Post-translational modifications (PTMs) on proteins significantly enlarge the physicochemical diversity present in biological macromolecules, altering function, localization, and interactions. Despite their critical role in regulating cellular processes, theoretical methods are not yet fully capable of coping with this diversity. These limitations are particularly more marked for coarse-grained (CG) models, in which comprehensive and self-consistent parametrizations are less frequent. Here we present a set of topologies and interaction parameters for the most common PTMs, fully compatible with the SIRAH force field. The PTMs introduced here reach the same level of structural description of the existing SIRAH force field, expanding the chemical spectrum with promising applications in dynamical protein-protein interactions in large and complex cellular environments.
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http://dx.doi.org/10.1021/acs.jcim.9b00900 | DOI Listing |
bioRxiv
November 2024
Department of Chemistry, College of Staten Island, City University of New York, 2800 Victory Blvd., 6S-238, Staten Island, NY 10314.
This study investigates nucleosome dynamics using both all-atom and coarse-grained (CG) molecular dynamics simulations, focusing on the SIRAH force field. Simulations are performed for two nucleosomal DNA sequences-ASP and Widom-601-over six microseconds at physiological salt concentrations. Comparative analysis of structural parameters, such as groove widths and base pair geometries, reveals good agreement between atomistic and CG models, though CG simulations exhibit broader conformational sampling and greater breathing motion of DNA ends.
View Article and Find Full Text PDFJ Phys Chem B
December 2024
Área Bioinformática, Departamento DETEMA, Facultad de Química, Universidad de la República, General Flores 2124, Montevideo 11600, Uruguay.
Molecular dynamics (MD) simulations provide an invaluable platform for exploring the dynamics of complex biomolecular systems at atomic resolution. However, compatibility issues between force fields and MD software engines can limit the interoperability and transferability of simulations. This work demonstrates the successful use of the coarse-grained SIRAH force field on the widely used NAMD MD engine across a range of increasingly complex biomolecular systems.
View Article and Find Full Text PDFInt J Mol Sci
June 2024
Institute of Physics Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland.
Intrinsically disordered proteins (IDPs) pose challenges to conventional experimental techniques due to their large-scale conformational fluctuations and transient structural elements. This work presents computational methods for studying IDPs at various resolutions using the Amber and Gromacs packages with both all-atom (Amber ff19SB with the OPC water model) and coarse-grained (Martini 3 and SIRAH) approaches. The effectiveness of these methodologies is demonstrated by examining the monomeric form of amyloid-β (Aβ42), an IDP, with and without disulfide bonds at different resolutions.
View Article and Find Full Text PDFJ Chem Theory Comput
January 2024
Biomolecular Simulations Group, Institut Pasteur de Montevideo, Mataojo 2020, CP 11400 Montevideo, Uruguay.
Glycans constitute one of the most complex families of biological molecules. Despite their crucial role in a plethora of biological processes, they remain largely uncharacterized because of their high complexity. Their intrinsic flexibility and the vast variability associated with the many combination possibilities have hampered their experimental determination.
View Article and Find Full Text PDFData Brief
August 2023
Biomolecular Simulations Group, Institut Pasteur de Montevideo, Mataojo 2020, CP 11400 Montevideo, Uruguay.
The small soluble aggregates of Aβ are broadly documented as potential targets for the development of new compounds with the capacity to inhibit the early stages of Alzheimer´s disease. Nevertheless, Aβ peptides show an intrinsically disordered character with a high propensity for aggregation, which complicates the identification of conserved structural patterns. Because of this, experimental techniques find substantial difficulties in the characterization of such soluble oligomers.
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