de Química e Bioquímica and Departamento de Química
e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Edifı́cio C8 Campo Grande, 1749-016 Lisboa, Portugal
| | - Vitor H. Teixeira
- Centro
de Química e Bioquímica and Departamento de Química
e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Edifı́cio C8 Campo Grande, 1749-016 Lisboa, Portugal
| | - António M. Baptista
- Instituto
de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Miguel Machuqueiro
- Centro
de Química e Bioquímica and Departamento de Química
e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Edifı́cio C8 Campo Grande, 1749-016 Lisboa, Portugal
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63
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Protein flexibility and cysteine reactivity: influence of mobility on the H-bond network and effects on pKa prediction. Protein J 2015; 33:323-36. [PMID: 24809821 DOI: 10.1007/s10930-014-9564-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Thanks to its chemical plasticity, cysteine (Cys) is a very versatile player in proteins. A major determinant of Cys reactivity is pKa: the ability to predict it is deemed critical in redox bioinformatics. I considered different computational methods for pKa predictions and ultimately applied one (propka, ppka1) to various datasets; for all residues I assessed the effect of (1) hydrogen bonding, electrostatics and solvation on predictions and (2) protein mobility on pKa variability. Particularly for Cys, exposure and H-bond contributions heavily dictated propka predictions. The prominence of H-bond contributions was previously reported: this may explain the effectiveness of ppka1 (with Cys, tested in a benchmark). However ppka1 was also very sensitive to protein mobility; I assessed the effects of mobility on particularly large (compared to previous studies) datasets of structural ensembles; I found that exposed Cys presented the highest pKa variability, ascribable to correspondingly high H-bond fluctuations associated with protein flexibility. The benefit of including protein dynamics in pKa predictions was previously proposed, but empirical methods were never tested in this sense; instead, giving their outstanding speed, they could lend particularly well to this purpose. I devised a strategy combining short range molecular dynamics with ppka1; the protocol aimed to mitigate high ppka1 variability by including a "statistical view" of fast conformational changes. Tested in a benchmark, the strategy lead to improved performances. These results provide new insights on Cys bioinformatics (pKa prediction protocols) and Cys biology (effect of mobility on exposed Cys properties).
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64
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Dissanayake T, Swails JM, Harris ME, Roitberg AE, York DM. Interpretation of pH-activity profiles for acid-base catalysis from molecular simulations. Biochemistry 2015; 54:1307-13. [PMID: 25615525 DOI: 10.1021/bi5012833] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The measurement of reaction rate as a function of pH provides essential information about mechanism. These rates are sensitive to the pK(a) values of amino acids directly involved in catalysis that are often shifted by the enzyme active site environment. Experimentally observed pH-rate profiles are usually interpreted using simple kinetic models that allow estimation of "apparent pK(a)" values of presumed general acid and base catalysts. One of the underlying assumptions in these models is that the protonation states are uncorrelated. In this work, we introduce the use of constant pH molecular dynamics simulations in explicit solvent (CpHMD) with replica exchange in the pH-dimension (pH-REMD) as a tool to aid in the interpretation of pH-activity data of enzymes and to test the validity of different kinetic models. We apply the methods to RNase A, a prototype acid-base catalyst, to predict the macroscopic and microscopic pK(a) values, as well as the shape of the pH-rate profile. Results for apo and cCMP-bound RNase A agree well with available experimental data and suggest that deprotonation of the general acid and protonation of the general base are not strongly coupled in transphosphorylation and hydrolysis steps. Stronger coupling, however, is predicted for the Lys41 and His119 protonation states in apo RNase A, leading to the requirement for a microscopic kinetic model. This type of analysis may be important for other catalytic systems where the active forms of the implicated general acid and base are oppositely charged and more highly correlated. These results suggest a new way for CpHMD/pH-REMD simulations to bridge the gap with experiments to provide a molecular-level interpretation of pH-activity data in studies of enzyme mechanisms.
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Affiliation(s)
- Thakshila Dissanayake
- Center for Integrative Proteomics Research, BioMaPS Institute, and Department of Chemistry & Chemical Biology, Rutgers University , 174 Frelinghuysen Road, Piscataway, New Jersey 08854-8076, United States
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65
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Reif MM, Oostenbrink C. Toward the correction of effective electrostatic forces in explicit-solvent molecular dynamics simulations: restraints on solvent-generated electrostatic potential and solvent polarization. Theor Chem Acc 2015; 134:2. [PMID: 26097404 PMCID: PMC4470580 DOI: 10.1007/s00214-014-1600-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 11/19/2014] [Indexed: 11/26/2022]
Abstract
Despite considerable advances in computing power, atomistic simulations under nonperiodic boundary conditions, with Coulombic electrostatic interactions and in systems large enough to reduce finite-size associated errors in thermodynamic quantities to within the thermal energy, are still not affordable. As a result, periodic boundary conditions, systems of microscopic size and effective electrostatic interaction functions are frequently resorted to. Ensuing artifacts in thermodynamic quantities are nowadays routinely corrected a posteriori, but the underlying configurational sampling still descends from spurious forces. The present study addresses this problem through the introduction of on-the-fly corrections to the physical forces during an atomistic molecular dynamics simulation. Two different approaches are suggested, where the force corrections are derived from special potential energy terms. In the first approach, the solvent-generated electrostatic potential sampled at a given atom site is restrained to a target value involving corrections for electrostatic artifacts. In the second approach, the long-range regime of the solvent polarization around a given atom site is restrained to the Born polarization, i.e., the solvent polarization corresponding to the ideal situation of a macroscopic system under nonperiodic boundary conditions and governed by Coulombic electrostatic interactions. The restraints are applied to the explicit-water simulation of a hydrated sodium ion, and the effect of the restraints on the structural and energetic properties of the solvent is illustrated. Furthermore, by means of the calculation of the charging free energy of a hydrated sodium ion, it is shown how the electrostatic potential restraint translates into the on-the-fly consideration of the corresponding free-energy correction terms. It is discussed how the restraints can be generalized to situations involving several solute particles. Although the present study considers a very simple system only, it is an important step toward the on-the-fly elimination of finite-size and approximate-electrostatic artifacts during atomistic molecular dynamics simulations.
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Affiliation(s)
- Maria M. Reif
- Institute for Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190 Vienna, Austria
| | - Chris Oostenbrink
- Institute for Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190 Vienna, Austria
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66
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Vila-Viçosa D, Teixeira VH, Santos HAF, Baptista AM, Machuqueiro M. Treatment of Ionic Strength in Biomolecular Simulations of Charged Lipid Bilayers. J Chem Theory Comput 2014; 10:5483-92. [DOI: 10.1021/ct500680q] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Diogo Vila-Viçosa
- Centro
de Química e Bioquímica and Departamento de Química
e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Vitor H. Teixeira
- Centro
de Química e Bioquímica and Departamento de Química
e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Hugo A. F. Santos
- Faculty
of Sciences, BioFIG−Centre for Biodiversity, Functional and
Integrative Genomics, University of Lisboa, 1649-004 Lisboa, Portugal
| | - António M. Baptista
- Instituto
de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Miguel Machuqueiro
- Centro
de Química e Bioquímica and Departamento de Química
e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
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67
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Chen W, Shen JK. Effects of system net charge and electrostatic truncation on all-atom constant pH molecular dynamics. J Comput Chem 2014; 35:1986-96. [PMID: 25142416 PMCID: PMC4165709 DOI: 10.1002/jcc.23713] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 07/20/2014] [Accepted: 08/03/2014] [Indexed: 12/21/2022]
Abstract
Constant pH molecular dynamics offers a means to rigorously study the effects of solution pH on dynamical processes. Here, we address two critical questions arising from the most recent developments of the all-atom continuous constant pH molecular dynamics (CpHMD) method: (1) What is the effect of spatial electrostatic truncation on the sampling of protonation states? (2) Is the enforcement of electrical neutrality necessary for constant pH simulations? We first examined how the generalized reaction field and force-shifting schemes modify the electrostatic forces on the titration coordinates. Free energy simulations of model compounds were then carried out to delineate the errors in the deprotonation free energy and salt-bridge stability due to electrostatic truncation and system net charge. Finally, CpHMD titration of a mini-protein HP36 was used to understand the manifestation of the two types of errors in the calculated pK(a) values. The major finding is that enforcing charge neutrality under all pH conditions and at all time via cotitrating ions significantly improves the accuracy of protonation-state sampling. We suggest that such finding is also relevant for simulations with particle mesh Ewald, considering the known artifacts due to charge-compensating background plasma.
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Affiliation(s)
- Wei Chen
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201
| | - Jana K. Shen
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201
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68
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Cote Y, Fu IW, Dobson ET, Goldberger JE, Nguyen HD, Shen JK. Mechanism of the pH-Controlled Self-Assembly of Nanofibers from Peptide Amphiphiles. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2014; 118:16272-16278. [PMID: 25089166 PMCID: PMC4111372 DOI: 10.1021/jp5048024] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Revised: 06/27/2014] [Indexed: 05/23/2023]
Abstract
Stimuli-responsive, self-assembling nanomaterials hold a great promise to revolutionize medicine and technology. However, current discovery is slow and often serendipitous. Here we report a multiscale modeling study to elucidate the pH-controlled self-assembly of nanofibers from the peptide amphiphiles, palmitoyl-I-A3E4-NH2. The coarse-grained simulations revealed the formation of random-coil based spherical micelles at strong electrostatic repulsion. However, at weak or no electrostatic repulsion, the micelles merge into a nanofiber driven by the β-sheet formation between the peptide segments. The all-atom constant pH molecular dynamics revealed a cooperative transition between random coil and β-sheet in the pH range 6-7, matching the CD data. Interestingly, although the bulk pKa is more than one unit below the transition pH, consistent with the titration data, the highest pKa's coincide with the transition pH, suggesting that the latter may be tuned by modulating the pKa's of a few solvent-buried Glu side chains. Together, these data offer, to our best knowledge, the first multiresolution and quantitative view of the pH-dependent self-assembly of nanofibers. The novel protocols and insights gained are expected to advance the computer-aided design and discovery of pH-responsive nanomaterials.
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Affiliation(s)
- Yoann Cote
- The Institute of Genetics and Molecular and Cellular
Biology, 67404 Illkirch Cedex, France
| | - Iris W. Fu
- Department
of Chemical Engineering and Materials Science, The Henry Samueli School
of Engineering, University of California, Irvine, California 92697, United States
| | - Eric T. Dobson
- Department of Chemistry, Ohio State University, Columbus, Ohio 43210, United States
| | - Joshua E. Goldberger
- Department of Chemistry, Ohio State University, Columbus, Ohio 43210, United States
| | - Hung D. Nguyen
- Department
of Chemical Engineering and Materials Science, The Henry Samueli School
of Engineering, University of California, Irvine, California 92697, United States
| | - Jana K. Shen
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, United States
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69
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Lee J, Miller BT, Damjanović A, Brooks BR. Constant pH Molecular Dynamics in Explicit Solvent with Enveloping Distribution Sampling and Hamiltonian Exchange. J Chem Theory Comput 2014; 10:2738-2750. [PMID: 25061443 PMCID: PMC4095908 DOI: 10.1021/ct500175m] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Indexed: 12/21/2022]
Abstract
We present a new computational approach for constant pH simulations in explicit solvent based on the combination of the enveloping distribution sampling (EDS) and Hamiltonian replica exchange (HREX) methods. Unlike constant pH methods based on variable and continuous charge models, our method is based on discrete protonation states. EDS generates a hybrid Hamiltonian of different protonation states. A smoothness parameter s is used to control the heights of energy barriers of the hybrid-state energy landscape. A small s value facilitates state transitions by lowering energy barriers. Replica exchange between EDS potentials with different s values allows us to readily obtain a thermodynamically accurate ensemble of multiple protonation states with frequent state transitions. The analysis is performed with an ensemble obtained from an EDS Hamiltonian without smoothing, s = ∞, which strictly follows the minimum energy surface of the end states. The accuracy and efficiency of this method is tested on aspartic acid, lysine, and glutamic acid, which have two protonation states, a histidine with three states, a four-residue peptide with four states, and snake cardiotoxin with eight states. The pKa values estimated with the EDS-HREX method agree well with the experimental pKa values. The mean absolute errors of small benchmark systems range from 0.03 to 0.17 pKa units, and those of three titratable groups of snake cardiotoxin range from 0.2 to 1.6 pKa units. This study demonstrates that EDS-HREX is a potent theoretical framework, which gives the correct description of multiple protonation states and good calculated pKa values.
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Affiliation(s)
- Juyong Lee
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - Benjamin T Miller
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - Ana Damjanović
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland 20892, United States ; Department of Biophysics, Johns Hopkins University , Baltimore, Maryland, United States
| | - Bernard R Brooks
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland 20892, United States
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70
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Chen W, Morrow BH, Shi C, Shen JK. Recent development and application of constant pH molecular dynamics. MOLECULAR SIMULATION 2014; 40:830-838. [PMID: 25309035 DOI: 10.1080/08927022.2014.907492] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Solution pH is a critical environmental factor for chemical and biological processes. Over the last decade, significant efforts have been made in the development of constant pH molecular dynamics (pHMD) techniques for gaining detailed insights into pH-coupled dynamical phenomena. In this article we review the advancement of this field in the past five years, placing a special emphasis on the development of the all-atom continuous pHMD technique. We discuss various applications, including the prediction of pKa shifts for proteins, nucleic acids and surfactant assemblies, elucidation of pH-dependent population shifts, protein-protein and protein-RNA binding, as well as the mechanisms of pH-dependent self-assembly and phase transitions of surfactants and peptides. We also discuss future directions for the further improvement of the pHMD techniques.
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Affiliation(s)
- Wei Chen
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201, USA
| | - Brian H Morrow
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201, USA
| | - Chuanyin Shi
- Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, China
| | - Jana K Shen
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201, USA
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71
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Chen W, Wallace JA, Yue Z, Shen JK. Introducing titratable water to all-atom molecular dynamics at constant pH. Biophys J 2014; 105:L15-7. [PMID: 23972860 DOI: 10.1016/j.bpj.2013.06.036] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2013] [Revised: 06/06/2013] [Accepted: 06/25/2013] [Indexed: 11/25/2022] Open
Abstract
Recent development of titratable coions has paved the way for realizing all-atom molecular dynamics at constant pH. To further improve physical realism, here we describe a technique in which proton titration of the solute is directly coupled to the interconversion between water and hydroxide or hydronium. We test the new method in replica-exchange continuous constant pH molecular dynamics simulations of three proteins, HP36, BBL, and HEWL. The calculated pKa values based on 10-ns sampling per replica have the average absolute and root-mean-square errors of 0.7 and 0.9 pH units, respectively. Introducing titratable water in molecular dynamics offers a means to model proton exchange between solute and solvent, thus opening a door to gaining new insights into the intricate details of biological phenomena involving proton translocation.
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72
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Swails JM, York DM, Roitberg AE. Constant pH Replica Exchange Molecular Dynamics in Explicit Solvent Using Discrete Protonation States: Implementation, Testing, and Validation. J Chem Theory Comput 2014; 10:1341-1352. [PMID: 24803862 PMCID: PMC3985686 DOI: 10.1021/ct401042b] [Citation(s) in RCA: 176] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Indexed: 12/24/2022]
Abstract
![]()
By
utilizing Graphics Processing Units, we show that constant pH
molecular dynamics simulations (CpHMD) run in Generalized Born (GB)
implicit solvent for long time scales can yield poor pKa predictions as a result of sampling unrealistic conformations.
To address this shortcoming, we present a method for performing constant
pH molecular dynamics simulations (CpHMD) in explicit solvent using
a
discrete protonation state model. The method involves standard molecular
dynamics (MD) being propagated in explicit solvent followed by protonation
state changes being attempted in GB implicit solvent at fixed intervals.
Replica exchange along the pH-dimension (pH-REMD) helps to obtain
acceptable titration behavior with the proposed method. We analyzed
the effects of various parameters and settings on the titration behavior
of CpHMD and pH-REMD in explicit solvent, including the size of the
simulation unit cell and the length of the relaxation dynamics following
protonation state changes. We tested the method with the amino acid
model compounds, a small pentapeptide with two titratable sites, and
hen egg white lysozyme (HEWL). The proposed method yields superior
predicted pKa values for HEWL over hundreds
of nanoseconds of simulation relative to corresponding predicted values
from simulations run in implicit solvent.
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Affiliation(s)
- Jason M Swails
- Quantum Theory Project, Chemistry Department, University of Florida , Gainesville, Florida 32611, United States
| | - Darrin M York
- BioMaPS Institute for Quantitative Biology, Center for Integrative Proteomics Research, and Department of Chemistry and Chemical Biology, Rutgers University , Piscataway, New Jersey 08901, United States
| | - Adrian E Roitberg
- Quantum Theory Project, Chemistry Department, University of Florida , Gainesville, Florida 32611, United States
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73
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Goh GB, Hulbert BS, Zhou H, Brooks CL. Constant pH molecular dynamics of proteins in explicit solvent with proton tautomerism. Proteins 2014; 82:1319-31. [PMID: 24375620 DOI: 10.1002/prot.24499] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Revised: 11/13/2013] [Accepted: 12/12/2013] [Indexed: 12/14/2022]
Abstract
pH is a ubiquitous regulator of biological activity, including protein-folding, protein-protein interactions, and enzymatic activity. Existing constant pH molecular dynamics (CPHMD) models that were developed to address questions related to the pH-dependent properties of proteins are largely based on implicit solvent models. However, implicit solvent models are known to underestimate the desolvation energy of buried charged residues, increasing the error associated with predictions that involve internal ionizable residue that are important in processes like hydrogen transport and electron transfer. Furthermore, discrete water and ions cannot be modeled in implicit solvent, which are important in systems like membrane proteins and ion channels. We report on an explicit solvent constant pH molecular dynamics framework based on multi-site λ-dynamics (CPHMD(MSλD)). In the CPHMD(MSλD) framework, we performed seamless alchemical transitions between protonation and tautomeric states using multi-site λ-dynamics, and designed novel biasing potentials to ensure that the physical end-states are predominantly sampled. We show that explicit solvent CPHMD(MSλD) simulations model realistic pH-dependent properties of proteins such as the Hen-Egg White Lysozyme (HEWL), binding domain of 2-oxoglutarate dehydrogenase (BBL) and N-terminal domain of ribosomal protein L9 (NTL9), and the pKa predictions are in excellent agreement with experimental values, with a RMSE ranging from 0.72 to 0.84 pKa units. With the recent development of the explicit solvent CPHMD(MSλD) framework for nucleic acids, accurate modeling of pH-dependent properties of both major class of biomolecules-proteins and nucleic acids is now possible.
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Affiliation(s)
- Garrett B Goh
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109
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74
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Morrow BH, Koenig PH, Shen JK. Self-assembly and bilayer-micelle transition of fatty acids studied by replica-exchange constant pH molecular dynamics. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:14823-14830. [PMID: 24215478 PMCID: PMC3946477 DOI: 10.1021/la403398n] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Recent interest in the development of surfactant-based nanodelivery systems targeting tumor sites has sparked our curiosity in understanding the detailed mechanism of the self-assembly and phase transitions of pH-sensitive surfactants. Toward this goal, we applied a state-of-the-art simulation technique, continuous constant pH molecular dynamics (CpHMD) with the hybrid-solvent scheme and pH-based replica-exchange protocol, to study the de novo self-assembly of 30 and 40 lauric acids, a simple model titratable surfactant. We observed the formation of a gel-state bilayer at low and intermediate pH and a spherical micelle at high pH, with the phase transition starting at 20-30% ionization and being completed at 50%. The degree of cooperativity for the transition increases from the 30-mer to the 40-mer. The calculated apparent or bulk pKa value is 7.0 for the 30-mer and 7.5 for the 40-mer. Congruent with experiment, these data demonstrate that CpHMD is capable of accurately modeling large conformational transitions of surfactant systems while allowing the simultaneous proton titration of constituent molecules. We suggest that CpHMD simulations may become a useful tool in aiding in the design and development of pH-sensitive nanocarriers for a variety of biomedical and technological applications.
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Affiliation(s)
- Brian H. Morrow
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201
| | - Peter H. Koenig
- Computational Chemistry, Modeling & Simulation GCO, Procter and Gamble, Cincinnati, OH
| | - Jana K. Shen
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201
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75
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Morrow BH, Koenig PH, Shen JK. Atomistic simulations of pH-dependent self-assembly of micelle and bilayer from fatty acids. J Chem Phys 2013. [PMID: 23181330 DOI: 10.1063/1.4766313] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Detailed knowledge of the self-assembly and phase behavior of pH-sensitive surfactants has implications in areas such as targeted drug delivery. Here we present a study of the formation of micelle and bilayer from lauric acids using a state-of-the-art simulation technique, continuous constant pH molecular dynamics (CpHMD) with conformational sampling in explicit solvent and the pH-based replica-exchange protocol. We find that at high pH conditions a spherical micelle is formed, while at low pH conditions a bilayer is formed with a considerable degree of interdigitation. The mid-point of the phase transition is in good agreement with experiment. Preliminary investigation also reveals that the effect of counterions and salt screening shifts the transition mid-point and does not change the structure of the surfactant assembly. Based on these data we suggest that CpHMD simulations may be applied to computational design of surfactant-based nano devices in the future.
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Affiliation(s)
- Brian H Morrow
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201, USA
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