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Hatch HW, Shen VK, Corti DS. Theory and Monte Carlo simulation of the ideal gas with shell particles in the canonical, isothermal-isobaric, grand canonical, and Gibbs ensembles. J Chem Phys 2024; 161:084106. [PMID: 39171706 DOI: 10.1063/5.0224305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Accepted: 08/05/2024] [Indexed: 08/23/2024] Open
Abstract
Theories of small systems play an important role in the fundamental understanding of finite size effects in statistical mechanics, as well as the validation of molecular simulation results as no computer can simulate fluids in the thermodynamic limit. Previously, a shell particle was included in the isothermal-isobaric ensemble in order to resolve an ambiguity in the resulting partition function. The shell particle removed either redundant volume states or redundant translational degrees of freedom of the system and yielded quantitative differences from traditional simulations in this ensemble. In this work, we investigate the effect of including a shell particle in the canonical, grand canonical, and Gibbs ensembles. For systems comprised of a pure component ideal gas, analytical expressions for various thermodynamic properties are obtained. We also derive the Metropolis Monte Carlo simulation acceptance criteria for these ensembles with shell particles, and the results of the simulations of an ideal gas are in excellent agreement with the theoretical predictions. The system size dependence of various important ensemble averages is also analyzed.
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Affiliation(s)
- Harold W Hatch
- Chemical Informatics Research Group, Chemical Sciences Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899-8380, USA
| | - Vincent K Shen
- Chemical Informatics Research Group, Chemical Sciences Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899-8380, USA
| | - David S Corti
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, Indiana 47907-2100, USA
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2
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Janek J, Kolafa J. Novel barostat implementation for molecular dynamics. J Chem Phys 2024; 160:184111. [PMID: 38728273 DOI: 10.1063/5.0193281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 04/24/2024] [Indexed: 05/12/2024] Open
Abstract
We propose a novel implementation of the extended-dynamics equations for isothermal-isobaric ensemble in molecular dynamics, as the Martyna-Tobias-Klein thermostat and barostat. This method is suitable for systems with constraints and the Verlet-family integrators. Instead of iterations or the Trotter-expansion-based methods, both velocities and box sizes (scaling of bond lengths) are predicted. The algorithm begins with force calculation, requiring neither quarter nor half time steps, and necessitating iterations only inside SHAKE. Several tests demonstrate that the quality is comparable to other implementations. It is found that the formula relating the extended barostat mass to the characteristic time of volume fluctuations is inaccurate for condensed systems, which has consequences for the parameter setup. Emphasis is also put on the verification of the precise isothermal-isobaric ensemble and finite-size effects.
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Affiliation(s)
- Jiří Janek
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, Technická 5, 166 28 Prague 6, Czech Republic
| | - Jiří Kolafa
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, Technická 5, 166 28 Prague 6, Czech Republic
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3
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Allouch A, Mougenot J, Prasanna S, Michau A, Seydou M, Maurel F, Brault P, Hassouni K. Statistical abundance and stability of carbon nanostructures by combined condensation-annealing molecular dynamics simulations. COMPUT THEOR CHEM 2021. [DOI: 10.1016/j.comptc.2021.113252] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Salekeen R, Barua J, Shaha PR, Islam KMD, Islam ME, Billah MM, Rahman SMM. Marine phycocompound screening reveals a potential source of novel senotherapeutics. J Biomol Struct Dyn 2021; 40:6071-6085. [PMID: 33533325 DOI: 10.1080/07391102.2021.1877822] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Cells undergo a controlled and systematic cycle of growth, replication and death. However, the integrity of this process gradually declines, leading to accumulation of senescent cells, a major hallmark of biological ageing. Dietary algae, particularly marine algae, have been long reported to exert anti-ageing benefits as cosmeceuticals and nutraceuticals with limited understanding of the molecular mechanisms underlying their activity. In this study, we have incorporated 1,202 previously reported bioactive small phycocompounds and subjected them to cheminformatic queries to assess these interactions. In-silico ADMET, 2-phase docking, metabolic pathway interaction and molecular dynamics simulations reveal multiple marine phycocompounds to have safe and effective senolytic potentials. We employed a novel deep convolutional neural network driven screening approach to identify (2R*, 3S*, 6R*, 7S*, 10R*, 13R*)-7,13-Dihydroxy-2,6-cyclo-1(9),14-xenicadiene-18,19-dial derived from Dilophus Fasciola, Laurendecumenyne A from Laurencia decumbens and 4-Bromo-3-ethyl-9-[(2E)-2-penten-4-yn-1-yl]-2,8-dioxabicyclo[5.2.1]decan-6-ol from Laurencia sp. to be potent inhibitors of multiple target senescent-cell anti-apoptotic pathway proteins. We simulated the best overall target inhibitors, specific protein inhibitors and molecular pathway regulators with each target protein and found stable interactions with minimum deviations (mean RMSD = 0.17 ± 0.01 nm) and gyrations (mean Rg = 1.64 ± 0.16 nm) of the simulated protein-compound complexes. Finally, molecular mechanics calculation suggests potent (mean ΔG = -69.56 ± 27.19 kCal/mol) and frequent hydrophobic interactions between the top performing marine phycocompounds and target proteins.
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Affiliation(s)
- Rahagir Salekeen
- Biotechnology and Genetic Engineering Discipline, Life Science School, Khulna University, Khulna, Bangladesh
| | - Joydip Barua
- Biotechnology and Genetic Engineering Discipline, Life Science School, Khulna University, Khulna, Bangladesh
| | - Punam Rani Shaha
- Biotechnology and Genetic Engineering Discipline, Life Science School, Khulna University, Khulna, Bangladesh
| | - Kazi Mohammed Didarul Islam
- Biotechnology and Genetic Engineering Discipline, Life Science School, Khulna University, Khulna, Bangladesh
| | - Md Emdadul Islam
- Biotechnology and Genetic Engineering Discipline, Life Science School, Khulna University, Khulna, Bangladesh
| | - Md Morsaline Billah
- Biotechnology and Genetic Engineering Discipline, Life Science School, Khulna University, Khulna, Bangladesh
| | - S M Mahbubur Rahman
- Biotechnology and Genetic Engineering Discipline, Life Science School, Khulna University, Khulna, Bangladesh
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5
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In silico and saturation transfer difference NMR approaches to unravel the binding mode of an andrographolide derivative to K-Ras oncoprotein. Future Med Chem 2020; 12:1611-1631. [PMID: 32892640 DOI: 10.4155/fmc-2020-0104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Background: Andrographolide and its benzylidene derivatives, SRJ09 and SRJ23, potentially bind oncogenic K-Ras to exert anticancer activity. Their molecular interactions with K-Ras oncoproteins that lead to effective biological activity are of major interest. Methods & results: In silico docking and molecular dynamics simulation were performed using Glide and Desmond, respectively; while saturation transfer difference NMR was performed using GDP-bound K-RasG12V. SRJ23 was found to bind strongly and selectively to K-RasG12V, by anchoring to a binding pocket (namely p2) principally via hydrogen bond and hydrophobic interactions. The saturation transfer difference NMR analysis revealed the proximity of protons of functional moieties in SRJ23 to K-RasG12V, suggesting positive binding. Conclusion: SRJ23 binds strongly and interacts stably with K-RasG12V to exhibit its inhibitory activity.
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Bone MA, Macquart T, Hamerton I, Howlin BJ. A Novel Approach to Atomistic Molecular Dynamics Simulation of Phenolic Resins Using Symthons. Polymers (Basel) 2020; 12:polym12040926. [PMID: 32316377 PMCID: PMC7240706 DOI: 10.3390/polym12040926] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 04/08/2020] [Accepted: 04/15/2020] [Indexed: 11/26/2022] Open
Abstract
Materials science is beginning to adopt computational simulation to eliminate laboratory trial and error campaigns—much like the pharmaceutical industry of 40 years ago. To further computational materials discovery, new methodology must be developed that enables rapid and accurate testing on accessible computational hardware. To this end, the authors utilise a novel methodology concept of intermediate molecules as a starting point, for which they propose the term ‘symthon’ (The term ‘Symthon’ is being used as a simulation equivalent of the synthon, popularised by Dr Stuart Warren in ‘Organic Synthesis: The Disconnection Approach’, OUP: Oxford, 1983.) rather than conventional monomers. The use of symthons eliminates the initial monomer bonding phase, reducing the number of iterations required in the simulation, thereby reducing the runtime. A novel approach to molecular dynamics, with an NVT (Canonical) ensemble and variable unit cell geometry, was used to generate structures with differing physical and thermal properties. Additional script methods were designed and tested, which enabled a high degree of cure in all sampled structures. This simulation has been trialled on large-scale atomistic models of phenolic resins, based on a range of stoichiometric ratios of formaldehyde and phenol. Density and glass transition temperature values were produced, and found to be in good agreement with empirical data and other simulated values in the literature. The runtime of the simulation was a key consideration in script design; cured models can be produced in under 24 h on modest hardware. The use of symthons has been shown as a viable methodology to reduce simulation runtime whilst generating accurate models.
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Affiliation(s)
- Matthew A. Bone
- Department of Chemistry & Faculty of Engineering and Physical Sciences, University of Surrey, Guildford, Surrey GU2 7XH, UK;
- Bristol Composites Institute (ACCIS), Department of Aerospace Engineering, School of Civil, Aerospace, and Mechanical Engineering, University of Bristol, Queen’s Building, University Walk, Bristol BS8 1TR, UK; (T.M.); (I.H.)
- Correspondence:
| | - Terence Macquart
- Bristol Composites Institute (ACCIS), Department of Aerospace Engineering, School of Civil, Aerospace, and Mechanical Engineering, University of Bristol, Queen’s Building, University Walk, Bristol BS8 1TR, UK; (T.M.); (I.H.)
| | - Ian Hamerton
- Bristol Composites Institute (ACCIS), Department of Aerospace Engineering, School of Civil, Aerospace, and Mechanical Engineering, University of Bristol, Queen’s Building, University Walk, Bristol BS8 1TR, UK; (T.M.); (I.H.)
| | - Brendan J. Howlin
- Department of Chemistry & Faculty of Engineering and Physical Sciences, University of Surrey, Guildford, Surrey GU2 7XH, UK;
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Day AL, Greisen P, Doyle L, Schena A, Stella N, Johnsson K, Baker D, Stoddard B. Unintended specificity of an engineered ligand-binding protein facilitated by unpredicted plasticity of the protein fold. Protein Eng Des Sel 2019; 31:375-387. [PMID: 30566669 DOI: 10.1093/protein/gzy031] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 10/02/2018] [Accepted: 11/07/2018] [Indexed: 12/25/2022] Open
Abstract
Attempts to create novel ligand-binding proteins often focus on formation of a binding pocket with shape complementarity against the desired ligand (particularly for compounds that lack distinct polar moieties). Although designed proteins often exhibit binding of the desired ligand, in some cases they display unintended recognition behavior. One such designed protein, that was originally intended to bind tetrahydrocannabinol (THC), was found instead to display binding of 25-hydroxy-cholecalciferol (25-D3) and was subjected to biochemical characterization, further selections for enhanced 25-D3 binding affinity and crystallographic analyses. The deviation in specificity is due in part to unexpected altertion of its conformation, corresponding to a significant change of the orientation of an α-helix and an equally large movement of a loop, both of which flank the designed ligand-binding pocket. Those changes led to engineered protein constructs that exhibit significantly more contacts and complementarity towards the 25-D3 ligand than the initial designed protein had been predicted to form towards its intended THC ligand. Molecular dynamics simulations imply that the initial computationally designed mutations may contribute to the movement of the helix. These analyses collectively indicate that accurate prediction and control of backbone dynamics conformation, through a combination of improved conformational sampling and/or de novo structure design, represents a key area of further development for the design and optimization of engineered ligand-binding proteins.
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Affiliation(s)
- Austin L Day
- Departments of Bioengineering and Biochemistry, University of Washington, Molecular Engineering and Sciences, Seattle, WA, USA
| | - Per Greisen
- Departments of Bioengineering and Biochemistry, University of Washington, Molecular Engineering and Sciences, Seattle, WA, USA
| | - Lindsey Doyle
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA, USA
| | - Alberto Schena
- Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Nephi Stella
- Departments of Bioengineering and Biochemistry, University of Washington, Molecular Engineering and Sciences, Seattle, WA, USA
| | - Kai Johnsson
- Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - David Baker
- Departments of Bioengineering and Biochemistry, University of Washington, Molecular Engineering and Sciences, Seattle, WA, USA
| | - Barry Stoddard
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA, USA
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Ahmad S, Murtaza UA, Raza S, Azam SS. Blocking the catalytic mechanism of MurC ligase enzyme from Acinetobacter baumannii: An in Silico guided study towards the discovery of natural antibiotics. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.02.051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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9
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Combating tigecycline resistant Acinetobacter baumannii: A leap forward towards multi-epitope based vaccine discovery. Eur J Pharm Sci 2019; 132:1-17. [DOI: 10.1016/j.ejps.2019.02.023] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 01/31/2019] [Accepted: 02/16/2019] [Indexed: 01/27/2023]
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10
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Kim M, Kim E, Lee S, Kim JS, Lee S. New Method for Constant- NPT Molecular Dynamics. J Phys Chem A 2019; 123:1689-1699. [PMID: 30715880 DOI: 10.1021/acs.jpca.8b09082] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The well-established molecular dynamics simulation methods for constant- NPT ensemble systems such as the Andersen-Nosé-Hoover method and their variants may alter the dynamic properties of the molecules under consideration, because their equations of motion are modified by the coupling with thermostat or barostat. To circumvent this artifact, we propose a new molecular dynamics simulation algorithm, by which only the molecules near the wall of the simulation box are coupled to the thermostat and barostat and the molecules of interest placed in the inner part of the simulation box remain intact. We test the efficiency of our algorithm in attaining the target temperature and pressure and the conformity of the calculated equilibrium and dynamic properties to those of a constant- NPT ensemble system.
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Affiliation(s)
- Minjung Kim
- Department of Chemistry , Seoul National University , Seoul 08826 , South Korea
| | - Eunji Kim
- Department of Chemistry , Seoul National University , Seoul 08826 , South Korea
| | - Seunghoon Lee
- Department of Chemistry , Seoul National University , Seoul 08826 , South Korea
| | - Jun Soo Kim
- Department of Chemistry and Nanoscience , Ewha Womans University , Seoul 03760 , South Korea
| | - Sangyoub Lee
- Department of Chemistry , Seoul National University , Seoul 08826 , South Korea
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11
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Barua H, Gunnam A, Yadav B, Nangia A, Shastri NR. An ab initio molecular dynamics method for cocrystal prediction: validation of the approach. CrystEngComm 2019. [DOI: 10.1039/c9ce01436e] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cocrystal formation prediction by ab initio molecular dynamics and validation based on the experimental results of 145 coformers for six drugs.
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Affiliation(s)
- Harsh Barua
- Solid State Pharmaceutical Research Group (SSPRG)
- Department of Pharmaceutics
- National Institute of Pharmaceutical Education and Research (NIPER)
- Hyderabad 500037
- India
| | - Anilkumar Gunnam
- School of Chemistry
- University of Hyderabad
- Hyderabad 500 046
- India
| | - Balvant Yadav
- Solid State Pharmaceutical Research Group (SSPRG)
- Department of Pharmaceutics
- National Institute of Pharmaceutical Education and Research (NIPER)
- Hyderabad 500037
- India
| | - Ashwini Nangia
- School of Chemistry
- University of Hyderabad
- Hyderabad 500 046
- India
| | - Nalini R. Shastri
- Solid State Pharmaceutical Research Group (SSPRG)
- Department of Pharmaceutics
- National Institute of Pharmaceutical Education and Research (NIPER)
- Hyderabad 500037
- India
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12
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Li Z, Corti DS. Monte Carlo simulations in the isothermal-isobaric ensemble: use of a ‘shell’ particle for simulating polyatomic fluids. MOLECULAR SIMULATION 2018. [DOI: 10.1080/08927022.2018.1518579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Zhao Li
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN, USA
| | - David S. Corti
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN, USA
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Frutapin, a lectin from Artocarpus incisa (breadfruit): cloning, expression and molecular insights. Biosci Rep 2017; 37:BSR20170969. [PMID: 28684550 PMCID: PMC5520216 DOI: 10.1042/bsr20170969] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 07/02/2017] [Accepted: 07/04/2017] [Indexed: 12/22/2022] Open
Abstract
Artocarpus incisa (breadfruit) seeds contain three different lectins (Frutalin, Frutapin (FTP) and Frutackin) with distinct carbohydrate specificities. The most abundant lectin is Frutalin, an α-D-galactose-specific carbohydrate-binding glycoprotein with antitumour properties and potential for tumour biomarker discovery as already reported. FTP is the second most abundant, but proved difficult to purify with very low yields and contamination with Frutalin frustrating its characterization. Here, we report for the first time high-level production and isolation of biologically active recombinant FTP in Escherichia coli BL21, optimizing conditions with the best set yielding >40 mg/l culture of soluble active FTP. The minimal concentration for agglutination of red blood cells was 62.5 µg/ml of FTP, a process effectively inhibited by mannose. Apo-FTP, FTP–mannose and FTP–glucose crystals were obtained, and they diffracted X-rays to a resolution of 1.58 (P212121), 1.70 (P3121) and 1.60 (P3121) Å respectively. The best solution showed four monomers per asymmetric unit. Molecular dynamics (MD) simulation suggested that FTP displays higher affinity for mannose than glucose. Cell studies revealed that FTP was non-cytotoxic to cultured mouse fibroblast 3T3 cells below 0.5 mg/ml and was also capable of stimulating cell migration at 50 µg/ml. In conclusion, our optimized expression system allowed high amounts of correctly folded soluble FTP to be isolated. This recombinant bioactive lectin will now be tested in future studies for therapeutic potential; for example in wound healing and tissue regeneration.
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