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Islam S, Shibly AZ. Exploring Bryophyllum pinnatum compounds as potential inhibitors for Vespula vulgaris allergen proteins: A systematic computational approach. Heliyon 2024; 10:e34713. [PMID: 39170106 PMCID: PMC11336329 DOI: 10.1016/j.heliyon.2024.e34713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 07/12/2024] [Accepted: 07/15/2024] [Indexed: 08/23/2024] Open
Abstract
Vespula vulgaris (V. vulgaris), commonly known as the common wasp, poses a significant health threat due to its venom-induced allergic reactions. This research focused on the exploration of bioactive compounds from Bryophyllum pinnatum as potential inhibitors for V. vulgaris allergen proteins, including Phospholipase A1 (Ves V1), Hyaluronoglucosaminidase (Ves V2), and Antigen 5 (Ves V5). Through a multidisciplinary approach involving literature reviews, molecular docking analyses, ADMET assessments and Molecular Dynamics Simulations (MDS) of 100ns we identified two promising drug candidates from four bioactive compounds- Bryophyllin A, Bryophyllin B, Bryotoxin A, and Bryotoxin B of Bryophyllum pinnatum. Molecular docking results revealed strong binding interactions, with Bryophyllin B and Bryotoxin A consistently exhibiting the highest affinity (-9.6 kcal/mol and -10.0 kcal/mol) across the allergen proteins. ADMET analyses highlighted Bryophyllin B as a favorable candidate, showing high absorption (HIA: 92.1 %), minimal metabolic interactions (CYP1A2: No), and a low toxicity profile (LD50 (rat): 2.431). MDS analysis revealed Bryophyllin B and Bryotoxin A as promising drug inhibitors, exhibiting the highest binding stability with the allergen proteins of V. vulgaris, as indicated by the lowest Root Mean Square Deviation (RMSD), Root Mean Square Fluctuation (RMSF), Radius of Gyration (RG) values and highest protein-ligand contacts. Our study provides valuable insights into the therapeutic potential of Bryophyllum pinnatum compounds as inhibitors for V. vulgaris allergen proteins having two promising candidates- Bryophyllin B and Bryotoxin A.
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Affiliation(s)
- Sirajul Islam
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, Santosh, 1902, Bangladesh
| | - Abu Zaffar Shibly
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, Santosh, 1902, Bangladesh
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2
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Islam S, Amin MA, Rengasamy KR, Mohiuddin AKM, Mahmud S. Structure-based pharmacophore modeling for precision inhibition of mutant ESR2 in breast cancer: A systematic computational approach. Cancer Med 2024; 13:e70074. [PMID: 39101505 PMCID: PMC11299079 DOI: 10.1002/cam4.70074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 07/04/2024] [Accepted: 07/24/2024] [Indexed: 08/06/2024] Open
Abstract
BACKGROUND Breast cancer, a leading cause of female mortality, is closely linked to mutations in estrogen receptor beta (ESR2), particularly in the ligand-binding domain, which contributed to altered signaling pathways and uncontrolled cell growth. OBJECTIVES/AIMS This study investigates the molecular and structural aspects of ESR2 mutant proteins to identify shared pharmacophoric regions of ESR2 mutant proteins and potential therapeutic targets aligned within the pharmacophore model. METHODS This study was initiated by establishing a common pharmacophore model among three mutant ESR2 proteins (PDB ID: 2FSZ, 7XVZ, and 7XWR). The generated shared feature pharmacophore (SFP) includes four primary binding interactions: Hydrogen bond donors (HBD), hydrogen bond acceptors (HBA), hydrophobic interactions (HPho), and Aromatic interactions (Ar), along with halogen bond donors (XBD) and totalling 11 features (HBD: 2, HBA: 3, HPho: 3, Ar: 2, XBD: 1). By employing an in-house Python script, these 11 features distributed into 336 combinations, which were used as query to isolate a drug library of 41,248 compounds and subjected to virtual screening through the generated SFP. RESULTS The virtual screening demonstrated 33 hits showing potential pharmacophoric fit scores and low RMSD value. The top four compounds: ZINC94272748, ZINC79046938, ZINC05925939, and ZINC59928516 showed a fit score of more than 86% and satisfied the Lipinski rule of five. These four compounds and a control underwent molecular (XP Glide mode) docking analysis against wild-type ESR2 protein (PDB ID: 1QKM), resulting in binding affinity of -8.26, -5.73, -10.80, and -8.42 kcal/mol, respectively, along with the control -7.2 kcal/mol. Furthermore, the stability of the selected candidates was determined through molecular dynamics (MD) simulations of 200 ns and MM-GBSA analysis. CONCLUSION Based on MD simulations and MM-GBSA analysis, our study identified ZINC05925939 as a promising ESR2 inhibitor among the top four hits. However, it is essential to conduct further wet lab evaluation to assess its efficacy.
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Affiliation(s)
- Sirajul Islam
- Department of Biotechnology and Genetic EngineeringMawlana Bhashani Science and Technology UniversitySantoshTangail1902Bangladesh
| | - Md. Al Amin
- Department of Biotechnology and Genetic EngineeringMawlana Bhashani Science and Technology UniversitySantoshTangail1902Bangladesh
| | - Kannan R.R. Rengasamy
- Laboratory of Natural Products and Medicinal Chemistry (LNPMC), Center for Global Health Research, Saveetha Medical College and HospitalSaveetha Institute of Medical and Technical Sciences (SIMATS)ThandalamChennai602105India
| | - A. K. M. Mohiuddin
- Department of Biotechnology and Genetic EngineeringMawlana Bhashani Science and Technology UniversitySantoshTangail1902Bangladesh
| | - Shahin Mahmud
- Department of Biotechnology and Genetic EngineeringMawlana Bhashani Science and Technology UniversitySantoshTangail1902Bangladesh
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Chew PY, Reinhardt A. Phase diagrams-Why they matter and how to predict them. J Chem Phys 2023; 158:030902. [PMID: 36681642 DOI: 10.1063/5.0131028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Understanding the thermodynamic stability and metastability of materials can help us to, for example, gauge whether crystalline polymorphs in pharmaceutical formulations are likely to be durable. It can also help us to design experimental routes to novel phases with potentially interesting properties. In this Perspective, we provide an overview of how thermodynamic phase behavior can be quantified both in computer simulations and machine-learning approaches to determine phase diagrams, as well as combinations of the two. We review the basic workflow of free-energy computations for condensed phases, including some practical implementation advice, ranging from the Frenkel-Ladd approach to thermodynamic integration and to direct-coexistence simulations. We illustrate the applications of such methods on a range of systems from materials chemistry to biological phase separation. Finally, we outline some challenges, questions, and practical applications of phase-diagram determination which we believe are likely to be possible to address in the near future using such state-of-the-art free-energy calculations, which may provide fundamental insight into separation processes using multicomponent solvents.
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Affiliation(s)
- Pin Yu Chew
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Aleks Reinhardt
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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Kumar H, Jimah JR, Misal SA, Salinas ND, Fried M, Schlesinger PH, Tolia NH. Implications of conformational flexibility, lipid binding, and regulatory domains in cell traversal-protein CelTOS for apicomplexan migration. J Biol Chem 2022; 298:102241. [PMID: 35809642 PMCID: PMC9400078 DOI: 10.1016/j.jbc.2022.102241] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 06/29/2022] [Accepted: 07/05/2022] [Indexed: 12/04/2022] Open
Abstract
Malaria and other apicomplexan-caused diseases affect millions of humans, agricultural animals, and pets. Cell traversal is a common feature used by multiple apicomplexan parasites to migrate through host cells and can be exploited to develop therapeutics against these deadly parasites. Here, we provide insights into the mechanism of the Cell-traversal protein for ookinetes and sporozoites (CelTOS), a conserved cell-traversal protein in apicomplexan parasites and malaria vaccine candidate. CelTOS has previously been shown to form pores in cell membranes to enable traversal of parasites through cells. We establish roles for the distinct protein regions of Plasmodium vivax CelTOS and examine the mechanism of pore formation. We further demonstrate that CelTOS dimer dissociation is required for pore formation, as disulfide bridging between monomers inhibits pore formation, and this inhibition is rescued by disulfide-bridge reduction. We also show that a helix-destabilizing amino acid, Pro127, allows CelTOS to undergo significant conformational changes to assemble into pores. The flexible C terminus of CelTOS is a negative regulator that limits pore formation. Finally, we highlight that lipid binding is a prerequisite for pore assembly as mutation of a phospholipids-binding site in CelTOS resulted in loss of lipid binding and abrogated pore formation. These findings identify critical regions in CelTOS and will aid in understanding the egress mechanism of malaria and other apicomplexan parasites as well as have implications for studying the function of other essential pore-forming proteins.
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Affiliation(s)
- Hirdesh Kumar
- Host-Pathogen Interactions and Structural Vaccinology Section, Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Disease, National Institutes of Health Bethesda, Maryland
| | - John R Jimah
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
| | - Santosh A Misal
- Molecular Pathogenesis and Biomarkers Section, Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Disease, National Institutes of Health Bethesda, Maryland
| | - Nichole D Salinas
- Host-Pathogen Interactions and Structural Vaccinology Section, Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Disease, National Institutes of Health Bethesda, Maryland
| | - Michal Fried
- Molecular Pathogenesis and Biomarkers Section, Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Disease, National Institutes of Health Bethesda, Maryland
| | - Paul H Schlesinger
- Department of Cell Biology and Physiology, Washington, University School of Medicine, Saint Louis, United States
| | - Niraj H Tolia
- Host-Pathogen Interactions and Structural Vaccinology Section, Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Disease, National Institutes of Health Bethesda, Maryland.
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5
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Ma Y, Zhang S, Zhou L, Zhang L, Zhang P, Ma S. Exploration of the inhibitory mechanism of PC190723 on FtsZ protein by molecular dynamics simulation. J Mol Graph Model 2022; 114:108189. [DOI: 10.1016/j.jmgm.2022.108189] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 04/03/2022] [Accepted: 04/04/2022] [Indexed: 12/30/2022]
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6
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Primorac T, Požar M, Sokolić F, Zoranić L. The influence of binary mixtures' structuring on the calculation of Kirkwood-Buff integrals: A molecular dynamics study. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.114773] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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8
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Sharma V, Wakode S. Investigating the role of N-terminal domain in phosphodiesterase 4B-inhibition by molecular dynamics simulation. J Biomol Struct Dyn 2020; 39:4270-4278. [PMID: 32552529 DOI: 10.1080/07391102.2020.1780154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Phosphodiesterase 4B (PDE4B) is a potential therapeutic target for the inflammatory respiratory diseases such as congestive obstructive pulmonary disease (COPD) and asthma. The sequence identity of ∼88% with its isoform PDE4D is the key barrier in developing selective PDE4B inhibitors which may help to overcome associated side effects. Despite high sequence identity, both isoforms differ in few residues present in N-terminal (UCR2) and C-terminal (CR3) involved in catalytic site formation. Previously, we designed and tested specific PDE4B inhibitors considering N-terminal residues as a part of the catalytic cavity. In continuation, current work thoroughly presents an MD simulation-based analysis of N-terminal residues and their role in ligand binding. The various parameters viz. root mean square deviation (RMSD), radius of gyration (Rg), root mean square fluctuation (RMSF), principal component analysis (PCA), dynamical cross-correlation matrix (DCCM) analysis, secondary structure analysis and residue interaction mapping were investigated to establish rational. Results showed that UCR2 reduced RMSF values for the metal binding pocket (31.5 ± 11 to 13.12 ± 6 Å2) and the substrate-binding pocket (38.8 ± 32 to 17.3 ± 11 Å2). UCR2 enhanced anti-correlated motion at the active site region that led to the improved ligand-binding affinity of PDE4B from -24.57 ± 3 to -35.54 ± 2 kcal/mol. Further, the atomic-level analysis indicated that T-π and π-π interactions between inhibitors and residues are vital forces that regulate inhibitor association to PDE4B with high affinity. In conclusion, UCR2, the N-terminal domain, embraces the dynamics of PDE4B active site and stabilizes PDE4B inhibitor interactions. Therefore the N-terminal domain needs to be considered while designing next-generation, selective PDE4B-inhibitors as potential anti-inflammatory drugs. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Vidushi Sharma
- Department of Pharmaceutical Chemistry, Delhi Institute of Pharmaceutical Sciences & Research, New Delhi, India
| | - Sharad Wakode
- Department of Pharmaceutical Chemistry, Delhi Institute of Pharmaceutical Sciences & Research, New Delhi, India
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Bhattacharya S, Xu L, Thompson D. Revisiting the earliest signatures of amyloidogenesis: Roadmaps emerging from computational modeling and experiment. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2018. [DOI: 10.1002/wcms.1359] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Shayon Bhattacharya
- Department of Physics, Bernal InstituteUniversity of LimerickLimerickIreland
| | - Liang Xu
- Department of Physics, Bernal InstituteUniversity of LimerickLimerickIreland
| | - Damien Thompson
- Department of Physics, Bernal InstituteUniversity of LimerickLimerickIreland
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10
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Wang L, Yuan Y, Chen X, Chen J, Guo Y, Li M, Li C, Pu X. Probing the cooperative mechanism of the μ–δ opioid receptor heterodimer by multiscale simulation. Phys Chem Chem Phys 2018; 20:29969-29982. [DOI: 10.1039/c8cp06652c] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The activation-cooperativity of the μ–δ opioid receptor heterodimer was probed by multiscale simulation coupled with a protein structure network.
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Affiliation(s)
- Longrong Wang
- Faculty of Chemistry
- Sichuan University
- Chengdu
- People's Republic of China
| | - Yuan Yuan
- College of Management
- Southwest University for Nationalities
- Chengdu 610041
- P. R. China
| | - Xin Chen
- Faculty of Chemistry
- Sichuan University
- Chengdu
- People's Republic of China
| | - Jiangfan Chen
- Faculty of Chemistry
- Sichuan University
- Chengdu
- People's Republic of China
| | - Yanzhi Guo
- Faculty of Chemistry
- Sichuan University
- Chengdu
- People's Republic of China
| | - Menglong Li
- Faculty of Chemistry
- Sichuan University
- Chengdu
- People's Republic of China
| | - Chuan Li
- College of Computer Science
- Sichuan University
- Chengdu
- P. R. China
| | - Xuemei Pu
- Faculty of Chemistry
- Sichuan University
- Chengdu
- People's Republic of China
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11
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Bakó I, Lábas A, Hermansson K, Bencsura Á, Oláh J. How can we detect hydrogen bond local cooperativity in liquid water: A simulation study. J Mol Liq 2017. [DOI: 10.1016/j.molliq.2017.08.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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12
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Steinczinger Z, Jóvári P, Pusztai L. Comparison of 9 classical interaction potentials of liquid water: Simultaneous Reverse Monte Carlo modeling of X-ray and neutron diffraction results and partial radial distribution functions from computer simulations. J Mol Liq 2017. [DOI: 10.1016/j.molliq.2016.09.068] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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13
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Understanding the molecular mechanism for the differential inhibitory activities of compounds against MTH1. Sci Rep 2017; 7:40557. [PMID: 28074893 PMCID: PMC5225434 DOI: 10.1038/srep40557] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 12/08/2016] [Indexed: 01/18/2023] Open
Abstract
MTH1 can hydrolyze oxidized nucleotides and is required for cancer survival. The IC50 values were 0.8 nM for TH287 with a methyl substitution, 5.0 nM for TH588 with a cyclopropyl substitution, and 2.1 μM for TH650 with an oxetanyl substitution. Thus, it is very significant to understand inhibitory mechanisms of these structurally similar compounds against MTH1 and influences of the substituent on the bioactivities. Our MD researches indicate that TH287 maintains significant hydrogen bonds with Asn33 and Asp119, stabilizes the binding site, and induces MTH1 adopt a closed motion, leading to a high inhibitory activity. When bound with TH588, the binding site can be partially stabilized and take a semi-closed state, which is because the cyclopropyl group in TH588 has larger steric hindrance than a methyl group in TH287. So TH588 has a slightly reduced inhibitory activity compared to TH287. TH650 induces greater conformation fluctuations than TH588 and the binding site adopts an opening state, which is caused by the large bulk of oxetanyl group and the interference of solvent on the oxetanyl substituent, leading to the lowest inhibitory activity. Thus, the inhibitory activity follows a TH287 > TH588 > TH650 trend, which well matches with the experimental finding.
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14
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Wang J, Chen Q, Wang M, Zhong C. The opening/closure of the P-loop and hinge of BCR-ABL1 decodes the low/high bioactivities of dasatinib and axitinib. Phys Chem Chem Phys 2017; 19:22444-22453. [DOI: 10.1039/c7cp03443a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The open/closed conformations reveal the low/high bioactivities of the ligands.
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Affiliation(s)
- Jianyi Wang
- School of Chemistry and Chemical Engineering
- Guangxi University
- Nanning 530004
- China
| | - Qing Chen
- School of Chemistry and Chemical Engineering
- Guangxi University
- Nanning 530004
- China
| | - Mian Wang
- School of Chemistry and Chemical Engineering
- Guangxi University
- Nanning 530004
- China
- College of Life Science and Technology
| | - Cheng Zhong
- School of Computer
- Electronics and Information
- Guangxi University
- Nanning 530004
- China
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15
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Székely E, Varga IK, Baranyai A. Tetrahedrality and hydrogen bonds in water. J Chem Phys 2016; 144:224502. [PMID: 27306013 DOI: 10.1063/1.4953555] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
We carried out extensive calculations of liquid water at different temperatures and pressures using the BK3 model suggested recently [P. T. Kiss and A. Baranyai, J. Chem. Phys. 138, 204507 (2013)]. In particular, we were interested in undercooled regions to observe the propensity of water to form tetrahedral coordination of closest neighbors around a central molecule. We compared the found tetrahedral order with the number of hydrogen bonds and with the partial pair correlation functions unfolded as distributions of the closest, the second closest, etc. neighbors. We found that contrary to the number of hydrogen bonds, tetrahedrality changes substantially with state variables. Not only the number of tetrahedral arrangements increases with lowering the pressure, the density, and the temperature but the domain size of connecting tetrahedral structures as well. The difference in tetrahedrality is very pronounced between the two sides of the Widom line and even more so between the low density amorphous (LDA) and high density amorphous (HDA) phases. We observed that in liquid water and in HDA, the 5th water molecule, contrary to ice and LDA, is positioned between the first and the second coordination shell. We found no convincing evidence of structural heterogeneity or regions referring to structural transition.
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Affiliation(s)
- Eszter Székely
- Institute of Chemistry, Eötvös University, P.O. Box 32, Budapest 112 1518, Hungary
| | - Imre K Varga
- Institute of Chemistry, Eötvös University, P.O. Box 32, Budapest 112 1518, Hungary
| | - András Baranyai
- Institute of Chemistry, Eötvös University, P.O. Box 32, Budapest 112 1518, Hungary
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16
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Lobanova O, Avendaño C, Lafitte T, Müller EA, Jackson G. SAFT-γ force field for the simulation of molecular fluids: 4. A single-site coarse-grained model of water applicable over a wide temperature range. Mol Phys 2015. [DOI: 10.1080/00268976.2015.1004804] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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17
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Kutschan B, Morawetz K, Thoms S. Dynamical mechanism of antifreeze proteins to prevent ice growth. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 90:022711. [PMID: 25215762 DOI: 10.1103/physreve.90.022711] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Indexed: 06/03/2023]
Abstract
The fascinating ability of algae, insects, and fishes to survive at temperatures below normal freezing is realized by antifreeze proteins (AFPs). These are surface-active molecules and interact with the diffusive water-ice interface thus preventing complete solidification. We propose a dynamical mechanism on how these proteins inhibit the freezing of water. We apply a Ginzburg-Landau-type approach to describe the phase separation in the two-component system (ice, AFP). The free-energy density involves two fields: one for the ice phase with a low AFP concentration and one for liquid water with a high AFP concentration. The time evolution of the ice reveals microstructures resulting from phase separation in the presence of AFPs. We observed a faster clustering of pre-ice structure connected to a locking of grain size by the action of AFP, which is an essentially dynamical process. The adsorption of additional water molecules is inhibited and the further growth of ice grains stopped. The interfacial energy between ice and water is lowered allowing the AFPs to form smaller critical ice nuclei. Similar to a hysteresis in magnetic materials we observe a thermodynamic hysteresis leading to a nonlinear density dependence of the freezing point depression in agreement with the experiments.
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Affiliation(s)
- B Kutschan
- Münster University of Applied Science, Stegerwaldstrasse 39, 48565 Steinfurt, Germany
| | - K Morawetz
- Münster University of Applied Science, Stegerwaldstrasse 39, 48565 Steinfurt, Germany and International Institute of Physics (IIP), Federal University of Rio Grande do Norte, Av. Odilon Gomes de Lima 1722, 59078-400 Natal, Brazil and Max-Planck-Institute for the Physics of Complex Systems, 01187 Dresden, Germany
| | - S Thoms
- Alfred Wegener Institut, Am Handelshafen 12, D-27570 Bremerhaven, Germany
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18
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Fenley AT, Henriksen NM, Muddana HS, Gilson MK. Bridging Calorimetry and Simulation through Precise Calculations of Cucurbituril-Guest Binding Enthalpies. J Chem Theory Comput 2014; 10:4069-4078. [PMID: 25221445 PMCID: PMC4159218 DOI: 10.1021/ct5004109] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2014] [Indexed: 01/02/2023]
Abstract
We used microsecond time scale molecular dynamics simulations to compute, at high precision, binding enthalpies for cucurbit[7]uril (CB7) with eight guests in aqueous solution. The results correlate well with experimental data from previously published isothermal titration calorimetry studies, and decomposition of the computed binding enthalpies by interaction type provides plausible mechanistic insights. Thus, dispersion interactions appear to play a key role in stabilizing these complexes, due at least in part to the fact that their packing density is greater than that of water. On the other hand, strongly favorable Coulombic interactions between the host and guests are compensated by unfavorable solvent contributions, leaving relatively modest electrostatic contributions to the binding enthalpies. The better steric fit of the aliphatic guests into the circular host appears to explain why their binding enthalpies tend to be more favorable than those of the more planar aromatic guests. The present calculations also bear on the validity of the simulation force field. Somewhat unexpectedly, the TIP3P water yields better agreement with experiment than the TIP4P-Ew water model, although the latter is known to replicate the properties of pure water more accurately. More broadly, the present results demonstrate the potential for computational calorimetry to provide atomistic explanations for thermodynamic observations.
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Affiliation(s)
- Andrew T Fenley
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego , 9500 Gilman Drive, La Jolla, California 92093-0736, United States
| | - Niel M Henriksen
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego , 9500 Gilman Drive, La Jolla, California 92093-0736, United States
| | - Hari S Muddana
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego , 9500 Gilman Drive, La Jolla, California 92093-0736, United States
| | - Michael K Gilson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego , 9500 Gilman Drive, La Jolla, California 92093-0736, United States
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Mijaković M, Polok KD, Kežić B, Sokolić F, Perera A, Zoranić L. A comparison of force fields for ethanol–water mixtures. MOLECULAR SIMULATION 2014. [DOI: 10.1080/08927022.2014.923567] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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20
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Tian WY, Huang KM, Yang LJ, Guo YN, Liu FH. Investigate the microscopic properties and the non-thermal effect of the electrolyte solution under microwave irradiation. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2014.05.042] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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21
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Kreck CA, Mancera RL. Characterization of the Glass Transition of Water Predicted by Molecular Dynamics Simulations Using Nonpolarizable Intermolecular Potentials. J Phys Chem B 2014; 118:1867-80. [DOI: 10.1021/jp411716y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Cara A. Kreck
- School of Biomedical Sciences,
CHIRI Biosciences, Curtin University, GPO Box U1987, Perth, Western
Australia 6845, Australia
| | - Ricardo L. Mancera
- School of Biomedical Sciences,
CHIRI Biosciences, Curtin University, GPO Box U1987, Perth, Western
Australia 6845, Australia
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22
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Kiss PT, Baranyai A. A systematic development of a polarizable potential of water. J Chem Phys 2014; 138:204507. [PMID: 23742493 DOI: 10.1063/1.4807600] [Citation(s) in RCA: 110] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Based on extensive studies of existing potentials we propose a new molecular model for water. The new model is rigid and contains three Gaussian charges. Contrary to other models, all charges take part in the polarization of the molecule. They are connected by harmonic springs to their gas-phase positions: the negative charge to a prescribed point on the main axis of the molecule; the positive charges to the hydrogens. The mechanical equilibrium between the electrostatic forces and the spring forces determines the polarization of the molecule which is established by iteration at every timestep. The model gives excellent estimates for ambient liquid properties and reasonably good results from high-pressure solids to gas-phase clusters. We present a detailed description of the development of this model and a large number of calculated properties compared to the estimates of the nonpolarizable TIP4P∕2005 [J. L. F. Abascal and C. Vega, J. Chem. Phys. 123, 234505 (2005)], the polarizable GCPM [P. Paricaud, M. Predota, A. A. Chialvo, and P. T. Cummings, J. Chem. Phys. 122, 244511 (2005)], and our earlier BKd3 model [P. T. Kiss and A. Baranyai, J. Chem. Phys. 137, 084506 (2012)]. The best overall performance is shown by the new model.
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Affiliation(s)
- Péter T Kiss
- Institute of Chemistry, Eötvös University, P.O. Box 32, 1518 Budapest 112, Hungary
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Li D, Guo B, Liu B, Zhai Z, Zhang Y, Liu Y, Yu H, Liu L, Yang C. Investigation on bioactive protection of the amino acids derived from LEA protein on insulin by molecular simulation. MOLECULAR SIMULATION 2013. [DOI: 10.1080/08927022.2013.769682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Bakó I, Bencsura Á, Hermannson K, Bálint S, Grósz T, Chihaia V, Oláh J. Hydrogen bond network topology in liquid water and methanol: a graph theory approach. Phys Chem Chem Phys 2013; 15:15163-71. [DOI: 10.1039/c3cp52271g] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Reinhardt A, Doye JPK, Noya EG, Vega C. Local order parameters for use in driving homogeneous ice nucleation with all-atom models of water. J Chem Phys 2012. [DOI: 10.1063/1.4766362] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
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Pérez A, Rubio A. A molecular dynamics study of water nucleation using the TIP4P/2005 model. J Chem Phys 2012; 135:244505. [PMID: 22225167 DOI: 10.1063/1.3672063] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Extensive molecular dynamics simulations were conducted using the TIP4P/2005 water model of Abascal and Vega [J. Chem. Phys. 123, 234505 (2005)] to investigate its condensation from supersaturated vapor to liquid at 330 K. The mean first passage time method [J. Wedekind, R. Strey, and D. Reguera, J. Chem. Phys. 126, 134103 (2007); L. S. Bartell and D. T. Wu, 125, 194503 (2006)] was used to analyze the influence of finite size effects, thermostats, and charged species on the nucleation dynamics. We find that the Nosé-Hoover thermostat and the one proposed by Bussi et al. [J. Chem. Phys. 126, 014101 (2007)] give essentially the same averages. We identify the maximum thermostat coupling time to guarantee proper thermostating for these simulations. The presence of charged species has a dramatic impact on the dynamics, inducing a marked change towards a pure growth regime, which highlights the importance of ions in the formation of liquid droplets in the atmosphere. It was found a small but noticeable sign preference at intermediate cluster sizes (between 5 and 30 water molecules) corresponding mostly to the formation of the second solvation shell around the ion. The TIP4P/2005 water model predicts that anions induce faster formation of water clusters than cations of the same magnitude of charge.
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Affiliation(s)
- Alejandro Pérez
- Nano-bio Spectroscopy Group and ETSF Scientific Development Center, Department of Materials Science, Faculty of Chemistry, University of the Basque Country (UPV/EHU), Donostia-San Sebastián, Spain.
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Affiliation(s)
- Alberto Striolo
- School of Chemical, Biological and Materials Engineering, University of Oklahoma, Norman, OK 73019, U.S.A
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