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  1. Article ; Online: SIRAH Late Harvest: Coarse-Grained Models for Protein Glycosylation.

    Garay, Pablo G / Machado, Matias R / Verli, Hugo / Pantano, Sergio

    Journal of chemical theory and computation

    2024  Volume 20, Issue 2, Page(s) 963–976

    Abstract: 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 ... ...

    Abstract 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. Although theoretical methods have proven to be a valid alternative to the study of glycans, the large size associated with polysaccharides, proteoglycans, and glycolipids poses significant challenges to a fully atomistic description of biologically relevant glycoconjugates. On the other hand, the exquisite dependence on hydrogen bonds to determine glycans' structure makes the development of simplified or coarse-grained (CG) representations extremely challenging. This is particularly the case when glycan representations are expected to be compatible with CG force fields that include several molecular types. We introduce a CG representation able to simulate a wide variety of polysaccharides and common glycosylation motifs in proteins, which is fully compatible with the CG SIRAH force field. Examples of application to N-glycosylated proteins, including antibody recognition and calcium-mediated glycan-protein interactions, highlight the versatility of the enlarged set of CG molecules provided by SIRAH.
    MeSH term(s) Glycosylation ; Molecular Dynamics Simulation ; Proteins/chemistry ; Antibodies ; Polysaccharides
    Chemical Substances Proteins ; Antibodies ; Polysaccharides
    Language English
    Publishing date 2024-01-04
    Publishing country United States
    Document type Journal Article
    ISSN 1549-9626
    ISSN (online) 1549-9626
    DOI 10.1021/acs.jctc.3c00783
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Post-Translational Modifications at the Coarse-Grained Level with the SIRAH Force Field.

    Garay, Pablo G / Barrera, Exequiel E / Pantano, Sergio

    Journal of chemical information and modeling

    2020  Volume 60, Issue 2, Page(s) 964–973

    Abstract: 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, ...

    Abstract 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.
    MeSH term(s) Methylation ; Molecular Dynamics Simulation ; Phosphorylation ; Protein Conformation ; Protein Processing, Post-Translational ; Proteins/chemistry ; Proteins/metabolism
    Chemical Substances Proteins
    Language English
    Publishing date 2020-01-07
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 190019-5
    ISSN 1549-960X ; 0095-2338
    ISSN (online) 1549-960X
    ISSN 0095-2338
    DOI 10.1021/acs.jcim.9b00900
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: The SIRAH-CoV-2 Initiative: A Coarse-Grained Simulations' Dataset of the SARS-CoV-2 Proteome.

    Garay, Pablo G / Barrera, Exequiel E / Klein, Florencia / Machado, Matias R / Soñora, Martín / Pantano, Sergio

    Frontiers in medical technology

    2021  Volume 3, Page(s) 644039

    Language English
    Publishing date 2021-02-15
    Publishing country Switzerland
    Document type Journal Article
    ISSN 2673-3129
    ISSN (online) 2673-3129
    DOI 10.3389/fmedt.2021.644039
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Detection of methylation, acetylation and glycosylation of protein residues by monitoring (13)C chemical-shift changes: A quantum-chemical study.

    Garay, Pablo G / Martin, Osvaldo A / Scheraga, Harold A / Vila, Jorge A

    PeerJ

    2016  Volume 4, Page(s) e2253

    Abstract: Post-translational modifications of proteins expand the diversity of the proteome by several orders of magnitude and have a profound effect on several biological processes. Their detection by experimental methods is not free of limitations such as the ... ...

    Abstract Post-translational modifications of proteins expand the diversity of the proteome by several orders of magnitude and have a profound effect on several biological processes. Their detection by experimental methods is not free of limitations such as the amount of sample needed or the use of destructive procedures to obtain the sample. Certainly, new approaches are needed and, therefore, we explore here the feasibility of using (13)C chemical shifts of different nuclei to detect methylation, acetylation and glycosylation of protein residues by monitoring the deviation of the (13)C chemical shifts from the expected (mean) experimental value of the non-modified residue. As a proof-of-concept, we used (13)C chemical shifts, computed at the DFT-level of theory, to test this hypothesis. Moreover, as a validation test of this approach, we compare our theoretical computations of the (13)Cε chemical-shift values against existing experimental data, obtained from NMR spectroscopy, for methylated and acetylated lysine residues with good agreement within ∼1 ppm. Then, further use of this approach to select the most suitable (13)C-nucleus, with which to determine other modifications commonly seen, such as methylation of arginine and glycosylation of serine, asparagine and threonine, shows encouraging results.
    Language English
    Publishing date 2016-07-21
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2703241-3
    ISSN 2167-8359
    ISSN 2167-8359
    DOI 10.7717/peerj.2253
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Factors affecting the computation of the 13C shielding in disaccharides.

    Garay, Pablo G / Martin, Osvaldo A / Scheraga, Harold A / Vila, Jorge A

    Journal of computational chemistry

    2014  Volume 35, Issue 25, Page(s) 1854–1864

    Abstract: Knowledge of the three-dimensional structures of glycans and glycoproteins is useful for a full understanding of molecular processes in which glycans are involved, such as antigen-recognition and virus infection, to name a few. Among the ubiquitous ... ...

    Abstract Knowledge of the three-dimensional structures of glycans and glycoproteins is useful for a full understanding of molecular processes in which glycans are involved, such as antigen-recognition and virus infection, to name a few. Among the ubiquitous nuclei in glycan molecules, the (13)C nucleus is an attractive candidate for computation of theoretical chemical shifts at the quantum chemical level of theory to validate and determine glycan structures. For this purpose, it is important to determine, first, which carbons can be used as probes to sense conformational changes and, second, all factors that affect the computation of the shielding, at the density functional theory (DFT) level of theory, of those carbons. To answer such questions, we performed a series of analyses on low-energy conformations, obtained by sampling the glycosidic torsional angles (ϕ, ψ) every 10°, of 12 disaccharides. Our results provide evidence that: (i) the carbons that participate in the glycosidic linkage are the most sensitive probes with which to sense conformational changes of disaccharides; (ii) the rotation of the hydroxyl groups closest to the glycosidic linkage significantly affects the computation of the shieldings of the carbons that participate in the glycosidic linkage; (iii) it is not possible to obtain the shieldings of one disaccharide from the computed values of a different disaccharide or from those disaccharides that differ in the anomeric state; and (iv) a proper basis set distribution, a functional, and a step size, with which to sample the conformational space, are necessary to compute shieldings accurately and rapidly.
    MeSH term(s) Amylose/chemistry ; Carbon Isotopes/chemistry ; Disaccharides/chemistry ; Entropy ; Glycoproteins/chemistry ; Maltose/chemistry ; Molecular Conformation ; Quantum Theory
    Chemical Substances Carbon Isotopes ; Disaccharides ; Glycoproteins ; Maltose (69-79-4) ; Amylose (9005-82-7)
    Language English
    Publishing date 2014-07-28
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 1479181-X
    ISSN 1096-987X ; 0192-8651
    ISSN (online) 1096-987X
    ISSN 0192-8651
    DOI 10.1002/jcc.23697
    Database MEDical Literature Analysis and Retrieval System OnLINE

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