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Gogal RA, Nessler AJ, Thiel AC, Bernabe HV, Corrigan Grove RA, Cousineau LM, Litman JM, Miller JM, Qi G, Speranza MJ, Tollefson MR, Fenn TD, Michaelson JJ, Okada O, Piquemal JP, Ponder JW, Shen J, Smith RJH, Yang W, Ren P, Schnieders MJ. Force Field X: A computational microscope to study genetic variation and organic crystals using theory and experiment. J Chem Phys 2024; 161:012501. [PMID: 38958156 PMCID: PMC11223778 DOI: 10.1063/5.0214652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 06/17/2024] [Indexed: 07/04/2024] Open
Abstract
Force Field X (FFX) is an open-source software package for atomic resolution modeling of genetic variants and organic crystals that leverages advanced potential energy functions and experimental data. FFX currently consists of nine modular packages with novel algorithms that include global optimization via a many-body expansion, acid-base chemistry using polarizable constant-pH molecular dynamics, estimation of free energy differences, generalized Kirkwood implicit solvent models, and many more. Applications of FFX focus on the use and development of a crystal structure prediction pipeline, biomolecular structure refinement against experimental datasets, and estimation of the thermodynamic effects of genetic variants on both proteins and nucleic acids. The use of Parallel Java and OpenMM combines to offer shared memory, message passing, and graphics processing unit parallelization for high performance simulations. Overall, the FFX platform serves as a computational microscope to study systems ranging from organic crystals to solvated biomolecular systems.
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Affiliation(s)
- Rose A. Gogal
- Roy J. Carver Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa 52242, USA
| | - Aaron J. Nessler
- Roy J. Carver Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa 52242, USA
| | - Andrew C. Thiel
- Roy J. Carver Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa 52242, USA
| | - Hernan V. Bernabe
- Roy J. Carver Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa 52242, USA
| | - Rae A. Corrigan Grove
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - Leah M. Cousineau
- Department of Biochemistry and Molecular Biology, University of Iowa, Iowa City, Iowa 52242, USA
| | - Jacob M. Litman
- Department of Biochemistry and Molecular Biology, University of Iowa, Iowa City, Iowa 52242, USA
| | - Jacob M. Miller
- Roy J. Carver Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa 52242, USA
| | - Guowei Qi
- Department of Biochemistry and Molecular Biology, University of Iowa, Iowa City, Iowa 52242, USA
| | - Matthew J. Speranza
- Roy J. Carver Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa 52242, USA
| | - Mallory R. Tollefson
- Roy J. Carver Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa 52242, USA
| | - Timothy D. Fenn
- Analytical Development, LEXEO Therapeutics, New York, New York 10010, USA
| | - Jacob J. Michaelson
- Department of Psychiatry, University of Iowa Hospitals and Clinics, Iowa City, Iowa 52242, USA
| | - Okimasa Okada
- Sohyaku Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, 1000 Kamoshida-cho, Aoba-ku, Yokohama, Kanagawa 227-0033, Japan
| | | | - Jay W. Ponder
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, USA
| | - Jana Shen
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, USA
| | - Richard J. H. Smith
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology, University of Iowa Hospitals and Clinics, Iowa City, Iowa 52242, USA
| | | | - Pengyu Ren
- Department of Biomedical Engineering, University of Texas, Austin, Texas 78712, USA
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Nessler A, Okada O, Kinoshita Y, Nishimura K, Nagata H, Fukuzawa K, Yonemochi E, Schnieders MJ. Crystal Polymorph Search in the NPT Ensemble via a Deposition/Sublimation Alchemical Path. CRYSTAL GROWTH & DESIGN 2024; 24:3205-3217. [PMID: 38659664 PMCID: PMC11036363 DOI: 10.1021/acs.cgd.3c01358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 02/22/2024] [Accepted: 02/23/2024] [Indexed: 04/26/2024]
Abstract
The formulation of active pharmaceutical ingredients involves discovering stable crystal packing arrangements or polymorphs, each of which has distinct pharmaceutically relevant properties. Traditional experimental screening techniques utilizing various conditions are commonly supplemented with in silico crystal structure prediction (CSP) to inform the crystallization process and mitigate risk. Predictions are often based on advanced classical force fields or quantum mechanical calculations that model the crystal potential energy landscape but do not fully incorporate temperature, pressure, or solution conditions during the search procedure. This study proposes an innovative alchemical path that utilizes an advanced polarizable atomic multipole force field to predict crystal structures based on direct sampling of the NPT ensemble. The use of alchemical (i.e., nonphysical) intermediates, a novel Monte Carlo barostat, and an orthogonal space tempering bias combine to enhance the sampling efficiency of the deposition/sublimation phase transition. The proposed algorithm was applied to 2-((4-(2-(3,4-dichlorophenyl)ethyl)phenyl)amino)benzoic acid (Cambridge Crystallography Database Centre ID: XAFPAY) as a case study to showcase the algorithm. Each experimentally determined polymorph with one molecule in the asymmetric unit was successfully reproduced via approximately 1000 short 1 ns simulations per space group where each simulation was initiated from random rigid body coordinates and unit cell parameters. Utilizing two threads of a recent Intel CPU (a Xeon Gold 6330 CPU at 2.00 GHz), 1 ns of sampling using the polarizable AMOEBA force field can be acquired in 4 h (equating to more than 300 ns/day using all 112 threads/56 cores of a dual CPU node) within the Force Field X software (https://ffx.biochem.uiowa.edu). These results demonstrate a step forward in the rigorous use of the NPT ensemble during the CSP search process and open the door to future algorithms that incorporate solution conditions using continuum solvation methods.
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Affiliation(s)
- Aaron
J. Nessler
- Department
of Biomedical Engineering, University of
Iowa, 103 South Capitol
Street, 5601 Seamans Center for the Engineering Arts and Sciences, Iowa City, Iowa 52242, United States
| | - Okimasa Okada
- Sohyaku
Innovative Research Division, Mitsubishi
Tanabe Pharma Corporation, 1000 Kamoshida-cho, Aoba-ku, Yokohama, Kanagawa 227-0033, Japan
| | - Yuya Kinoshita
- Analytical
Development, Pharmaceutical Sciences, Takeda
Pharmaceutical Company Limited, 2-26-1, Muraoka-Higashi, Fujisawa 251-8555, Kanagawa, Japan
| | - Koki Nishimura
- Analytical
Development, Pharmaceutical Sciences, Takeda
Pharmaceutical Company Limited, 2-26-1, Muraoka-Higashi, Fujisawa 251-8555, Kanagawa, Japan
| | - Hiroomi Nagata
- CMC
Modality Technology Laboratories, Production Technology and Supply
Chain Management Division, Mitsubishi Tanabe
Pharma Corporation, Osaka 541-8505, Japan
| | - Kaori Fukuzawa
- Graduate
School of Pharmaceutical Sciences, Osaka
University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Etsuo Yonemochi
- Department
of Physical Chemistry, School of Pharmacy and Pharmaceutical Sciences, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo 142-8501, Japan
| | - Michael J. Schnieders
- Department
of Biomedical Engineering, University of
Iowa, 103 South Capitol
Street, 5601 Seamans Center for the Engineering Arts and Sciences, Iowa City, Iowa 52242, United States
- Department
of Biochemistry, University of Iowa, 51 Newton Road, 4-403 Bowen Science
Building, Iowa City, Iowa 52242, United States
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Jin S, Wang JN, Xue Y, Li P, Mei Y. Selectivity of parvalbumin B protein binding to Ca2+ and Mg2+ at an ab initio QM/MM level using the reference-potential method. CHINESE J CHEM PHYS 2021. [DOI: 10.1063/1674-0068/cjcp2109176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Shuwei Jin
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200062, China
| | - Jia-Ning Wang
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200062, China
| | - Yuanfei Xue
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200062, China
| | - Pengfei Li
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200062, China
- Silicon Therapeutics (Suzhou) Co., Ltd., Suzhou 215000, China
| | - Ye Mei
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200062, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan 030006, China
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Jing Z, Rackers JA, Pratt LR, Liu C, Rempe SB, Ren P. Thermodynamics of ion binding and occupancy in potassium channels. Chem Sci 2021; 12:8920-8930. [PMID: 34257893 PMCID: PMC8246295 DOI: 10.1039/d1sc01887f] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 06/01/2021] [Indexed: 12/15/2022] Open
Abstract
Potassium channels modulate various cellular functions through efficient and selective conduction of K+ ions. The mechanism of ion conduction in potassium channels has recently emerged as a topic of debate. Crystal structures of potassium channels show four K+ ions bound to adjacent binding sites in the selectivity filter, while chemical intuition and molecular modeling suggest that the direct ion contacts are unstable. Molecular dynamics (MD) simulations have been instrumental in the study of conduction and gating mechanisms of ion channels. Based on MD simulations, two hypotheses have been proposed, in which the four-ion configuration is an artifact due to either averaged structures or low temperature in crystallographic experiments. The two hypotheses have been supported or challenged by different experiments. Here, MD simulations with polarizable force fields validated by ab initio calculations were used to investigate the ion binding thermodynamics. Contrary to previous beliefs, the four-ion configuration was predicted to be thermodynamically stable after accounting for the complex electrostatic interactions and dielectric screening. Polarization plays a critical role in the thermodynamic stabilities. As a result, the ion conduction likely operates through a simple single-vacancy and water-free mechanism. The simulations explained crystal structures, ion binding experiments and recent controversial mutagenesis experiments. This work provides a clear view of the mechanism underlying the efficient ion conduction and demonstrates the importance of polarization in ion channel simulations. Polarization shapes the energy landscape of ion conduction in potassium channels.![]()
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Affiliation(s)
- Zhifeng Jing
- Department of Biomedical Engineering, The University of Texas at Austin Austin Texas 78712 USA
| | - Joshua A Rackers
- Center for Integrated Nanotechnologies, Sandia National Laboratories Albuquerque New Mexico 87185 USA
| | - Lawrence R Pratt
- Department of Chemical and Biomolecular Engineering, Tulane University New Orleans Louisiana 70118 USA
| | - Chengwen Liu
- Department of Biomedical Engineering, The University of Texas at Austin Austin Texas 78712 USA
| | - Susan B Rempe
- Center for Integrated Nanotechnologies, Sandia National Laboratories Albuquerque New Mexico 87185 USA
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin Austin Texas 78712 USA
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