101
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Abstract
By focusing on essential features, while averaging over less important details, coarse-grained (CG) models provide significant computational and conceptual advantages with respect to more detailed models. Consequently, despite dramatic advances in computational methodologies and resources, CG models enjoy surging popularity and are becoming increasingly equal partners to atomically detailed models. This perspective surveys the rapidly developing landscape of CG models for biomolecular systems. In particular, this review seeks to provide a balanced, coherent, and unified presentation of several distinct approaches for developing CG models, including top-down, network-based, native-centric, knowledge-based, and bottom-up modeling strategies. The review summarizes their basic philosophies, theoretical foundations, typical applications, and recent developments. Additionally, the review identifies fundamental inter-relationships among the diverse approaches and discusses outstanding challenges in the field. When carefully applied and assessed, current CG models provide highly efficient means for investigating the biological consequences of basic physicochemical principles. Moreover, rigorous bottom-up approaches hold great promise for further improving the accuracy and scope of CG models for biomolecular systems.
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Affiliation(s)
- W G Noid
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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102
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Plazinska A, Plazinski W, Jozwiak K. Fast, metadynamics-based method for prediction of the stereochemistry-dependent relative free energies of ligand-receptor interactions. J Comput Chem 2014; 35:876-82. [PMID: 24615679 DOI: 10.1002/jcc.23563] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Revised: 01/30/2014] [Accepted: 02/01/2014] [Indexed: 01/09/2023]
Abstract
The computational approach applicable for the molecular dynamics (MD)-based techniques is proposed to predict the ligand-protein binding affinities dependent on the ligand stereochemistry. All possible stereoconfigurations are expressed in terms of one set of force-field parameters [stereoconfiguration-independent potential (SIP)], which allows for calculating all relative free energies by only single simulation. SIP can be used for studying diverse, stereoconfiguration-dependent phenomena by means of various computational techniques of enhanced sampling. The method has been successfully tested on the β2-adrenergic receptor (β2-AR) binding the four fenoterol stereoisomers by both metadynamics simulations and replica-exchange MD. Both the methods gave very similar results, fully confirming the presence of stereoselective effects in the fenoterol-β2-AR interactions. However, the metadynamics-based approach offered much better efficiency of sampling which allows for significant reduction of the unphysical region in SIP.
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Affiliation(s)
- Anita Plazinska
- Department of Chemistry, Faculty of Pharmacy, Laboratory of Medicinal Chemistry and Neuroengineering, Medical University of Lublin, W. Chodzki Street, 4a, 20-093, Lublin, Poland
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103
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Molecular dynamics simulation of the crystallizable fragment of IgG1-insights for the design of Fcabs. Int J Mol Sci 2014; 15:438-55. [PMID: 24451126 PMCID: PMC3907818 DOI: 10.3390/ijms15010438] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Revised: 12/19/2013] [Accepted: 12/27/2013] [Indexed: 11/17/2022] Open
Abstract
An interesting format in the development of therapeutic monoclonal antibodies uses the crystallizable fragment of IgG1 as starting scaffold. Engineering of its structural loops allows generation of an antigen binding site. However, this might impair the molecule’s conformational stability, which can be overcome by introducing stabilizing point mutations in the CH3 domains. These point mutations often affect the stability and unfolding behavior of both the CH2 and CH3 domains. In order to understand this cross-talk, molecular dynamics simulations of the domains of the Fc fragment of human IgG1 are reported. The structure of human IgG1-Fc obtained from X-ray crystallography is used as a starting point for simulations of the wild-type protein at two different pH values. The stabilizing effect of a single point mutation in the CH3 domain as well as the impact of the hinge region and the glycan tree structure connected to the CH2 domains is investigated. Regions of high local flexibility were identified as potential sites for engineering antigen binding sites. Obtained data are discussed with respect to the available X-ray structure of IgG1-Fc, directed evolution approaches that screen for stability and use of the scaffold IgG1-Fc in the design of antigen binding Fc proteins.
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104
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Plazinski W, Drach M. The dynamics of the conformational changes in the hexopyranose ring: a transition path sampling approach. RSC Adv 2014. [DOI: 10.1039/c4ra03410d] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The transition paths corresponding to the conformational rearrangements in the ring of hexapyranose (α-d- and β-d-glucose) molecules were described by applying the transition path sampling method.
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Affiliation(s)
- Wojciech Plazinski
- Institute of Catalysis and Surface Chemistry
- Polish Academy of Sciences
- 30-239 Cracow, Poland
| | - Mateusz Drach
- Department of Theoretical Chemistry
- Faculty of Chemistry
- UMCS
- 20-031 Lublin, Poland
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105
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Abstract
Although carbohydrates represent one of the most important families of biomolecules, they remain under-studied in comparison to the other biomolecular families (peptides, nucleobases). Beyond their best-known function of energy source in living systems, they act as mediator of molecular recognition processes, carrying molecular information in the so-called "sugar code," just to name one of their countless functions. Owing to their high conformational flexibility, they encode extremely rich information conveyed via the non-covalent hydrogen bonds within the carbohydrate and with other biomolecular assemblies, such as peptide subunits of proteins. Over the last decade there has been tremendous progress in the study of the conformational preferences of neutral oligosaccharides, and of the interactions between carbohydrates and various molecular partners (water, aromatic models, and peptide models), using vibrational spectroscopy as a sensitive probe. In parallel, other spectroscopic techniques have recently become available to the study of carbohydrates in the gas phase (microwave spectroscopy, IRMPD on charged species).
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Affiliation(s)
- Emilio J Cocinero
- Departamento de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV - EHU), Apartado 644, 48940, Bilbao, Spain,
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106
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Stortz TA, De Moura DC, Laredo T, Marangoni AG. Molecular interactions of ethylcellulose with sucrose particles. RSC Adv 2014. [DOI: 10.1039/c4ra12010h] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Heat resistance in chocolate upon ethylcellulose addition is due to the formation of a jammed sugar network.
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Affiliation(s)
- Terri A. Stortz
- Department of Food Science
- University of Guelph
- Guelph, Canada
| | - Dref C. De Moura
- Biophysics Interdepartmental Group (BIG)
- University of Guelph
- Guelph, Canada
| | - Thamara Laredo
- Departments of Sustainability Science and Chemistry
- Lakehead University
- Orillia, Canada
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107
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Samoshin AV, Veselov IS, Chertkov VA, Yaroslavov AA, Grishina GV, Samoshina NM, Samoshin VV. Fliposomes: new amphiphiles based on trans-3,4-bis(acyloxy)-piperidine able to perform a pH-triggered conformational flip and cause an instant cargo release from liposomes. Tetrahedron Lett 2013. [DOI: 10.1016/j.tetlet.2013.07.156] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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108
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Kapla J, Wohlert J, Stevensson B, Engström O, Widmalm G, Maliniak A. Molecular dynamics simulations of membrane-sugar interactions. J Phys Chem B 2013; 117:6667-73. [PMID: 23662588 DOI: 10.1021/jp402385d] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
It is well documented that disaccharides in general and trehalose (TRH) in particular strongly affect physical properties and functionality of lipid bilayers. We investigate interactions between lipid membranes formed by 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and TRH by means of molecular dynamics (MD) computer simulations. Ten different TRH concentrations were studied in the range wTRH = 0-0.20 (w/w). The potential of mean force (PMF) for DMPC bilayer-TRH interactions was determined using two different force fields, and was subsequently used in a simple analytical model for description of sugar binding at the membrane interface. The MD results were in good agreement with the predictions of the model. The net affinities of TRH for the DMPC bilayer derived from the model and MD simulations were compared with experimental results. The area per lipid increases and the membrane becomes thinner with increased TRH concentration, which is interpreted as an intercalation effect of the TRH molecules into the polar part of the lipids, resulting in conformational changes in the chains. These results are consistent with recent experimental observations. The compressibility modulus related to the fluctuations of the membrane increases dramatically with increased TRH concentration, which indicates higher order and rigidity of the bilayer. This is also reflected in a decrease (by a factor of 15) of the lateral diffusion of the lipids. We interpret these observations as a formation of a glassy state at the interface of the membrane, which has been suggested in the literature as a hypothesis for the membrane-sugar interactions.
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Affiliation(s)
- Jon Kapla
- Department of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
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109
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Wang D, Ámundadóttir ML, van Gunsteren WF, Hünenberger PH. Intramolecular hydrogen-bonding in aqueous carbohydrates as a cause or consequence of conformational preferences: a molecular dynamics study of cellobiose stereoisomers. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2013; 42:521-37. [DOI: 10.1007/s00249-013-0901-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Revised: 03/19/2013] [Accepted: 03/28/2013] [Indexed: 10/26/2022]
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110
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Oborský P, Tvaroška I, Králová B, Spiwok V. Toward an accurate conformational modeling of iduronic acid. J Phys Chem B 2013; 117:1003-9. [PMID: 23286518 DOI: 10.1021/jp3100552] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Iduronic acid (IdoA), unlike most other monosaccharides, can adopt different ring conformations, depending on the context of the molecular structure. Accurate modeling of this building block is essential for understanding the role of glycosaminoglycans and other glycoconjugates. Here, we use metadynamics to predict equilibria of (1)C(4), (4)C(1) and (2)S(O) conformations of α-L-IdoA-OMe and α-L-IdoA2S-OMe. Different schemes of scaling of atoms separated by three bonds (1-4 interaction) were tested. It was found that scaling (reduction) of 1-4 electrostatic interactions significantly changes conformational preferences toward the (4)C(1) conformation. More interestingly, scaling of 1-4 van der Waals interaction favors skew-boat conformations. This shows that a minor modification of noncovalent 1-4 interactions parameters can provide a good agreement between populations of conformers of iduronic acid in water from simulations and experiments.
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Affiliation(s)
- Pavel Oborský
- Department of Biochemistry and Microbiology, Institute of Chemical Technology, Prague, Technická 3, Prague 6 166 28, Czech Republic
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111
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Reif MM, Winger M, Oostenbrink C. Testing of the GROMOS Force-Field Parameter Set 54A8: Structural Properties of Electrolyte Solutions, Lipid Bilayers, and Proteins. J Chem Theory Comput 2013; 9:1247-1264. [PMID: 23418406 PMCID: PMC3572754 DOI: 10.1021/ct300874c] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Indexed: 11/28/2022]
Abstract
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The GROMOS 54A8 force field [Reif et al. J. Chem.
Theory
Comput.2012, 8, 3705–3723]
is the first of its kind to contain nonbonded parameters for charged
amino acid side chains that are derived in a rigorously thermodynamic
fashion, namely a calibration against single-ion hydration free energies.
Considering charged moieties in solution, the most decisive signature
of the GROMOS 54A8 force field in comparison to its predecessor 54A7
can probably be found in the thermodynamic equilibrium between salt-bridged
ion pair formation and hydration. Possible shifts in this equilibrium
might crucially affect the properties of electrolyte solutions or/and
the stability of (bio)molecules. It is therefore important to investigate
the consequences of the altered description of charged oligoatomic
species in the GROMOS 54A8 force field. The present study focuses
on examining the ability of the GROMOS 54A8 force field to accurately
model the structural properties of electrolyte solutions, lipid bilayers,
and proteins. It is found that (i) aqueous electrolytes
involving oligoatomic species (sodium acetate, methylammonium chloride,
guanidinium chloride) reproduce experimental salt activity derivatives
for concentrations up to 1.0 m (1.0-molal) very well, and good agreement
between simulated and experimental data is also reached for sodium
acetate and methylammonium chloride at 2.0 m concentration, while
not even qualitative agreement is found for sodium chloride throughout
the whole range of examined concentrations, indicating a failure of
the GROMOS 54A7 and 54A8 force-field parameter sets to correctly account
for the balance between ion–ion and ion–water binding
propensities of sodium and chloride ions; (ii) the
GROMOS 54A8 force field reproduces the liquid crystalline-like phase
of a hydrated DPPC bilayer at a pressure of 1 bar and a temperature
of 323 K, the area per lipid being in agreement with experimental
data, whereas other structural properties (volume per lipid, bilayer
thickness) appear underestimated; (iii) the secondary
structure of a range of different proteins simulated with the GROMOS
54A8 force field at pH 7 is maintained and compatible with experimental
NMR data, while, as also observed for the GROMOS 54A7 force field,
α-helices are slightly overstabilized with respect to 310-helices; (iv) with the GROMOS 54A8 force
field, the side chains of arginine, lysine, aspartate, and glutamate
residues appear slightly more hydrated and present a slight excess
of oppositely-charged solution components in their vicinity, whereas
salt-bridge formation properties between charged residues at the protein
surface, as assessed by probability distributions of interionic distances,
are largely equivalent in the GROMOS 54A7 and 54A8 force-field parameter
sets.
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Affiliation(s)
- Maria M Reif
- Institute for Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, 1190 Vienna, Austria
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112
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López CA, de Vries AH, Marrink SJ. Amylose folding under the influence of lipids. Carbohydr Res 2012; 364:1-7. [DOI: 10.1016/j.carres.2012.10.007] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Revised: 10/04/2012] [Accepted: 10/06/2012] [Indexed: 11/25/2022]
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113
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Kimura H, Nakahara M, Matubayasi N. Noncatalytic Hydrothermal Elimination of the Terminal d-Glucose Unit from Malto- and Cello-Oligosaccharides through Transformation to d-Fructose. J Phys Chem A 2012; 116:10039-49. [DOI: 10.1021/jp3034165] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hiroshi Kimura
- Institute for Chemical
Research, Kyoto University, Uji, Kyoto
611-0011, Japan
| | - Masaru Nakahara
- Institute for Chemical
Research, Kyoto University, Uji, Kyoto
611-0011, Japan
| | - Nobuyuki Matubayasi
- Institute for Chemical
Research, Kyoto University, Uji, Kyoto
611-0011, Japan
- Japan Science
and Technology
Agency (JST), CREST, Kawaguchi, Saitama
332-0012, Japan
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114
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Pol-Fachin L, Rusu VH, Verli H, Lins RD. GROMOS 53A6GLYC, an Improved GROMOS Force Field for Hexopyranose-Based Carbohydrates. J Chem Theory Comput 2012; 8:4681-90. [PMID: 26605624 DOI: 10.1021/ct300479h] [Citation(s) in RCA: 110] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
An improved parameter set for explicit-solvent simulations of carbohydrates (referred to as GROMOS 53A6GLYC) is presented, allowing proper description of the most stable conformation of all 16 possible aldohexopyranose-based monosaccharides. This set includes refinement of torsional potential parameters associated with the determination of hexopyranose rings conformation by fitting to their corresponding quantum-mechanical profiles. Other parameters, as the rules for third and excluded neighbors, are taken directly from the GROMOS 53A6 force field. Comparisons of the herein presented parameter set to our previous version (GROMOS 45A4), the GLYCAM06 force field, and available NMR data are presented in terms of ring puckering free energies, conformational distribution of the hydroxymethyl group, and glycosidic linkage geometries for 16 selected monosaccharides and eight disaccharides. The proposed parameter modifications have shown a significant improvement for the above-mentioned quantities over the two tested force fields, while retaining full compatibility with the GROMOS 53A6 and 54A7 parameter sets for other classes of biomolecules.
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Affiliation(s)
- Laercio Pol-Fachin
- Center of Biotechnology, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Victor H Rusu
- Department of Fundamental Chemistry, Federal University of Pernambuco, Recife, PE, Brazil
| | - Hugo Verli
- Center of Biotechnology, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil.,College of Pharmacy, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Roberto D Lins
- Department of Fundamental Chemistry, Federal University of Pernambuco, Recife, PE, Brazil
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115
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Fuchs PFJ, Hansen HS, Hünenberger PH, Horta BAC. A GROMOS Parameter Set for Vicinal Diether Functions: Properties of Polyethyleneoxide and Polyethyleneglycol. J Chem Theory Comput 2012; 8:3943-63. [DOI: 10.1021/ct300245h] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Patrick F. J. Fuchs
- INSERM, U665, F-75739 Paris, France
- Univ Paris Diderot, Sorbonne Paris Cité, UMR_S 665, F-75739 Paris, France
- Institut National de la Transfusion Sanguine, F-75739 Paris, France
- CNRS, Laboratoire d’Imagerie Paramétrique, UMR 7623, 75006
Paris, France
| | - Halvor S. Hansen
- Laboratory
of Physical Chemistry, ETH Zürich, CH-8093 Zürich, Switzerland
| | | | - Bruno A. C. Horta
- Laboratory
of Physical Chemistry, ETH Zürich, CH-8093 Zürich, Switzerland
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116
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Sameera WMC, Pantazis DA. A Hierarchy of Methods for the Energetically Accurate Modeling of Isomerism in Monosaccharides. J Chem Theory Comput 2012; 8:2630-45. [PMID: 26592108 DOI: 10.1021/ct3002305] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- W. M. C. Sameera
- Institut Català d’Investigació
Química, Av. Països Catalans 16, 43007 Tarragona, Spain
| | - Dimitrios A. Pantazis
- Max-Planck-Institut für
Bioanorganische Chemie, Stiftstrasse 34-36, 45470 Mülheim an
der Ruhr, Germany
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117
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Foley BL, Tessier MB, Woods RJ. Carbohydrate force fields. WILEY INTERDISCIPLINARY REVIEWS. COMPUTATIONAL MOLECULAR SCIENCE 2012; 2:652-697. [PMID: 25530813 PMCID: PMC4270206 DOI: 10.1002/wcms.89] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Carbohydrates present a special set of challenges to the generation of force fields. First, the tertiary structures of monosaccharides are complex merely by virtue of their exceptionally high number of chiral centers. In addition, their electronic characteristics lead to molecular geometries and electrostatic landscapes that can be challenging to predict and model. The monosaccharide units can also interconnect in many ways, resulting in a large number of possible oligosaccharides and polysaccharides, both linear and branched. These larger structures contain a number of rotatable bonds, meaning they potentially sample an enormous conformational space. This article briefly reviews the history of carbohydrate force fields, examining and comparing their challenges, forms, philosophies, and development strategies. Then it presents a survey of recent uses of these force fields, noting trends, strengths, deficiencies, and possible directions for future expansion.
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Affiliation(s)
- B. Lachele Foley
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Matthew B. Tessier
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Robert J. Woods
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
- School of Chemistry, National University of Ireland, Galway, Ireland
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118
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Reif MM, Hünenberger PH, Oostenbrink C. New Interaction Parameters for Charged Amino Acid Side Chains in the GROMOS Force Field. J Chem Theory Comput 2012; 8:3705-23. [DOI: 10.1021/ct300156h] [Citation(s) in RCA: 161] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Maria M. Reif
- Institute for Molecular Modeling
and Simulation, University of Natural Resources and Life Sciences, 1190 Vienna, Austria
| | - Philippe H. Hünenberger
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology (ETH), 8093 Zurich,
Switzerland
| | - Chris Oostenbrink
- Institute for Molecular Modeling
and Simulation, University of Natural Resources and Life Sciences, 1190 Vienna, Austria
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119
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Ellis CR, Maiti B, Noid WG. Specific and nonspecific effects of glycosylation. J Am Chem Soc 2012; 134:8184-93. [PMID: 22524526 DOI: 10.1021/ja301005f] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Glycosylation regulates vital cellular processes and dramatically influences protein folding and stability. In particular, experiments have demonstrated that asparagine (N)-linked disaccharides drive a "conformational switch" in a model peptide. The present work investigates this conformational switch via extensive atomically detailed replica exchange molecular dynamics simulations in explicit solvent. To distinguish the effects of specific and nonspecific interactions upon the peptide conformational ensemble, these simulations considered model peptides that were N-linked to a disaccharide and to a steric crowder of the same shape. The simulations are remarkably consistent with experiment and provide detailed insight into the peptide structure ensemble. They suggest that steric crowding by N-linked disaccharides excludes extended conformations, but does not significantly impact the tetrahedral structure of the surrounding solvent or otherwise alter the peptide free energy surface. However, the combination of steric crowding with specific hydrogen bonds and hydrophobic stacking interactions more dramatically impacts the peptide ensemble and stabilizes new structures.
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Affiliation(s)
- Christopher R Ellis
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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120
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Wu S, Zhan HY, Wang HM, Ju Y. Secondary Structure Analysis of Native Cellulose by Molecular Dynamics Simulations with Coarse Grained Model. CHINESE J CHEM PHYS 2012. [DOI: 10.1088/1674-0068/25/02/191-198] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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121
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Mallajosyula SS, Guvench O, Hatcher E, MacKerell AD. CHARMM Additive All-Atom Force Field for Phosphate and Sulfate Linked to Carbohydrates. J Chem Theory Comput 2012; 8:759-776. [PMID: 22685386 PMCID: PMC3367516 DOI: 10.1021/ct200792v] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Presented is an extension of the CHARMM additive all-atom carbohydrate force field to enable the modeling of phosphate and sulfate linked to carbohydrates. The parameters are developed in a hierarchical fashion using model compounds containing the key atoms in the full carbohydrates. Target data for parameter optimization included full two-dimensional energy surfaces defined by the glycosidic dihedral angle pairs in the phosphate/sulfate model compound analogs of hexopyranose monosaccharide phosphates and sulfates, as determined by quantum mechanical (QM) MP2/cc-pVTZ single point energies on MP2/6-31+G(d) optimized structures. In order to achieve balanced, transferable dihedral parameters for the dihedral angles, surfaces for all possible anomeric and conformational states were included during the parametrization process. In addition, to model physiologically relevant systems both the mono- and di-anionic charged states were studied for the phosphates. This resulted in over 7000 MP2/cc-pVTZ//MP2/6-31G+(d) model compound conformational energies which, supplemented with QM geometries, were the main target data for the parametrization. Parameters were validated against crystals of relevant monosaccharide derivatives obtained from the Cambridge Structural Database (CSD) and larger systems, namely inositol-(tri/tetra/penta) phosphates non-covalently bound to the pleckstrin homology (PH) domain and oligomeric chondroitin sulfate in solution and in complex with cathepsin K protein.
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Affiliation(s)
- Sairam S. Mallajosyula
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn St., HSF II-629, Baltimore, MD 21201
| | - Olgun Guvench
- Department of Pharmaceutical Sciences, University of New England College of Pharmacy, Portland, Maine 04103
| | - Elizabeth Hatcher
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn St., HSF II-629, Baltimore, MD 21201
| | - Alexander D. MacKerell
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn St., HSF II-629, Baltimore, MD 21201
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122
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Matthews JF, Beckham GT, Bergenstråhle-Wohlert M, Brady JW, Himmel ME, Crowley MF. Comparison of Cellulose Iβ Simulations with Three Carbohydrate Force Fields. J Chem Theory Comput 2012; 8:735-48. [DOI: 10.1021/ct2007692] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
| | - Gregg T. Beckham
- Department of Chemical Engineering, Colorado School of Mines, Golden, Colorado, United
States
| | - Malin Bergenstråhle-Wohlert
- Department of Food
Science, Cornell University, Ithaca, New
York, United States
- Wallenberg
Wood Science Center, Royal Institute of Technology, Stockholm, Sweden
| | - John W. Brady
- Department of Food
Science, Cornell University, Ithaca, New
York, United States
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123
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Enjalbert Q, Racaud A, Lemoine J, Redon S, Ayhan MM, Andraud C, Chambert S, Bretonnière Y, Loison C, Antoine R, Dugourd P. Optical Properties of a Visible Push–Pull Chromophore Covalently Bound to Carbohydrates: Solution and Gas-Phase Spectroscopy Combined to Theoretical Investigations. J Phys Chem B 2012; 116:841-51. [DOI: 10.1021/jp2099015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Quentin Enjalbert
- Université de Lyon, F-69622, Lyon, France
- Université Lyon 1, 43, Bld du 11 Novembre 1918, F-69622 Villeurbanne, France
- Laboratoire de Spectrométrie Ionique et Moléculaire, UMR5579, CNRS, Université Lyon 1, France
- Laboratoire de Sciences Analytiques, UMR5180, CNRS, Université Lyon 1, France
| | - Amandine Racaud
- Université de Lyon, F-69622, Lyon, France
- Université Lyon 1, 43, Bld du 11 Novembre 1918, F-69622 Villeurbanne, France
- Laboratoire de Spectrométrie Ionique et Moléculaire, UMR5579, CNRS, Université Lyon 1, France
- Laboratoire de Sciences Analytiques, UMR5180, CNRS, Université Lyon 1, France
| | - Jérôme Lemoine
- Université de Lyon, F-69622, Lyon, France
- Université Lyon 1, 43, Bld du 11 Novembre 1918, F-69622 Villeurbanne, France
- Laboratoire de Sciences Analytiques, UMR5180, CNRS, Université Lyon 1, France
| | - Sébastien Redon
- Université de Lyon, F-69622, Lyon, France
- Université Lyon 1, 43, Bld du 11 Novembre 1918, F-69622 Villeurbanne, France
- Laboratoire de Chimie Organique et Bioorganique, INSA de Lyon, Lyon, France
- Institut de Chimie et de Biochimie Moléculaires et Supramoléculaires, UMR5246, CNRS, Université Lyon 1, INSA de Lyon, CPE-Lyon, Lyon, France
| | - Mehmet Menaf Ayhan
- Université de Lyon, F-69622, Lyon, France
- Laboratoire de Chimie de l’ENS Lyon, UMR5182, CNRS, ENS Lyon, 46 allée d’Italie, F-69364 Lyon, France
| | - Chantal Andraud
- Université de Lyon, F-69622, Lyon, France
- Laboratoire de Chimie de l’ENS Lyon, UMR5182, CNRS, ENS Lyon, 46 allée d’Italie, F-69364 Lyon, France
| | - Stéphane Chambert
- Université de Lyon, F-69622, Lyon, France
- Université Lyon 1, 43, Bld du 11 Novembre 1918, F-69622 Villeurbanne, France
- Laboratoire de Chimie Organique et Bioorganique, INSA de Lyon, Lyon, France
- Institut de Chimie et de Biochimie Moléculaires et Supramoléculaires, UMR5246, CNRS, Université Lyon 1, INSA de Lyon, CPE-Lyon, Lyon, France
| | - Yann Bretonnière
- Université de Lyon, F-69622, Lyon, France
- Laboratoire de Chimie de l’ENS Lyon, UMR5182, CNRS, ENS Lyon, 46 allée d’Italie, F-69364 Lyon, France
| | - Claire Loison
- Université de Lyon, F-69622, Lyon, France
- Université Lyon 1, 43, Bld du 11 Novembre 1918, F-69622 Villeurbanne, France
- Laboratoire de Spectrométrie Ionique et Moléculaire, UMR5579, CNRS, Université Lyon 1, France
| | - Rodolphe Antoine
- Université de Lyon, F-69622, Lyon, France
- Université Lyon 1, 43, Bld du 11 Novembre 1918, F-69622 Villeurbanne, France
- Laboratoire de Spectrométrie Ionique et Moléculaire, UMR5579, CNRS, Université Lyon 1, France
| | - Philippe Dugourd
- Université de Lyon, F-69622, Lyon, France
- Université Lyon 1, 43, Bld du 11 Novembre 1918, F-69622 Villeurbanne, France
- Laboratoire de Spectrométrie Ionique et Moléculaire, UMR5579, CNRS, Université Lyon 1, France
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Chen P, Nishiyama Y, Mazeau K. Torsional Entropy at the Origin of the Reversible Temperature-Induced Phase Transition of Cellulose. Macromolecules 2011. [DOI: 10.1021/ma201954s] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Pan Chen
- Centre de Recherches sur les Macromolécules Végétales (CERMAV-CNRS), BP 53, F-38041
Grenoble cedex 9, France
| | - Yoshiharu Nishiyama
- Centre de Recherches sur les Macromolécules Végétales (CERMAV-CNRS), BP 53, F-38041
Grenoble cedex 9, France
| | - Karim Mazeau
- Centre de Recherches sur les Macromolécules Végétales (CERMAV-CNRS), BP 53, F-38041
Grenoble cedex 9, France
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Guvench O, Mallajosyula SS, Raman EP, Hatcher E, Vanommeslaeghe K, Foster TJ, Jamison FW, MacKerell AD. CHARMM additive all-atom force field for carbohydrate derivatives and its utility in polysaccharide and carbohydrate-protein modeling. J Chem Theory Comput 2011; 7:3162-3180. [PMID: 22125473 PMCID: PMC3224046 DOI: 10.1021/ct200328p] [Citation(s) in RCA: 461] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Monosaccharide derivatives such as xylose, fucose, N-acetylglucosamine (GlcNAc), N-acetylgalactosamine (GlaNAc), glucuronic acid, iduronic acid, and N-acetylneuraminic acid (Neu5Ac) are important components of eukaryotic glycans. The present work details development of force-field parameters for these monosaccharides and their covalent connections to proteins via O-linkages to serine or threonine sidechains and via N-linkages to asparagine sidechains. The force field development protocol was designed to explicitly yield parameters that are compatible with the existing CHARMM additive force field for proteins, nucleic acids, lipids, carbohydrates, and small molecules. Therefore, when combined with previously developed parameters for pyranose and furanose monosaccharides, for glycosidic linkages between monosaccharides, and for proteins, the present set of parameters enables the molecular simulation of a wide variety of biologically-important molecules such as complex carbohydrates and glycoproteins. Parametrization included fitting to quantum mechanical (QM) geometries and conformational energies of model compounds, as well as to QM pair interaction energies and distances of model compounds with water. Parameters were validated in the context of crystals of relevant monosaccharides, as well NMR and/or x-ray crystallographic data on larger systems including oligomeric hyaluronan, sialyl Lewis X, O- and N-linked glycopeptides, and a lectin:sucrose complex. As the validated parameters are an extension of the CHARMM all-atom additive biomolecular force field, they further broaden the types of heterogeneous systems accessible with a consistently-developed force-field model.
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Affiliation(s)
- Olgun Guvench
- Department of Pharmaceutical Sciences, University of New England College of Pharmacy, Portland, Maine 04103
| | - Sairam S. Mallajosyula
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn St., HSF II-629, Baltimore, MD 21201
| | - E. Prabhu Raman
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn St., HSF II-629, Baltimore, MD 21201
| | - Elizabeth Hatcher
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn St., HSF II-629, Baltimore, MD 21201
| | - Kenno Vanommeslaeghe
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn St., HSF II-629, Baltimore, MD 21201
| | - Theresa J. Foster
- Department of Pharmaceutical Sciences, University of New England College of Pharmacy, Portland, Maine 04103
| | - Francis W. Jamison
- Department of Pharmaceutical Sciences, University of New England College of Pharmacy, Portland, Maine 04103
| | - Alexander D. MacKerell
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn St., HSF II-629, Baltimore, MD 21201
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