101
|
Glova AD, Melnikova SD, Mercurieva AA, Larin SV, Lyulin SV. Grafting-Induced Structural Ordering of Lactide Chains. Polymers (Basel) 2019; 11:polym11122056. [PMID: 31835722 PMCID: PMC6961058 DOI: 10.3390/polym11122056] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 12/06/2019] [Accepted: 12/09/2019] [Indexed: 01/05/2023] Open
Abstract
The structure of a grafted layer of lactide chains in the “dry brush” regime immersed in a melt of chemically similar polymer was examined while varying graft lengths. To this end, microsecond atomistic molecular dynamics simulations were performed. Almost no influence of graft length on the fraction of the grafted chains backfolded to the grafting surface was found. However, a structural ordering was unexpectedly observed in the system when the length of the grafted lactide chains was close to approximately 10 Kuhn segments. This ordering of the grafts is characterized by the formation of helical fragments whose structure is in good agreement with the experimental data for the α crystal of the lactide chains. Both the backfolding and the structural ordering may be viewed as the initial stage of the crystallization of the layer of grafted lactide chains. In contrast to the known behavior for conventional polymer brushes in the “dry brush” regime, the structure of the grafted lactide chains can be either amorphous or ordered, depending on the graft length N and the grafting density σ when their product Nσ is fixed.
Collapse
Affiliation(s)
- Artyom D. Glova
- Institute of Macromolecular Compounds, Russian Academy of Sciences, Bolshoj pr. 31 (V.O.), 199004 St. Petersburg, Russia; (A.D.G.); (A.A.M.); (S.V.L.)
| | - Sofya D. Melnikova
- Institute of Physics, Nanotechnology and Telecommunications, Peter the Great St. Petersburg Polytechnic University, Polytechnicheskaya st. 29, 195251 St. Petersburg, Russia;
| | - Anna A. Mercurieva
- Institute of Macromolecular Compounds, Russian Academy of Sciences, Bolshoj pr. 31 (V.O.), 199004 St. Petersburg, Russia; (A.D.G.); (A.A.M.); (S.V.L.)
| | - Sergey V. Larin
- Institute of Macromolecular Compounds, Russian Academy of Sciences, Bolshoj pr. 31 (V.O.), 199004 St. Petersburg, Russia; (A.D.G.); (A.A.M.); (S.V.L.)
| | - Sergey V. Lyulin
- Institute of Macromolecular Compounds, Russian Academy of Sciences, Bolshoj pr. 31 (V.O.), 199004 St. Petersburg, Russia; (A.D.G.); (A.A.M.); (S.V.L.)
- Correspondence: ; Tel.: +7-812-323-0216
| |
Collapse
|
102
|
Yutani K, Matsuura Y, Joti Y. Confirmation of the formation of salt bridges in the denatured state of CutA1 protein using molecular dynamics simulations. Biophys Physicobiol 2019; 16:176-184. [PMID: 31984170 PMCID: PMC6976010 DOI: 10.2142/biophysico.16.0_176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 04/25/2019] [Indexed: 12/01/2022] Open
Abstract
It remains unclear how the abundant charged residues in proteins from hyperthermophiles contribute to the stabilization of proteins. Previously, based on molecular dynamics (MD) simulations, we proposed that these charged residues decrease the entropic effect by forming salt bridges in the denatured state under physiological conditions (Yutani et al., Sci. Rep. 8, 7613 (2018)). Because the quality of MD results is strongly dependent on the force fields used, in this study we performed the MD simulations using a different force field (AMBER99SB) along with the one we used before (Gromos43a1), at the same temperatures examined previously as well as at higher temperatures. In these experiments, we used the same ionic mutant (Ec0VV6) of CutA1 from Escherichia coli as in the previous study. In MD simulations at 300 K, Lys87 and Arg88 in the loop region of Ec0VV6 formed salt bridges with different favorable pairs in different force fields. Furthermore, the helical content and radius of gyration differed slightly between two force fields. However, at a higher temperature (600 K), the average numbers of salt bridges for the six substituted residues of Ec0VV6 were 0.87 per residue for Gromos43a1 and 0.88 for AMBER99SB in 400-ns MD simulation, indicating that the values were similar despite the use of different force fields. These observations suggest that the charged residues in Ec0VV6 can form a considerable number of salt bridges, even in the denatured state with drastic fluctuation at 600 K. These results corroborate our previous proposal.
Collapse
Affiliation(s)
| | | | - Yasumasa Joti
- RIKEN SPring-8 Center, Sayo, Hyogo 679-5148, Japan.,Japan Synchrotron Radiation Research Institute, Sayo, Hyogo 679-5198 Japan
| |
Collapse
|
103
|
Glova A, Larin SV, Nazarychev VM, Kenny JM, Lyulin AV, Lyulin SV. Toward Predictive Molecular Dynamics Simulations of Asphaltenes in Toluene and Heptane. ACS OMEGA 2019; 4:20005-20014. [PMID: 31788635 PMCID: PMC6882142 DOI: 10.1021/acsomega.9b02992] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 10/31/2019] [Indexed: 06/10/2023]
Abstract
The conventional definition of asphaltenes is based on their solubility in toluene and their insolubility in heptane. We have utilized this definition to study the influence of partial charge parametrization on the aggregation behavior of asphaltenes using classical atomistic molecular dynamics simulations performed on the microsecond time scale. Under consideration here are toluene- and heptane-based systems with different partial charges parametrized using the general AMBER force field (GAFF). Systems with standard GAFF partial charges calculated by the AM1-BCC and HF/6-31G*(RESP) methods were simulated alongside systems without partial charges. The partial charges implemented differ in terms of the resulting electrical negativity of the asphaltene polyaromatic core, with the AM1-BCC method giving the greatest magnitude of the total core charge. Based on our analysis of the molecular relaxation and orientation, and on the aggregation behavior of asphaltenes in toluene and heptane, we proposed to use the partial charges obtained by the AM1-BCC method for the study of asphaltene aggregates. A good agreement with available experimental data was observed on the sizes of the aggregates, their fractal dimensions, and the solvent entrainment for the model asphaltenes in toluene and heptane. From the results obtained, we conclude that for a better predictive ability, simulation parameters must be carefully chosen, with particular attention paid to the partial charges owing to their influence on the electrical negativity of the asphaltene core and on the asphaltenes aggregation.
Collapse
Affiliation(s)
- Artyom
D. Glova
- Institute
of Macromolecular Compounds, Russian Academy
of Sciences, Bolshoi
pr. 31 (V.O.), 199004 St. Petersburg, Russia
| | - Sergey V. Larin
- Institute
of Macromolecular Compounds, Russian Academy
of Sciences, Bolshoi
pr. 31 (V.O.), 199004 St. Petersburg, Russia
| | - Victor M. Nazarychev
- Institute
of Macromolecular Compounds, Russian Academy
of Sciences, Bolshoi
pr. 31 (V.O.), 199004 St. Petersburg, Russia
| | - Josè M. Kenny
- Institute
of Macromolecular Compounds, Russian Academy
of Sciences, Bolshoi
pr. 31 (V.O.), 199004 St. Petersburg, Russia
| | - Alexey V. Lyulin
- Institute
of Macromolecular Compounds, Russian Academy
of Sciences, Bolshoi
pr. 31 (V.O.), 199004 St. Petersburg, Russia
- Theory
of Polymers and Soft Matter Group, Technische
Universiteit Eindhoven, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Sergey V. Lyulin
- Institute
of Macromolecular Compounds, Russian Academy
of Sciences, Bolshoi
pr. 31 (V.O.), 199004 St. Petersburg, Russia
| |
Collapse
|
104
|
Wei W, Champion C, Liu Z, Barigye SJ, Labute P, Moitessier N. Torsional Energy Barriers of Biaryls Could Be Predicted by Electron Richness/Deficiency of Aromatic Rings; Advancement of Molecular Mechanics toward Atom-Type Independence. J Chem Inf Model 2019; 59:4764-4777. [PMID: 31430147 DOI: 10.1021/acs.jcim.9b00585] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Biaryl molecules are ubiquitous pharmacophores found in natural products and pharmaceuticals. In spite of this, existing molecular mechanics force fields are unable to accurately reproduce their torsional energy profiles, except for a few well-parametrized cases. This effectively limits the ability of structure-based drug design methods to correctly identify hits involving biaryls with confidence (e.g., during virtual screening, employing docking and/or molecular dynamics simulations). Continuing in our endeavor to quantify organic chemistry principles, we showed that the torsional energy profile of biaryl compounds could be computed on-the-fly based on the electron richness/deficiency of the aromatic rings. This method, called H-TEQ 4.0, was developed using a set of 131 biaryls. It was subsequently validated on a separate set of 100 diverse biaryls, including multisubstituted, bicyclic and tricyclic druglike molecules, and produced an average root-mean-square error (RMSE) of 0.95 kcal·mol-1. For comparison, GAFF2 produced an RMSE of 3.88 kcal·mol-1, owing to problems associated with the transferability of torsion parameters. The success of H-TEQ 4.0 provided further evidence that force fields could transition to become atom-type independent, providing that the correct chemical principles are used. Overall, this method solved the problem of transferability of biaryl torsion parameters, while simultaneously improving the overall accuracy of the force field.
Collapse
Affiliation(s)
- Wanlei Wei
- Department of Chemistry , McGill University , 801 Sherbrooke Street West , Montréal , Quebec , Canada H3A 0B8
| | - Candide Champion
- Department of Chemistry , McGill University , 801 Sherbrooke Street West , Montréal , Quebec , Canada H3A 0B8
| | - Zhaomin Liu
- Department of Chemistry , McGill University , 801 Sherbrooke Street West , Montréal , Quebec , Canada H3A 0B8
| | - Stephen J Barigye
- Department of Chemistry , McGill University , 801 Sherbrooke Street West , Montréal , Quebec , Canada H3A 0B8
| | - Paul Labute
- Chemical Computing Group Inc. , 1010 Sherbrooke Street West , Montréal , Quebec , Canada H3A 2R7
| | - Nicolas Moitessier
- Department of Chemistry , McGill University , 801 Sherbrooke Street West , Montréal , Quebec , Canada H3A 0B8
| |
Collapse
|
105
|
Malliavin TE, Mucherino A, Lavor C, Liberti L. Systematic Exploration of Protein Conformational Space Using a Distance Geometry Approach. J Chem Inf Model 2019; 59:4486-4503. [PMID: 31442036 DOI: 10.1021/acs.jcim.9b00215] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The optimization approaches classically used during the determination of protein structure encounter various difficulties, especially when the size of the conformational space is large. Indeed, in such a case, algorithmic convergence criteria are more difficult to set up. Moreover, the size of the search space makes it difficult to achieve a complete exploration. The interval branch-and-prune (iBP) approach, based on the reformulation of the distance geometry problem (DGP) provides a theoretical frame for the generation of protein conformations, by systematically sampling the conformational space. When an appropriate subset of interatomic distances is known exactly, this worst-case exponential-time algorithm is provably complete and fixed-parameter tractable. These guarantees, however, immediately disappear as distance measurement errors are introduced. Here we propose an improvement of this approach: threading-augmented interval branch-and-prune (TAiBP), where the combinatorial explosion of the original iBP approach arising from its exponential complexity is alleviated by partitioning the input instances into consecutive peptide fragments and by using self-organizing maps (SOMs) to obtain clusters of similar solutions. A validation of the TAiBP approach is presented here on a set of proteins of various sizes and structures. The calculation inputs are a uniform covalent geometry extracted from force field covalent terms, the backbone dihedral angles with error intervals, and a few long-range distances. For most of the proteins smaller than 50 residues and interval widths of 20°, the TAiBP approach yielded solutions with RMSD values smaller than 3 Å with respect to the initial protein conformation. The efficiency of the TAiBP approach for proteins larger than 50 residues will require the use of nonuniform covalent geometry and may have benefits from the recent development of residue-specific force-fields.
Collapse
Affiliation(s)
- Thérèse E Malliavin
- Unité de Bioinformatique Structurale, UMR 3528, CNRS, and Departement de Bioinformatique, Biostatistique et Biologie Intégrative, USR 3756, CNRS , Institut Pasteur , 75015 Paris , France
| | | | - Carlile Lavor
- Applied Math Department , IMECC-University of Campinas , Campinas , SP 13083-970 , Brazil
| | - Leo Liberti
- LIX CNRS, Ecole Polytechnique , Institut Polytechnique de Paris , Route de Saclay , 91128 Palaiseau , France
| |
Collapse
|
106
|
Casalini T, Limongelli V, Schmutz M, Som C, Jordan O, Wick P, Borchard G, Perale G. Molecular Modeling for Nanomaterial-Biology Interactions: Opportunities, Challenges, and Perspectives. Front Bioeng Biotechnol 2019; 7:268. [PMID: 31681746 PMCID: PMC6811494 DOI: 10.3389/fbioe.2019.00268] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 09/27/2019] [Indexed: 12/17/2022] Open
Abstract
Injection of nanoparticles (NP) into the bloodstream leads to the formation of a so-called "nano-bio" interface where dynamic interactions between nanoparticle surfaces and blood components take place. A common consequence is the formation of the protein corona, that is, a network of adsorbed proteins that can strongly alter the surface properties of the nanoparticle. The protein corona and the resulting structural changes experienced by adsorbed proteins can lead to substantial deviations from the expected cellular uptake as well as biological responses such as NP aggregation and NP-induced protein fibrillation, NP interference with enzymatic activity, or the exposure of new antigenic epitopes. Achieving a detailed understanding of the nano-bio interface is still challenging due to the synergistic effects of several influencing factors like pH, ionic strength, and hydrophobic effects, to name just a few. Because of the multiscale complexity of the system, modeling approaches at a molecular level represent the ideal choice for a detailed understanding of the driving forces and, in particular, the early events at the nano-bio interface. This review aims at exploring and discussing the opportunities and perspectives offered by molecular modeling in this field through selected examples from literature.
Collapse
Affiliation(s)
- Tommaso Casalini
- Polymer Engineering Laboratory, Department of Innovative Technologies, Institute for Mechanical Engineering and Materials Technology, University of Applied Sciences and Arts of Southern Switzerland (SUPSI), Manno, Switzerland
| | - Vittorio Limongelli
- Faculty of Biomedical Sciences, Center for Computational Medicine in Cardiology, Institute of Computational Science, Università della Svizzera italiana (USI), Lugano, Switzerland
- Department of Pharmacy, University of Naples “Federico II”, Naples, Italy
| | - Mélanie Schmutz
- Technology and Society Laboratory, Swiss Federal Laboratories for Materials Science and Technology (Empa), St. Gallen, Switzerland
| | - Claudia Som
- Technology and Society Laboratory, Swiss Federal Laboratories for Materials Science and Technology (Empa), St. Gallen, Switzerland
| | - Olivier Jordan
- School of Pharmaceutical Sciences, University of Geneva, Genève, Switzerland
| | - Peter Wick
- Laboratory for Particles – Biology Interactions, Swiss Federal Laboratories for Materials Science and Technology (Empa), St. Gallen, Switzerland
| | - Gerrit Borchard
- School of Pharmaceutical Sciences, University of Geneva, Genève, Switzerland
| | - Giuseppe Perale
- Polymer Engineering Laboratory, Department of Innovative Technologies, Institute for Mechanical Engineering and Materials Technology, University of Applied Sciences and Arts of Southern Switzerland (SUPSI), Manno, Switzerland
- Ludwig Boltzmann Institute for Experimental and Clinical Traumatology, Wien, Austria
| |
Collapse
|
107
|
Recent Advances in Coarse-Grained Models for Biomolecules and Their Applications. Int J Mol Sci 2019; 20:ijms20153774. [PMID: 31375023 PMCID: PMC6696403 DOI: 10.3390/ijms20153774] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 07/28/2019] [Accepted: 07/30/2019] [Indexed: 12/23/2022] Open
Abstract
Molecular dynamics simulations have emerged as a powerful tool to study biological systems at varied length and timescales. The conventional all-atom molecular dynamics simulations are being used by the wider scientific community in routine to capture the conformational dynamics and local motions. In addition, recent developments in coarse-grained models have opened the way to study the macromolecular complexes for time scales up to milliseconds. In this review, we have discussed the principle, applicability and recent development in coarse-grained models for biological systems. The potential of coarse-grained simulation has been reviewed through state-of-the-art examples of protein folding and structure prediction, self-assembly of complexes, membrane systems and carbohydrates fiber models. The multiscale simulation approaches have also been discussed in the context of their emerging role in unravelling hierarchical level information of biosystems. We conclude this review with the future scope of coarse-grained simulations as a constantly evolving tool to capture the dynamics of biosystems.
Collapse
|
108
|
Qiu Y, Nerenberg PS, Head-Gordon T, Wang LP. Systematic Optimization of Water Models Using Liquid/Vapor Surface Tension Data. J Phys Chem B 2019; 123:7061-7073. [DOI: 10.1021/acs.jpcb.9b05455] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yudong Qiu
- Chemistry Department, University of California, Davis, Davis, California 95616, United States
| | - Paul S. Nerenberg
- Departments of Physics & Astronomy and Biological Sciences, California State University, Los Angeles, California 90032, United States
| | - Teresa Head-Gordon
- Pitzer Theory Center and Departments of Chemistry, Bioengineering and Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California 94720, United States
| | - Lee-Ping Wang
- Chemistry Department, University of California, Davis, Davis, California 95616, United States
| |
Collapse
|
109
|
Smith AA, Ernst M, Riniker S, Meier BH. Localized and Collective Motions in HET-s(218-289) Fibrils from Combined NMR Relaxation and MD Simulation. Angew Chem Int Ed Engl 2019; 58:9383-9388. [PMID: 31070275 PMCID: PMC6618077 DOI: 10.1002/anie.201901929] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 04/17/2019] [Indexed: 12/20/2022]
Abstract
Nuclear magnetic resonance (NMR) relaxation data and molecular dynamics (MD) simulations are combined to characterize the dynamics of the fungal prion HET-s(218-289) in its amyloid form. NMR data is analyzed with the dynamics detector method, which yields timescale-specific information. An analogous analysis is performed on MD trajectories. Because specific MD predictions can be verified as agreeing with the NMR data, MD was used for further interpretation of NMR results: for the different timescales, cross-correlation coefficients were derived to quantify the correlation of the motion between different residues. Short timescales are the result of very local motions, while longer timescales are found for longer-range correlated motion. Similar trends on ns- and μs-timescales suggest that μs motion in fibrils is the result of motion correlated over many fibril layers.
Collapse
Affiliation(s)
- Albert A. Smith
- Physical ChemistryETH ZurichVladimir-Prelog-Weg 28093ZurichSwitzerland
- Present address: Institut für Medizinische Physik und BiophysikUniversität LeipzigHärtelstraße 16–1804107LeipzigGermany
| | - Matthias Ernst
- Physical ChemistryETH ZurichVladimir-Prelog-Weg 28093ZurichSwitzerland
| | - Sereina Riniker
- Physical ChemistryETH ZurichVladimir-Prelog-Weg 28093ZurichSwitzerland
| | - Beat H. Meier
- Physical ChemistryETH ZurichVladimir-Prelog-Weg 28093ZurichSwitzerland
| |
Collapse
|
110
|
Smith AA, Ernst M, Riniker S, Meier BH. Localized and Collective Motions in HET‐s(218‐289) Fibrils from Combined NMR Relaxation and MD Simulation. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201901929] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Albert A. Smith
- Physical ChemistryETH Zurich Vladimir-Prelog-Weg 2 8093 Zurich Switzerland
- Present address: Institut für Medizinische Physik und BiophysikUniversität Leipzig Härtelstraße 16–18 04107 Leipzig Germany
| | - Matthias Ernst
- Physical ChemistryETH Zurich Vladimir-Prelog-Weg 2 8093 Zurich Switzerland
| | - Sereina Riniker
- Physical ChemistryETH Zurich Vladimir-Prelog-Weg 2 8093 Zurich Switzerland
| | - Beat H. Meier
- Physical ChemistryETH Zurich Vladimir-Prelog-Weg 2 8093 Zurich Switzerland
| |
Collapse
|
111
|
Casalini T, Perale G. From Microscale to Macroscale: Nine Orders of Magnitude for a Comprehensive Modeling of Hydrogels for Controlled Drug Delivery. Gels 2019; 5:E28. [PMID: 31096685 PMCID: PMC6631542 DOI: 10.3390/gels5020028] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 04/14/2019] [Accepted: 05/06/2019] [Indexed: 12/21/2022] Open
Abstract
Because of their inherent biocompatibility and tailorable network design, hydrogels meet an increasing interest as biomaterials for the fabrication of controlled drug delivery devices. In this regard, mathematical modeling can highlight release mechanisms and governing phenomena, thus gaining a key role as complementary tool for experimental activity. Starting from the seminal contribution given by Flory-Rehner equation back in 1943 for the determination of matrix structural properties, over more than 70 years, hydrogel modeling has not only taken advantage of new theories and the increasing computational power, but also of the methods offered by computational chemistry, which provide details at the fundamental molecular level. Simulation techniques such as molecular dynamics act as a "computational microscope" and allow for obtaining a new and deeper understanding of the specific interactions between the solute and the polymer, opening new exciting possibilities for an in silico network design at the molecular scale. Moreover, system modeling constitutes an essential step within the "safety by design" paradigm that is becoming one of the new regulatory standard requirements also in the field-controlled release devices. This review aims at providing a summary of the most frequently used modeling approaches (molecular dynamics, coarse-grained models, Brownian dynamics, dissipative particle dynamics, Monte Carlo simulations, and mass conservation equations), which are here classified according to the characteristic length scale. The outcomes and the opportunities of each approach are compared and discussed with selected examples from literature.
Collapse
Affiliation(s)
- Tommaso Casalini
- Biomaterials Laboratory, Institute for Mechanical Engineering and Materials Technology, SUPSI-University of Applied Sciences and Arts of Southern Switzerland, Via Cantonale 2C, Galleria 2, 6928 Manno, Switzerland.
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, 8093 Zurich, Switzerland.
| | - Giuseppe Perale
- Biomaterials Laboratory, Institute for Mechanical Engineering and Materials Technology, SUPSI-University of Applied Sciences and Arts of Southern Switzerland, Via Cantonale 2C, Galleria 2, 6928 Manno, Switzerland.
- Department of Surgical Sciences and Integrated Diagnostics, Orthopaedic Clinic-IRCCS Ospedale Policlinico San Martino, Faculty of Biomedical Sciences, University of Genova, Largo R. Benzi 10, 16132 Genova, Italy.
| |
Collapse
|
112
|
Hahn DF, Milić JV, Hünenberger PH. Vase
‐
Kite
Equilibrium of Resorcin[4]arene Cavitands Investigated Using Molecular Dynamics Simulations with Ball‐and‐Stick Local Elevation Umbrella Sampling. Helv Chim Acta 2019. [DOI: 10.1002/hlca.201900060] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- David F. Hahn
- Laboratory of Physical Chemistry, Department of Chemistry and Applied BiosciencesETH Zürich Vladimir-Prelog-Weg 2 CH-8093 Zürich Switzerland
| | - Jovana V. Milić
- Laboratory of Photonics and InterfacesÉcole Polytechnique Fédérale de Lausanne, EPFL SB ISIC LPI, Station 6 CH-1015 Lausanne Switzerland
| | - Philippe H. Hünenberger
- Laboratory of Physical Chemistry, Department of Chemistry and Applied BiosciencesETH Zürich Vladimir-Prelog-Weg 2 CH-8093 Zürich Switzerland
| |
Collapse
|
113
|
Marrink SJ, Corradi V, Souza PC, Ingólfsson HI, Tieleman DP, Sansom MS. Computational Modeling of Realistic Cell Membranes. Chem Rev 2019; 119:6184-6226. [PMID: 30623647 PMCID: PMC6509646 DOI: 10.1021/acs.chemrev.8b00460] [Citation(s) in RCA: 432] [Impact Index Per Article: 86.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Indexed: 12/15/2022]
Abstract
Cell membranes contain a large variety of lipid types and are crowded with proteins, endowing them with the plasticity needed to fulfill their key roles in cell functioning. The compositional complexity of cellular membranes gives rise to a heterogeneous lateral organization, which is still poorly understood. Computational models, in particular molecular dynamics simulations and related techniques, have provided important insight into the organizational principles of cell membranes over the past decades. Now, we are witnessing a transition from simulations of simpler membrane models to multicomponent systems, culminating in realistic models of an increasing variety of cell types and organelles. Here, we review the state of the art in the field of realistic membrane simulations and discuss the current limitations and challenges ahead.
Collapse
Affiliation(s)
- Siewert J. Marrink
- Groningen
Biomolecular Sciences and Biotechnology Institute & Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Valentina Corradi
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Paulo C.T. Souza
- Groningen
Biomolecular Sciences and Biotechnology Institute & Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Helgi I. Ingólfsson
- Biosciences
and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
| | - D. Peter Tieleman
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Mark S.P. Sansom
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K.
| |
Collapse
|
114
|
Mehmood R, Qi HW, Steeves AH, Kulik HJ. The Protein’s Role in Substrate Positioning and Reactivity for Biosynthetic Enzyme Complexes: The Case of SyrB2/SyrB1. ACS Catal 2019. [DOI: 10.1021/acscatal.9b00865] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
|
115
|
Qi HW, Kulik HJ. Evaluating Unexpectedly Short Non-covalent Distances in X-ray Crystal Structures of Proteins with Electronic Structure Analysis. J Chem Inf Model 2019; 59:2199-2211. [DOI: 10.1021/acs.jcim.9b00144] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Helena W. Qi
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Heather J. Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| |
Collapse
|
116
|
Visscher KM, Geerke DP. Deriving Force-Field Parameters from First Principles Using a Polarizable and Higher Order Dispersion Model. J Chem Theory Comput 2019; 15:1875-1883. [PMID: 30763086 PMCID: PMC6581419 DOI: 10.1021/acs.jctc.8b01105] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Indexed: 11/30/2022]
Abstract
In this work we propose a strategy based on quantum mechanical (QM) calculations to parametrize a polarizable force field for use in molecular dynamics (MD) simulations. We investigate the use of multiple atoms-in-molecules (AIM) strategies to partition QM determined molecular electron densities into atomic subregions. The partitioned atomic densities are subsequently used to compute atomic dispersion coefficients from effective exchange-hole-dipole moment (XDM) calculations. In order to derive values for the repulsive van der Waals parameters from first principles, we use a simple volume relation to scale effective atomic radii. Explicit inclusion of higher order dispersion coefficients was tested for a series of alkanes, and we show that combining C6 and C8 attractive terms together with a C11 repulsive potential yields satisfying models when used in combination with our van der Waals parameters and electrostatic and bonded parameters as directly obtained from quantum calculations as well. This result highlights that explicit inclusion of higher order dispersion terms could be viable in simulation, and it suggests that currently available QM analysis methods allow for first-principles parametrization of molecular mechanics models.
Collapse
Affiliation(s)
- Koen M. Visscher
- AIMMS Division of Molecular Toxicology,
Department of Chemistry and Pharmaceutical Sciences, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, the Netherlands
| | - Daan P. Geerke
- AIMMS Division of Molecular Toxicology,
Department of Chemistry and Pharmaceutical Sciences, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, the Netherlands
| |
Collapse
|
117
|
Abstract
In addition to the underlying basic concepts and early recognition of halogen bonding, this paper reviews the conflicting views that consistently appear in the area of noncovalent interactions and the ability of covalently bonded halogen atoms in molecules to participate in noncovalent interactions that contribute to packing in the solid-state. It may be relatively straightforward to identify Type-II halogen bonding between atoms using the conceptual framework of σ-hole theory, especially when the interaction is linear and is formed between the axial positive region (σ-hole) on the halogen in one monomer and a negative site on a second interacting monomer. A σ-hole is an electron density deficient region on the halogen atom X opposite to the R–X covalent bond, where R is the remainder part of the molecule. However, it is not trivial to do so when secondary interactions are involved as the directionality of the interaction is significantly affected. We show, by providing some specific examples, that halogen bonds do not always follow the strict Type-II topology, and the occurrence of Type-I and -III halogen-centered contacts in crystals is very difficult to predict. In many instances, Type-I halogen-centered contacts appear simultaneously with Type-II halogen bonds. We employed the Independent Gradient Model, a recently proposed electron density approach for probing strong and weak interactions in molecular domains, to show that this is a very useful tool in unraveling the chemistry of halogen-assisted noncovalent interactions, especially in the weak bonding regime. Wherever possible, we have attempted to connect some of these results with those reported previously. Though useful for studying interactions of reasonable strength, IUPAC’s proposed “less than the sum of the van der Waals radii” criterion should not always be assumed as a necessary and sufficient feature to reveal weakly bound interactions, since in many crystals the attractive interaction happens to occur between the midpoint of a bond, or the junction region, and a positive or negative site.
Collapse
|
118
|
Yang Z, Mehmood R, Wang M, Qi HW, Steeves AH, Kulik HJ. Revealing quantum mechanical effects in enzyme catalysis with large-scale electronic structure simulation. REACT CHEM ENG 2019; 4:298-315. [PMID: 31572618 PMCID: PMC6768422 DOI: 10.1039/c8re00213d] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Enzymes have evolved to facilitate challenging reactions at ambient conditions with specificity seldom matched by other catalysts. Computational modeling provides valuable insight into catalytic mechanism, and the large size of enzymes mandates multi-scale, quantum mechanical-molecular mechanical (QM/MM) simulations. Although QM/MM plays an essential role in balancing simulation cost to enable sampling with full QM treatment needed to understand electronic structure in enzyme active sites, the relative importance of these two strategies for understanding enzyme mechanism is not well known. We explore challenges in QM/MM for studying the reactivity and stability of three diverse enzymes: i) Mg2+-dependent catechol O-methyltransferase (COMT), ii) radical enzyme choline trimethylamine lyase (CutC), and iii) DNA methyltransferase (DNMT1), which has structural Zn2+ binding sites. In COMT, strong non-covalent interactions lead to long range coupling of electronic structure properties across the active site, but the more isolated nature of the metallocofactor in DNMT1 leads to faster convergence of some properties. We quantify these effects in COMT by computing covariance matrices of by-residue electronic structure properties during dynamics and along the reaction coordinate. In CutC, we observe spontaneous bond cleavage following initiation events, highlighting the importance of sampling and dynamics. We use electronic structure analysis to quantify the relative importance of CHO and OHO non-covalent interactions in imparting reactivity. These three diverse cases enable us to provide some general recommendations regarding QM/MM simulation of enzymes.
Collapse
Affiliation(s)
- Zhongyue Yang
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Rimsha Mehmood
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Mengyi Wang
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Helena W. Qi
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Adam H. Steeves
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Heather J. Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| |
Collapse
|
119
|
Arantes PR, Polêto MD, John EBO, Pedebos C, Grisci BI, Dorn M, Verli H. Development of GROMOS-Compatible Parameter Set for Simulations of Chalcones and Flavonoids. J Phys Chem B 2019; 123:994-1008. [DOI: 10.1021/acs.jpcb.8b10139] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Pablo R. Arantes
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS 91500-970, Brazil
| | - Marcelo D. Polêto
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS 91500-970, Brazil
| | - Elisa B. O. John
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS 91500-970, Brazil
| | - Conrado Pedebos
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS 91500-970, Brazil
- School of Pharmacy, University of Nottingham, University Park, Nottingham, U.K
- CAPES Foundation, Ministry of Education of Brazil, Brasília, 70040-020, Brazil
| | - Bruno I. Grisci
- Instituto de Informática, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS 91501-970, Brazil
| | - Marcio Dorn
- Instituto de Informática, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS 91501-970, Brazil
| | - Hugo Verli
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS 91500-970, Brazil
| |
Collapse
|
120
|
Abstract
All-atom, classical force fields for protein molecular dynamics (MD) simulations currently occupy a sweet spot in the universe of computational models, sufficiently detailed to be of predictive value in many cases, yet also simple enough that some biologically relevant time scales (microseconds or more) can now be sampled via specialized hardware or enhanced sampling methods. However, due to their long evolutionary history, there is now a myriad of force field branches in current use, which can make it hard for those entering the simulation field to know which would be the best set of parameters for a given application. In this chapter, I try to give an overview of the historical motivation for the different force fields available, suggestions for how to determine the most appropriate model and what to do if the results are in conflict with experimental evidence.
Collapse
Affiliation(s)
- Robert B Best
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.
| |
Collapse
|
121
|
Braun E, Gilmer J, Mayes HB, Mobley DL, Monroe JI, Prasad S, Zuckerman DM. Best Practices for Foundations in Molecular Simulations [Article v1.0]. LIVING JOURNAL OF COMPUTATIONAL MOLECULAR SCIENCE 2018; 1:5957. [PMID: 31788666 PMCID: PMC6884151 DOI: 10.33011/livecoms.1.1.5957] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This document provides a starting point for approaching molecular simulations, guiding beginning practitioners to what issues they need to know about before and while starting their first simulations, and why those issues are so critical. This document makes no claims to provide an adequate introduction to the subject on its own. Instead, our goal is to help people know what issues are critical before beginning, and to provide references to good resources on those topics. We also provide a checklist of key issues to consider before and while setting up molecular simulations which may serve as a foundation for other best practices documents.
Collapse
Affiliation(s)
| | | | | | | | | | - Samarjeet Prasad
- National Institutes of Health and Johns Hopkins University, Baltimore
| | | |
Collapse
|
122
|
Mobley DL, Bannan CC, Rizzi A, Bayly CI, Chodera JD, Lim VT, Lim NM, Beauchamp KA, Slochower DR, Shirts MR, Gilson MK, Eastman PK. Escaping Atom Types in Force Fields Using Direct Chemical Perception. J Chem Theory Comput 2018; 14:6076-6092. [PMID: 30351006 PMCID: PMC6245550 DOI: 10.1021/acs.jctc.8b00640] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Traditional approaches to specifying a molecular mechanics force field encode all the information needed to assign force field parameters to a given molecule into a discrete set of atom types. This is equivalent to a representation consisting of a molecular graph comprising a set of vertices, which represent atoms labeled by atom type, and unlabeled edges, which represent chemical bonds. Bond stretch, angle bend, and dihedral parameters are then assigned by looking up bonded pairs, triplets, and quartets of atom types in parameter tables to assign valence terms and using the atom types themselves to assign nonbonded parameters. This approach, which we call indirect chemical perception because it operates on the intermediate graph of atom-typed nodes, creates a number of technical problems. For example, atom types must be sufficiently complex to encode all necessary information about the molecular environment, making it difficult to extend force fields encoded this way. Atom typing also results in a proliferation of redundant parameters applied to chemically equivalent classes of valence terms, needlessly increasing force field complexity. Here, we describe a new approach to assigning force field parameters via direct chemical perception. Rather than working through the intermediary of the atom-typed graph, direct chemical perception operates directly on the unmodified chemical graph of the molecule to assign parameters. In particular, parameters are assigned to each type of force field term (e.g., bond stretch, angle bend, torsion, and Lennard-Jones) based on standard chemical substructure queries implemented via the industry-standard SMARTS chemical perception language, using SMIRKS extensions that permit labeling of specific atoms within a chemical pattern. We use this to implement a new force field format, called the SMIRKS Native Open Force Field (SMIRNOFF) format. We demonstrate the power and generality of this approach using examples of specific molecules that pose problems for indirect chemical perception and construct and validate a minimalist yet very general force field, SMIRNOFF99Frosst. We find that a parameter definition file only ∼300 lines long provides coverage of all but <0.02% of a 5 million molecule drug-like test set. Despite its simplicity, the accuracy of SMIRNOFF99Frosst for small molecule hydration free energies and selected properties of pure organic liquids is similar to that of the General Amber Force Field, whose specification requires thousands of parameters. This force field provides a starting point for further optimization and refitting work to follow.
Collapse
Affiliation(s)
- David L Mobley
- Department of Pharmaceutical Science , University of California , Irvine , California 92697 , United States
- Department of Chemistry , University of California , Irvine , California 92697 , United States
| | - Caitlin C Bannan
- Department of Chemistry , University of California , Irvine , California 92697 , United States
| | - Andrea Rizzi
- Tri-Institutional Program in Computational Biology and Medicine , New York , New York 10065 , United States
- Computational and Systems Biology Program , Memorial Sloan Kettering Cancer Center , New York , New York 10065 , United States
| | | | - John D Chodera
- Computational and Systems Biology Program , Memorial Sloan Kettering Cancer Center , New York , New York 10065 , United States
| | - Victoria T Lim
- Department of Chemistry , University of California , Irvine , California 92697 , United States
| | - Nathan M Lim
- Department of Pharmaceutical Science , University of California , Irvine , California 92697 , United States
| | - Kyle A Beauchamp
- Counsyl , South San Francisco , California 94080 , United States
| | - David R Slochower
- Skaggs School of Pharmacy and Pharmaceutical Sciences , University of California, San Diego , La Jolla , California 92093 , United States
| | - Michael R Shirts
- Department of Chemical and Biological Engineering , University of Colorado Boulder , Boulder , Colorado 80309 , United States
| | - Michael K Gilson
- Skaggs School of Pharmacy and Pharmaceutical Sciences , University of California, San Diego , La Jolla , California 92093 , United States
| | - Peter K Eastman
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| |
Collapse
|
123
|
Rezaian M, Maleki R, Dahri Dahroud M, Alamdari A, Alimohammadi M. pH-Sensitive Co-Adsorption/Release of Doxorubicin and Paclitaxel by Carbon Nanotube, Fullerene, and Graphene Oxide in Combination with N-isopropylacrylamide: A Molecular Dynamics Study. Biomolecules 2018; 8:E127. [PMID: 30380660 PMCID: PMC6316683 DOI: 10.3390/biom8040127] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 10/16/2018] [Accepted: 10/19/2018] [Indexed: 12/16/2022] Open
Abstract
Nanotechnology based drug delivery systems for cancer therapy have been the topic of interest for many researchers and scientists. In this research, we have studied the pH sensitive co-adsorption and release of doxorubicin (DOX) and paclitaxel (PAX) by carbon nanotube (CNT), fullerene, and graphene oxide (GO) in combination with N-isopropylacrylamide (PIN). This simulation study has been performed by use of molecular dynamics. Interaction energies, hydrogen bond, and gyration radius were investigated. Results reveal that, compared with fullerene and GO, CNT is a better carrier for the co-adsorption and co-release of DOX and PAX. It can adsorb the drugs in plasma pH and release it in vicinity of cancerous tissues which have acidic pH. Investigating the number of hydrogen bonds revealed that PIN created many hydrogen bonds with water resulting in high hydrophilicity of PIN, hence making it more stable in the bloodstream while preventing from its accumulation. It is also concluded from this study that CNT and PIN would make a suitable combination for the delivery of DOX and PAX, because PIN makes abundant hydrogen bonds and CNT makes stable interactions with these drugs.
Collapse
Affiliation(s)
- Milad Rezaian
- Department of Pharmacology, School of Medicine, Shahid Beheshti University of Medical Sciences, 19839-63113 Tehran, Iran.
| | - Reza Maleki
- Department of Chemical Engineering, School of Chemical and Petroleum Engineering, Shiraz University, Shiraz 71345, Iran.
| | - Mohammad Dahri Dahroud
- Student Research Committee, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz 71345, Iran.
| | - Abdolmohammad Alamdari
- Department of Chemical Engineering, School of Chemical and Petroleum Engineering, Shiraz University, Shiraz 71345, Iran.
| | | |
Collapse
|
124
|
Walz MM, Ghahremanpour MM, van Maaren PJ, van der Spoel D. Phase-Transferable Force Field for Alkali Halides. J Chem Theory Comput 2018; 14:5933-5948. [DOI: 10.1021/acs.jctc.8b00507] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Marie-Madeleine Walz
- Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, SE-75124 Uppsala, Sweden
| | - Mohammad M. Ghahremanpour
- Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, SE-75124 Uppsala, Sweden
| | - Paul J. van Maaren
- Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, SE-75124 Uppsala, Sweden
| | - David van der Spoel
- Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, SE-75124 Uppsala, Sweden
| |
Collapse
|
125
|
Baz J, Gebhardt J, Kraus H, Markthaler D, Hansen N. Insights into Noncovalent Binding Obtained from Molecular Dynamics Simulations. CHEM-ING-TECH 2018. [DOI: 10.1002/cite.201800050] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Jörg Baz
- University of Stuttgart; Institute of Thermodynamics and Thermal Process Engineering; Pfaffenwaldring 9 70569 Stuttgart Germany
| | - Julia Gebhardt
- University of Stuttgart; Institute of Thermodynamics and Thermal Process Engineering; Pfaffenwaldring 9 70569 Stuttgart Germany
| | - Hamzeh Kraus
- University of Stuttgart; Institute of Thermodynamics and Thermal Process Engineering; Pfaffenwaldring 9 70569 Stuttgart Germany
| | - Daniel Markthaler
- University of Stuttgart; Institute of Thermodynamics and Thermal Process Engineering; Pfaffenwaldring 9 70569 Stuttgart Germany
| | - Niels Hansen
- University of Stuttgart; Institute of Thermodynamics and Thermal Process Engineering; Pfaffenwaldring 9 70569 Stuttgart Germany
| |
Collapse
|
126
|
Bashardanesh Z, van der Spoel D. Impact of Dispersion Coefficient on Simulations of Proteins and Organic Liquids. J Phys Chem B 2018; 122:8018-8027. [DOI: 10.1021/acs.jpcb.8b05770] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Zahedeh Bashardanesh
- Uppsala Center for Computational Chemistry, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, P.O. Box 596, SE-75124 Uppsala, Sweden
| | - David van der Spoel
- Uppsala Center for Computational Chemistry, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, P.O. Box 596, SE-75124 Uppsala, Sweden
| |
Collapse
|
127
|
Walters ET, Mohebifar M, Johnson ER, Rowley CN. Evaluating the London Dispersion Coefficients of Protein Force Fields Using the Exchange-Hole Dipole Moment Model. J Phys Chem B 2018; 122:6690-6701. [DOI: 10.1021/acs.jpcb.8b02814] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Evan T. Walters
- Department of Chemistry, Memorial University of Newfoundland, St. John’s A1C 5S7, Newfoundland and Labrador, Canada
| | - Mohamad Mohebifar
- Department of Chemistry, Memorial University of Newfoundland, St. John’s A1C 5S7, Newfoundland and Labrador, Canada
| | - Erin R. Johnson
- Department of Chemistry, Dalhousie University, Halifax B3H 4R2, Nova Scotia, Canada
| | - Christopher N. Rowley
- Department of Chemistry, Memorial University of Newfoundland, St. John’s A1C 5S7, Newfoundland and Labrador, Canada
| |
Collapse
|