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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
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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
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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
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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
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Article ; Online: Recommendations for eye care during the alarm state by the coronavirus disease pandemic COVID-19.

Gegúndez-Fernández, J A / Zarranz-Ventura, J / Garay-Aramburu, G / Muñoz-Negrete, F J / Mendicute Del Barrio, J / Pablo-Júlvez, L / García-Delpech, S / López-Alemany, A / Arnalich-Montiel, F / Cordero-Coma, M / Cárceles, J A

Archivos de la Sociedad Espanola de Oftalmologia

2020 Volume 95, Issue 6, Page(s) 300–310

Abstract: Objective: Minimize exposure to the SARS-CoV-2, reduce the chances of cross-transmission between patients and healthcare personnel, and prevent the development of postoperative complications from the management of patients with eye diseases during the ... ...

Title translation	Recomendaciones para la atención oftalmológica durante el estado de alarma por la pandemia de enfermedad por coronavirus COVID-19.
Abstract	Objective: Minimize exposure to the SARS-CoV-2, reduce the chances of cross-transmission between patients and healthcare personnel, and prevent the development of postoperative complications from the management of patients with eye diseases during the 2019 coronavirus disease pandemic (COVID-19). Methods: COVID-19 literature review and consensus establishment between different Spanish ophthalmology societies in order to provide guidelines and recommendations of maximum resources primarily conditioned by the state of alert, confinement and social distancing that occurs in Spain since March 16, 2020. Results: The recommendations will promote the adoption of action and protection measures for eye care in outpatient clinics, surgical areas and hospitalization, for unconfirmed (asymptomatic and symptomatic) and confirmed COVID-19 patients. Measures must be adapted to the circumstances and availability of personal protective equipment in each of the centers and Autonomous Communities, which will be updated according to the pandemic phases and the measures adopted by the Spanish Government. Conclusions: During the COVID-19 pandemic, attention to the potential health risks to the population caused by coronavirus should prevail over the possible progression of the common eye diseases. Ophthalmologists and other eye care professionals must assume a possible progression of these diseases due to the impossibility of adequate patient follow-up.
MeSH term(s)	Antimalarials/therapeutic use ; Asymptomatic Diseases ; Betacoronavirus ; Blood Safety ; COVID-19 ; Chloroquine/therapeutic use ; Contact Lenses ; Coronavirus Infections/diagnosis ; Coronavirus Infections/epidemiology ; Coronavirus Infections/prevention & control ; Coronavirus Infections/transmission ; Disease Progression ; Eye Diseases/diagnosis ; Eye Diseases/therapy ; Humans ; Hydroxychloroquine/therapeutic use ; Infectious Disease Transmission, Patient-to-Professional/prevention & control ; Ophthalmologic Surgical Procedures/adverse effects ; Ophthalmologic Surgical Procedures/methods ; Ophthalmology ; Pandemics/prevention & control ; Pneumonia, Viral/diagnosis ; Pneumonia, Viral/epidemiology ; Pneumonia, Viral/prevention & control ; Pneumonia, Viral/transmission ; Postoperative Complications/prevention & control ; Risk Factors ; SARS-CoV-2 ; Societies, Medical ; Spain ; Symptom Assessment/methods ; Withholding Treatment
Chemical Substances	Antimalarials ; Hydroxychloroquine (4QWG6N8QKH) ; Chloroquine (886U3H6UFF)
Keywords	covid19
Language	Spanish
Publishing date	2020-04-25
Publishing country	Spain
Document type	Journal Article ; Practice Guideline ; Review
ISSN	2173-5794
ISSN (online)	2173-5794
DOI	10.1016/j.oftal.2020.04.002
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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
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Article: Challenges in familial chylomicronemia syndrome diagnosis and management across Latin American countries: An expert panel discussion.

Santos, Raul D / Lorenzatti, Alberto / Corral, Pablo / Nogueira, Juan Patricio / Cafferata, Alberto M / Aimone, Daniel / Lourenço, Charles M / Izar, Maria Cristina / Lima, Josivan G / Lottenberg, Ana Maria / Alonso, Rodrigo / Garay, Karla / Morales, Alvaro Ruiz / Vargas-Uricoechea, Hernando / Peña, Christian A Colón / Roman-González, Alejandro

Journal of clinical lipidology

2021 Volume 15, Issue 5, Page(s) 620–624

Abstract: Familial chylomicronemia syndrome (FCS) is a rare genetic disorder characterized by extremely high triglyceride levels due to impaired clearance of chylomicrons from plasma. This paper is the result of a panel discussion with Latin American specialists ... ...

Abstract	Familial chylomicronemia syndrome (FCS) is a rare genetic disorder characterized by extremely high triglyceride levels due to impaired clearance of chylomicrons from plasma. This paper is the result of a panel discussion with Latin American specialists who raised the main issues on diagnosis and management of FCS in their countries. Overall FCS is diagnosed late on the course of the disease, is characterized by heterogeneity on the occurrence of pancreatitis, and remains a long time in care of different specialists until reaching a lipidologist. Pancreatitis and secondary diabetes are frequently seen, often due to late diagnosis and inadequate care. Molecular diagnosis is unusual; however, loss of function variants on the lipoprotein lipase gene are apparently the most frequent etiology. A founder effect of the glycosylphosphatidylinositol anchored high density lipoprotein binding protein 1 gene has been described in the northeast of Brazil. Low awareness of the disease amongst health professionals contributes to inadequate care and an inadequate patient journey.
MeSH term(s)	Chylomicrons/blood ; Diabetes Mellitus/etiology ; Female ; Glycosylphosphatidylinositols/metabolism ; Humans ; Hyperlipoproteinemia Type I/blood ; Hyperlipoproteinemia Type I/diagnosis ; Hyperlipoproteinemia Type I/etiology ; Hyperlipoproteinemia Type I/therapy ; Latin America ; Lipoprotein Lipase/genetics ; Loss of Function Mutation ; Male ; Pancreatitis/etiology ; RNA-Binding Proteins/genetics ; RNA-Binding Proteins/metabolism ; Triglycerides/blood
Chemical Substances	Chylomicrons ; Glycosylphosphatidylinositols ; RNA-Binding Proteins ; Triglycerides ; high density lipoprotein binding protein (147605-06-9) ; Lipoprotein Lipase (EC 3.1.1.34)
Language	English
Publishing date	2021-12-15
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2365061-8
ISSN	1876-4789 ; 1933-2874
ISSN (online)	1876-4789
ISSN	1933-2874
DOI	10.1016/j.jacl.2021.10.004
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Article ; Online: Fluorescent Amorphous Distyrylnaphthalene-Based Polymers: Synthesis, Characterization and Thin-Film Nanomolar Sensing of Nitroaromatics in Water.

Garay, Raúl O / Schvval, Ana B / Almassio, Marcela F / Del Rosso, Pablo G / Romagnoli, Maria J / Montani, Rosana S

Polymers

2018 Volume 10, Issue 12

Abstract: Two new fluorescent segmented conjugated polymers with either 1,4- or 2,6-distyrylnaphthalene chromophores and their model compounds were synthesized and the chemosensing abilities of the polymeric thin films to detect nitroaromatics (NACs) in aqueous ... ...

Abstract	Two new fluorescent segmented conjugated polymers with either 1,4- or 2,6-distyrylnaphthalene chromophores and their model compounds were synthesized and the chemosensing abilities of the polymeric thin films to detect nitroaromatics (NACs) in aqueous media were evaluated. The structural, thermal and optical properties of the polymers were correlated with those displayed by their corresponding model compounds. Changes in the connectivity of naphthylene units caused minor differences in optical properties, morphology and quenching efficiencies. Molecular modeling highlighted the extremely bent character of polymer microstructures that explains their high solubility and amorphous character. Polymeric films are amorphous, strongly fluorescent and showed remarkable quenching efficiencies in the nanomolar range with picric acid (PA) and trinitrotoluene (TNT). Quenching experiments using either different nitroaromatic quenchers, excitation wavelengths, excitation beam path-lengths, or time of exposure of the film to the quenching solution evidenced the dominant role of inner filter effects (IFE) in the polymer response to NACs in the micromolar range. The sensing response towards PA, a quencher that strongly absorbs at the excitation wavelength, has an IFE contribution even at the nanomolar range, while the response towards the non-absorbing TNT depends only on the quenching occurring after diffusion of the analyte into the film.
Language	English
Publishing date	2018-12-10
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2527146-5
ISSN	2073-4360 ; 2073-4360
ISSN (online)	2073-4360
ISSN	2073-4360
DOI	10.3390/polym10121366
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Article ; Online: Airway Pathological Alterations Selectively Associated With Acute Respiratory Distress Syndrome and Diffuse Alveolar Damage - Narrative Review.

Ortiz, Guillermo / Garay, Manuel / Capelozzi, Vera / Cardinal-Fernández, Pablo

Archivos de bronconeumologia

2018 Volume 55, Issue 1, Page(s) 31–37

Abstract: Acute respiratory distress syndrome (ARDS) is a frequent and life-threatening entity. Recently, it has been demonstrated that diffuse alveolar damage (DAD), which is considered the histological hallmark in spite of presenting itself in only half of ... ...

Abstract	Acute respiratory distress syndrome (ARDS) is a frequent and life-threatening entity. Recently, it has been demonstrated that diffuse alveolar damage (DAD), which is considered the histological hallmark in spite of presenting itself in only half of living patients with ARDS, exerts a relevant effect in the ARDS outcome. Despite the fact that the bronchial tree constitutes approximately 1% of the lung volume, discovering a relation between DAD and bronchial tree findings could be of paramount importance for a few reasons; (a) it could improve the description of ARDS with DAD as a clinical-pathological entity, (b) it could subrogate DAD findings with the advantage of their more accessible and safer analysis and (c) it could allow the discovery of new therapeutic targets. This narrative review is focused on pathological airway changes associated to Diffuse Alveolar Damage in the context of Acute Respiratory Distress Syndrome. It is organized into five sections: main anatomical and functional features of the human airway, why it is necessary to study airway features associated to DAD in patients with ARDS, pathological airway changes associated with DAD in animal models of ARDS, pathological airway changes associated with DAD in patients with ARDS, and the newest techniques for studying the histology of the bronchial tree and lung parenchyma.
MeSH term(s)	Animals ; Bronchi/anatomy & histology ; Disease Models, Animal ; Guinea Pigs ; Humans ; Lung/pathology ; Pulmonary Alveoli/pathology ; Rabbits ; Rats ; Respiratory Distress Syndrome/complications ; Respiratory Distress Syndrome/pathology
Language	English
Publishing date	2018-05-28
Document type	Journal Article ; Systematic Review
ZDB-ID	733126-5
ISSN	1579-2129 ; 0300-2896
ISSN (online)	1579-2129
ISSN	0300-2896
DOI	10.1016/j.arbres.2018.03.006
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Article ; Online: Recommendations for eye care during the alarm state by the coronavirus disease pandemic COVID-19

Gegúndez-Fernández, J.A. / Zarranz-Ventura, J. / Garay-Aramburu, G. / Muñoz-Negrete, F.J. / Mendicute del Barrio, J. / Pablo-Júlvez, L. / García-Delpech, S. / López-Alemany, A. / Arnalich-Montiel, F. / Cordero-Coma, M. / Cárceles, J.A.

Archivos de la Sociedad Española de Oftalmología (English Edition)

2020 Volume 95, Issue 6, Page(s) 300–310

Keywords	covid19
Language	English
Publisher	Elsevier BV
Publishing country	us
Document type	Article ; Online
ISSN	2173-5794
DOI	10.1016/j.oftale.2020.04.001
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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