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Stylianakis I, Zervos N, Lii JH, Pantazis DA, Kolocouris A. Conformational energies of reference organic molecules: benchmarking of common efficient computational methods against coupled cluster theory. J Comput Aided Mol Des 2023; 37:607-656. [PMID: 37597063 PMCID: PMC10618395 DOI: 10.1007/s10822-023-00513-5] [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] [Received: 05/09/2023] [Accepted: 06/03/2023] [Indexed: 08/21/2023]
Abstract
We selected 145 reference organic molecules that include model fragments used in computer-aided drug design. We calculated 158 conformational energies and barriers using force fields, with wide applicability in commercial and free softwares and extensive application on the calculation of conformational energies of organic molecules, e.g. the UFF and DREIDING force fields, the Allinger's force fields MM3-96, MM3-00, MM4-8, the MM2-91 clones MMX and MM+, the MMFF94 force field, MM4, ab initio Hartree-Fock (HF) theory with different basis sets, the standard density functional theory B3LYP, the second-order post-HF MP2 theory and the Domain-based Local Pair Natural Orbital Coupled Cluster DLPNO-CCSD(T) theory, with the latter used for accurate reference values. The data set of the organic molecules includes hydrocarbons, haloalkanes, conjugated compounds, and oxygen-, nitrogen-, phosphorus- and sulphur-containing compounds. We reviewed in detail the conformational aspects of these model organic molecules providing the current understanding of the steric and electronic factors that determine the stability of low energy conformers and the literature including previous experimental observations and calculated findings. While progress on the computer hardware allows the calculations of thousands of conformations for later use in drug design projects, this study is an update from previous classical studies that used, as reference values, experimental ones using a variety of methods and different environments. The lowest mean error against the DLPNO-CCSD(T) reference was calculated for MP2 (0.35 kcal mol-1), followed by B3LYP (0.69 kcal mol-1) and the HF theories (0.81-1.0 kcal mol-1). As regards the force fields, the lowest errors were observed for the Allinger's force fields MM3-00 (1.28 kcal mol-1), ΜΜ3-96 (1.40 kcal mol-1) and the Halgren's MMFF94 force field (1.30 kcal mol-1) and then for the MM2-91 clones MMX (1.77 kcal mol-1) and MM+ (2.01 kcal mol-1) and MM4 (2.05 kcal mol-1). The DREIDING (3.63 kcal mol-1) and UFF (3.77 kcal mol-1) force fields have the lowest performance. These model organic molecules we used are often present as fragments in drug-like molecules. The values calculated using DLPNO-CCSD(T) make up a valuable data set for further comparisons and for improved force field parameterization.
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Affiliation(s)
- Ioannis Stylianakis
- Department of Medicinal Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, Panepistimioupolis Zografou, 15771, Athens, Greece
| | - Nikolaos Zervos
- Department of Medicinal Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, Panepistimioupolis Zografou, 15771, Athens, Greece
| | - Jenn-Huei Lii
- Department of Chemistry, National Changhua University of Education, Changhua City, Taiwan
| | - Dimitrios A Pantazis
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
| | - Antonios Kolocouris
- Department of Medicinal Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, Panepistimioupolis Zografou, 15771, Athens, Greece.
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, 15771, Athens, Greece.
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Molecular modeling, molecular dynamics simulation, and essential dynamics analysis of grancalcin: An upregulated biomarker in experimental autoimmune encephalomyelitis mice. Heliyon 2022; 8:e11232. [PMID: 36340004 PMCID: PMC9626934 DOI: 10.1016/j.heliyon.2022.e11232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 05/30/2022] [Accepted: 10/20/2022] [Indexed: 11/06/2022] Open
Abstract
The experimental autoimmune encephalomyelitis mouse model is the most commonly used animal model, and it best represents multiple sclerosis. Grancalcin (GCA) was discovered to be upregulated in EAE mice. GCA comprises 220 amino acids that have been assigned the UniprotKB ID Q8VC88. It is a calcium-binding protein that helps neutrophils adhere to fibronectin and the formation of focal adhesions. However, the protein data bank does not contain the crystal structure of mouse GCA. The current study aims to analyze the structural and physicochemical properties of GCA. Mouse GCA showed a high percentage identity (87%) with the crystal structure of des (1–52) grancalcin with bound calcium (chain A) from Homo sapiens identified by its PDB id 1k94_A. Using the SWISS-MODEL server, we used 1k94_A as a template protein to model the mouse GCA protein. Compared to the template structure 1K94, three potential binding sites for calcium-binding have been proposed, ranging from 13 to 20, 80 to 91, and 109 to 120 amino acids. On an i5 personal computer with 8GB of RAM, GROMACS 2020.1 was utilized to run a 100 ns molecular dynamics (MD) simulation. RMSD, Rg, and RMSF analysis of an MD simulation trajectory indicate a stable and compact state throughout the simulation period of modeled proteins. We found that GCA is primarily alpha helical (Class 1), with eight alpha helices. The essential dynamics analysis captures PCA and SASA, culminating in the biological motions that correspond to the last 1000 frames. These findings will aid the development of potential inhibitors as well as the determination of binding pockets and residues for drug-like molecules.
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Hajibabaei A, Ha M, Pourasad S, Kim J, Kim KS. Machine Learning of First-Principles Force-Fields for Alkane and Polyene Hydrocarbons. J Phys Chem A 2021; 125:9414-9420. [PMID: 34657427 DOI: 10.1021/acs.jpca.1c05819] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Machine learning (ML) interatomic potentials (ML-IAPs) are generated for alkane and polyene hydrocarbons using on-the-fly adaptive sampling and a sparse Gaussian process regression (SGPR) algorithm. The ML model is generated based on the PBE+D3 level of density functional theory (DFT) with molecular dynamics (MD) for small alkane and polyene molecules. Intermolecular interactions are also trained with clusters and condensed phases of small molecules. It shows excellent transferability to long alkanes and closely describes the ab inito potential energy surface for polyenes. Simulation of liquid ethane also shows reasonable agreement with experimental reports. This is a promising initiative toward a universal ab initio quality force-field for hydrocarbons and organic molecules.
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Affiliation(s)
- Amir Hajibabaei
- Center for Superfunctional Materials, Department of Chemistry, Ulsan National Institute of Science and Technology, 50 UNIST-gil, Ulsan 44919, Korea
| | - Miran Ha
- Center for Superfunctional Materials, Department of Chemistry, Ulsan National Institute of Science and Technology, 50 UNIST-gil, Ulsan 44919, Korea
| | - Saeed Pourasad
- Center for Superfunctional Materials, Department of Chemistry, Ulsan National Institute of Science and Technology, 50 UNIST-gil, Ulsan 44919, Korea
| | - Junu Kim
- Center for Superfunctional Materials, Department of Chemistry, Ulsan National Institute of Science and Technology, 50 UNIST-gil, Ulsan 44919, Korea
| | - Kwang S Kim
- Center for Superfunctional Materials, Department of Chemistry, Ulsan National Institute of Science and Technology, 50 UNIST-gil, Ulsan 44919, Korea
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Abreu CRA, Tuckerman ME. Hamiltonian based resonance-free approach for enabling very large time steps in multiple time-scale molecular dynamics. Mol Phys 2021. [DOI: 10.1080/00268976.2021.1923848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Charlles R. A. Abreu
- Chemical Engineering Department, Escola de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Mark E. Tuckerman
- Department of Chemistry, New York University, New York, NY, USA
- Courant Institute of Mathematical Sciences, New York University, New York, NY, USA
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, People's Republic of China
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Designing a multi-epitope vaccine against the Lassa virus through reverse vaccinology, subtractive proteomics, and immunoinformatics approaches. INFORMATICS IN MEDICINE UNLOCKED 2021. [DOI: 10.1016/j.imu.2021.100683] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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Kashefolgheta S, Oliveira MP, Rieder SR, Horta BAC, Acree WE, Hünenberger PH. Evaluating Classical Force Fields against Experimental Cross-Solvation Free Energies. J Chem Theory Comput 2020; 16:7556-7580. [DOI: 10.1021/acs.jctc.0c00688] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Sadra Kashefolgheta
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Marina P. Oliveira
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Salomé R. Rieder
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Bruno A. C. Horta
- Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-909, Brazil
| | - William E. Acree
- Department of Chemistry, University of North Texas, 1155 Union Circle Drive #305070, Denton, Texas 76203, United States
| | - Philippe H. Hünenberger
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
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Kamiya N, Kayanuma M, Fujitani H, Shinoda K. A New Lipid Force Field (FUJI). J Chem Theory Comput 2020; 16:3664-3676. [PMID: 32384238 DOI: 10.1021/acs.jctc.9b01195] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
To explore inhomogeneous and anisotropic systems such as lipid bilayers, the Lennard-Jones particle mesh Ewald (LJ-PME) method has been applied without a conventional isotropic dispersion correction. As the popular AMBER and CHARMM lipid force fields were developed using a cutoff scheme, their lipid bilayers unacceptably shrink when using the LJ-PME method. In this study, a new all-atom lipid force field (FUJI) was developed on the basis of the AMBER force-field scheme including the Lipid14 van der Waals parameters. Point charges were calculated using the restrained electrostatic potentials of many lipid conformers. Further, torsion energy profiles were calculated using high-level ab initio molecular orbitals (LCCSD(T)/Aug-cc-pVTZ//LMP2/Aug-cc-pVTZ), following which the molecular mechanical dihedral parameters were derived through a fast Fourier transform. By incorporation of these parameters into a new lipid force field without fitting experimental data, the desired lipid characteristics such as the area per lipid and lateral diffusion coefficients were obtained through GROMACS molecular dynamics simulations using the LJ-PME method and virtual hydrogen sites. The calculated area per lipid and lateral diffusion coefficients showed satisfactory agreement with experimental data. Furthermore, the electron-density profiles along the membrane normal were calculated for pure lipid bilayers, and the resulting membrane thicknesses agreed well with the experimental values. As the new lipid force field is compatible with FUJI for protein and small molecules, the new FUJI force field will offer accurate modeling for complex systems consisting of various membrane proteins and lipids.
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Affiliation(s)
- Nozomu Kamiya
- Fujitsu Limited Bio-IT R&D Office, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Megumi Kayanuma
- Research Center for Computational Design of Advanced Functional Materials, National Institute of Advanced Industrial Science and Technology, 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
| | - Hideaki Fujitani
- Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Keiko Shinoda
- Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
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Arcangeli C, Lico C, Baschieri S, Mancuso M. Characterization Of Blood-Brain Barrier Crossing And Tumor Homing Peptides By Molecular Dynamics Simulations. Int J Nanomedicine 2020; 14:10123-10136. [PMID: 31920308 PMCID: PMC6941700 DOI: 10.2147/ijn.s225793] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 10/17/2019] [Indexed: 01/25/2023] Open
Abstract
Introduction The new frontier of tumor diagnosis and treatment relies on the development of delivery strategies capable of allowing the specific targeting of the diagnostic agents/chemotherapeutics, avoiding side effects. In the case of brain tumors, achieving this goal is made more difficult by the presence of the blood–brain barrier (BBB). Peptides have been revealed as excellent candidates for both BBB crossing and specific cancer homing. Nanoparticles (NPs), functionalized with BBB crossing and tumor homing (TH) peptides, are emerging as smart theranostic systems. However, there is still poor knowledge concerning the molecular structure and dynamical properties of these peptides, essential requirements for a suitable functionalization of the delivery systems themselves. Methods In this work, by means of molecular dynamics (MD) simulations, we have extensively characterized the structural and dynamical behavior of several peptides, known to be endowed of BBB crossing and TH properties. Results The simulations point out that, on the basis of their conformational dynamics, the peptides can be classified in two main groups: 1) peptides assuming a specific structural conformation, a feature that could be important for interacting with the molecular target but that may limit their use as functionalizing molecules and 2) highly flexible peptides whose interaction with the target may be independent of a particular structural conformation and that may represent good candidates for the functionalization of theranostic NP-based platforms. Discussion Such findings may be useful for the de novo designing of NP-based delivery systems. ![]()
Point your SmartPhone at the code above. If you have a QR code reader the video abstract will appear. Or use: https://youtu.be/wp8npbWb754
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Affiliation(s)
- Caterina Arcangeli
- Laboratory of Health and Environment, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, ENEA, Rome, Italy
| | - Chiara Lico
- Laboratory of Biotechnology, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, ENEA, Rome, Italy
| | - Selene Baschieri
- Laboratory of Biotechnology, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, ENEA, Rome, Italy
| | - Mariateresa Mancuso
- Laboratory of Biomedical Technologies, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, ENEA, Rome, Italy
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Kubincová A, Riniker S, Hünenberger PH. Reaction-field electrostatics in molecular dynamics simulations: development of a conservative scheme compatible with an atomic cutoff. Phys Chem Chem Phys 2020; 22:26419-26437. [DOI: 10.1039/d0cp03835k] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Shifting and switching schemes are developed to enable strict energy conservation in molecular dynamics simulations relying on reaction-field electrostatic (as well as Lennard-Jones) interactions with an atom-based cutoff truncation.
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Affiliation(s)
| | - Sereina Riniker
- Laboratory of Physical Chemistry
- ETH Zurich
- 8093 Zurich
- Switzerland
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10
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Yang S, Liu H, Zhang Y, Lu H, Chen H. Residue-Specific Force Field Improving the Sample of Intrinsically Disordered Proteins and Folded Proteins. J Chem Inf Model 2019; 59:4793-4805. [DOI: 10.1021/acs.jcim.9b00647] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sheng Yang
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, SJTU−Yale Joint Center for Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Hao Liu
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, SJTU−Yale Joint Center for Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Yangpeng Zhang
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, SJTU−Yale Joint Center for Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Hui Lu
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, SJTU−Yale Joint Center for Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
- SJTU-Yale Joint Center for Biostatistics and Data Science, 800 Dongchuan Road, Shanghai, 200240, China
| | - Haifeng Chen
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, SJTU−Yale Joint Center for Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
- Shanghai Center for Bioinformation Technology, 1278 Keyuan Road, Shanghai, 200235, China
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11
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Paul S, Nair NN, Vashisth H. Phase space and collective variable based simulation methods for studies of rare events. MOLECULAR SIMULATION 2019. [DOI: 10.1080/08927022.2019.1634268] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Sanjib Paul
- Department of Chemical Engineering, University of New Hampshire, Durham, NH, USA
| | - Nisanth N. Nair
- Department of Chemistry, Indian Institute of Technology, Kanpur, India
| | - Harish Vashisth
- Department of Chemical Engineering, University of New Hampshire, Durham, NH, USA
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12
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Yamashita T. Toward rational antibody design: recent advancements in molecular dynamics simulations. Int Immunol 2019; 30:133-140. [PMID: 29346652 DOI: 10.1093/intimm/dxx077] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 01/11/2018] [Indexed: 01/02/2023] Open
Abstract
Because antibodies have become an important therapeutic tool, rational antibody design is a challenging issue involving various science and technology fields. From the computational aspect, many types of design-assist methods have been developed, but their accuracy is not fully satisfactory. Because of recent advancements in computational power, molecular dynamics (MD) simulation has become a helpful tool to trace the motion of proteins and to characterize their properties. Thus, MD simulation has been applied to various systems involving antigen-antibody complexes and has been shown to provide accurate insight into antigen-antibody interactions and dynamics at an atomic resolution. Therefore, it is highly possible that MD simulation will play several roles complementing the conventional antibody design. In this review, we address several important features of MD simulation in the context of rational antibody design.
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Affiliation(s)
- Takefumi Yamashita
- Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, Japan
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13
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Awasthi S, Nair NN. Exploring high‐dimensional free energy landscapes of chemical reactions. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2018. [DOI: 10.1002/wcms.1398] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Shalini Awasthi
- Department of Chemistry Indian Institute of Technology Kanpur Uttar Pradesh India
| | - Nisanth N. Nair
- Department of Chemistry Indian Institute of Technology Kanpur Uttar Pradesh India
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14
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Cuendet MA, Margul DT, Schneider E, Vogt-Maranto L, Tuckerman ME. Endpoint-restricted adiabatic free energy dynamics approach for the exploration of biomolecular conformational equilibria. J Chem Phys 2018; 149:072316. [DOI: 10.1063/1.5027479] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Affiliation(s)
- Michel A. Cuendet
- Molecular Modeling Group, Swiss Institute of Bioinformatics, UNIL Sorge, 1015 Lausanne, Switzerland
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York 10065, USA
| | - Daniel T. Margul
- Department of Chemistry, New York University, New York, New York 10003, USA
| | - Elia Schneider
- Department of Chemistry, New York University, New York, New York 10003, USA
| | | | - Mark E. Tuckerman
- Department of Chemistry, New York University, New York, New York 10003, USA
- Courant Institute of Mathematical Sciences, New York University, New York, New York 10012, USA
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, 3663 Zhongshan Road North, Shanghai 200062, China
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Schneider E, Dai L, Topper RQ, Drechsel-Grau C, Tuckerman ME. Stochastic Neural Network Approach for Learning High-Dimensional Free Energy Surfaces. PHYSICAL REVIEW LETTERS 2017; 119:150601. [PMID: 29077427 DOI: 10.1103/physrevlett.119.150601] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Indexed: 05/27/2023]
Abstract
The generation of free energy landscapes corresponding to conformational equilibria in complex molecular systems remains a significant computational challenge. Adding to this challenge is the need to represent, store, and manipulate the often high-dimensional surfaces that result from rare-event sampling approaches employed to compute them. In this Letter, we propose the use of artificial neural networks as a solution to these issues. Using specific examples, we discuss network training using enhanced-sampling methods and the use of the networks in the calculation of ensemble averages.
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Affiliation(s)
- Elia Schneider
- Department of Chemistry, New York University, New York, New York 10003, USA
| | - Luke Dai
- Department of Chemistry, New York University, New York, New York 10003, USA
| | - Robert Q Topper
- Department of Chemistry, The Cooper Union for the Advancement of Science and Art, 41 Cooper Square, New York, New York 10003, USA
| | | | - Mark E Tuckerman
- Department of Chemistry, New York University, New York, New York 10003, USA
- Courant Institute of Mathematical Science, New York University, New York, New York 10003, USA
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, 3663 Zhongshan Road North, Shanghai 200062, China
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Rubio-Martinez J, Tomas MS, Perez JJ. Effect of the solvent on the conformational behavior of the alanine dipeptide deduced from MD simulations. J Mol Graph Model 2017; 78:118-128. [PMID: 29055185 DOI: 10.1016/j.jmgm.2017.10.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 10/07/2017] [Accepted: 10/09/2017] [Indexed: 11/19/2022]
Abstract
In general, peptides do not exhibit a well-defined conformational profile in solution. However, despite the experimental blurred picture associated with their structure, compelling spectroscopic evidence shows that peptides exhibit local order. The conformational profile of a peptide is the result of a balance between intramolecular interactions between different atoms of the molecule and intermolecular interactions between atoms of the molecule and the solvent. Accordingly, the conformational profile of a peptide will change upon the properties of the solvent it is soaked. To get insight into the balance between intra- and intermolecular interactions on the conformational preferences of the peptide backbone we have studied the conformational profile of the alanine dipeptide in diverse solvents using molecular dynamics as sampling technique. Solvents studied include chloroform, methanol, dimethyl sulfoxide, water and N-methylacetamide. Different treatments of the solvent have been studied in the present work including explicit solvent molecules, a generalized Born model and using the bulk dielectric constant of the solvent. The diverse calculations identify four major conformations with different populations in the diverse solvents: the C7eq only sampled in chloroform; the C5 or extended conformation; the polyproline (PII) conformation and the right-handed α-helix conformation (αR). The results of present calculations permit to analyze how the balance between intra- and intermolecular interactions explains the populations of the diverse conformations observed.
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Affiliation(s)
- Jaime Rubio-Martinez
- Dept. of Physical Chemistry, Faculty of Chemistry, Universitat de Barcelona and the Institut de Recerca en Quimica Teorica i Computacional (IQTCUB), Mati i Franques 1-3, 08028 Barcelona, Spain
| | - M Santos Tomas
- Department of Architecture Technology, Universitat Politecnica de Catalunya, Av. Diagonal, 649, E-08028 Barcelona, Spain
| | - Juan J Perez
- Department of Chemical Engineering, Universitat Politecnica de Catalunya- Barcelona Tech, Av. Diagonal, 647, 08028 Barcelona, Spain.
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17
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Polimeni M, Petridis L, Smith JC, Arcangeli C. Dynamics at a Peptide-TiO 2 Anatase (101) Interface. J Phys Chem B 2017; 121:8869-8877. [PMID: 28851213 DOI: 10.1021/acs.jpcb.7b04707] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The interface between biological matter and inorganic materials is a widely investigated research topic due to possible applications in biomedicine and nanotechnology. In this context, the molecular level adsorption mechanism that drives specific recognition between small peptide sequences and inorganic surfaces represents an important topic likely to provide much information useful for designing bioderived materials. Here, we investigate the dynamics at the interface between a Ti-binding peptide sequence (AMRKLPDAPGMHC) and a TiO2 anatase surface by using molecular dynamics (MD) simulations. In the simulations the adsorption mechanism is characterized by diffusion of the peptide from the bulk water phase toward the TiO2 surface, followed by the anchoring of the peptide to the surface. The anchoring is mediated by the interfacial water layers by means of the charged groups of the side chains of the peptide. The peptide samples anchored and dissociated states from the surface and its conformation is not affected by the surface when anchored.
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Affiliation(s)
- Marco Polimeni
- NAST Centre, Deptartment of Physics, "Roma Tor Vergata" University , 00133 Rome, Italy
| | - Loukas Petridis
- Center for Molecular Biophysics, Oak Ridge National Laboratory , P.O. Box 2008, Oak Ridge, Tennessee 37830, United States
| | - Jeremy C Smith
- Center for Molecular Biophysics, Oak Ridge National Laboratory , P.O. Box 2008, Oak Ridge, Tennessee 37830, United States
| | - Caterina Arcangeli
- R.C. Casaccia, ENEA Italian National Agency for New Technologies, Energy and Sustainable Economic Development , Via Anguillarese, 301, 00123 Rome, Italy
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Cendejas K, Parker HE, Molina D, Choudhury R. Supramolecular self-assembly of water-soluble cavitands: investigated by molecular dynamics simulation. J INCL PHENOM MACRO 2017. [DOI: 10.1007/s10847-017-0750-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Moitra P, Subramanian Y, Bhattacharya S. Concentration Dependent Self-Assembly of TrK-NGF Receptor Derived Tripeptide: New Insights from Experiment and Computer Simulations. J Phys Chem B 2017; 121:815-824. [DOI: 10.1021/acs.jpcb.6b10511] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Parikshit Moitra
- Department
of Organic Chemistry, Indian Institute of Science, Bangalore 560012, India
| | - Yashonath Subramanian
- Solid
State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
- Condensed
Matter Theory Unit, Jawaharlal Nehru Center for Advanced Scientific Research, Bangalore 560064, India
| | - Santanu Bhattacharya
- Department
of Organic Chemistry, Indian Institute of Science, Bangalore 560012, India
- Director’s
Research Unit, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
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20
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Cuendet MA, Weinstein H, LeVine MV. The Allostery Landscape: Quantifying Thermodynamic Couplings in Biomolecular Systems. J Chem Theory Comput 2016; 12:5758-5767. [PMID: 27766843 PMCID: PMC5156960 DOI: 10.1021/acs.jctc.6b00841] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
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Allostery plays a fundamental role
in most biological processes.
However, little theory is available to describe it outside of two-state
models. Here we use a statistical mechanical approach to show that
the allosteric coupling between two collective variables is not a
single number, but instead a two-dimensional thermodynamic coupling
function that is directly related to the mutual information from information
theory and the copula density function from probability theory. On
this basis, we demonstrate how to quantify the contribution of specific
energy terms to this thermodynamic coupling function, enabling an
approximate decomposition that reveals the mechanism of allostery.
We illustrate the thermodynamic coupling function and its use by showing
how allosteric coupling in the alanine dipeptide molecule contributes
to the overall shape of the Φ/Ψ free energy surface, and
by identifying the interactions that are necessary for this coupling.
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Affiliation(s)
- Michel A Cuendet
- Swiss Institute of Bioinformatics, UNIL Sorge, 1015 Lausanne, Switzerland
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21
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Hakulinen R, Puranen S. Probabilistic model to treat flexibility in molecular contacts. Mol Phys 2016. [DOI: 10.1080/00268976.2016.1225129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Riku Hakulinen
- Structural Bioinformatics Laboratory/Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
| | - Santeri Puranen
- Department of Computer Science, Aalto University, Espoo, Finland
- Department of Computer Science, University of Helsinki, Helsinki, Finland
- Helsinki Institute for Information Technology HIIT, Helsinki, Finland
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22
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Erler J, Zhang R, Petridis L, Cheng X, Smith JC, Langowski J. The role of histone tails in the nucleosome: a computational study. Biophys J 2016; 107:2911-2922. [PMID: 25517156 DOI: 10.1016/j.bpj.2014.10.065] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 10/13/2014] [Accepted: 10/15/2014] [Indexed: 11/29/2022] Open
Abstract
Histone tails play an important role in gene transcription and expression. We present here a systematic computational study of the role of histone tails in the nucleosome, using replica exchange molecular dynamics simulations with an implicit solvent model and different well-established force fields. We performed simulations for all four histone tails, H4, H3, H2A, and H2B, isolated and with inclusion of the nucleosome. The results confirm predictions of previous theoretical studies for the secondary structure of the isolated tails but show a strong dependence on the force field used. In the presence of the entire nucleosome for all force fields, the secondary structure of the histone tails is destabilized. Specific contacts are found between charged lysine and arginine residues and DNA phosphate groups and other binding sites in the minor and major DNA grooves. Using cluster analysis, we found a single dominant configuration of binding to DNA for the H4 and H2A histone tails, whereas H3 and H2B show multiple binding configurations with an equal probability. The leading stabilizing contribution for those binding configurations is the attractive interaction between the positively charged lysine and arginine residues and the negatively charged phosphate groups, and thus the resulting charge neutralization. Finally, we present results of molecular dynamics simulations in explicit solvent to confirm our conclusions. Results from both implicit and explicit solvent models show that large portions of the histone tails are not bound to DNA, supporting the complex role of these tails in gene transcription and expression and making them possible candidates for binding sites of transcription factors, enzymes, and other proteins.
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Affiliation(s)
- Jochen Erler
- Division of Biophysics of Macromolecules, German Cancer Research Center, Heidelberg, Germany
| | - Ruihan Zhang
- Division of Biophysics of Macromolecules, German Cancer Research Center, Heidelberg, Germany
| | - Loukas Petridis
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Xiaolin Cheng
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Jeremy C Smith
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Jörg Langowski
- Division of Biophysics of Macromolecules, German Cancer Research Center, Heidelberg, Germany.
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23
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Baldauf C, Rossi M. Going clean: structure and dynamics of peptides in the gas phase and paths to solvation. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2015; 27:493002. [PMID: 26598600 DOI: 10.1088/0953-8984/27/49/493002] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The gas phase is an artificial environment for biomolecules that has gained much attention both experimentally and theoretically due to its unique characteristic of providing a clean room environment for the comparison between theory and experiment. In this review we give an overview mainly on first-principles simulations of isolated peptides and the initial steps of their interactions with ions and solvent molecules: a bottom up approach to the complexity of biological environments. We focus on the accuracy of different methods to explore the conformational space, the connections between theory and experiment regarding collision cross section evaluations and (anharmonic) vibrational spectra, and the challenges faced in this field.
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Affiliation(s)
- Carsten Baldauf
- Fritz Haber Institute, Faradayweg 4-6, 14195 Berlin, Germany
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24
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Cormanich RA, Bühl M, Rittner R. Understanding the conformational behaviour of Ac-Ala-NHMe in different media. A joint NMR and DFT study. Org Biomol Chem 2015. [PMID: 26219244 DOI: 10.1039/c5ob01296a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The conformational behaviour of Ac-Ala-NHMe was studied in the gas-phase and in solution by theoretical calculations (B3LYP-D3/aug-cc-pVDZ level) and experimental (1)H NMR. The conformational preferences of this compound were shown to result from a complex interplay between the strengths of possible intramolecular hydrogen bonds, steric interactions, hyperconjugation, entropy effects and the overall dipole moments. The Ac-Ala-N(Me)2 derivative was studied in addition, to design a system akin to Ac-Ala-NHMe, but with disrupted intramolecular hydrogen bonds involving the -NHMe group, mimicking the effect of polar protic solvents.
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Affiliation(s)
- Rodrigo A Cormanich
- Chemistry Institute, University of Campinas, Campinas, SP 13083-970, Brazil.
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25
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Robertson M, Tirado-Rives J, Jorgensen WL. Improved Peptide and Protein Torsional Energetics with the OPLSAA Force Field. J Chem Theory Comput 2015; 11:3499-509. [PMID: 26190950 PMCID: PMC4504185 DOI: 10.1021/acs.jctc.5b00356] [Citation(s) in RCA: 482] [Impact Index Per Article: 53.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Indexed: 11/28/2022]
Abstract
The development and validation of new peptide dihedral parameters are reported for the OPLS-AA force field. High accuracy quantum chemical methods were used to scan φ, ψ, χ1, and χ2 potential energy surfaces for blocked dipeptides. New Fourier coefficients for the dihedral angle terms of the OPLS-AA force field were fit to these surfaces, utilizing a Boltzmann-weighted error function and systematically examining the effects of weighting temperature. To prevent overfitting to the available data, a minimal number of new residue-specific and peptide-specific torsion terms were developed. Extensive experimental solution-phase and quantum chemical gas-phase benchmarks were used to assess the quality of the new parameters, named OPLS-AA/M, demonstrating significant improvement over previous OPLS-AA force fields. A Boltzmann weighting temperature of 2000 K was determined to be optimal for fitting the new Fourier coefficients for dihedral angle parameters. Conclusions are drawn from the results for best practices for developing new torsion parameters for protein force fields.
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Affiliation(s)
- Michael
J. Robertson
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Julian Tirado-Rives
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - William L. Jorgensen
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
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26
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Yamashita T, Ueda A, Mitsui T, Tomonaga A, Matsumoto S, Kodama T, Fujitani H. The Feasibility of an Efficient Drug Design Method with High-Performance Computers. Chem Pharm Bull (Tokyo) 2015; 63:147-55. [DOI: 10.1248/cpb.c14-00596] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Takefumi Yamashita
- Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo
| | - Akihiko Ueda
- Bio-IT R&D Office, Next-Generation Healthcare Innovation Center, Fujitsu Limited
| | - Takashi Mitsui
- Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo
- Bio-IT R&D Office, Next-Generation Healthcare Innovation Center, Fujitsu Limited
| | - Atsushi Tomonaga
- Bio-IT R&D Office, Next-Generation Healthcare Innovation Center, Fujitsu Limited
| | - Shunji Matsumoto
- Bio-IT R&D Office, Next-Generation Healthcare Innovation Center, Fujitsu Limited
| | - Tatsuhiko Kodama
- Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo
| | - Hideaki Fujitani
- Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo
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