1
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Niu SJ, Ren FD. Finite Temperature String with Order Parameter as Collective Variables for Molecular Crystal: A Case of Polymorphic Transformation of TNT under External Electric Field. Molecules 2024; 29:2549. [PMID: 38893427 PMCID: PMC11173574 DOI: 10.3390/molecules29112549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Revised: 05/08/2024] [Accepted: 05/08/2024] [Indexed: 06/21/2024] Open
Abstract
An external electric field is an effective tool to induce the polymorphic transformation of molecular crystals, which is important practically in the chemical, material, and energy storage industries. However, the understanding of this mechanism is poor at the molecular level. In this work, two types of order parameters (OPs) were constructed for the molecular crystal based on the intermolecular distance, bond orientation, and molecular orientation. Using the K-means clustering algorithm for the sampling of OPs based on the Euclidean distance and density weight, the polymorphic transformation of TNT was investigated using a finite temperature string (FTS) under external electric fields. The potential of mean force (PMF) was obtained, and the essence of the polymorphic transformation between o-TNT and m-TNT was revealed, which verified the effectiveness of the FTS method based on K-means clustering to OPs. The differences in PMFs between the o-TNT and transition state were decreased under external electric fields in comparison with those in no field. The fields parallel to the c-axis obviously affected the difference in PMF, and the relationship between the changes in PMFs and field strengths was found. Although the external electric field did not promote the convergence, the time of the polymorphic transformation was reduced under the external electric field in comparison to its absence. Moreover, under the external electric field, the polymorphic transformation from o-TNT to m-TNT occurred while that from m-TNT to o-TNT was prevented, which was explained by the dipole moment of molecule, relative permittivity, chemical potential difference, nucleation work and nucleation rate. This confirmed that the polymorphic transformation orientation of the molecular crystal could be controlled by the external electric field. This work provides an effective way to explore the polymorphic transformation of the molecular crystals at a molecular level, and it is useful to control the production process and improve the performance of energetic materials by using the external electric fields.
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Affiliation(s)
- Shi-Jie Niu
- School of Chemistry and Chemical Engineering, North University of China, Taiyuan 030051, China;
- School of Management, Wuhan Polytechnic University, Wuhan 430040, China
| | - Fu-De Ren
- School of Chemistry and Chemical Engineering, North University of China, Taiyuan 030051, China;
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2
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Ren F, Wang X, Zhang Q, Wang X, Chang L, Zhang Z. Experimental and Theoretical Investigation of External Electric-Field-Induced Crystallization of TKX-50 from Solution by Finite-Temperature String with Order Parameters as Collective Variables for Ionic Crystals. Molecules 2024; 29:1159. [PMID: 38474669 DOI: 10.3390/molecules29051159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 02/26/2024] [Accepted: 02/28/2024] [Indexed: 03/14/2024] Open
Abstract
External electric fields are an effective tool to induce phase transformations. The crystallization of ionic crystals from solution is a common phase transformation. However, understanding of mechanisms is poor at the molecular level. In this work, we carried out an experimental and theoretical investigation of the external electric-field-induced crystallization of TKX-50 from saturated formic acid solution by finite-temperature string (FTS) with order parameters (OPs) as collective variables for ionic crystals. The minimum-free-energy path was sketched by the string method in collective variables. The results show that the K-means clustering algorithm based on Euclidean distance and density weights can be used for enhanced sampling of the OPs in external electric-field-induced crystallization of ionic crystal from solution, which improves the conventional FTS. The crystallization from solution is a process of surface-mediated nucleation. The external electric field can accelerate the evolution of the string and decrease the difference in the potential of mean forces between the crystal and the transition state. Due to the significant change in OPs induced by the external electric field in nucleation, the crystalline quality was enhanced, which explains the experimental results that the external electric field enhanced the density, detonation velocity, and detonation pressure of TKX-50. This work provides an effective way to explore the crystallization of ionic crystals from solution at the molecular level, and it is useful for improving the properties of ionic crystal explosives by using external electric fields.
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Affiliation(s)
- Fude Ren
- School of Chemistry and Chemical Engineering, North University of China, Taiyuan 030051, China
| | - Xiaolei Wang
- School of Chemistry and Chemical Engineering, North University of China, Taiyuan 030051, China
| | - Qing Zhang
- School of Chemistry and Chemical Engineering, North University of China, Taiyuan 030051, China
| | - Xiaojun Wang
- Gansu Yinguang Chemical Industry Group, Baiyin 730900, China
| | - Lingling Chang
- School of Chemistry and Chemical Engineering, North University of China, Taiyuan 030051, China
| | - Zhiteng Zhang
- School of Chemistry and Chemical Engineering, North University of China, Taiyuan 030051, China
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3
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Ren FD, Liu YZ, Ding KW, Chang LL, Cao DL, Liu S. Finite temperature string by K-means clustering sampling with order parameters as collective variables for molecular crystals: application to polymorphic transformation between β-CL-20 and ε-CL-20. Phys Chem Chem Phys 2024; 26:3500-3515. [PMID: 38206084 DOI: 10.1039/d3cp05389j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
Polymorphic transformation of molecular crystals is a fundamental phase transition process, and it is important practically in the chemical, material, biopharmaceutical, and energy storage industries. However, understanding of the transformation mechanism at the molecular level is poor due to the extreme simulating challenges in enhanced sampling and formulating order parameters (OPs) as the collective variables that can distinguish polymorphs with quite similar and complicated structures so as to describe the reaction coordinate. In this work, two kinds of OPs for CL-20 were constructed by the bond distances, bond orientations and relative orientations. A K-means clustering algorithm based on the Euclidean distance and sample weight was used to smooth the initial finite temperature string (FTS), and the minimum free energy path connecting β-CL-20 and ε-CL-20 was sketched by the string method in collective variables, and the free energy profile along the path and the nucleation kinetics were obtained by Markovian milestoning with Voronoi tessellations. In comparison with the average-based sampling, the K-means clustering algorithm provided an improved convergence rate of FTS. The simulation of transformation was independent of OP types but was affected greatly by finite-size effects. A surface-mediated local nucleation mechanism was confirmed and the configuration located at the shoulder of potential of mean force, rather than overall maximum, was confirmed to be the critical nucleus formed by the cooperative effect of the intermolecular interactions. This work provides an effective way to explore the polymorphic transformation of caged molecular crystals at the molecular level.
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Affiliation(s)
- Fu-de Ren
- School of Chemical Engineering and Technology, North University of China, Taiyuan 030051, China.
| | - Ying-Zhe Liu
- Xi'an Modern Chemistry Research Institute, Xi'an 710065, China
| | - Ke-Wei Ding
- Xi'an Modern Chemistry Research Institute, Xi'an 710065, China
| | - Ling-Ling Chang
- School of Chemical Engineering and Technology, North University of China, Taiyuan 030051, China.
| | - Duan-Lin Cao
- School of Chemical Engineering and Technology, North University of China, Taiyuan 030051, China.
| | - Shubin Liu
- Research Computing Center, University of North Carolina, Chapel Hill, North Carolina 27599-3420, USA.
- Depaertment of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA
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4
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Abstract
![]()
We
explore the process of base-flipping for four central bases,
adenine, guanine, cytosine, and thymine, in a deoxyribonucleic acid
(DNA) duplex using the energy landscape perspective. NMR imino-proton
exchange and fluorescence correlation spectroscopy studies have been
used in previous experiments to obtain lifetimes for bases in paired
and extrahelical states. However, the difference of almost 4 orders
of magnitude in the base-flipping rates obtained by the two methods
implies that they are exploring different pathways and possibly different
open states. Our results support the previous suggestion that minor
groove opening may be favored by distortions in the DNA backbone and
reveal links between sequence effects and the direction of opening,
i.e., whether the base flips toward the major or the minor groove
side. In particular, base flipping along the minor groove pathway
was found to align toward the 5′ side of the backbone. We find
that bases align toward the 3′ side of the backbone when flipping
along the major groove pathway. However, in some cases for cytosine
and thymine, the base flipping along the major groove pathway also
aligns toward the 5′ side. The sequence effect may be caused
by the polar interactions between the flipping-base and its neighboring
bases on either of the strands. For guanine flipping toward the minor
groove side, we find that the equilibrium constant for opening is
large compared to flipping via the major groove. We find that the
estimated rates of base opening, and hence the lifetimes of the closed
state, obtained for thymine flipping through small and large angles
along the major groove differ by 6 orders of magnitude, whereas for
thymine flipping through small angles along the minor groove and large
angles along the major groove, the rates differ by 3 orders of magnitude.
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Affiliation(s)
- Nicy
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, U.K
| | - Debayan Chakraborty
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - David J. Wales
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, U.K
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5
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Abstract
The opening of a Watson-Crick double helix is required for crucial cellular processes, including replication, repair, and transcription. It has long been assumed that RNA or DNA base pairs are broken by the concerted symmetric movement of complementary nucleobases. By analyzing thousands of base-pair opening and closing events from molecular simulations, here, we uncover a systematic stepwise process driven by the asymmetric flipping-out probability of paired nucleobases. We demonstrate experimentally that such asymmetry strongly biases the unwinding efficiency of DNA helicases toward substrates that bear highly dynamic nucleobases, such as pyrimidines, on the displaced strand. Duplex substrates with identical thermodynamic stability are thus shown to be more easily unwound from one side than the other, in a quantifiable and predictable manner. Our results indicate a possible layer of gene regulation coded in the direction-dependent unwindability of the double helix.
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6
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Peng X, Zhang Y, Li Y, Liu Q, Chu H, Zhang D, Li G. Integrating Multiple Accelerated Molecular Dynamics To Improve Accuracy of Free Energy Calculations. J Chem Theory Comput 2018; 14:1216-1227. [DOI: 10.1021/acs.jctc.7b01211] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Xiangda Peng
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
- Chinese
Academy of Science, University of Chinese Academy Sciences, Beijing 100049, P. R. China
| | - Yuebin Zhang
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Yan Li
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - QingLong Liu
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Huiying Chu
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Dinglin Zhang
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Guohui Li
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
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7
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Self-Assembly of 3D DNA Crystals Containing a Torsionally Stressed Component. Cell Chem Biol 2017; 24:1401-1406.e2. [DOI: 10.1016/j.chembiol.2017.08.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 07/06/2017] [Accepted: 08/18/2017] [Indexed: 11/15/2022]
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8
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Ma N, van der Vaart A. Free Energy Coupling between DNA Bending and Base Flipping. J Chem Inf Model 2017; 57:2020-2026. [PMID: 28696686 DOI: 10.1021/acs.jcim.7b00215] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Free energy simulations are presented to probe the energetic coupling between DNA bending and the flipping of a central thymine in double stranded DNA 13mers. The energetics are shown to depend on the neighboring base pairs, and upstream C or T or downstream C tended to make flipping more costly. Flipping to the major groove side was generally preferred. Bending aids flipping, by pushing the system up in free energy, but for small and intermediate bending angles the two were uncorrelated. At higher bending angles, bending and flipping became correlated, and bending primed the system for base flipping toward the major groove. Flipping of the 6-4 pyrimidine-pyrimidone and pyrimidine dimer photoproducts is shown to be more facile than for undamaged DNA. For the damages, major groove flipping was preferred, and DNA bending was much facilitated in the 6-4 pyrimidine-pyrimidone damaged system. Aspects of the calculations were verified by structural analyses of protein-DNA complexes with flipped bases.
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Affiliation(s)
- Ning Ma
- Department of Chemistry, University of South Florida , 4202 East Fowler Avenue CHE 205, Tampa, Florida 33620, United States
| | - Arjan van der Vaart
- Department of Chemistry, University of South Florida , 4202 East Fowler Avenue CHE 205, Tampa, Florida 33620, United States
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9
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Lindahl V, Villa A, Hess B. Sequence dependency of canonical base pair opening in the DNA double helix. PLoS Comput Biol 2017; 13:e1005463. [PMID: 28369121 PMCID: PMC5393899 DOI: 10.1371/journal.pcbi.1005463] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 04/17/2017] [Accepted: 03/17/2017] [Indexed: 12/15/2022] Open
Abstract
The flipping-out of a DNA base from the double helical structure is a key step of many cellular processes, such as DNA replication, modification and repair. Base pair opening is the first step of base flipping and the exact mechanism is still not well understood. We investigate sequence effects on base pair opening using extensive classical molecular dynamics simulations targeting the opening of 11 different canonical base pairs in two DNA sequences. Two popular biomolecular force fields are applied. To enhance sampling and calculate free energies, we bias the simulation along a simple distance coordinate using a newly developed adaptive sampling algorithm. The simulation is guided back and forth along the coordinate, allowing for multiple opening pathways. We compare the calculated free energies with those from an NMR study and check assumptions of the model used for interpreting the NMR data. Our results further show that the neighboring sequence is an important factor for the opening free energy, but also indicates that other sequence effects may play a role. All base pairs are observed to have a propensity for opening toward the major groove. The preferred opening base is cytosine for GC base pairs, while for AT there is sequence dependent competition between the two bases. For AT opening, we identify two non-canonical base pair interactions contributing to a local minimum in the free energy profile. For both AT and CG we observe long-lived interactions with water and with sodium ions at specific sites on the open base pair. The DNA double helix, a molecule that stores biological information, has become an iconic image of biomedical research. In order to use or repair the information it carries, the bases that are stacked in the helix need to be chemically exposed. This can happen either by separating the two strands in the helix or by flipping out individual bases. Here, we focus on the latter process. Usually proteins are involved in interactions with bases, but it is still unclear if bases are pulled out actively by proteins or if they act on spontaneously flipped bases. Although experiments can detect base pair opening, it is difficult to detect which base moves in which direction. Here, we present results from molecular dynamics simulations using a recently developed sampling method which improves the statistics in the simulations by enhancing the probability of the base pair opening event. We observe differences in probability, modes and mechanism of opening that depend not only on the types of the bases in the pair, but also strongly on their neighbors. This provides essential information for understanding how DNA functions.
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Affiliation(s)
- Viveca Lindahl
- Department of Physics and Swedish e-Science Research Center, KTH Royal Institute of Technology, Stockholm, Sweden
- Science for Life Laboratory, Stockholm and Uppsala, Stockholm, Sweden
| | - Alessandra Villa
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Berk Hess
- Department of Physics and Swedish e-Science Research Center, KTH Royal Institute of Technology, Stockholm, Sweden
- Science for Life Laboratory, Stockholm and Uppsala, Stockholm, Sweden
- * E-mail:
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10
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Fu H, Shao X, Chipot C, Cai W. Extended Adaptive Biasing Force Algorithm. An On-the-Fly Implementation for Accurate Free-Energy Calculations. J Chem Theory Comput 2016; 12:3506-13. [PMID: 27398726 DOI: 10.1021/acs.jctc.6b00447] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Proper use of the adaptive biasing force (ABF) algorithm in free-energy calculations needs certain prerequisites to be met, namely, that the Jacobian for the metric transformation and its first derivative be available and the coarse variables be independent and fully decoupled from any holonomic constraint or geometric restraint, thereby limiting singularly the field of application of the approach. The extended ABF (eABF) algorithm circumvents these intrinsic limitations by applying the time-dependent bias onto a fictitious particle coupled to the coarse variable of interest by means of a stiff spring. However, with the current implementation of eABF in the popular molecular dynamics engine NAMD, a trajectory-based post-treatment is necessary to derive the underlying free-energy change. Usually, such a posthoc analysis leads to a decrease in the reliability of the free-energy estimates due to the inevitable loss of information, as well as to a drop in efficiency, which stems from substantial read-write accesses to file systems. We have developed a user-friendly, on-the-fly code for performing eABF simulations within NAMD. In the present contribution, this code is probed in eight illustrative examples. The performance of the algorithm is compared with traditional ABF, on the one hand, and the original eABF implementation combined with a posthoc analysis, on the other hand. Our results indicate that the on-the-fly eABF algorithm (i) supplies the correct free-energy landscape in those critical cases where the coarse variables at play are coupled to either each other or to geometric restraints or holonomic constraints, (ii) greatly improves the reliability of the free-energy change, compared to the outcome of a posthoc analysis, and (iii) represents a negligible additional computational effort compared to regular ABF. Moreover, in the proposed implementation, guidelines for choosing two parameters of the eABF algorithm, namely the stiffness of the spring and the mass of the fictitious particles, are proposed. The present on-the-fly eABF implementation can be viewed as the second generation of the ABF algorithm, expected to be widely utilized in the theoretical investigation of recognition and association phenomena relevant to physics, chemistry, and biology.
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Affiliation(s)
| | - Xueguang Shao
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300071, China
| | - Christophe Chipot
- Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana-Champaign, Unité Mixte de Recherche No. 7565, Université de Lorraine , B.P. 70239, 54506 Vandœuvre-lès-Nancy cedex, France.,Theoretical and Computational Biophysics Group, Beckman Institute, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.,Department of Physics, University of Illinois at Urbana-Champaign , 1110 West Green Street, Urbana, Illinois 61801, United States
| | - Wensheng Cai
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300071, China
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11
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Cao L, Cheng L, Tang T, Liu J, Zhang D, Xu P, Li G. Understanding enzyme reactions using enhanced sampling techniques. MOLECULAR SIMULATION 2016. [DOI: 10.1080/08927022.2015.1132316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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12
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Wu D, Fajer MI, Cao L, Cheng X, Yang W. Generalized Ensemble Sampling of Enzyme Reaction Free Energy Pathways. Methods Enzymol 2016; 577:57-74. [PMID: 27498634 PMCID: PMC4978182 DOI: 10.1016/bs.mie.2016.05.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Free energy path sampling plays an essential role in computational understanding of chemical reactions, particularly those occurring in enzymatic environments. Among a variety of molecular dynamics simulation approaches, the generalized ensemble sampling strategy is uniquely attractive for the fact that it not only can enhance the sampling of rare chemical events but also can naturally ensure consistent exploration of environmental degrees of freedom. In this review, we plan to provide a tutorial-like tour on an emerging topic: generalized ensemble sampling of enzyme reaction free energy path. The discussion is largely focused on our own studies, particularly ones based on the metadynamics free energy sampling method and the on-the-path random walk path sampling method. We hope that this minipresentation will provide interested practitioners some meaningful guidance for future algorithm formulation and application study.
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Affiliation(s)
- D Wu
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, United States
| | - M I Fajer
- UT-ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN, United States; Florida State University, Tallahassee, FL, United States
| | - L Cao
- Florida State University, Tallahassee, FL, United States
| | - X Cheng
- UT-ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN, United States; The University of Tennessee, Knoxville, TN, United States.
| | - W Yang
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, United States; Florida State University, Tallahassee, FL, United States.
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13
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Lv C, Aitchison EW, Wu D, Zheng L, Cheng X, Yang W. Comparative exploration of hydrogen sulfide and water transmembrane free energy surfaces via orthogonal space tempering free energy sampling. J Comput Chem 2016; 37:567-74. [PMID: 26119423 PMCID: PMC4959446 DOI: 10.1002/jcc.23982] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 05/24/2015] [Indexed: 01/22/2023]
Abstract
Hydrogen sulfide (H2 S), a commonly known toxic gas compound, possesses unique chemical features that allow this small solute molecule to quickly diffuse through cell membranes. Taking advantage of the recent orthogonal space tempering (OST) method, we comparatively mapped the transmembrane free energy landscapes of H2 S and its structural analogue, water (H2 O), seeking to decipher the molecular determinants that govern their drastically different permeabilities. As revealed by our OST sampling results, in contrast to the highly polar water solute, hydrogen sulfide is evidently amphipathic, and thus inside membrane is favorably localized at the interfacial region, that is, the interface between the polar head-group and nonpolar acyl chain regions. Because the membrane binding affinity of H2 S is mainly governed by its small hydrophobic moiety and the barrier height inbetween the interfacial region and the membrane center is largely determined by its moderate polarity, the transmembrane free energy barriers to encounter by this toxic molecule are very small. Moreover when H2 S diffuses from the bulk solution to the membrane center, the above two effects nearly cancel each other, so as to lead to a negligible free energy difference. This study not only explains why H2 S can quickly pass through cell membranes but also provides a practical illustration on how to use the OST free energy sampling method to conveniently analyze complex molecular processes. © 2015 Wiley Periodicals, Inc.
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Affiliation(s)
- Chao Lv
- Department of Chemistry & Biochemistry, Florida State University, Tallahassee, Florida 32306
| | - Erick W. Aitchison
- Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306
| | - Dongsheng Wu
- Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306
| | - Lianqing Zheng
- Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306
| | - Xiaolin Cheng
- UT-ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37830
- Department of Biochemistry, Cellular and Molecular Biology, the University of Tennessee, Knoxville, Tennessee, 37996
| | - Wei Yang
- Department of Chemistry & Biochemistry, Florida State University, Tallahassee, Florida 32306
- Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306
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14
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Lv C, Li X, Wu D, Zheng L, Yang W. Predictive Sampling of Rare Conformational Events in Aqueous Solution: Designing a Generalized Orthogonal Space Tempering Method. J Chem Theory Comput 2016; 12:41-52. [PMID: 26636477 PMCID: PMC4968881 DOI: 10.1021/acs.jctc.5b00953] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In aqueous solution, solute conformational transitions are governed by intimate interplays of the fluctuations of solute-solute, solute-water, and water-water interactions. To promote molecular fluctuations to enhance sampling of essential conformational changes, a common strategy is to construct an expanded Hamiltonian through a series of Hamiltonian perturbations and thereby broaden the distribution of certain interactions of focus. Due to a lack of active sampling of configuration response to Hamiltonian transitions, it is challenging for common expanded Hamiltonian methods to robustly explore solvent mediated rare conformational events. The orthogonal space sampling (OSS) scheme, as exemplified by the orthogonal space random walk and orthogonal space tempering methods, provides a general framework for synchronous acceleration of slow configuration responses. To more effectively sample conformational transitions in aqueous solution, in this work, we devised a generalized orthogonal space tempering (gOST) algorithm. Specifically, in the Hamiltonian perturbation part, a solvent-accessible-surface-area-dependent term is introduced to implicitly perturb near-solute water-water fluctuations; more importantly in the orthogonal space response part, the generalized force order parameter is generalized as a two-dimension order parameter set, in which essential solute-solvent and solute-solute components are separately treated. The gOST algorithm is evaluated through a molecular dynamics simulation study on the explicitly solvated deca-alanine (Ala10) peptide. On the basis of a fully automated sampling protocol, the gOST simulation enabled repetitive folding and unfolding of the solvated peptide within a single continuous trajectory and allowed for detailed constructions of Ala10 folding/unfolding free energy surfaces. The gOST result reveals that solvent cooperative fluctuations play a pivotal role in Ala10 folding/unfolding transitions. In addition, our assessment analysis suggests that because essential conformational events are mainly driven by the compensating fluctuations of essential solute-solvent and solute-solute interactions, commonly employed "predictive" sampling methods are unlikely to be effective on this seemingly "simple" system. The gOST development presented in this paper illustrates how to employ the OSS scheme for physics-based sampling method designs.
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Affiliation(s)
- Chao Lv
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, 32306
| | - Xubin Li
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, 32306
| | - Dongsheng Wu
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, 32306
| | - Lianqing Zheng
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, 32306
| | - Wei Yang
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, 32306
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, 32306
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15
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Branduardi D, Marinelli F, Faraldo-Gómez JD. Atomic-resolution dissection of the energetics and mechanism of isomerization of hydrated ATP-Mg(2+) through the SOMA string method. J Comput Chem 2015; 37:575-86. [PMID: 26149527 DOI: 10.1002/jcc.23991] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Revised: 06/09/2015] [Accepted: 06/11/2015] [Indexed: 01/28/2023]
Abstract
The atomic mechanisms of isomerization of ATP-Mg(2+) in solution are characterized using the recently developed String Method with Optimal Molecular Alignment (SOMA) and molecular-dynamics simulations. Bias-Exchange Metadynamics simulations are first performed to identify the primary conformers of the ATP-Mg(2+) complex and their connectivity. SOMA is then used to elucidate the minimum free-energy path (MFEP) for each transition, in a 48-dimensional space. Analysis of the per-atom contributions to the global free-energy profiles reveals that the mechanism of these transitions is controlled by the Mg(2+) ion and its coordinating oxygen atoms in the triphosphate moiety, as well as by the ion-hydration shell. Metadynamics simulations in path collective variables based on the MFEP demonstrate these isomerizations proceed across a narrow channel of configurational space, thus validating the premise underlying SOMA. This study provides a roadmap for the examination of conformational changes in biomolecules, based on complementary enhanced-sampling techniques with different strengths. © 2015 Wiley Periodicals, Inc.
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Affiliation(s)
- Davide Branduardi
- Theoretical Molecular Biophysics Group, Max Planck Institute of Biophysics, Max-von-Laue Strasse 3, Frankfurt-am-Main, DE 60438, Germany
| | - Fabrizio Marinelli
- Theoretical Molecular Biophysics Section, National Heart, Lung and Blood Institute, National Institutes of Health, Building 5635FL, Suite T-800, Bethesda, Maryland, 20892
| | - José D Faraldo-Gómez
- Theoretical Molecular Biophysics Group, Max Planck Institute of Biophysics, Max-von-Laue Strasse 3, Frankfurt-am-Main, DE 60438, Germany.,Theoretical Molecular Biophysics Section, National Heart, Lung and Blood Institute, National Institutes of Health, Building 5635FL, Suite T-800, Bethesda, Maryland, 20892
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16
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Hudson PS, White JK, Kearns FL, Hodoscek M, Boresch S, Lee Woodcock H. Efficiently computing pathway free energies: New approaches based on chain-of-replica and Non-Boltzmann Bennett reweighting schemes. Biochim Biophys Acta Gen Subj 2014; 1850:944-953. [PMID: 25239198 DOI: 10.1016/j.bbagen.2014.09.016] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 09/09/2014] [Accepted: 09/10/2014] [Indexed: 11/25/2022]
Abstract
BACKGROUND Accurately modeling condensed phase processes is one of computation's most difficult challenges. Include the possibility that conformational dynamics may be coupled to chemical reactions, where multiscale (i.e., QM/MM) methods are needed, and this task becomes even more daunting. METHODS Free energy simulations (i.e., molecular dynamics), multiscale modeling, and reweighting schemes. RESULTS Herein, we present two new approaches for mitigating the aforementioned challenges. The first is a new chain-of-replica method (off-path simulations, OPS) for computing potentials of mean force (PMFs) along an easily defined reaction coordinate. This development is coupled with a new distributed, highly-parallel replica framework (REPDstr) within the CHARMM package. Validation of these new schemes is carried out on two processes that undergo conformational changes. First is the simple torsional rotation of butane, while a much more challenging glycosidic rotation (in vacuo and solvated) is the second. Additionally, a new approach that greatly improves (i.e., possibly an order of magnitude) the efficiency of computing QM/MM PMFs is introduced and compared to standard schemes. Our efforts are grounded in the recently developed method for efficiently computing QM-based free energies (i.e., QM-Non-Boltzmann Bennett, QM-NBB). Again, we validate this new technique by computing the QM/MM PMF of butane's torsional rotation. CONCLUSIONS The OPS-REPDstr method is a promising new approach that overcomes many limitations of standard pathway simulations in CHARMM. The combination of QM-NBB with pathway techniques is very promising as it offers significant advantages over current procedures. GENERAL SIGNIFICANCE Efficiently computing potentials of mean force is a major, unresolved, area of interest. This article is part of a Special Issue entitled Recent developments of molecular dynamics.
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Affiliation(s)
- Phillip S Hudson
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave., CHE205, Tampa, FL 33620-5250, USA
| | - Justin K White
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave., CHE205, Tampa, FL 33620-5250, USA
| | - Fiona L Kearns
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave., CHE205, Tampa, FL 33620-5250, USA
| | - Milan Hodoscek
- Center for Molecular Modeling, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Stefan Boresch
- Department of Computational Biological Chemistry, Faculty of Chemistry, University of Vienna, Währingerstraße 17, A-1090 Vienna, Austria
| | - H Lee Woodcock
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave., CHE205, Tampa, FL 33620-5250, USA.
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Moradi M, Tajkhorshid E. Computational Recipe for Efficient Description of Large-Scale Conformational Changes in Biomolecular Systems. J Chem Theory Comput 2014; 10:2866-2880. [PMID: 25018675 PMCID: PMC4089915 DOI: 10.1021/ct5002285] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Indexed: 11/30/2022]
Abstract
Characterizing large-scale structural transitions in biomolecular systems poses major technical challenges to both experimental and computational approaches. On the computational side, efficient sampling of the configuration space along the transition pathway remains the most daunting challenge. Recognizing this issue, we introduce a knowledge-based computational approach toward describing large-scale conformational transitions using (i) nonequilibrium, driven simulations combined with work measurements and (ii) free energy calculations using empirically optimized biasing protocols. The first part is based on designing mechanistically relevant, system-specific reaction coordinates whose usefulness and applicability in inducing the transition of interest are examined using knowledge-based, qualitative assessments along with nonequilirbrium work measurements which provide an empirical framework for optimizing the biasing protocol. The second part employs the optimized biasing protocol resulting from the first part to initiate free energy calculations and characterize the transition quantitatively. Using a biasing protocol fine-tuned to a particular transition not only improves the accuracy of the resulting free energies but also speeds up the convergence. The efficiency of the sampling will be assessed by employing dimensionality reduction techniques to help detect possible flaws and provide potential improvements in the design of the biasing protocol. Structural transition of a membrane transporter will be used as an example to illustrate the workings of the proposed approach.
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Affiliation(s)
- Mahmoud Moradi
- Department of Biochemistry,
Center for Biophysics and Computational Biology, and Beckman Institute
for Advanced Science and Technology, University
of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Emad Tajkhorshid
- Department of Biochemistry,
Center for Biophysics and Computational Biology, and Beckman Institute
for Advanced Science and Technology, University
of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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Li W, Ma A. Recent developments in methods for identifying reaction coordinates. MOLECULAR SIMULATION 2014; 40:784-793. [PMID: 25197161 PMCID: PMC4152980 DOI: 10.1080/08927022.2014.907898] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
In the study of rare events in complex systems with many degrees of freedom, a key element is to identify the reaction coordinates of a given process. Over recent years, a number of methods and protocols have been developed to extract the reaction coordinates based on limited information from molecular dynamics simulations. In this review, we provide a brief survey over a number of major methods developed in the past decade, some of which are discussed in greater detail, to provide an overview of the problems that are partially solved and challenges that still remain. A particular emphasis has been placed on methods for identifying reaction coordinates that are related to the committor.
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Affiliation(s)
- Wenjin Li
- Department of Bioengineering, The University of Illinois at Chicago, 851 South Morgan Street, Chicago, IL 60607, USA
| | - Ao Ma
- Department of Bioengineering, The University of Illinois at Chicago, 851 South Morgan Street, Chicago, IL 60607, USA
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