A5017891381- DNA and Nucleic Acid Chemistry
- Protein Structure and Dynamics
- Advanced biosensing and bioanalysis techniques
- Carbohydrate Chemistry and Synthesis
- RNA and protein synthesis mechanisms
- Trypanosoma species research and implications
- Glycosylation and Glycoproteins Research
- Microplastics and Plastic Pollution
- Plant nutrient uptake and metabolism
- Scientific Computing and Data Management
- Enzyme Structure and Function
- Chemical Synthesis and Analysis
- Biochemical effects in animals
- Methane Hydrates and Related Phenomena
- Analytical Chemistry and Chromatography
- Computational Drug Discovery Methods
- Phytase and its Applications
- Research Data Management Practices
- Luminescence and Fluorescent Materials
- Microbial metabolism and enzyme function
- Synthesis and Catalytic Reactions
- Protein Hydrolysis and Bioactive Peptides
- Proteins in Food Systems
- Molecular Sensors and Ion Detection
- Distributed and Parallel Computing Systems
Virginia Tech
2021-2024
Universidade Federal do Rio Grande do Sul
2015-2024
Universidade Federal de Viçosa
2015-2023
Universidade Federal de Ciências da Saúde de Porto Alegre
2019
University of Southampton
2019
Centro Universitário Cesmac
2019
Science for Life Laboratory
2018
Uppsala University
2018
University of Rio Grande and Rio Grande Community College
2015
The structure of ribonucleic acid (RNA) polymers is strongly dependent on the presence of, in particular Mg2+ cations to stabilize structural features. Only high-resolution X-ray crystallography structures can ions be identified reliably. Here, we perform molecular dynamics simulations 24 RNA with varying ion concentrations. Twelve were helical and others complex folded. aim study predict positions but also evaluate impact different types (Na+ or Mg2+) ionic strength stability variations...
Dysregulation of pre-mRNA splicing machinery activity has been related to the biogenesis several diseases. The serine/arginine-rich protein kinase family (SRPKs) plays a critical role in regulating events through extensive phosphorylation factors from proteins (SR proteins). Previous investigations have described overexpression SRPK1 and SRPK2 leukemia other cancer types, suggesting that they would be useful targets for developing novel antitumor strategies. Herein, we evaluated effect...
The identification of lead compounds usually includes a step chemical diversity generation. Its rationale may be supported by both qualitative (SAR) and quantitative (QSAR) approaches, offering models the putative ligand-receptor interactions. In scenarios, our understanding which interactions functional groups can perform is mostly based on their nature (such as electronegativity, volume, melting point, lipophilicity etc.) instead dynamics in aqueous, biological solutions (solvent...
Abstract The development of accurate protein force fields has been the cornerstone molecular simulations for past 50 years. During this period, many lessons have learned regarding use experimental target data and parameter fitting procedures. Here, we review recent advances in field development. We discuss emergence polarizable role electronic polarization areas which additive fall short. automated methods inclusion additional solution during parametrization is discussed as a means to...
Abstract We introduce TUPÃ, a Python‐based algorithm to calculate and analyze electric fields in molecular simulations. To demonstrate the features we present three test cases which orientation magnitude of field exerted by biomolecules help explain biological phenomena or observed kinetics. As part also provide PyMOL plugin researchers visualize how are organized within simulation system. The code is freely available can be obtained at https://mdpoleto.github.io/tupa/ .
The West Nile Virus (WNV) NS2B-NS3 protease is an attractive target for the development of therapeutics against this arboviral pathogen. In present investigation, screening a small library fifty-eight synthetic compounds NS2-NB3 WNV described. following groups were evaluated: 3-(2-aryl-2-oxoethyl)isobenzofuran-1(3H)-ones; eugenol derivatives bearing 1,2,3-triazolic functionalities; and indan-1,3-diones with functionalities. most promising these was derivative, namely...
Hexaphyrin-based anion chemosensors are reported for the first time.
Abstract PIK‐75 is a phosphoinositide‐3‐kinase (PI3K) α‐isoform‐selective inhibitor with high potency. Although published structure–activity relationship data show the importance of NO 2 and Br substituents in PIK‐75, none studies could correctly determine underlying reason for their importance. In this publication, we report first X‐ray crystal structure complex kinase GSK‐3β. The shows an unusual U‐shaped conformation within active site GSK‐3β that likely stabilized by atypical...
Tospovirus is a plant-infecting genus within the family Bunyaviridae, which also includes four animal-infecting genera: Hantavirus, Nairovirus, Phlebovirus and Orthobunyavirus. Compared to these members, structures of proteins still are poorly understood. Despite multiple studies have attempted identify candidate N protein regions involved in RNA binding multimerization for tospovirus using yeast two-hybrid systems (Y2HS) site-directed mutagenesis, ribonucleocapsids (RNPs) remains largely...
The molecular dynamics of the Pseudomonas fluorescens 07A metalloprotease in presence structural Ca2+ and Mn2+ ions was evaluated. Seven are primarily bound to C-terminus, while a divalent cation is located at catalytic site, acting as cofactor. observed enzyme's experimental activity suggests that could compete for active site enzyme with Ca2+, Zn2+ or other cations, thus providing greater power enzyme. Our simulations suggest these partially protect structure from thermal denaturation....
Methyl-coenzyme M reductase (MCR) is a central player in methane biogeochemistry, governing methanogenesis and the anaerobic oxidation of (AOM) methanogens methanotrophs (ANME), respectively. The prosthetic group MCR coenzyme F430, nickel-containing tetrahydrocorphin. Several modified versions F430 have been discovered, including 172-methylthio-F430 (mtF430) used by ANME-1 MCR. Here, we employ molecular dynamics (MD) simulations to investigate active site from Methanosarcina acetivorans when...
The environmental and economic challenges posed by the widespread use disposal of plastics, particularly poly(ethylene terephthalate) (PET), require innovative solutions to mitigate their impact. Such mitigation begins with understanding physical properties polymer that could enable new recycling technologies. Although molecular simulations have provided valuable insights into PET interactions various hydrolases, current nonpolarizable force fields neglect electronic polarization effects...
Electrospray mass spectrometry/mass spectrometry was used to investigate the gas-phase properties of protonated expanded porphyrins, in order correlate those with their structure and conformation. We have selected five meso-pentafluorophenyl respectively, a pair oxidized/reduced fused pentaphyrins (22 24 π electrons), regular hexaphyrins (26 28 electrons) doubly N-fused hexaphyrin (28 electrons). The behavior species oxidized reduced porphyrins is different. (aromatic Hückel systems)...
Chalcones and flavonoids constitute a large family of plant secondary metabolites that have been explored as potential source novel pharmaceutical products. While the simulation these compounds by molecular dynamics (MD) can be valuable strategy to assess their conformational properties so further develop role in drug discovery, there are no set force field parameters specifically designed experimentally validated for description condensed phase. So current work developed new parameter MD...
The Envelope (E) protein of SARS-CoV-2 plays a key role in virus maturation, assembly, and virulence mechanisms. E is characterized by the presence PDZ-binding motif (PBM) at its C-terminus that allows it to interact with several PDZ-containing proteins intracellular environment. One main binding partners PDZ2 domain ZO1, crucial formation epithelial endothelial tight junctions (TJs). In this work, through combination analytical ultracentrifugation analysis equilibrium kinetic folding...
The angiotensin-converting enzyme (ACE) plays a key role in blood pressure regulation process, and its inhibition is one of the main drug targets for treatment hypertension. Though various peptides from milk proteins are well-known their ACE-inhibitory capacity, research devoted to understand molecular bases such property remain scarce, specifically peptides. Therefore, this work, computational docking dynamics calculations were performed enlighten intermolecular interactions involved ACE by...
Rotational Profiler provides an analytical algorithm to compute sets of classical torsional dihedral parameters by fitting empirical energy profile a reference one that can be obtained experimentally or quantum-mechanical methods. The resulting profiles are compatible with the functional forms in most widely used biomolecular force fields (e.g., GROMOS, AMBER, OPLS, and CHARMM). linear least-squares regression method is generate best satisfy fitting. free use, analytical, field/package...
The formation of G-quadruplexes (GQs) occurs in guanine-rich sequences DNA and RNA, producing highly stable structurally diverse noncanonical nucleic acid structures. GQs play crucial roles regulating transcription, translation, replication maintaining the genome, among others; thus, changes to their structures can lead diseases such as cancer. Previous studies using polarizable molecular dynamics simulations have shown differences ion binding properties between telomeric repeat-containing...