Local and long range potentials for heparin‐protein systems for coarse‐grained simulations

Samsonov, Sergey A.; Lubecka, Emilia A.; Bojarski, Krzysztof K.; Ganzynkowicz, Robert; Liwo, Adam

doi:10.1002/bip.23269

Cited by 8 publications

(14 citation statements)

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“…The UNIfied COarse gRaiNed model (UNICORN) [ 26 , 47 ] is the most heavily coarse-grained model of those described in this section. It has been created by merging the models specific for proteins (UNRES) [ 24 , 47 , 80 , 146 ], nucleic acids (NARES-2P) [ 147 ] and for polysaccharides (SUGRES-1P) [ 47 , 148 , 149 ]. Recently, its extension to treat protein–nucleic acid complexes has been developed [ 150 ].…”

Section: Theory and Methodologymentioning

confidence: 99%

“…SUGRES-1P is still under development [ 148 , 149 ]. It is being extended [ 149 ] to include glycosaminoglycans (GAGs), for which the CG force fields are scarce despite their high biological significance. The other force fields developed for glycosoaminoglycans are described in Section 2.3.7 .…”

Section: Theory and Methodologymentioning

confidence: 99%

Section: Unicornmentioning

confidence: 99%

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Theory and Practice of Coarse-Grained Molecular Dynamics of Biologically Important Systems

et al. 2021

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Molecular dynamics with coarse-grained models is nowadays extensively used to simulate biomolecular systems at large time and size scales, compared to those accessible to all-atom molecular dynamics. In this review article, we describe the physical basis of coarse-grained molecular dynamics, the coarse-grained force fields, the equations of motion and the respective numerical integration algorithms, and selected practical applications of coarse-grained molecular dynamics. We demonstrate that the motion of coarse-grained sites is governed by the potential of mean force and the friction and stochastic forces, resulting from integrating out the secondary degrees of freedom. Consequently, Langevin dynamics is a natural means of describing the motion of a system at the coarse-grained level and the potential of mean force is the physical basis of the coarse-grained force fields. Moreover, the choice of coarse-grained variables and the fact that coarse-grained sites often do not have spherical symmetry implies a non-diagonal inertia tensor. We describe selected coarse-grained models used in molecular dynamics simulations, including the most popular MARTINI model developed by Marrink’s group and the UNICORN model of biological macromolecules developed in our laboratory. We conclude by discussing examples of the application of coarse-grained molecular dynamics to study biologically important processes.

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Section: Theory and Methodologymentioning

confidence: 99%

Section: Theory and Methodologymentioning

confidence: 99%

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Theory and Practice of Coarse-Grained Molecular Dynamics of Biologically Important Systems

et al. 2021

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“…Of particular interest is the investigation of the effect of polymer length and degree and pattern of deacetylation on the polymer properties . (ii) From the extracellular matrix, GAGs, ,− and other polysaccharides such as α(1-3) glucan. , In most cases, these applications study the interactions of these polysaccharides with proteins.…”

Section: Polysaccharidesmentioning

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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“…In this study, we present the implementation and calibration of the SUGRES-1P CG model. , We based our implementation on the theoretical background and initial parametrization of the sugar rings with each other published by our group. , Furthermore, we have fine tune the weights and parameters of the force field and applied the SUGRES-1P force field to the simulation of free HP of degree of polymerization (dp) ranging from 6 to 68. The conformations obtained from CG simulations were compared to experimentally determined HP structures. , The results show a good agreement with the experimental data in terms of the general shape and conformation of the CG HP molecules as well as their global characteristics: end-to-end distance (EED) and radius of gyration ( R g ).…”

Section: Introductionmentioning

confidence: 99%

Extension of the SUGRES-1P Coarse-Grained Model of Polysaccharides to Heparin

Danielsson,

Samsonov,

Liwo

et al. 2023

J. Chem. Theory Comput.

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Heparin is an unbranched periodic polysaccharide composed of negatively charged monomers and involved in key biological processes, including anticoagulation, angiogenesis, and inflammation. Its structure and dynamics have been studied extensively using experimental as well as theoretical approaches. The conventional approach of computational chemistry applied to the analysis of biomolecules is all-atom molecular dynamics, which captures the interactions of individual atoms by solving Newton’s equation of motion. An alternative is molecular dynamics simulations using coarse-grained models of biomacromolecules, which offer a reduction of the representation and consequently enable us to extend the time and size scale of simulations by orders of magnitude. In this work, we extend the UNIfied COarse-gRaiNed (UNICORN) model of biological macromolecules developed in our laboratory to heparin. We carried out extensive tests to estimate the optimal weights of energy terms of the effective energy function as well as the optimal Debye–Hückel screening factor for electrostatic interactions. We applied the model to study unbound heparin molecules of polymerization degree ranging from 6 to 68 residues. We compare the obtained coarse-grained heparin conformations with models obtained from X-ray diffraction studies of heparin. The SUGRES-1P force field was able to accurately predict the general shape and global characteristics of heparin molecules.

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Local and long range potentials for heparin‐protein systems for coarse‐grained simulations

Cited by 8 publications

References 45 publications

Theory and Practice of Coarse-Grained Molecular Dynamics of Biologically Important Systems

Theory and Practice of Coarse-Grained Molecular Dynamics of Biologically Important Systems

Multifaceted Computational Modeling in Glycoscience

Extension of the SUGRES-1P Coarse-Grained Model of Polysaccharides to Heparin

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