Adrián G. Turjanski

University of Buenos Aires

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Marcelo A. Martí

Consejo Nacional de Investigaciones Científicas y Técnicas

Lucas A. Defelipe

European Molecular Biology Laboratory

Ezequiel Sosa

Fundación Ciencias Exactas y Naturales

Darío Fernández Do Porto

Fundación Ciencias Exactas y Naturales

Darío A. Estrı́n

University of Buenos Aires

Carlos P. Modenutti

Fundación Ciencias Exactas y Naturales

Esteban Lanzarotti

Fundación Ciencias Exactas y Naturales

Juan Pablo Arcon

Institute for Research in Biomedicine

Leandro Radusky

University of Buenos Aires

Agustín Pardo

University of Buenos Aires

Cooperative Institutions

Consejo Nacional de Investigaciones Científicas y Técnicas

220

University of Buenos Aires

170

Fundación Ciencias Exactas y Naturales

121

Instituto de Química y Fisicoquímica Biológicas

Centro Científico Tecnológico - San Juan

Centro Científico Tecnológico - Tucumán

Garrahan Hospital

Universidade Federal de Minas Gerais

National Agricultural Technology Institute

Administración Nacional de Laboratorios e Institutos de Salud

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Reactions of Melatonin and Related Indoles with Free Radicals: A Computational Study

Journal of Medicinal Chemistry (1998)

Adrián G. Turjanski Ruth E. Rosenstein Darío A. Estrı́n

Melatonin is being increasingly promoted as a therapeutic agent for the treatment of jet lag and insomnia and has been recently suggested to act as an efficient free-radical scavenger. In the present work, its mechanisms of action for scavenging hydroxyl radicals have been investigated using semiempirical AM1 and density functional theory (DFT) computational tools. Two different reactions were proposed as follows: one involving the abstraction of an indolic hydrogen to yield a neutral radical and another involving the addition of the hydroxyl radical to the indolic moiety. Our results show that, from a thermodynamical standpoint, melatonin may directly scavenge hydroxyl radicals both in vacuum and in aqueous solution. The structural requirements for free-radical-trapping ability have been examined comparing melatonin with related indoles. Computational data suggest that 5-methoxy and N-acetyl groups of melatonin do not significantly affect its thermodynamical capacity of free-radical trapping. The present results support experimental data on the potential of melatonin as a physiological or pharmacological antioxidant agent.

Scavenger

Moiety

Hydroxyl radical

Free radical scavenger

Hydrogen atom abstraction

10.1021/jm980117m

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Citations (69)

Thiol redox biochemistry: insights from computer simulations

Biophysical Reviews (2014)

Ari Zeida Carlos M. Guardia Pablo Lichtig Laura L. Perissinotti Lucas A. Defelipe

Thiol

Hypochlorous acid

Reactivity

Nitrosylation

Sulfenic acid

S-Nitrosylation

10.1007/s12551-013-0127-x

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Citations (41)

Reverse Engineering of an Aspirin-Responsive Transcriptional Regulator in Escherichia coli

ACS Synthetic Biology (2019)

Lummy Maria Oliveira Monteiro Letícia Arruda Ananda Sanches-Medeiros Leonardo Martins‐Santana Luana de Fátima Alves

Bacterial transcription factors (TFs) are key devices for the engineering of complex circuits in many biotechnological applications, yet there are few well-characterized inducer-responsive TFs that could be used in the context of an animal or human host. We have deciphered the inducer recognition mechanism of two AraC/XylS regulators from Pseudomonas putida (BenR and XylS) for creating a novel expression system responsive to acetyl salicylate (i.e., aspirin). Using protein homology modeling and molecular docking with the cognate inducer benzoate and a suite of chemical analogues, we identified the conserved binding pocket of BenR and XylS. By means of site-directed mutagenesis, we identified a single amino acid position required for efficient inducer recognition and transcriptional activation. Whereas this modification in BenR abolishes protein activity, in XylS, it increases the response to several inducers, including acetyl salicylic acid, to levels close to those achieved by the canonical inducer. Moreover, by constructing chimeric proteins with swapped N-terminal domains, we created novel regulators with mixed promoter and inducer recognition profiles. As a result, a collection of engineered TFs was generated with an enhanced response to benzoate, 3-methylbenzoate, 2-methylbenzoate, 4-methylbenzoate, salicylic acid, aspirin, and acetylsalicylic acid molecules for eliciting gene expression in E. coli.

Inducer

10.1021/acssynbio.9b00191

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Citations (15)

Structured and Unstructured Binding of an Intrinsically Disordered Protein as Revealed by Atomistic Simulations

Journal of the American Chemical Society (2016)

Raúl Esteban Ithuralde Adrián E. Roitberg Adrián G. Turjanski

Intrinsically disordered proteins (IDPs) are a set of proteins that lack a definite secondary structure in solution. IDPs can acquire tertiary structure when bound to their partners; therefore, the recognition process must also involve protein folding. The nature of the transition state (TS), structured or unstructured, determines the binding mechanism. The characterization of the TS has become a major challenge for experimental techniques and molecular simulations approaches since diffusion, recognition, and binding is coupled to folding. In this work we present atomistic molecular dynamics (MD) simulations that sample the free energy surface of the coupled folding and binding of the transcription factor c-myb to the cotranscription factor CREB binding protein (CBP). This process has been recently studied and became a model to study IDPs. Despite the plethora of available information, we still do not know how c-myb binds to CBP. We performed a set of atomistic biased MD simulations running a total of 15.6 μs. Our results show that c-myb folds very fast upon binding to CBP with no unique pathway for binding. The process can proceed through both structured or unstructured TS's with similar probabilities. This finding reconciles previous seemingly different experimental results. We also performed Go-type coarse-grained MD of several structured and unstructured models that indicate that coupled folding and binding follows a native contact mechanism. To the best of our knowledge, this is the first atomistic MD simulation that samples the free energy surface of the coupled folding and binding processes of IDPs.

Intrinsically Disordered Proteins

Folding (DSP implementation)

Energy landscape

MYB

10.1021/jacs.6b02016

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Citations (33)

Overview of the SARS-CoV-2 genotypes circulating in Latin America during 2021

Frontiers in Public Health (2023)

José Arturo Molina-Mora Jhonnatan Reales-González Erwin Camacho Francisco Duarte-Martínez Pablo Tsukayama

Latin America is one of the regions in which the COVID-19 pandemic has a stronger impact, with more than 72 million reported infections and 1.6 million deaths until June 2022. Since this region is ecologically diverse and is affected by enormous social inequalities, efforts to identify genomic patterns of the circulating SARS-CoV-2 genotypes are necessary for the suitable management of the pandemic. To contribute to the genomic surveillance of the SARS-CoV-2 in Latin America, we extended the number of SARS-CoV-2 genomes available from the region by sequencing and analyzing the viral genome from COVID-19 patients from seven countries (Argentina, Brazil, Costa Rica, Colombia, Mexico, Bolivia, and Peru). Subsequently, we analyzed the genomes circulating mainly during 2021 including records from GISAID database from Latin America. A total of 1,534 genome sequences were generated from seven countries, demonstrating the laboratory and bioinformatics capabilities for genomic surveillance of pathogens that have been developed locally. For Latin America, patterns regarding several variants associated with multiple re-introductions, a relatively low percentage of sequenced samples, as well as an increment in the mutation frequency since the beginning of the pandemic, are in line with worldwide data. Besides, some variants of concern (VOC) and variants of interest (VOI) such as Gamma, Mu and Lambda, and at least 83 other lineages have predominated locally with a country-specific enrichments. This work has contributed to the understanding of the dynamics of the pandemic in Latin America as part of the local and international efforts to achieve timely genomic surveillance of SARS-CoV-2.

Pandemic

10.3389/fpubh.2023.1095202

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Citations (14)

Solvation and Conformational Properties of Melatonin: a Computational Study

Journal of Molecular Modeling (1999)

Adrián G. Turjanski Ruth E. Rosenstein Darío A. Estrı́n

Dihedral angle

HOMO/LUMO

Moiety

Implicit solvation

Mulliken population analysis

10.1007/s0089490050271

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Citations (7)

MRSA dynamic circulation between the community and the hospital setting: New insights from a cohort study

Journal of Infection (2019)

Danilo Barcudi Ezequiel Sosa Ricardo Lamberghini Analía Garnero Dario Tosoroni

10.1016/j.jinf.2019.10.001

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Citations (27)

Genome sequencing and analysis of black flounder (Paralichthys orbignyanus) reveals new insights into Pleuronectiformes genomic size and structure

BMC Genomics (2024)

Fernando Villarreal Germán Burguener Ezequiel Sosa Nicolás Stocchi Gustavo M. Somoza

Black flounder (Paralichthys orbignyanus, Pleuronectiformes) is a commercially significant marine fish with promising aquaculture potential in Argentina. Despite extensive studies on Black flounder aquaculture, its limited genetic information available hampers the crucial role genetics plays in the development of this activity. In this study, we first employed Illumina sequencing technology to sequence the entire genome of Black flounder. Utilizing two independent libraries-one from a female and another from a male-with 150 bp paired-end reads, a mean insert length of 350 bp, and over 35 X-fold coverage, we achieved assemblies resulting in a genome size of ~ 538 Mbp. Analysis of the assemblies revealed that more than 98% of the core genes were present, with more than 78% of them having more than 50% coverage. This indicates a somehow complete and accurate genome at the coding sequence level. This genome contains 25,231 protein-coding genes, 445 tRNAs, 3 rRNAs, and more than 1,500 non-coding RNAs of other types. Black flounder, along with pufferfishes, seahorses, pipefishes, and anabantid fish, displays a smaller genome compared to most other teleost groups. In vertebrates, the number of transposable elements (TEs) is often correlated with genome size. However, it remains unclear whether the sizes of introns and exons also play a role in determining genome size. Hence, to elucidate the potential factors contributing to this reduced genome size, we conducted a comparative genomic analysis between Black flounder and other teleost orders to determine if the small genomic size could be explained by repetitive elements or gene features, including the whole genome genes and introns sizes. We show that the smaller genome size of flounders can be attributed to several factors, including changes in the number of repetitive elements, and decreased gene size, particularly due to lower amount of very large and small introns. Thus, these components appear to be involved in the genome reduction in Black flounder. Despite these insights, the full implications and potential benefits of genome reduction in Black flounder for reproduction and aquaculture remain incompletely understood, necessitating further research.

Genome size

10.1186/s12864-024-10081-z

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Citations (1)

A computational study of the interaction of the foot and mouth disease virus VP1 with monoclonal antibodies

Journal of Immunological Methods (2015)

Rubén Marrero Ramiro Rodríguez Limardo Elisa Carrillo G König Adrián G. Turjanski

Epitope mapping

10.1016/j.jim.2015.06.008

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Citations (5)

Yerba mate (Ilex paraguariensis) genome provides new insights into convergent evolution of caffeine biosynthesis

eLife (2025)

Federico A. Vignale Andrea Hernandez Garcia Carlos P. Modenutti Ezequiel Sosa Lucas A. Defelipe

Yerba mate (YM, Ilex paraguariensis ) is an economically important crop marketed for the elaboration of mate, the third-most widely consumed caffeine-containing infusion worldwide. Here, we report the first genome assembly of this species, which has a total length of 1.06 Gb and contains 53,390 protein-coding genes. Comparative analyses revealed that the large YM genome size is partly due to a whole-genome duplication (Ip-α) during the early evolutionary history of Ilex , in addition to the hexaploidization event (γ) shared by core eudicots. Characterization of the genome allowed us to clone the genes encoding methyltransferase enzymes that catalyse multiple reactions required for caffeine production. To our surprise, this species has converged upon a different biochemical pathway compared to that of coffee and tea. In order to gain insight into the structural basis for the convergent enzyme activities, we obtained a crystal structure for the terminal enzyme in the pathway that forms caffeine. The structure reveals that convergent solutions have evolved for substrate positioning because different amino acid residues facilitate a different substrate orientation such that efficient methylation occurs in the independently evolved enzymes in YM and coffee. While our results show phylogenomic constraint limits the genes coopted for convergence of caffeine biosynthesis, the X-ray diffraction data suggest structural constraints are minimal for the convergent evolution of individual reactions.

Convergent evolution

Comparative Genomics

10.7554/elife.104759

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Citations (0)