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Chen L, Li X, Xie Y, Liu N, Qin X, Chen X, Bu Y. Modulation of proton-coupled electron transfer reactions in lysine-containing alpha-helixes: alpha-helixes promoting long-range electron transfer. Phys Chem Chem Phys 2022; 24:14592-14602. [PMID: 35667661 DOI: 10.1039/d2cp00666a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The proton-coupled electron transfer (PCET) reaction plays an important role in promoting many biological and chemical reactions. Usually, the rate of the PCET reaction increases with an increase in the electron transfer distance because long-range electron transfer requires more free energy barriers. Our density functional theory calculations here reveal that the mechanism of PCET occurring in lysine-containing alpha(α)-helixes changes with an increasing number of residues in the α-helical structure and the different conformations because of the modulation of the excess electron distribution by the α-helical structures. The rate constants of the corresponding PCET reactions are independent of or substantially shallower dependent on the electron transfer distances along α-helixes. This counter-intuitive behavior can be attributed to the fact that the formation of larger macro-cylindrical dipole moments in longer helixes can promote electron transfer along the α-helix with a low energy barrier. These findings may be useful to gain insights into long-range electron transfer in proteins and design α-helix-based electronics via the regulation of short-range proton transfer.
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Affiliation(s)
- Long Chen
- Chongqing Key Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 401331, P. R. China.
| | - Xin Li
- Chongqing Key Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 401331, P. R. China.
| | - Yuxin Xie
- Chongqing Key Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 401331, P. R. China.
| | - Nian Liu
- Chongqing Key Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 401331, P. R. China.
| | - Xin Qin
- Chongqing Key Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 401331, P. R. China.
| | - Xiaohua Chen
- Chongqing Key Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 401331, P. R. China.
| | - Yuxiang Bu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong, 250100, P. R. China.
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Lemkul JA. Pairwise-additive and polarizable atomistic force fields for molecular dynamics simulations of proteins. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 170:1-71. [PMID: 32145943 DOI: 10.1016/bs.pmbts.2019.12.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Protein force fields have been undergoing continual development since the first complete parameter sets were introduced nearly four decades ago. The functional forms that underlie these models have many common elements for the treatment of bonded and nonbonded forces, which are reviewed here. The most widely used force fields to date use a fixed-charge convention in which electronic polarization effects are treated via a mean-field approximation during partial charge assignment. Despite success in modeling folded proteins over many years, the fixed-charge assumption has limitations that cannot necessarily be overcome within their potential energy equations. To overcome these limitations, several force fields have recently been derived that explicitly treat electronic polarization effects with straightforward extensions of the potential energy functions used by nonpolarizable force fields. Here, we review the history of the most popular nonpolarizable force fields (AMBER, CHARMM, OPLS, and GROMOS) as well as studies that have validated them and applied them to studies of protein folding and misfolding. Building upon these force fields are more recent polarizable interaction potentials, including fluctuating charge models, POSSIM, AMOEBA, and the classical Drude oscillator. These force fields differ in their implementations but all attempt to model electronic polarization in a computationally tractable manner. Despite their recent emergence in the field of protein folding, several studies have already applied these polarizable models to challenging problems in this domain, including the role of polarization in folding free energies and sequence-specific effects on the stability of α-helical structures.
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Affiliation(s)
- Justin A Lemkul
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, United States.
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Sharma I, Kaminski GA. Using polarizable POSSIM force field and fuzzy-border continuum solvent model to calculate pK(a) shifts of protein residues. J Comput Chem 2017; 38:65-80. [PMID: 27785788 PMCID: PMC5123858 DOI: 10.1002/jcc.24519] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 09/22/2016] [Accepted: 10/02/2016] [Indexed: 12/26/2022]
Abstract
Our Fuzzy-Border (FB) continuum solvent model has been extended and modified to produce hydration parameters for small molecules using POlarizable Simulations Second-order Interaction Model (POSSIM) framework with an average error of 0.136 kcal/mol. It was then used to compute pKa shifts for carboxylic and basic residues of the turkey ovomucoid third domain (OMTKY3) protein. The average unsigned errors in the acid and base pKa values were 0.37 and 0.4 pH units, respectively, versus 0.58 and 0.7 pH units as calculated with a previous version of polarizable protein force field and Poisson Boltzmann continuum solvent. This POSSIM/FB result is produced with explicit refitting of the hydration parameters to the pKa values of the carboxylic and basic residues of the OMTKY3 protein; thus, the values of the acidity constants can be viewed as additional fitting target data. In addition to calculating pKa shifts for the OMTKY3 residues, we have studied aspartic acid residues of Rnase Sa. This was done without any further refitting of the parameters and agreement with the experimental pKa values is within an average unsigned error of 0.65 pH units. This result included the Asp79 residue that is buried and thus has a high experimental pKa value of 7.37 units. Thus, the presented model is capable or reproducing pKa results for residues in an environment that is significantly different from the solvated protein surface used in the fitting. Therefore, the POSSIM force field and the FB continuum solvent parameters have been demonstrated to be sufficiently robust and transferable. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Ity Sharma
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, MA 01609
| | - George A. Kaminski
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, MA 01609
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Cvitkovic JP, Kaminski GA. Developing multisite empirical force field models for Pt(II) and cisplatin. J Comput Chem 2016; 38:161-168. [PMID: 27859392 DOI: 10.1002/jcc.24665] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 10/12/2016] [Accepted: 10/26/2016] [Indexed: 12/15/2022]
Abstract
We have developed empirical force field parameters for Pt(II) and cisplatin. Two force field frameworks were used-modified OPLS-AA and our second-order polarizable POSSIM. A seven-site model was used for the Pt(II) ion. The goal was to create transferable parameter sets compatible with the force field models for proteins and general organic compounds. A number of properties of the Pt(II) ion and its coordination compounds have been considered, including geometries and energies of the complexes, hydration free energy, and radial distribution functions in water. Comparison has been made with experimental and quantum mechanical results. We have demonstrated that both versions are generally capable of reproducing key properties of the system, but the second-order polarizable POSSIM formalism permits more accurate quantitative results to be obtained. For example, the energy of formation of cisplatin as calculated with the modified OPLS-AA exhibited an error of 9.9%, while the POSSIM error for the same quantity was 6.2%. The produced parameter sets are transferable and suitable to be used in protein-metal binding simulations in which position or even coordination of the ion does not have to be constrained using preexisting knowledge. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- John P Cvitkovic
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, 100 Institute Rd, Worcester, Massachusetts, 01609
| | - George A Kaminski
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, 100 Institute Rd, Worcester, Massachusetts, 01609
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Abstract
It is known that a C-terminal lysine stabilizes helix formation in polyalanine peptides that have seven or more residues. Using a combination of cold ion spectroscopy and DFT calculations, we demonstrate that even a three-residue peptide, Ac-Phe-Ala-LysH(+), adopts a structure in which the lysine side chain forms three hydrogen bonds with backbone carbonyls, reproducing the capping motif of larger polyalanine helices. This is confirmed by comparison with Ac-Phe-(Ala)5-LysH(+), which forms a 310 helix containing the same structural feature. In both molecules, we identified the vibrational bands of the N- and C-terminal amide NH stretches, which lack strong hydrogen bonds with carbonyls and consequently appear in a characteristic region above 3400 cm(-1). A similar pattern is also present in the even longer peptide Ac-Phe-(Ala)10-LysH(+), illustrating the generality of this capping motif. The two longer peptides contain additional, characteristic amide NH stretch bands below 3400 cm(-1), which form the core of the helix.
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Affiliation(s)
- Aleksandra V Zabuga
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Thomas R Rizzo
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
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Li X, Ponomarev SY, Sigalovsky DL, Cvitkovic JP, Kaminski GA. POSSIM: Parameterizing Complete Second-Order Polarizable Force Field for Proteins. J Chem Theory Comput 2014; 10:4896-4910. [PMID: 25400518 PMCID: PMC4230370 DOI: 10.1021/ct500243k] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Indexed: 12/13/2022]
Abstract
![]()
Previously,
we reported development of a fast polarizable force
field and software named POSSIM (POlarizable Simulations with Second
order Interaction Model). The second-order approximation permits the speed up of the polarizable component of the calculations by ca. an order
of magnitude. We have now expanded the POSSIM framework to include
a complete polarizable force field for proteins. Most of the parameter
fitting was done to high-level quantum mechanical data. Conformational
geometries and energies for dipeptides have been reproduced within
average errors of ca. 0.5 kcal/mol for energies of the conformers
(for the electrostatically neutral residues) and 9.7° for key
dihedral angles. We have also validated this force field by running
Monte Carlo simulations of collagen-like proteins in water. The resulting
geometries were within 0.94 Å root-mean-square deviation (RMSD)
from the experimental data. We have performed additional validation
by studying conformational properties of three oligopeptides relevant
in the context of N-glycoprotein secondary structure. These systems
have been previously studied with combined experimental and computational
methods, and both POSSIM and benchmark OPLS-AA simulations that we
carried out produced geometries within ca. 0.9 Å RMSD of the
literature structures. Thus, the performance of POSSIM in reproducing
the structures is comparable with that of the widely used OPLS-AA
force field. Furthermore, our fitting of the force field parameters
for peptides and proteins has been streamlined compared with the
previous generation of the complete polarizable force field and relied
more on transferability of parameters for nonbonded interactions (including
the electrostatic component). The resulting deviations from the quantum
mechanical data are similar to those achieved with the previous generation;
thus, the technique is robust, and the parameters are transferable.
At the same time, the number of parameters used in this work was noticeably
smaller than that of the previous generation of our complete polarizable
force field for proteins; thus, the transferability of this set can
be expected to be greater, and the danger of force field fitting artifacts
is lower. Therefore, we believe that this force field can be successfully
applied in a wide variety of applications to proteins and protein–ligand
complexes.
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Affiliation(s)
- Xinbi Li
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute , Worcester, Massachusetts 01609, United States
| | - Sergei Y Ponomarev
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute , Worcester, Massachusetts 01609, United States
| | - Daniel L Sigalovsky
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute , Worcester, Massachusetts 01609, United States
| | - John P Cvitkovic
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute , Worcester, Massachusetts 01609, United States
| | - George A Kaminski
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute , Worcester, Massachusetts 01609, United States
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Morrison LJ, Wysocki VH. Gas-Phase Helical Peptides Mimic Solution-Phase Behavior. J Am Chem Soc 2014; 136:14173-83. [PMID: 25203898 DOI: 10.1021/ja507298e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Lindsay J. Morrison
- Ohio State University, 484
West 12th Avenue, Columbus, Ohio 43210, United States
| | - Vicki H. Wysocki
- Ohio State University, 484
West 12th Avenue, Columbus, Ohio 43210, United States
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Li X, Ponomarev SY, Sa Q, Sigalovsky DL, Kaminski GA. Polarizable simulations with second order interaction model (POSSIM) force field: developing parameters for protein side-chain analogues. J Comput Chem 2013; 34:1241-50. [PMID: 23420678 PMCID: PMC3633718 DOI: 10.1002/jcc.23248] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 01/20/2013] [Indexed: 12/16/2022]
Abstract
A previously introduced polarizable simulations with second-order interaction model (POSSIM) force field has been extended to include parameters for small molecules serving as models for peptide and protein side-chains. Parameters have been fitted to permit reproducing many-body energies, gas-phase dimerization energies, and geometries and liquid-phase heats of vaporization and densities. Quantum mechanical and experimental data have been used as the target for the fitting. The POSSIM framework combines accuracy of a polarizable force field and computational efficiency of the second-order approximation of the full-scale induced point dipole polarization formalism. The resulting parameters can be used for simulations of the parameterized molecules themselves or their analogues. In addition to this, these force field parameters are currently being used in further development of the POSSIM fast polarizable force field for proteins.
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