Modification of 56ACARBO force field for molecular dynamic calculations of chitosan and its derivatives

Naumov, V.S.; Ignatov, Stanislav K.

doi:10.1007/s00894-017-3421-x

Cited by 14 publications

(25 citation statements)

References 53 publications

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“…The RSFF2+ model corrects both of these features and thus improves accuracy over a broad temperature range.) The GLYCAM06 potential, , with recent modifications specific to chitosan, is used for chitosan. Bond lengths within peptide molecules are constrained within the LINCS algorithm, and those within water molecules are constrained within the SETTLE algorithm .…”

Section: Methodsmentioning

confidence: 99%

Polyelectrolyte Influence on Beta-Hairpin Peptide Stability: A Simulation Study

Moses

Tassel

2022

J. Phys. Chem. B

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Assemblies of proteins and charged macromolecules (polyelectrolytes) find important applications as pharmaceutical formulations, biocatalysts, and cell-contacting substrates. A key question is how the polymer component influences the structure and function of the protein. The present paper addresses the influence of charged polymers on the thermal stability of two model beta-hairpin-forming peptides through an all-atom, replica exchange molecular dynamics simulation. The (negatively charged) peptides consist of the terminal 16 amino acids of the B1 domain of Protein G (GB1) and a variant with three of the GB1 residues substituted with tryptophan (Tryptophan Zipper 4, or TZ4). A (cationic) lysine polymer is seen to thermally stabilize TZ4 and destabilize GB1, while a (also cationic) chitosan polymer slightly stabilizes GB1 but has essentially no effect on TZ4. Free energy profiles reveal folded and unfolded conformations to be separated by kinetic barriers generally acting in the direction of the thermodynamically favored state. Through application of an Ising-like statistical mechanical model, a mechanism is proposed based on competition between (indirect) entropic stabilization of folded versus unfolded states and (direct) competition for hydrogen-bonding and hydrophobic interactions. These findings have important implications to the design of polyelectrolyte-based materials for biomedical and biotechnological applications.

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Section: Methodsmentioning

confidence: 99%

Polyelectrolyte Influence on Beta-Hairpin Peptide Stability: A Simulation Study

Moses

Tassel

2022

J. Phys. Chem. B

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“…26 These MD simulations were based on the united-atom G53A6 force-field and its G53A6 CARBO modification, which were recently re-parameterized for hexopyranose-based oligosaccharides such as cellulose, 27,28 glucose, 29,30 sucrose, 31 and chitosan. 32 Through a combination of experimental techniques and MD simulations, we were able to demonstrate that the HA-alkyl chain supramolecular properties were closely related to alkyl chain length. Here we further validate this approach for HA polymer-dye interactions dependence on the nature of the hydrophobic ligands.…”

Section: Introductionmentioning

confidence: 92%

Probing the self-assembly dynamics and internal structure of amphiphilic hyaluronic acid conjugates by fluorescence spectroscopy and molecular dynamics simulations

et al. 2018

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Polymeric nanoparticles are increasingly used as biocompatible carriers for drugs and imaging agents. Understanding their self-assembly dynamics and morphology is of ultimate importance to develop nanoformulations with optimal characteristics. To achieve better performance, it is vital to account for cargo-carrier interactions at the molecular level. The self-assembly dynamics were studied and the internal structure of nanoparticles derived from a series of hydrophobically modified hyaluronic acid was revealed. Environment-sensitive ratiometric fluorescent probes provide valuable information about the nanoparticle's interior morphology, and molecular dynamics simulations complement the overall picture with insights into intramolecular and intermolecular interactions of the polymer, as well as its interactions with the small-molecule load. van der Waals and π-π interactions of the hydrophobic side fragments play a leading role in self-assembly and loading of hydrophobic small molecules. Aliphatic substituents form more extensive hydrophobic domains, while aromatic moieties allow more interaction of the loaded small molecules with the surrounding solvent.

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Section: Computational Concepts and Toolsmentioning

confidence: 99%

“…With the GROMOS engine, several implementations have provided a series of improved parametrizations to account for particular important carbohydrate features. The following describes the main steps of such endeavors and their areas of application: GROMOS 45A4 and GROMOS 53A6GLYC hexopyranose in an explicit solvent, 46 GROMOS 56ACARBO, 47,48 ring conformational equilibria in hexopyranose, 49 GROMOS 56ACARBO_CHT chitosan and its derivatives, 50 GROMOS 56ACARBO/CARBO_R furanosebased carbohydrates, 51 and GROMOS96 43A1 glycan structure simulation in glycoproteins. 52,53 The continuous developments of the all-atom optimized potentials for liquid simulations (OPLS) 54,55 force field provide improvement to correct the performances in the estimation of the conformational changes around the glycosidic torsion angles and treatment of the carbohydrate-carbohydrate interactions in solution and explicit-water simulations.…”

Section: Force Fields For Carbohydratesmentioning

confidence: 99%

Multifaceted Computational Modeling in Glycoscience

Pérez

Makshakova

2022

Chem. Rev.

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Glycoscience assembles all the scientific disciplines involved in studying various molecules and macromolecules containing carbohydrates and complex glycans. Such an ensemble involves one of the most extensive sets of molecules in quantity and occurrence since they occur in all microorganisms and higher organisms. Once the compositions and sequences of these molecules are established, the determination of their three-dimensional structural and dynamical features is a step toward understanding the molecular basis underlying their properties and functions. The range of the relevant computational methods capable of addressing such issues is anchored by the specificity of stereoelectronic effects from quantum chemistry to mesoscale modeling throughout molecular dynamics and mechanics and coarse-grained and docking calculations. The Review leads the reader through the detailed presentations of the applications of computational modeling. The illustrations cover carbohydrate−carbohydrate interactions, glycolipids, and N-and O-linked glycans, emphasizing their role in SARS-CoV-2. The presentation continues with the structure of polysaccharides in solution and solid-state and lipopolysaccharides in membranes. The full range of protein-carbohydrate interactions is presented, as exemplified by carbohydrate-active enzymes, transporters, lectins, antibodies, and glycosaminoglycan binding proteins. A final section features a list of 150 tools and databases to help address the many issues of structural glycobioinformatics. CONTENTS 5.1. N-and O-Linked Glycans 5.2. Structure and Dynamics of SARS-CoV-2 5.3. Structure, Function, and Dynamics of Glycolipids 6. Polysaccharides 6.1. Polysaccharides in Solution 6.2. Polysaccharides in the Solid-State 6.3. Lipolysaccharides in Membranes 7. Protein Carbohydrate Interactions 7.1. Presentation: Synopsis of the Protein Families 7.2. Insights into Glycosyltransferases 7.3. Insights into Glycosyl Hydrolases 7.4. Enzymatic Degradation of Polysaccharides in the Solid-State

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Modification of 56ACARBO force field for molecular dynamic calculations of chitosan and its derivatives

Cited by 14 publications

References 53 publications

Polyelectrolyte Influence on Beta-Hairpin Peptide Stability: A Simulation Study

Polyelectrolyte Influence on Beta-Hairpin Peptide Stability: A Simulation Study

Probing the self-assembly dynamics and internal structure of amphiphilic hyaluronic acid conjugates by fluorescence spectroscopy and molecular dynamics simulations

Multifaceted Computational Modeling in Glycoscience

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