51
|
Panczyk K, Gaweda K, Drach M, Plazinski W. Extension of the GROMOS 56a6 CARBO/CARBO_R Force Field for Charged, Protonated, and Esterified Uronates. J Phys Chem B 2018; 122:3696-3710. [PMID: 29558620 DOI: 10.1021/acs.jpcb.7b11548] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
An extension of the GROMOS 56a6CARBO/CARBO_R force field for hexopyranose-based carbohydrates is presented. The additional parameters describe the conformational properties of uronate residues. The three distinct chemical states of the carboxyl group are considered: deprotonated (negatively charged), protonated (neutral), and esterified (neutral). The parametrization procedure was based on quantum-chemical calculations, and the resulting parameters were tested in the context of (i) flexibility of the pyranose rings under different pH conditions, (ii) conformation of the glycosidic linkage of the (1 → 4)-type for uronates with different chemical states of carboxyl moieties, (iii) conformation of the exocyclic (i.e., carboxylate and lactol) moieties, and (iv) structure of the Ca2+-linked chain-chain complexes of uronates. The presently proposed parameters in combination with the 56a6CARBO/CARBO_R set can be used to describe the naturally occurring polyuronates, composed either of homogeneous (e.g., glucuronans) or heterogeneous (e.g., pectins, alginates) segments. The results of simulations relying on the new set of parameters indicate that the conformation of glycosidic linkage is nearly unaffected by the chemical state of the carboxyl group, in contrary to the ring conformational equilibria. The calculations for the poly(α-d-galacturonate)-Ca2+ and poly(α-l-guluronate)-Ca2+ complexes show that both parallel and anitiparallel arrangements of uronate chains are possible but differ in several structural aspects.
Collapse
Affiliation(s)
- Karina Panczyk
- Jerzy Haber Institute of Catalysis and Surface Chemistry , Polish Academy of Sciences , ul. Niezapominajek 8 , 30-239 Cracow , Poland
| | - Karolina Gaweda
- Jerzy Haber Institute of Catalysis and Surface Chemistry , Polish Academy of Sciences , ul. Niezapominajek 8 , 30-239 Cracow , Poland
| | - Mateusz Drach
- Department of Theoretical Chemistry, Faculty of Chemistry , M. Curie-Sklodowska University , pl. M. Curie-Sklodowskiej 3 , 20-031 Lublin , Poland
| | - Wojciech Plazinski
- Jerzy Haber Institute of Catalysis and Surface Chemistry , Polish Academy of Sciences , ul. Niezapominajek 8 , 30-239 Cracow , Poland
| |
Collapse
|
52
|
Skariyachan S, Manjunath M, Bachappanavar N. Screening of potential lead molecules against prioritised targets of multi-drug-resistant-Acinetobacter baumannii - insights from molecular docking, molecular dynamic simulations and in vitro assays. J Biomol Struct Dyn 2018. [PMID: 29529934 DOI: 10.1080/07391102.2018.1451387] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Acinetobacter baumannii, an opportunistic pathogen, has become multi-drug resistant (MDR) to major classes of antibacterial and poses grave threat to public health. The current study focused to screen novel phytotherapeutics against prioritised targets of Acinetobacter baumannii by computational investigation. Fourteen potential drug targets were screened based on their functional role in various biosynthetic pathways and the 3D structures of 9 targets were retrieved from Protein Data Bank and others were computationally predicted. By extensive literature survey, 104 molecules from 48 herbal sources were screened and subjected to virtual screening. Ten clinical isolates of A. baumannii were tested for antibiotic susceptibility towards clinafloxacin, imipenem and polymyxin-E. Computational screening suggested that Ajmalicine ((19α)-16, 17-didehydro-19-methyloxayohimban-16-carboxylic acid methyl ester from Rauwolfia serpentina), Strictamin (Akuammilan-17-oic acid methyl ester from Alstonia scholaris) and Limonin (7, 16-dioxo-7, 16-dideoxylimondiol from Citrus sps) exhibited promising binding towards multiple drug targets of A. baumannii in comparison with the binding between standard drugs and their targets. Limonin displayed promising binding potential (binding energy -9.8 kcal/mol) towards diaminopimelate epimerase (DapF) and UDP-N-acetylglucosamine 1-carboxyvinyltransferase (MurA). Ajmalicine and Strictamin demonstrated good binding potential (-9.5, -8.5 kcal/mol, respectively) towards MurA and shikimate dehydrogenase (-7.8 kcal/mol). Molecular dynamic simulations further validated the docking results. In vitro assay suggested that the tested isolates exhibited resistance to clinafloxacin, imipenem and polymyxin-E and the herbal preparations (crude extract) demonstrated a significant antibacterial potential (p ≤ .05). The study suggests that the aforementioned lead candidates and targets can be used for structure-based drug screening towards MDR A. baumannii.
Collapse
Affiliation(s)
- Sinosh Skariyachan
- a Department of Biotechnology Engineering , Dayananda Sagar Institutions , Bengaluru 560 078 , Karnataka , India.,b Visvesvaraya Technological University , Belagavi , India
| | - Meghna Manjunath
- a Department of Biotechnology Engineering , Dayananda Sagar Institutions , Bengaluru 560 078 , Karnataka , India.,b Visvesvaraya Technological University , Belagavi , India
| | - Nikhil Bachappanavar
- a Department of Biotechnology Engineering , Dayananda Sagar Institutions , Bengaluru 560 078 , Karnataka , India.,b Visvesvaraya Technological University , Belagavi , India
| |
Collapse
|
53
|
Affiliation(s)
- Noura Dawass
- Process & Energy Laboratory, Delft University of Technology, Delft, The Netherlands
| | - Peter Krüger
- Graduate School of Science and Engineering, Chiba University, Chiba, Japan
| | | | - Thijs J. H. Vlugt
- Process & Energy Laboratory, Delft University of Technology, Delft, The Netherlands
| |
Collapse
|
54
|
Milzetti J, Nayar D, van der Vegt NFA. Convergence of Kirkwood–Buff Integrals of Ideal and Nonideal Aqueous Solutions Using Molecular Dynamics Simulations. J Phys Chem B 2018; 122:5515-5526. [DOI: 10.1021/acs.jpcb.7b11831] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jasmin Milzetti
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Center of Smart Interfaces, Technische Universität Darmstadt, Alarich-Weiss-Straße 10, 64287, Darmstadt, Germany
| | - Divya Nayar
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Center of Smart Interfaces, Technische Universität Darmstadt, Alarich-Weiss-Straße 10, 64287, Darmstadt, Germany
| | - Nico F. A. van der Vegt
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Center of Smart Interfaces, Technische Universität Darmstadt, Alarich-Weiss-Straße 10, 64287, Darmstadt, Germany
| |
Collapse
|
55
|
Jandova Z, Fast D, Setz M, Pechlaner M, Oostenbrink C. Saturation Mutagenesis by Efficient Free-Energy Calculation. J Chem Theory Comput 2018; 14:894-904. [PMID: 29262673 PMCID: PMC5813279 DOI: 10.1021/acs.jctc.7b01099] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Single-point mutations
in proteins can greatly influence protein
stability, binding affinity, protein function or its expression per
se. Here, we present accurate and efficient predictions of the free
energy of mutation of amino acids. We divided the complete mutational
free energy into an uncharging step, which we approximate by a third-power
fitting (TPF) approach, and an annihilation step, which we approximate
using the one-step perturbation (OSP) method. As a diverse set of
test systems, we computed the solvation free energy of all amino acid
side chain analogues and obtained an excellent agreement with thermodynamic
integration (TI) data. Moreover, we calculated mutational free energies
in model tripeptides and established an efficient protocol involving
a single reference state. Again, the approximate methods agreed excellently
with the TI references, with a root-mean-square error of only 3.6
kJ/mol over 17 mutations. Our combined TPF+OSP approach does show
not only a very good agreement but also a 2-fold higher efficiency
than full blown TI calculations.
Collapse
Affiliation(s)
- Zuzana Jandova
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences , Vienna A-1190, Austria
| | - Daniel Fast
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences , Vienna A-1190, Austria
| | - Martina Setz
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences , Vienna A-1190, Austria
| | - Maria Pechlaner
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences , Vienna A-1190, Austria
| | - Chris Oostenbrink
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences , Vienna A-1190, Austria
| |
Collapse
|
56
|
Jandova Z, Trosanova Z, Weisova V, Oostenbrink C, Hritz J. Free energy calculations on the stability of the 14-3-3ζ protein. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1866:442-450. [PMID: 29203375 DOI: 10.1016/j.bbapap.2017.11.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 10/31/2017] [Accepted: 11/25/2017] [Indexed: 01/08/2023]
Abstract
Mutations of cysteine are often introduced to e.g. avoid formation of non-physiological inter-molecular disulfide bridges in in-vitro experiments, or to maintain specificity in labeling experiments. Alanine or serine is typically preferred, which usually do not alter the overall protein stability, when the original cysteine was surface exposed. However, selecting the optimal mutation for cysteines in the hydrophobic core of the protein is more challenging. In this work, the stability of selected Cys mutants of 14-3-3ζ was predicted by free-energy calculations and the obtained data were compared with experimentally determined stabilities. Both the computational predictions as well as the experimental validation point at a significant destabilization of mutants C94A and C94S. This destabilization could be attributed to the formation of hydrophobic cavities and a polar solvation of a hydrophilic side chain. A L12E, M78K double mutant was further studied in terms of its reduced dimerization propensity. In contrast to naïve expectations, this double mutant did not lead to the formation of strong salt bridges, which was rationalized in terms of a preferred solvation of the ionic species. Again, experiments agreed with the calculations by confirming the monomerization of the double mutants. Overall, the simulation data is in good agreement with experiments and offers additional insight into the stability and dimerization of this important family of regulatory proteins.
Collapse
Affiliation(s)
- Zuzana Jandova
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Zuzana Trosanova
- CEITEC-MU, Masaryk University, Kamenice 753/5, Bohunice, Brno, Czech Republic
| | - Veronika Weisova
- CEITEC-MU, Masaryk University, Kamenice 753/5, Bohunice, Brno, Czech Republic
| | - Chris Oostenbrink
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, Vienna, Austria.
| | - Jozef Hritz
- CEITEC-MU, Masaryk University, Kamenice 753/5, Bohunice, Brno, Czech Republic.
| |
Collapse
|
57
|
Bakarić D, Petrov D, Mouvenchery YK, Heiβler S, Oostenbrink C, Schaumann GE. Ion-induced modification of the sucrose network and its impact on melting of freeze-dried liposomes. DSC and molecular dynamics study. Chem Phys Lipids 2017; 210:38-46. [PMID: 29179944 DOI: 10.1016/j.chemphyslip.2017.11.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 11/14/2017] [Accepted: 11/23/2017] [Indexed: 02/07/2023]
Abstract
Disaccharides play an important role in survival of anhydrobiotic organisms during extreme environmental conditions. A key protection feature is their capability to form the hydrogen bond (HB) network in a similar fashion as the one made by water. Since various ions also affect the HB network in completely hydrated systems, it is of a great interest to understand how they impact preservation when incorporated in a disaccharide network. To address this, we employ a combination of experimental and modeling techniques to study behavior of multilamellar 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) liposomes freeze-dried with sucrose in presence of NaCl or NaH2PO4·H2O at various concentrations (0.01-1M). Differential scanning calorimetry (DSC) was employed in order to determine the cooperative unit size (CUS), the number of lipid molecules that constitute a domain of cooperative motion in the liposome, and the melting temperature (Tm). In the absence of salt CUS was estimated to be 122±12, whereas in the presence of NaCl CUS increases more (347±34 for c=1M) than for NaH2PO4·H2O (193±26 for 1M). When it comes to Tm, the situation is reversed; NaCl induces increase by about 1K, while NaH2PO4·H2O by about 10K. These findings clearly demonstrate how different interaction forces-hydrogen bonding, charge pairing, and van der Waals interactions between acyl chains-affect CUS and Tm. Their interplay and contribution of particular interaction was further analyzed with molecular dynamics (MD) simulations. This analysis demonstrated that the HB network of DMPC and sucrose is partially disrupted in the presence of NaCl ions, and even to a greater extent in the case of NaH2PO4·H2O ions. Notably, H2PO4- ions outcompete and replace the sucrose molecules at the DMPC surface, which in turn alters the nature of the DMPC-surrounding interactions, from a weaker HB-dominated to a stronger CP-dominated interaction network.
Collapse
Affiliation(s)
- Danijela Bakarić
- University of Koblenz-Landau, Institute for Environmental Sciences, Group of Environmental and Soil Chemistry, Fortstraße 7, D-76829 Landau, Germany.
| | - Dražen Petrov
- Department of Material Sciences and Process Engineering, Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences Vienna, Muthgasse 18, A-1190 Vienna, Austria
| | - Yamuna Kunhi Mouvenchery
- University of Koblenz-Landau, Institute for Environmental Sciences, Group of Environmental and Soil Chemistry, Fortstraße 7, D-76829 Landau, Germany
| | - Stefan Heiβler
- Institute for Functional Interfaces, Karlsruhe Institute for Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Chris Oostenbrink
- Department of Material Sciences and Process Engineering, Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences Vienna, Muthgasse 18, A-1190 Vienna, Austria
| | - Gabriele E Schaumann
- University of Koblenz-Landau, Institute for Environmental Sciences, Group of Environmental and Soil Chemistry, Fortstraße 7, D-76829 Landau, Germany.
| |
Collapse
|
58
|
Frederix PWJM, Idé J, Altay Y, Schaeffer G, Surin M, Beljonne D, Bondarenko AS, Jansen TLC, Otto S, Marrink SJ. Structural and Spectroscopic Properties of Assemblies of Self-Replicating Peptide Macrocycles. ACS NANO 2017; 11:7858-7868. [PMID: 28723067 PMCID: PMC5616102 DOI: 10.1021/acsnano.7b02211] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Self-replication at the molecular level is often seen as essential to the early origins of life. Recently a mechanism of self-replication has been discovered in which replicator self-assembly drives the process. We have studied one of the examples of such self-assembling self-replicating molecules to a high level of structural detail using a combination of computational and spectroscopic techniques. Molecular Dynamics simulations of self-assembled stacks of peptide-derived replicators provide insights into the structural characteristics of the system and serve as the basis for semiempirical calculations of the UV-vis, circular dichroism (CD) and infrared (IR) absorption spectra that reflect the chiral organization and peptide secondary structure of the stacks. Two proposed structural models are tested by comparing calculated spectra to experimental data from electron microscopy, CD and IR spectroscopy, resulting in a better insight into the specific supramolecular interactions that lead to self-replication. Specifically, we find a cooperative self-assembly process in which β-sheet formation leads to well-organized structures, while also the aromatic core of the macrocycles plays an important role in the stability of the resulting fibers.
Collapse
Affiliation(s)
- Pim W. J. M. Frederix
- University
of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute, Nijenborgh 7, 9747AG Groningen, The Netherlands
- University
of Groningen, Center for Systems Chemistry, Stratingh Institute for
Chemistry, Nijenborgh
4, 9747AG Groningen, The Netherlands
- E-mail:
| | - Julien Idé
- Laboratory
of Chemistry of Novel Materials, University
of Mons − UMONS, Place du Parc 20, B-7000 Mons, Belgium
| | - Yigit Altay
- University
of Groningen, Center for Systems Chemistry, Stratingh Institute for
Chemistry, Nijenborgh
4, 9747AG Groningen, The Netherlands
| | - Gaël Schaeffer
- University
of Groningen, Center for Systems Chemistry, Stratingh Institute for
Chemistry, Nijenborgh
4, 9747AG Groningen, The Netherlands
| | - Mathieu Surin
- Laboratory
of Chemistry of Novel Materials, University
of Mons − UMONS, Place du Parc 20, B-7000 Mons, Belgium
| | - David Beljonne
- Laboratory
of Chemistry of Novel Materials, University
of Mons − UMONS, Place du Parc 20, B-7000 Mons, Belgium
| | - Anna S. Bondarenko
- University
of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747AG Groningen, The Netherlands
| | - Thomas L. C. Jansen
- University
of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747AG Groningen, The Netherlands
| | - Sijbren Otto
- University
of Groningen, Center for Systems Chemistry, Stratingh Institute for
Chemistry, Nijenborgh
4, 9747AG Groningen, The Netherlands
- University
of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747AG Groningen, The Netherlands
- E-mail:
| | - Siewert J. Marrink
- University
of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute, Nijenborgh 7, 9747AG Groningen, The Netherlands
- University
of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747AG Groningen, The Netherlands
- E-mail:
| |
Collapse
|
59
|
Williams-Noonan BJ, Yuriev E, Chalmers DK. Free Energy Methods in Drug Design: Prospects of “Alchemical Perturbation” in Medicinal Chemistry. J Med Chem 2017; 61:638-649. [DOI: 10.1021/acs.jmedchem.7b00681] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Billy J. Williams-Noonan
- Medicinal Chemistry, Monash
Institute of Pharmaceutical Sciences, Monash University, 381 Royal
Parade, Parkville, Victoria 3052, Australia
| | - Elizabeth Yuriev
- Medicinal Chemistry, Monash
Institute of Pharmaceutical Sciences, Monash University, 381 Royal
Parade, Parkville, Victoria 3052, Australia
| | - David K. Chalmers
- Medicinal Chemistry, Monash
Institute of Pharmaceutical Sciences, Monash University, 381 Royal
Parade, Parkville, Victoria 3052, Australia
| |
Collapse
|
60
|
Sandoval-Perez A, Pluhackova K, Böckmann RA. Critical Comparison of Biomembrane Force Fields: Protein-Lipid Interactions at the Membrane Interface. J Chem Theory Comput 2017; 13:2310-2321. [PMID: 28388089 DOI: 10.1021/acs.jctc.7b00001] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Molecular dynamics (MD) simulations offer the possibility to study biological processes at high spatial and temporal resolution often not reachable by experiments. Corresponding biomolecular force field parameters have been developed for a wide variety of molecules ranging from inorganic ligands and small organic molecules over proteins and lipids to nucleic acids. Force fields have typically been parametrized and validated on thermodynamic observables and structural characteristics of individual compounds, e.g. of soluble proteins or lipid bilayers. Less strictly, due to the added complexity and missing experimental data to compare to, force fields have hardly been tested on the properties of mixed systems, e.g. on protein-lipid systems. Their selection and combination for mixed systems is further complicated by the partially differing parametrization strategies. Additionally, the presence of other compounds in the system may shift the subtle balance of force field parameters. Here, we assessed the protein-lipid interactions as described in the four atomistic force fields GROMOS54a7, CHARMM36 and the two force field combinations Amber14sb/Slipids and Amber14sb/Lipid14. Four observables were compared, focusing on the membrane-water interface: the conservation of the secondary structure of transmembrane proteins, the positioning of transmembrane peptides relative to the lipid bilayer, the insertion depth of side chains of unfolded peptides absorbed at the membrane interface, and the ability to reproduce experimental insertion energies of Wimley-White peptides at the membrane interface. Significant differences between the force fields were observed that affect e.g. membrane insertion depths and tilting of transmembrane peptides.
Collapse
Affiliation(s)
- Angelica Sandoval-Perez
- Computational Biology, Department of Biology, Friedrich-Alexander University of Erlangen-Nürnberg , Staudtstrassre 5, 91058 Erlangen, Germany
| | - Kristyna Pluhackova
- Computational Biology, Department of Biology, Friedrich-Alexander University of Erlangen-Nürnberg , Staudtstrassre 5, 91058 Erlangen, Germany
| | - Rainer A Böckmann
- Computational Biology, Department of Biology, Friedrich-Alexander University of Erlangen-Nürnberg , Staudtstrassre 5, 91058 Erlangen, Germany
| |
Collapse
|
61
|
Margreitter C, Reif MM, Oostenbrink C. Update on phosphate and charged post-translationally modified amino acid parameters in the GROMOS force field. J Comput Chem 2017; 38:714-720. [DOI: 10.1002/jcc.24733] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Revised: 12/28/2016] [Accepted: 12/29/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Christian Margreitter
- Department of Material Sciences and Process Engineering; Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences; Vienna Austria
| | - Maria M. Reif
- Physics Department T38; Technical University of Munich; Munich Germany
| | - Chris Oostenbrink
- Department of Material Sciences and Process Engineering; Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences; Vienna Austria
| |
Collapse
|
62
|
Mohamed NA, Bradshaw RT, Essex JW. Evaluation of solvation free energies for small molecules with the AMOEBA polarizable force field. J Comput Chem 2016; 37:2749-2758. [PMID: 27757978 PMCID: PMC5111595 DOI: 10.1002/jcc.24500] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 09/05/2016] [Accepted: 09/07/2016] [Indexed: 01/24/2023]
Abstract
The effects of electronic polarization in biomolecular interactions will differ depending on the local dielectric constant of the environment, such as in solvent, DNA, proteins, and membranes. Here the performance of the AMOEBA polarizable force field is evaluated under nonaqueous conditions by calculating the solvation free energies of small molecules in four common organic solvents. Results are compared with experimental data and equivalent simulations performed with the GAFF pairwise-additive force field. Although AMOEBA results give mean errors close to "chemical accuracy," GAFF performs surprisingly well, with statistically significantly more accurate results than AMOEBA in some solvents. However, for both models, free energies calculated in chloroform show worst agreement to experiment and individual solutes are consistently poor performers, suggesting non-potential-specific errors also contribute to inaccuracy. Scope for the improvement of both potentials remains limited by the lack of high quality experimental data across multiple solvents, particularly those of high dielectric constant. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Noor Asidah Mohamed
- Computational Systems Chemistry, School of ChemistryUniversity of SouthamptonHighfieldSouthamptonSO17 1BJUK
| | - Richard T. Bradshaw
- Computational Systems Chemistry, School of ChemistryUniversity of SouthamptonHighfieldSouthamptonSO17 1BJUK
| | - Jonathan W. Essex
- Computational Systems Chemistry, School of ChemistryUniversity of SouthamptonHighfieldSouthamptonSO17 1BJUK
| |
Collapse
|
63
|
An extensive simulation study of lipid bilayer properties with different head groups, acyl chain lengths, and chain saturations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:3093-3104. [PMID: 27664502 DOI: 10.1016/j.bbamem.2016.09.016] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 09/14/2016] [Accepted: 09/19/2016] [Indexed: 12/21/2022]
Abstract
Previous MD simulations of six phosphocholine (PC) lipid bilayers demonstrated the accuracy of the CHARMM36 force field (C36FF) for PC bilayer simulation at varied temperatures (BBA-Biomembranes, 1838 (2014): 2520-2529). In this work, we further examine the accuracy of C36FF over a wide temperature range for a broader range of lipid types such as various head groups (phosphatidic acid (PA), PC, phosphoethanolamine (PE), phosphoglycerol (PG), and phosphoserine (PS)), and tails (saturated, mono-, mixed- and poly-unsaturated acyl chains with varied chain lengths). The structural properties (surface area per lipid (SA/lip), overall bilayer thickness, hydrophobic thickness, headgroup-to-headgroup thickness, deuterium order parameter (SCD), and spin-lattice relaxation time (T1)) obtained from simulations agree well with nearly all available experimental data. Our analyses indicate that PS lipids have the most inter-lipid hydrogen bonds, while PG lipids have the most intra-lipid hydrogen bonds, which play the main role in their low SA/lip in PS lipids and low thicknesses in PG lipids, respectively. PS, PE, and PA lipids have the largest contact clusters with on average 5-8 lipids per cluster, while PC and PG have clusters of 4 lipids based on a cutoff distance of 6.5Å. PS lipids have much slower lipid wobble (i.e., higher correlation time) than other head groups at a given temperature as the hydrogen bonded network significantly reduces a lipid's mobility, and the rate of lipid wobble increases dramatically as temperature increases. These in-depth analyses facilitate further understanding of lipid bilayers at the atomic level.
Collapse
|
64
|
Ruiter AD, Oostenbrink C. Extended Thermodynamic Integration: Efficient Prediction of Lambda Derivatives at Nonsimulated Points. J Chem Theory Comput 2016; 12:4476-86. [PMID: 27494138 DOI: 10.1021/acs.jctc.6b00458] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Thermodynamic integration (TI) is one of the most commonly used free-energy calculation methods. The derivative of the Hamiltonian with respect to lambda, ⟨∂H/∂λ⟩, is determined at multiple λ-points. Because a numerical integration step is necessary, high curvature regions require simulations at densely spaced λ-points. Here, the principle of extended TI is introduced, where ⟨∂H/∂λ⟩ values are predicted at nonsimulated λ-points. On the basis of three model systems, it is shown that extended TI requires significantly fewer λ-points than regular TI to obtain similar accuracy.
Collapse
Affiliation(s)
- Anita de Ruiter
- Institute for Molecular Modeling and Simulation, University of Natural Resources and Life Sciences (BOKU) Vienna, 1180 Wien, Austria
| | - Chris Oostenbrink
- Institute for Molecular Modeling and Simulation, University of Natural Resources and Life Sciences (BOKU) Vienna, 1180 Wien, Austria
| |
Collapse
|
65
|
Vermaas JV, Trebesch N, Mayne CG, Thangapandian S, Shekhar M, Mahinthichaichan P, Baylon JL, Jiang T, Wang Y, Muller MP, Shinn E, Zhao Z, Wen PC, Tajkhorshid E. Microscopic Characterization of Membrane Transporter Function by In Silico Modeling and Simulation. Methods Enzymol 2016; 578:373-428. [PMID: 27497175 PMCID: PMC6404235 DOI: 10.1016/bs.mie.2016.05.042] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Membrane transporters mediate one of the most fundamental processes in biology. They are the main gatekeepers controlling active traffic of materials in a highly selective and regulated manner between different cellular compartments demarcated by biological membranes. At the heart of the mechanism of membrane transporters lie protein conformational changes of diverse forms and magnitudes, which closely mediate critical aspects of the transport process, most importantly the coordinated motions of remotely located gating elements and their tight coupling to chemical processes such as binding, unbinding and translocation of transported substrate and cotransported ions, ATP binding and hydrolysis, and other molecular events fueling uphill transport of the cargo. An increasing number of functional studies have established the active participation of lipids and other components of biological membranes in the function of transporters and other membrane proteins, often acting as major signaling and regulating elements. Understanding the mechanistic details of these molecular processes require methods that offer high spatial and temporal resolutions. Computational modeling and simulations technologies empowered by advanced sampling and free energy calculations have reached a sufficiently mature state to become an indispensable component of mechanistic studies of membrane transporters in their natural environment of the membrane. In this article, we provide an overview of a number of major computational protocols and techniques commonly used in membrane transporter modeling and simulation studies. The article also includes practical hints on effective use of these methods, critical perspectives on their strengths and weak points, and examples of their successful applications to membrane transporters, selected from the research performed in our own laboratory.
Collapse
Affiliation(s)
- J V Vermaas
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States; University of Illinois at Urbana-Champaign, Urbana, IL, United States; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - N Trebesch
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States; University of Illinois at Urbana-Champaign, Urbana, IL, United States; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - C G Mayne
- University of Illinois at Urbana-Champaign, Urbana, IL, United States; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - S Thangapandian
- University of Illinois at Urbana-Champaign, Urbana, IL, United States; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - M Shekhar
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States; University of Illinois at Urbana-Champaign, Urbana, IL, United States; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - P Mahinthichaichan
- University of Illinois at Urbana-Champaign, Urbana, IL, United States; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - J L Baylon
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States; University of Illinois at Urbana-Champaign, Urbana, IL, United States; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - T Jiang
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States; University of Illinois at Urbana-Champaign, Urbana, IL, United States; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Y Wang
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States; University of Illinois at Urbana-Champaign, Urbana, IL, United States; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - M P Muller
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States; University of Illinois at Urbana-Champaign, Urbana, IL, United States; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, United States; College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - E Shinn
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States; University of Illinois at Urbana-Champaign, Urbana, IL, United States; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Z Zhao
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States; University of Illinois at Urbana-Champaign, Urbana, IL, United States; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - P-C Wen
- University of Illinois at Urbana-Champaign, Urbana, IL, United States; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - E Tajkhorshid
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States; University of Illinois at Urbana-Champaign, Urbana, IL, United States; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, United States; College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, United States.
| |
Collapse
|
66
|
Horta BAC, Merz PT, Fuchs PFJ, Dolenc J, Riniker S, Hünenberger PH. A GROMOS-Compatible Force Field for Small Organic Molecules in the Condensed Phase: The 2016H66 Parameter Set. J Chem Theory Comput 2016; 12:3825-50. [DOI: 10.1021/acs.jctc.6b00187] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Bruno A. C. Horta
- Laboratory
of Physical Chemistry, ETH Zürich, CH-8093 Zürich, Switzerland
- Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-909, Brazil
| | - Pascal T. Merz
- Laboratory
of Physical Chemistry, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Patrick F. J. Fuchs
- Institut Jacques Monod, UMR 7592 CNRS, Université Paris-Diderot, Sorbonne Paris Cité, F-75205 Paris, France
| | - Jozica Dolenc
- Laboratory
of Physical Chemistry, ETH Zürich, CH-8093 Zürich, Switzerland
- Chemistry,
Biology and Pharmacy Information Center, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Sereina Riniker
- Laboratory
of Physical Chemistry, ETH Zürich, CH-8093 Zürich, Switzerland
| | | |
Collapse
|
67
|
Pineda De Castro LF, Dopson M, Friedman R. Biological Membranes in Extreme Conditions: Simulations of Anionic Archaeal Tetraether Lipid Membranes. PLoS One 2016; 11:e0155287. [PMID: 27167213 PMCID: PMC4864297 DOI: 10.1371/journal.pone.0155287] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 03/29/2016] [Indexed: 01/25/2023] Open
Abstract
In contrast to the majority of organisms that have cells bound by di-ester phospholipids, archaeal membranes consist of di- and tetraether phospholipids. Originating from organisms that withstand harsh conditions (e.g., low pH and a wide range of temperatures) such membranes have physical properties that make them attractive materials for biological research and biotechnological applications. We developed force-field parameters based on the widely used Generalized Amber Force Field (GAFF) to enable the study of anionic tetraether membranes of the model archaean Sulfolobus acidocaldarius by computer simulations. The simulations reveal that the physical properties of these unique membranes depend on the number of cyclopentane rings included in each lipid unit, and on the size of cations that are used to ensure charge neutrality. This suggests that the biophysical properties of Sulfolobus acidocaldarius cells depend not only on the compositions of their membranes but also on the media in which they grow.
Collapse
Affiliation(s)
- Luis Felipe Pineda De Castro
- Computational Chemistry and Biochemistry research Group (CCBG), Department of Chemistry and Biomedical Sciences, Linnæus University, 391 82 Kalmar, Sweden
- Centre of Excellence “Biomaterials Chemistry”, Linnæus University, 391 82 Kalmar, Sweden
| | - Mark Dopson
- Systems Biology of Microorganisms Research Group (SBMR), Centre for Ecology and Evolution in Microbial model Systems (EEMiS), Linnæus University, 391 82 Kalmar, Sweden
| | - Ran Friedman
- Computational Chemistry and Biochemistry research Group (CCBG), Department of Chemistry and Biomedical Sciences, Linnæus University, 391 82 Kalmar, Sweden
- Centre of Excellence “Biomaterials Chemistry”, Linnæus University, 391 82 Kalmar, Sweden
- * E-mail:
| |
Collapse
|
68
|
Bonthuis DJ, Mamatkulov SI, Netz RR. Optimization of classical nonpolarizable force fields for OH− and H3O+. J Chem Phys 2016; 144:104503. [DOI: 10.1063/1.4942771] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Douwe Jan Bonthuis
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Oxford OX1 3NP, United Kingdom
| | - Shavkat I. Mamatkulov
- Ion-Plasma and Laser Technologies Institute of the Uzbekistan AS, Tashkent, Uzbekistan
| | - Roland R. Netz
- Fachbereich Physik, Freie Universität Berlin, 14195 Berlin, Germany
| |
Collapse
|
69
|
Catte A, Girych M, Javanainen M, Loison C, Melcr J, Miettinen MS, Monticelli L, Määttä J, Oganesyan VS, Ollila OHS, Tynkkynen J, Vilov S. Molecular electrometer and binding of cations to phospholipid bilayers. Phys Chem Chem Phys 2016; 18:32560-32569. [DOI: 10.1039/c6cp04883h] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The molecular electrometer – reorientation of lipid head due to bound charge – allows direct quantitative vetting of simulations against noninvasive NMR experiments; most simulation models overestimated lipid–cation affinities.
Collapse
|
70
|
Papaleo E. Integrating atomistic molecular dynamics simulations, experiments, and network analysis to study protein dynamics: strength in unity. Front Mol Biosci 2015; 2:28. [PMID: 26075210 PMCID: PMC4445042 DOI: 10.3389/fmolb.2015.00028] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 05/08/2015] [Indexed: 12/11/2022] Open
Abstract
In the last years, we have been observing remarkable improvements in the field of protein dynamics. Indeed, we can now study protein dynamics in atomistic details over several timescales with a rich portfolio of experimental and computational techniques. On one side, this provides us with the possibility to validate simulation methods and physical models against a broad range of experimental observables. On the other side, it also allows a complementary and comprehensive view on protein structure and dynamics. What is needed now is a better understanding of the link between the dynamic properties that we observe and the functional properties of these important cellular machines. To make progresses in this direction, we need to improve the physical models used to describe proteins and solvent in molecular dynamics, as well as to strengthen the integration of experiments and simulations to overcome their own limitations. Moreover, now that we have the means to study protein dynamics in great details, we need new tools to understand the information embedded in the protein ensembles and in their dynamic signature. With this aim in mind, we should enrich the current tools for analysis of biomolecular simulations with attention to the effects that can be propagated over long distances and are often associated to important biological functions. In this context, approaches inspired by network analysis can make an important contribution to the analysis of molecular dynamics simulations.
Collapse
Affiliation(s)
- Elena Papaleo
- Structural Biology and Nuclear Magnetic Resonance Laboratory, Department of Biology, University of Copenhagen Copenhagen, Denmark
| |
Collapse
|
71
|
Goh GB, Eike DM, Murch BP, Brooks CL. Accurate Modeling of Ionic Surfactants at High Concentration. J Phys Chem B 2015; 119:6217-24. [DOI: 10.1021/acs.jpcb.5b01765] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Garrett B. Goh
- Department
of Chemistry, University of Michigan, 930 N. University, Ann Arbor, Michigan 48109, United States
| | - David M. Eike
- Computational Chemistry, Modeling and Simulation, The Procter & Gamble Company, 8611 Beckett Road, West Chester, Ohio 45069, United States
| | - Bruce P. Murch
- Computational Chemistry, Modeling and Simulation, The Procter & Gamble Company, 8611 Beckett Road, West Chester, Ohio 45069, United States
| | - Charles L. Brooks
- Department
of Chemistry, University of Michigan, 930 N. University, Ann Arbor, Michigan 48109, United States
- Biophysics
Program, University of Michigan, 930 N. University, Ann Arbor, Michigan 48109, United States
| |
Collapse
|
72
|
Church AT, Hughes ZE, Walsh TR. Improving the description of interactions between Ca2+ and protein carboxylate groups, including γ-carboxyglutamic acid: revised CHARMM22* parameters. RSC Adv 2015. [DOI: 10.1039/c5ra11268k] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
We show that the CHARMM22* force-field over-binds the interaction between aqueous carboxylates and Ca2+, and introduce a modification that can recover experimentally-determined binding free energies for these systems.
Collapse
Affiliation(s)
- Andrew T. Church
- Institute for Frontier Materials
- Deakin University
- Geelong
- Australia
| | - Zak E. Hughes
- Institute for Frontier Materials
- Deakin University
- Geelong
- Australia
| | - Tiffany R. Walsh
- Institute for Frontier Materials
- Deakin University
- Geelong
- Australia
| |
Collapse
|
73
|
Leman JK, Ulmschneider MB, Gray JJ. Computational modeling of membrane proteins. Proteins 2015; 83:1-24. [PMID: 25355688 PMCID: PMC4270820 DOI: 10.1002/prot.24703] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 10/01/2014] [Accepted: 10/18/2014] [Indexed: 02/06/2023]
Abstract
The determination of membrane protein (MP) structures has always trailed that of soluble proteins due to difficulties in their overexpression, reconstitution into membrane mimetics, and subsequent structure determination. The percentage of MP structures in the protein databank (PDB) has been at a constant 1-2% for the last decade. In contrast, over half of all drugs target MPs, only highlighting how little we understand about drug-specific effects in the human body. To reduce this gap, researchers have attempted to predict structural features of MPs even before the first structure was experimentally elucidated. In this review, we present current computational methods to predict MP structure, starting with secondary structure prediction, prediction of trans-membrane spans, and topology. Even though these methods generate reliable predictions, challenges such as predicting kinks or precise beginnings and ends of secondary structure elements are still waiting to be addressed. We describe recent developments in the prediction of 3D structures of both α-helical MPs as well as β-barrels using comparative modeling techniques, de novo methods, and molecular dynamics (MD) simulations. The increase of MP structures has (1) facilitated comparative modeling due to availability of more and better templates, and (2) improved the statistics for knowledge-based scoring functions. Moreover, de novo methods have benefited from the use of correlated mutations as restraints. Finally, we outline current advances that will likely shape the field in the forthcoming decade.
Collapse
Affiliation(s)
- Julia Koehler Leman
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Martin B. Ulmschneider
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Jeffrey J. Gray
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| |
Collapse
|
74
|
Tuszynski JA, Winter P, White D, Tseng CY, Sahu KK, Gentile F, Spasevska I, Omar SI, Nayebi N, Churchill CD, Klobukowski M, El-Magd RMA. Mathematical and computational modeling in biology at multiple scales. Theor Biol Med Model 2014; 11:52. [PMID: 25542608 PMCID: PMC4396153 DOI: 10.1186/1742-4682-11-52] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 11/25/2014] [Indexed: 01/08/2023] Open
Abstract
A variety of topics are reviewed in the area of mathematical and computational modeling in biology, covering the range of scales from populations of organisms to electrons in atoms. The use of maximum entropy as an inference tool in the fields of biology and drug discovery is discussed. Mathematical and computational methods and models in the areas of epidemiology, cell physiology and cancer are surveyed. The technique of molecular dynamics is covered, with special attention to force fields for protein simulations and methods for the calculation of solvation free energies. The utility of quantum mechanical methods in biophysical and biochemical modeling is explored. The field of computational enzymology is examined.
Collapse
Affiliation(s)
- Jack A Tuszynski
- Department of Physics and Department of Oncology, University of Alberta, Edmonton, Canada.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
75
|
Cerutti DS, Swope WC, Rice J, Case DA. ff14ipq: A Self-Consistent Force Field for Condensed-Phase Simulations of Proteins. J Chem Theory Comput 2014; 10:4515-4534. [PMID: 25328495 PMCID: PMC4196740 DOI: 10.1021/ct500643c] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2014] [Indexed: 01/25/2023]
Abstract
We present the ff14ipq force field, implementing the previously published IPolQ charge set for simulations of complete proteins. Minor modifications to the charge derivation scheme and van der Waals interactions between polar atoms are introduced. Torsion parameters are developed through a generational learning approach, based on gas-phase MP2/cc-pVTZ single-point energies computed of structures optimized by the force field itself rather than the quantum benchmark. In this manner, we sacrifice information about the true quantum minima in order to ensure that the force field maintains optimal agreement with the MP2/cc-pVTZ benchmark for the ensembles it will actually produce in simulations. A means of making the gas-phase torsion parameters compatible with solution-phase IPolQ charges is presented. The ff14ipq model is an alternative to ff99SB and other Amber force fields for protein simulations in programs that accommodate pair-specific Lennard-Jones combining rules. The force field gives strong performance on α-helical and β-sheet oligopeptides as well as globular proteins over microsecond time scale simulations, although it has not yet been tested in conjunction with lipid and nucleic acid models. We show how our choices in parameter development influence the resulting force field and how other choices that may have appeared reasonable would actually have led to poorer results. The tools we developed may also aid in the development of future fixed-charge and even polarizable biomolecular force fields.
Collapse
Affiliation(s)
- David S. Cerutti
- Department
of Chemistry and
Chemical Biology and BioMaPS Institute, Rutgers University, 610 Taylor Road, Piscataway, New Jersey 08854-8066, United States
| | - William C. Swope
- Department
of Chemistry and
Chemical Biology and BioMaPS Institute, Rutgers University, 610 Taylor Road, Piscataway, New Jersey 08854-8066, United States
| | - Julia
E. Rice
- Department
of Chemistry and
Chemical Biology and BioMaPS Institute, Rutgers University, 610 Taylor Road, Piscataway, New Jersey 08854-8066, United States
| | - David A. Case
- Department
of Chemistry and
Chemical Biology and BioMaPS Institute, Rutgers University, 610 Taylor Road, Piscataway, New Jersey 08854-8066, United States
| |
Collapse
|
76
|
Hansen N, van Gunsteren WF. Practical Aspects of Free-Energy Calculations: A Review. J Chem Theory Comput 2014; 10:2632-47. [PMID: 26586503 DOI: 10.1021/ct500161f] [Citation(s) in RCA: 289] [Impact Index Per Article: 28.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Free-energy calculations in the framework of classical molecular dynamics simulations are nowadays used in a wide range of research areas including solvation thermodynamics, molecular recognition, and protein folding. The basic components of a free-energy calculation, that is, a suitable model Hamiltonian, a sampling protocol, and an estimator for the free energy, are independent of the specific application. However, the attention that one has to pay to these components depends considerably on the specific application. Here, we review six different areas of application and discuss the relative importance of the three main components to provide the reader with an organigram and to make nonexperts aware of the many pitfalls present in free energy calculations.
Collapse
Affiliation(s)
- Niels Hansen
- Institute of Thermodynamics and Thermal Process Engineering, University of Stuttgart , D-70569 Stuttgart, Germany.,Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH , CH-8093 Zürich, Switzerland
| | - Wilfred F van Gunsteren
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH , CH-8093 Zürich, Switzerland
| |
Collapse
|
77
|
Kahlen J, Salimi L, Sulpizi M, Peter C, Donadio D. Interaction of Charged Amino-Acid Side Chains with Ions: An Optimization Strategy for Classical Force Fields. J Phys Chem B 2014; 118:3960-72. [DOI: 10.1021/jp412490c] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jens Kahlen
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Leila Salimi
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
- Johannes Gutenberg University Mainz, Staudinger Weg 7, 55099 Mainz, Germany
| | - Marialore Sulpizi
- Johannes Gutenberg University Mainz, Staudinger Weg 7, 55099 Mainz, Germany
| | - Christine Peter
- University of Konstanz, P.O. Box 718, 78547 Konstanz, Germany
| | - Davide Donadio
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| |
Collapse
|
78
|
Tang X, Koenig PH, Larson RG. Molecular Dynamics Simulations of Sodium Dodecyl Sulfate Micelles in Water—The Effect of the Force Field. J Phys Chem B 2014; 118:3864-80. [DOI: 10.1021/jp410689m] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Xueming Tang
- Department
of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Peter H. Koenig
- Computational Chemistry, Modeling and Simulation, The Procter & Gamble Company, 8611 Beckett Road, West Chester, Ohio 45069, United States
| | - Ronald G. Larson
- Department
of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
| |
Collapse
|
79
|
Lin Z, Oostenbrink C, van Gunsteren WF. On the use of one-step perturbation to investigate the dependence of NOE-derived atom–atom distance bound violations of peptides upon a variation of force-field parameters. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2014; 43:113-9. [DOI: 10.1007/s00249-014-0943-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Revised: 01/13/2014] [Accepted: 01/17/2014] [Indexed: 11/28/2022]
|
80
|
Nagy G, Oostenbrink C. Dihedral-based segment identification and classification of biopolymers I: proteins. J Chem Inf Model 2014; 54:266-77. [PMID: 24364820 PMCID: PMC3904766 DOI: 10.1021/ci400541d] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Indexed: 12/29/2022]
Abstract
A new structure classification scheme for biopolymers is introduced, which is solely based on main-chain dihedral angles. It is shown that by dividing a biopolymer into segments containing two central residues, a local classification can be performed. The method is referred to as DISICL, short for Dihedral-based Segment Identification and Classification. Compared to other popular secondary structure classification programs, DISICL is more detailed as it offers 18 distinct structural classes, which may be simplified into a classification in terms of seven more general classes. It was designed with an eye to analyzing subtle structural changes as observed in molecular dynamics simulations of biomolecular systems. Here, the DISICL algorithm is used to classify two databases of protein structures, jointly containing more than 10 million segments. The data is compared to two alternative approaches in terms of the amount of classified residues, average occurrence and length of structural elements, and pair wise matches of the classifications by the different programs. In an accompanying paper (Nagy, G.; Oostenbrink, C. Dihedral-based segment identification and classification of biopolymers II: Polynucleotides. J. Chem. Inf. Model. 2013, DOI: 10.1021/ci400542n), the analysis of polynucleotides is described and applied. Overall, DISICL represents a potentially useful tool to analyze biopolymer structures at a high level of detail.
Collapse
Affiliation(s)
- Gabor Nagy
- University of Natural Resources
and Life Sciences, Institute for Molecular
Modeling and Simulation, Muthgasse 18, 1190 Vienna, Austria
| | - Chris Oostenbrink
- University of Natural Resources
and Life Sciences, Institute for Molecular
Modeling and Simulation, Muthgasse 18, 1190 Vienna, Austria
| |
Collapse
|