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Cao S, Kalin ML, Huang X. EPISOL: A software package with expanded functions to perform 3D-RISM calculations for the solvation of chemical and biological molecules. J Comput Chem 2023; 44:1536-1549. [PMID: 36856731 DOI: 10.1002/jcc.27088] [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: 10/29/2022] [Revised: 12/24/2022] [Accepted: 01/29/2023] [Indexed: 03/02/2023]
Abstract
Integral equation theory (IET) provides an effective solvation model for chemical and biological systems that balances computational efficiency and accuracy. We present a new software package, the expanded package for IET-based solvation (EPISOL), that performs 3D-reference interaction site model (3D-RISM) calculations to obtain the solvation structure and free energies of solute molecules in different solvents. In EPISOL, we have implemented 22 different closures, multiple free energy functionals, and new variations of 3D-RISM theory, including the recent hydrophobicity-induced density inhomogeneity (HI) theory for hydrophobic solutes and ion-dipole correction (IDC) theory for negatively charged solutes. To speed up the convergence and enhance the stability of the self-consistent iterations, we have introduced several numerical schemes in EPISOL, including a newly developed dynamic mixing approach. We show that these schemes have significantly reduced the failure rate of 3D-RISM calculations compared to AMBER-RISM software. EPISOL consists of both a user-friendly graphic interface and a kernel library that allows users to call its routines and adapt them to other programs. EPISOL is compatible with the force-field and coordinate files from both AMBER and GROMACS simulation packages. Moreover, EPISOL is equipped with an internal memory control to efficiently manage the use of physical memory, making it suitable for performing calculations on large biomolecules. We demonstrate that EPISOL can efficiently and accurately calculate solvation density distributions around various solute molecules (including a protein chaperone consisting of 120,715 atoms) and obtain solvent free energy for a wide range of organic compounds. We expect that EPISOL can be widely applied as a solvation model for chemical and biological systems. EPISOL is available at https://github.com/EPISOLrelease/EPISOL.
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Affiliation(s)
- Siqin Cao
- Department of Chemistry, Theoretical Chemistry Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Michael L Kalin
- Biophysics Graduate Program, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Xuhui Huang
- Department of Chemistry, Theoretical Chemistry Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
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2
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Cao S, Qiu Y, Unarta IC, Goonetilleke EC, Huang X. The Ion-Dipole Correction of the 3DRISM Solvation Model to Accurately Compute Water Distributions around Negatively Charged Biomolecules. J Phys Chem B 2022; 126:8632-8645. [PMID: 36282904 DOI: 10.1021/acs.jpcb.2c04431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The 3D reference interaction site model (3DRISM) provides an efficient grid-based solvation model to compute the structural and thermodynamic properties of biomolecules in aqueous solutions. However, it remains challenging for existing 3DRISM methods to correctly predict water distributions around negatively charged solute molecules. In this paper, we first show that this challenge is mainly due to the orientation of water molecules in the first solvation shell of the negatively charged solute molecules. To properly consider this orientational preference, position-dependent two-body intramolecular correlations of solvent need to be included in the 3DRISM theory, but direct evaluations of these position-dependent two-body intramolecular correlations remain numerically intractable. To address this challenge, we introduce the Ion-Dipole Correction (IDC) to the 3DRISM theory, in which we incorporate the orientation preference of water molecules via an additional solute-solvent interaction term (i.e., the ion-dipole interaction) while keeping the formulism of the 3DRISM equation unchanged. We prove that this newly introduced IDC term is equivalent to an effective direct correlation function which can effectively consider the orientation effect that arises from position dependent two-body correlations. We first quantitatively validate our 3DRISM-IDC theory combined with the PSE3 closure on Cl-, [ClO]- (a two-site anion), and [NO2]- (a three-site anion). For all three anions, we show that our 3DRISM-IDC theory significantly outperforms the 3DRISM theory in accurately predicting the solvation structures in comparison to MD simulations, including RDFs and 3D water distributions. Furthermore, we have also demonstrated that the 3DRISM-IDC can improve the accuracy of hydration free-energy calculation for Cl-. We further demonstrate that our 3DRISM-IDC theory yields significant improvements over the 3DRISM theory when applied to compute the solvation structures for various negatively charged solute molecules, including adenosine triphosphate (ATP), a short peptide containing 19 residues, a DNA hairpin containing 24 nucleotides, and a riboswitch RNA molecule with 77 nucleotides. We expect that our 3DRISM-IDC-PSE3 solvation model holds great promise to be widely applied to study solvation properties for nucleic acids and other biomolecules containing negatively charged functional groups.
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Affiliation(s)
- Siqin Cao
- Theoretical Chemistry Institute, Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin53706, United States
| | - Yunrui Qiu
- Theoretical Chemistry Institute, Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin53706, United States
| | - Ilona C Unarta
- Theoretical Chemistry Institute, Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin53706, United States
| | - Eshani C Goonetilleke
- Theoretical Chemistry Institute, Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin53706, United States
| | - Xuhui Huang
- Theoretical Chemistry Institute, Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin53706, United States
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3
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Setnickova K, Huang TC, Wang CT, Lin YC, Lee SL, Zhuang GL, Tung KL, Tseng HH, Uchytil P. Realizing the impact of the intermediate layer structure on the CO2/CH4 separation performance of carbon molecular sieving membranes: Insights from experimental synthesis and molecular simulation. Sep Purif Technol 2021. [DOI: 10.1016/j.seppur.2021.118627] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Nguyen H, Thai NQ, Truong DT, Li MS. Remdesivir Strongly Binds to Both RNA-Dependent RNA Polymerase and Main Protease of SARS-CoV-2: Evidence from Molecular Simulations. J Phys Chem B 2020; 124:11337-11348. [PMID: 33264025 PMCID: PMC7724981 DOI: 10.1021/acs.jpcb.0c07312] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 11/12/2020] [Indexed: 02/07/2023]
Abstract
The outbreak of a new coronavirus SARS-CoV-2 (severe acute respiratory syndrome-coronavirus 2) has caused a global COVID-19 (coronavirus disease 2019) pandemic, resulting in millions of infections and thousands of deaths around the world. There is currently no drug or vaccine for COVID-19, but it has been revealed that some commercially available drugs are promising, at least for treating symptoms. Among them, remdesivir, which can block the activity of RNA-dependent RNA polymerase (RdRp) in old SARS-CoV and MERS-CoV viruses, has been prescribed to COVID-19 patients in many countries. A recent experiment showed that remdesivir binds to SARS-CoV-2 with an inhibition constant of μM, but the exact target has not been reported. In this work, combining molecular docking, steered molecular dynamics, and umbrella sampling, we examined its binding affinity to two targets including the main protease (Mpro), also known as 3C-like protease, and RdRp. We showed that remdesivir binds to Mpro slightly weaker than to RdRp, and the corresponding inhibition constants, consistent with the experiment, fall to the μM range. The binding mechanisms of remdesivir to two targets differ in that the electrostatic interaction is the main force in stabilizing the RdRp-remdesivir complex, while the van der Waals interaction dominates in the Mpro-remdesivir case. Our result indicates that remdesivir can target not only RdRp but also Mpro, which can be invoked to explain why this drug is effective in treating COVID-19. We have identified residues of the target protein that make the most important contribution to binding affinity, and this information is useful for drug development for this disease.
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Affiliation(s)
- Hoang
Linh Nguyen
- Life Science Lab, Institute for Computational Science and Technology, Quang Trung Software City, Tan Chanh
Hiep Ward, District 12, Ho Chi Minh City 700000, Vietnam
| | - Nguyen Quoc Thai
- Life Science Lab, Institute for Computational Science and Technology, Quang Trung Software City, Tan Chanh
Hiep Ward, District 12, Ho Chi Minh City 700000, Vietnam
- Dong
Thap University, 783 Pham Huu Lau Street, Ward 6, Cao Lanh
City 870000, Dong Thap, Vietnam
| | - Duc Toan Truong
- Life Science Lab, Institute for Computational Science and Technology, Quang Trung Software City, Tan Chanh
Hiep Ward, District 12, Ho Chi Minh City 700000, Vietnam
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, Warsaw 02-668, Poland
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Miyata T, Yabuki N, Leung J. Transferability of Sigma Enlarging Bridge Function for Lennard-Jones Diatomic Solute Using Monatomic Solvent Correlation Obtained from Molecular Dynamics Simulation. CHEM LETT 2020. [DOI: 10.1246/cl.200521] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Tatsuhiko Miyata
- Department of Physics, Ehime University, 2-5 Bunkyo-Cho, Matsuyama, Ehime 790-8577, Japan
| | - Naoya Yabuki
- Department of Physics, Ehime University, 2-5 Bunkyo-Cho, Matsuyama, Ehime 790-8577, Japan
| | - Jackie Leung
- Department of Physics, Ehime University, 2-5 Bunkyo-Cho, Matsuyama, Ehime 790-8577, Japan
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Miyata T. Sigma enlarging bridge function for heteronuclear Lennard-Jones diatomic solute solvated in a Lennard-Jones monatomic solvent in terms of the parameter transferability. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2020.137777] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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8
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Nguyen HL, Lan PD, Thai NQ, Nissley DA, O'Brien EP, Li MS. Does SARS-CoV-2 Bind to Human ACE2 More Strongly Than Does SARS-CoV? J Phys Chem B 2020; 124:7336-7347. [PMID: 32790406 PMCID: PMC7433338 DOI: 10.1021/acs.jpcb.0c04511] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
![]()
The
2019 novel coronavirus (SARS-CoV-2) epidemic, which was first
reported in December 2019 in Wuhan, China, was declared a pandemic
by the World Health Organization in March 2020. Genetically, SARS-CoV-2
is closely related to SARS-CoV, which caused a global epidemic with
8096 confirmed cases in more than 25 countries from 2002 to 2003.
Given the significant morbidity and mortality rate, the current pandemic
poses a danger to all of humanity, prompting us to understand the
activity of SARS-CoV-2 at the atomic level. Experimental studies have
revealed that spike proteins of both SARS-CoV-2 and SARS-CoV bind
to angiotensin-converting enzyme 2 (ACE2) before entering the cell
for replication. However, the binding affinities reported by different
groups seem to contradict each other. Wrapp et al. (Science2020, 367, 1260–1263) showed
that the spike protein of SARS-CoV-2 binds to the ACE2 peptidase domain
(ACE2-PD) more strongly than does SARS-CoV, and this fact may be associated
with a greater severity of the new virus. However, Walls et al. (Cell2020, 181, 281–292)
reported that SARS-CoV-2 exhibits a higher binding affinity, but the
difference between the two variants is relatively small. To understand
the binding mechnism and experimental results, we investigated how
the receptor binding domain (RBD) of SARS-CoV (SARS-CoV-RBD) and SARS-CoV-2
(SARS-CoV-2-RBD) interacts with a human ACE2-PD using molecular modeling.
We applied a coarse-grained model to calculate the dissociation constant
and found that SARS-CoV-2 displays a 2-fold higher binding affinity.
Using steered all-atom molecular dynamics simulations, we demonstrate
that, like a coarse-grained simulation, SARS-CoV-2-RBD was associated
with ACE2-PD more strongly than was SARS-CoV-RBD, as evidenced by
a higher rupture force and larger pulling work. We show that the binding
affinity of both viruses to ACE2 is driven by electrostatic interactions.
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Affiliation(s)
- Hoang Linh Nguyen
- Life Science Lab, Institute for Computational Science and Technology, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Vietnam
| | - Pham Dang Lan
- Life Science Lab, Institute for Computational Science and Technology, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Vietnam.,Faculty of Physics and Engineering Physics, VNUHCM-University of Science, 227, Nguyen Van Cu Street, District 5, Ho Chi Minh City, Vietnam
| | - Nguyen Quoc Thai
- Life Science Lab, Institute for Computational Science and Technology, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Vietnam.,Dong Thap University, 783 Pham Huu Lau Street, Ward 6, Cao Lanh City, Dong Thap, Vietnam
| | - Daniel A Nissley
- Department of Statistics, University of Oxford, Oxford OX1 2JD, United Kingdom
| | - Edward P O'Brien
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, United States.,Bioinformatics and Genomics Graduate Program, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, United States.,Institute for Computational and Data Sciences, Pennsylvania State University, University Park, Pennsylvania 16802,United States
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, 02-668 Warsaw, Poland
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Abstract
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Accurate determination
of the binding affinity of the ligand to
the receptor remains a difficult problem in computer-aided drug design.
Here, we study and compare the efficiency of Jarzynski’s equality
(JE) combined with steered molecular dynamics and the linear interaction
energy (LIE) method by assessing the binding affinity of 23 small
compounds to six receptors, including β-lactamase, thrombin,
factor Xa, HIV-1 protease (HIV), myeloid cell leukemia-1, and cyclin-dependent
kinase 2 proteins. It was shown that Jarzynski’s nonequilibrium
binding free energy ΔGneqJar correlates with the available
experimental data with the correlation levels R =
0.89, 0.86, 0.83, 0.80, 0.83, and 0.81 for six data sets, while for
the binding free energy ΔGLIE obtained
by the LIE method, we have R = 0.73, 0.80, 0.42,
0.23, 0.85, and 0.01. Therefore, JE is recommended to be used for
ranking binding affinities as it provides accurate and robust results.
In contrast, LIE is not as reliable as JE, and it should be used with
caution, especially when it comes to new systems.
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Affiliation(s)
- Kiet Ho
- Institute for Computational Sciences and Technology, Quang Trung Software City, SBI Building, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Vietnam
| | - Duc Toan Truong
- Institute for Computational Sciences and Technology, Quang Trung Software City, SBI Building, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Vietnam.,Department of Theoretical Physics, Faculty of Physics and Engineering Physics, Ho Chi Minh University of Science, Ho Chi Minh City, Vietnam
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
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10
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Shevkunov SV. Water Vapor Nucleation on a Surface with Nanoscopic Grooves. 2. Features of Thermodynamic Behavior. COLLOID JOURNAL 2019. [DOI: 10.1134/s1061933x19030141] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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11
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Thangsunan P, Wongsaipun S, Kittiwachana S, Suree N. Effective prediction model and determination of binding residues influential for inhibitors targeting HIV-1 integrase-LEDGF/p75 interface by employing solvent accessible surface area energy as key determinant. J Biomol Struct Dyn 2019; 38:460-473. [PMID: 30744499 DOI: 10.1080/07391102.2019.1580219] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Development of a highly accurate prediction model for protein-ligand inhibition has been a major challenge in drug discovery. Herein, we describe a novel predictive model for the inhibition of HIV-1 integrase (IN)-LEDGF/p75 protein-protein interaction. The model was constructed using energy parameters approximated from molecular dynamics (MD) simulations and molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) calculations. Chemometric analysis using partial least squares (PLS) regression revealed that solvent accessible surface area energy (ΔGSASA) is the major determinant parameter contributing greatly to the prediction accuracy. PLS prediction model on the ΔGSASA values collected from 41 complexes yielded a strong correlation between the predicted and the actual inhibitory activities (R2 = 0.9666, RMSEC of pIC50 values = 0.0890). Additionally, for the test set of 14 complexes, the model performed satisfactorily with very low pIC50 errors (Q2 = 0.5168, RMSEP = 0.3325). A strong correlation between the buried surface areas on the IN protein, when bound with IN-LEDGF/p75 inhibitors, and the respective ΔGSASA values was also obtained. Furthermore, the current method could identify 'hot spots'of amino acid residues highly influential to the inhibitory activity prediction. This could present fruitful implications in binding site determination and future inhibitor developments targeting protein-protein interactions.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Patcharapong Thangsunan
- Interdisciplinary Program in Biotechnology, Graduate School, Chiang Mai University, Muang, Chiang Mai, Thailand.,Division of Biochemistry and Biochemical Technology, Department of Chemistry, Faculty of Science, Chiang Mai University, Muang, Chiang Mai, Thailand
| | - Sakunna Wongsaipun
- Department of Chemistry, Faculty of Science, Chiang Mai University, Muang, Chiang Mai, Thailand
| | - Sila Kittiwachana
- Department of Chemistry, Faculty of Science, Chiang Mai University, Muang, Chiang Mai, Thailand
| | - Nuttee Suree
- Division of Biochemistry and Biochemical Technology, Department of Chemistry, Faculty of Science, Chiang Mai University, Muang, Chiang Mai, Thailand.,Department of Chemistry, Faculty of Science, Chiang Mai University, Muang, Chiang Mai, Thailand.,Center of Excellence in Materials Science and Technology, Chiang Mai University, Chiang Mai, Thailand
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12
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Performance of Kobryn-Gusarov-Kovalenko closure from a thermodynamic viewpoint for one-component Lennard-Jones fluids. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.04.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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13
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Shevkunov SV. High-temperature stability of the hydrate shell of a Na+ cation in a flat nanopore with hydrophobic walls. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2017. [DOI: 10.1134/s0036024417150018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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14
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Correction of Kovalenko-Hirata closure in Ornstein-Zernike integral equation theory for Lennard-Jones fluids. J Mol Liq 2017. [DOI: 10.1016/j.molliq.2017.05.134] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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15
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Miyata T. A Parameterization of Empirical Sigma Enlarging Bridge Correction of Kovalenko-Hirata Closure in Ornstein-Zernike Theory for Lennard-Jones Fluids. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2017. [DOI: 10.1246/bcsj.20170203] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Tatsuhiko Miyata
- Department of Physics, Ehime University, 2-5 Bunkyo-Cho, Matsuyama, Ehime 790-8577
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16
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Munaò G, Saija F. Integral equation study of soft-repulsive dimeric fluids. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2017; 29:115101. [PMID: 28155850 DOI: 10.1088/1361-648x/aa5306] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We study fluid structure and water-like anomalies of a system constituted by dimeric particles interacting via a purely repulsive core-softened potential by means of integral equation theories. In our model, dimers interact through a repulsive pair potential of inverse-power form with a softened repulsion strength. By employing the Ornstein-Zernike approach and the reference interaction site model (RISM) theory, we study the behavior of water-like anomalies upon progressively increasing the elongation λ of the dimers from the monomeric case ([Formula: see text]) to the tangent configuration ([Formula: see text]). For each value of the elongation we consider two different values of the interaction potential, corresponding to one and two length scales, with the aim to provide a comprehensive description of the possible fluid scenarios of this model. Our theoretical results are systematically compared with already existing or newly generated Monte Carlo data: we find that theories and simulations agree in providing the picture of a fluid exhibiting density and structural anomalies for low values of λ and for both the two values of the interaction potential. Integral equation theories give accurate predictions for pressure and radial distribution functions, whereas the temperatures where anomalies occur are underestimated. Upon increasing the elongation, the RISM theory still predicts the existence of anomalies; the latter are no longer observed in simulations, since their development is likely precluded by the onset of crystallization. We discuss our results in terms of the reliability of integral equation theories in predicting the existence of water-like anomalies in core-softened fluids.
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Affiliation(s)
- Gianmarco Munaò
- Dipartimento di Scienze Matematiche e Informatiche, Scienze Fisiche e Scienze della Terra, Università degli Studi di Messina, Viale F. Stagno d'Alcontres 31, 98166 Messina, Italy
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17
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Miyata T, Thapa J. Accuracy of solvation free energy calculated by hypernetted chain and Kovalenko–Hirata approximations for two-component system of Lennard-Jones liquid. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2014.05.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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18
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Wickstrom L, He P, Gallicchio E, Levy RM. Large scale affinity calculations of cyclodextrin host-guest complexes: Understanding the role of reorganization in the molecular recognition process. J Chem Theory Comput 2013; 9:3136-3150. [PMID: 25147485 DOI: 10.1021/ct400003r] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Host-guest inclusion complexes are useful models for understanding the structural and energetic aspects of molecular recognition. Due to their small size relative to much larger protein-ligand complexes, converged results can be obtained rapidly for these systems thus offering the opportunity to more reliably study fundamental aspects of the thermodynamics of binding. In this work, we have performed a large scale binding affinity survey of 57 β-cyclodextrin (CD) host guest systems using the binding energy distribution analysis method (BEDAM) with implicit solvation (OPLS-AA/AGBNP2). Converged estimates of the standard binding free energies are obtained for these systems by employing techniques such as parallel Hamitionian replica exchange molecular dynamics, conformational reservoirs and multistate free energy estimators. Good agreement with experimental measurements is obtained in terms of both numerical accuracy and affinity rankings. Overall, average effective binding energies reproduce affinity rank ordering better than the calculated binding affinities, even though calculated binding free energies, which account for effects such as conformational strain and entropy loss upon binding, provide lower root mean square errors when compared to measurements. Interestingly, we find that binding free energies are superior rank order predictors for a large subset containing the most flexible guests. The results indicate that, while challenging, accurate modeling of reorganization effects can lead to ligand design models of superior predictive power for rank ordering relative to models based only on ligand-receptor interaction energies.
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Affiliation(s)
- Lauren Wickstrom
- BioMaPS Institute for Quantitative Biology and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854 ; Department of Chemistry, Lehman College, The City University of New York, Bronx, NY 10468
| | - Peng He
- BioMaPS Institute for Quantitative Biology and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854
| | - Emilio Gallicchio
- BioMaPS Institute for Quantitative Biology and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854
| | - Ronald M Levy
- BioMaPS Institute for Quantitative Biology and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854
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19
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Maruyama Y, Hirata F. Modified Anderson Method for Accelerating 3D-RISM Calculations Using Graphics Processing Unit. J Chem Theory Comput 2012; 8:3015-21. [PMID: 26605714 DOI: 10.1021/ct300355r] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A fast algorithm is proposed to solve the three-dimensional reference interaction site model (3D-RISM) theory on a graphics processing unit (GPU). 3D-RISM theory is a powerful tool for investigating biomolecular processes in solution; however, such calculations are often both memory-intensive and time-consuming. We sought to accelerate these calculations using GPUs, but to work around the problem of limited memory size in GPUs, we modified the less memory-intensive "Anderson method" to give faster convergence to 3D-RISM calculations. Using this method on a Tesla C2070 GPU, we reduced the total computational time by a factor of 8, 1.4 times by the modified Andersen method and 5.7 times by GPU, compared to calculations on an Intel Xeon machine (eight cores, 3.33 GHz) with the conventional method.
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Affiliation(s)
- Yutaka Maruyama
- Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Okazaki 444-8585, Japan
| | - Fumio Hirata
- Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Okazaki 444-8585, Japan.,Department of Functional Molecular Science, The Graduate University for Advanced Studies, Okazaki 444-8585, Japan
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20
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Luchko T, Joung IS, Case DA. Integral Equation Theory of Biomolecules and Electrolytes. INNOVATIONS IN BIOMOLECULAR MODELING AND SIMULATIONS 2012. [DOI: 10.1039/9781849735049-00051] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The so-called three-dimensional version (3D-RISM) can be used to describe the interactions of solvent components (here we treat water and ions) with a chemical or biomolecular solute of arbitrary size and shape. Here we give an overview of the current status of such models, describing some aspects of “pure” electrolytes (water plus simple ions) and of ionophores, proteins and nucleic acids in the presence of water and salts. Here we focus primarily on interactions with water and dissolved salts; as a practical matter, the discussion is mostly limited to monovalent ions, since studies of divalent ions present many difficult problems that have not yet been addressed. This is not a comprehensive review, but covers a few recent examples that illustrate current issues.
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Affiliation(s)
- Tyler Luchko
- Department of Chemistry and Chemical Biology and BioMaPS Institute Rutgers University Piscataway NJ 08854, USA
| | - In Suk Joung
- Department of Chemistry and Chemical Biology and BioMaPS Institute Rutgers University Piscataway NJ 08854, USA
| | - David A. Case
- Department of Chemistry and Chemical Biology and BioMaPS Institute Rutgers University Piscataway NJ 08854, USA
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21
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Lapelosa M, Gallicchio E, Levy RM. Conformational Transitions and Convergence of Absolute Binding Free Energy Calculations. J Chem Theory Comput 2011; 8:47-60. [PMID: 22368530 DOI: 10.1021/ct200684b] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The Binding Energy Distribution Analysis Method (BEDAM) is employed to compute the standard binding free energies of a series of ligands to a FK506 binding protein (FKBP12) with implicit solvation. Binding free energy estimates are in reasonably good agreement with experimental affinities. The conformations of the complexes identified by the simulations are in good agreement with crystallographic data, which was not used to restrain ligand orientations. The BEDAM method is based on λ -hopping Hamiltonian parallel Replica Exchange (HREM) molecular dynamics conformational sampling, the OPLS-AA/AGBNP2 effective potential, and multi-state free energy estimators (MBAR). Achieving converged and accurate results depends on all of these elements of the calculation. Convergence of the binding free energy is tied to the level of convergence of binding energy distributions at critical intermediate states where bound and unbound states are at equilibrium, and where the rate of binding/unbinding conformational transitions is maximal. This finding mirrors similar observations in the context of order/disorder transitions as for example in protein folding. Insights concerning the physical mechanism of ligand binding and unbinding are obtained. Convergence for the largest FK506 ligand is achieved only after imposing strict conformational restraints, which however require accurate prior structural knowledge of the structure of the complex. The analytical AGBNP2 model is found to underestimate the magnitude of the hydrophobic driving force towards binding in these systems characterized by loosely packed protein-ligand binding interfaces. Rescoring of the binding energies using a numerical surface area model corrects this deficiency. This study illustrates the complex interplay between energy models, exploration of conformational space, and free energy estimators needed to obtain robust estimates from binding free energy calculations.
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Affiliation(s)
- Mauro Lapelosa
- BioMaPS Institute for Quantitative Biology and Department of Chemistry and Chemical Biology, Rutgers the State University of New Jersey, Piscataway, NJ 08854
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Munaó G, Costa D, Sciortino F, Caccamo C. Simulation and theory of a model for tetrahedral colloidal particles. J Chem Phys 2011; 134:194502. [DOI: 10.1063/1.3582904] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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Miyata T, Ikuta Y, Hirata F. Free energy calculation using molecular dynamics simulation combined with the three-dimensional reference interaction site model theory. II. Thermodynamic integration along a spatial reaction coordinate. J Chem Phys 2011; 134:044127. [DOI: 10.1063/1.3532078] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
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Katsumoto Y, Kubosaki N, Miyata T. Molecular Approach To Understand the Tacticity Effects on the Hydrophilicity of Poly(N-isopropylacrylamide): Solubility of Dimer Model Compounds in Water. J Phys Chem B 2010; 114:13312-8. [DOI: 10.1021/jp107442h] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yukiteru Katsumoto
- Graduate School of Science, Hiroshima University, Kagamiyama 1-3-1, Higashi-Hiroshima 739-8526, Japan and Department of Physics, Ehime University, 2-5 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Noriyuki Kubosaki
- Graduate School of Science, Hiroshima University, Kagamiyama 1-3-1, Higashi-Hiroshima 739-8526, Japan and Department of Physics, Ehime University, 2-5 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Tatsuhiko Miyata
- Graduate School of Science, Hiroshima University, Kagamiyama 1-3-1, Higashi-Hiroshima 739-8526, Japan and Department of Physics, Ehime University, 2-5 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
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