Marcelo D. Polêto

Marcelo D. Polêto
Virginia Polytechnic Institute and State University | VT · Department of Biochemistry

PhD in Cell and Molecular Biology

About

36
Publications
6,698
Reads
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204
Citations
Introduction
I am interested in the conformational dynamics of biomolecules in different conditions and their impact on molecular recognition. In this sense, I often use a range of molecular modeling techniques, such as comparative modeling and molecular dynamics simulations, in order to study biophysical events in atomic-scale resolution.
Additional affiliations
April 2019 - September 2020
Universidade Federal de Viçosa (UFV)
Position
  • PostDoc Position
March 2019 - April 2020
Universidade Federal de Viçosa (UFV)
Position
  • Research Associate
December 2013 - July 2014
Uppsala University
Position
  • Exchange student
Education
August 2016 - March 2019
Universidade Federal do Rio Grande do Sul
Field of study
  • Molecular Dynamics Simulations and Force Field Development
March 2015 - July 2016
Universidade Federal do Rio Grande do Sul
Field of study
  • Molecular Dynamics Simulations and Force Field Development
March 2009 - December 2014
Universidade Federal de Viçosa (UFV)
Field of study
  • Molecular Modeling

Publications

Publications (36)
Article
We introduce TUPÃ, a Python‐based algorithm to calculate and analyze electric fields in molecular simulations. To demonstrate the features in TUPÃ, we present three test cases in which the orientation and magnitude of the electric field exerted by biomolecules help explain biological phenomena or observed kinetics. As part of TUPÃ, we also provide...
Article
Full-text available
The development of accurate protein force fields has been the cornerstone of molecular simulations for the past 50 years. During this period, many lessons have been learned regarding the use of experimental target data and parameter fitting procedures. Here, we review recent advances in protein force field development. We discuss the recent emergen...
Article
We used computational molecular dynamics (MD) to assess molecular conformations of apo- and holo-forms (respectively without and with Ca2+) of bovine α-lactalbumin (α-La) at different temperatures, and to correlate them with the protein’s foaming properties. At 4 ºC and 25 ºC no major protein conformation changes occurred. At 75 ºC, lots of changes...
Article
We present a user-friendly front-end for running molecular dynamics (MD) simulations using the OpenMM toolkit on the Google Colab framework. Our goals are (1) to highlight the usage of a cloud-computing scheme for educational purposes for a hands-on approach when learning MD simulations and (2) to exemplify how low-income research groups can perfor...
Preprint
Full-text available
We present a user-friendly front-end for running molecular dynamics (MD) simulations using OpenMM toolkit on the Google Colab framework. Our goals are: 1) to highlight the usage of a cloud-computing scheme for educational purposes for a hands-on approach when learning MD simulations and 2) to exemplify how low-income research 1 groups can perform M...
Preprint
We present a user-friendly front-end for running molecular dynamics (MD) simulations using OpenMM toolkit on the Google Colab framework. Our goals are: 1) to highlight the usage of a cloud-computing scheme for educational purposes for a hands-on approach when learning MD simulations and 2) to exemplify how low-income research groups can perform MD...
Article
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 the treatment of hypertension. Though various peptides from milk proteins are well-known for their ACE-inhibitory capacity, research devoted to understand the molecular bases of such property remain s...
Article
Rotational Profiler provides an analytical algorithm to compute sets of classical torsional dihedral parameters by fitting an empirical energy profile to a reference one that can be obtained experimentally or by quantum-mechanical methods. The resulting profiles are compatible with the functional forms in the most widely used biomolecular force fie...
Article
Abstract: ENTPDases are enzymes known for hydrolyzing extracellular nucleotides and playing an essential role in controlling the nucleotide signaling via nucleotide/purinergic receptors P2. Moreover, ENTPDases, together with Ecto-5´-nucleotidase activity, affect the adenosine signaling via P1 receptors. These signals control many biological process...
Article
Full-text available
Hypertension is nowadays one of the major world concerns in public health. Several food proteins, among which caseins, can be substrates for generating peptides with antihypertensive potential. With the increasingly evolution of computational tools, in silico molecular modeling has gained prominence in studies of protein-ligand complexes in differe...
Article
Motivation The conformational space of small molecules can be vast and difficult to assess. Molecular dynamics simulations of free ligands in solution have been applied to predict conformational populations, but their characterization is often based on clustering algorithms or manual efforts. Results Here, we introduce ConfID, an analytical tool...
Article
Lipid-linked oligosaccharides (LLOs) plays an important role in the N-glycosylation pathway as the donor substrate of oligosaccharyltransferases (OSTs), which are responsible for the en bloc transfer of glycan chains onto a nascent polypeptide. The lipid component of LLO in both eukarya and archaea consists of a dolichol, and an undecaprenol in pro...
Article
Full-text available
The West Nile Virus (WNV) NS2B-NS3 protease is an attractive target for the development of therapeutics against this arboviral pathogen. In the present investigation, the screening of a small library of fifty-eight synthetic compounds against the NS2-NB3 protease of WNV is described. The following groups of compounds were evaluated: 3-(2-aryl-2-oxo...
Preprint
Full-text available
div> Lipid-linked oligosaccharides (LLOs) plays an important role in the N-glycosylation pathway as the donor substrate of oligosaccharyltransferases (OSTs), which are respon- sible for the en bloc transfer of glycan chains onto a nascent polypeptide. The lipid component of LLO in both eukarya and archaea consists of a dolichol, and an unde- capr...
Article
Chalcones and flavonoids constitute a large family of plant secondary metabolites that has been explored as a potential source of novel pharmaceutical products. While the simulation of these compounds by molecular dynamics (MD) can be a valuable strategy to assess their conformational properties and so further develop their role in drug discovery,...
Article
PIK‐75 is a phosphoinositide‐3‐kinase (PI3K) α‐isoform‐selective inhibitor with high potency. Although published SAR data show the importance of the NO2 and the Br substituents in PIK‐75, none of the published studies could correctly assign the underlying reason for their importance. In this publication, we report the first X‐ray crystal structure...
Article
PIK‐75 is a phosphoinositide‐3‐kinase (PI3K) α‐isoform‐selective inhibitor with high potency. Although published SAR data show the importance of the NO2 and the Br substituents in PIK‐75, none of the published studies could correctly assign the underlying reason for their importance. In this publication, we report the first X‐ray crystal structure...
Article
Full-text available
The structure of ribonucleic acid (RNA) polymers is strongly dependent on the presence of, in particular Mg2+ cations to stabilize structural features. Only in high-resolution X-ray crystallography structures can ions be identified reliably. Here, we perform molecular dynamics simulations of 24 RNA structures with varying ion concentrations. Twelve...
Article
The identification of lead compounds usually includes a step of chemical diversity generation. Its rationale may be supported by both qualitative (SAR) and quantitative (QSAR) approaches, offering models of the putative ligand-receptor interactions. In both scenarios, our understanding of which interactions functional groups can perform is mostly b...
Article
Full-text available
Background 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, the structures of Tospovirus proteins still are poorly understood. Despite multiple studies have attempted to identify candidate N prot...
Article
Bovine cysticercosis is a zoonotic infection widely spread throughout Brazil, creating a burden on hygiene maintenance and the economy. Diagnosis of cysticercosis usually relies on post mortem inspection of carcasses in slaughterhouses. This detection method provides only low sensitivity. Recent advancements have improved the performance of serolog...
Article
Electrospray mass spectrometry/mass spectrometry was used to investigate the gas-phase properties of protonated expanded porphyrins, in order to correlate those with their structure and conformation. We have selected five expanded meso-pentafluorophenyl porphyrins, respectively, a pair of oxidized/reduced fused pentaphyrins (22 and 24 π electrons),...
Article
Full-text available
Porcine circovirus-2 (PCV2) is the etiologic agent of several diseases in pigs, including multi-systemic wasting syndrome (PMWS). In this work, a new mutant PCV2b was isolated from PMWS-affected pigs on a Brazilian farm. Its genome showed high sequence similarity ([99 % identity) to those from a group of emerging mutants isolated from cases of PMWS...
Article
Full-text available
Dysregulation of pre-mRNA splicing machinery activity has been related to the biogenesis of several diseases. The serine/arginine-rich protein kinase family (SRPKs) plays a critical role in regulating pre-mRNA splicing events through the extensive phosphorylation of splicing factors from the family of serine/arginine-rich proteins (SR proteins). Pr...
Article
Full-text available
Hexaphyrin-based anion chemosensors are reported for the first time. The meso-hexakis(ethylenediamine)-substituted [28]hexaphyrins and revealed strong affinity for F(-), AcO(-) and H2PO4(-). Adsorption constants in aqueous media were determined on a gold piezoelectric crystal coated with and . (1)H NMR titrations and molecular dynamics simulations...

Questions

Question (1)
Question
Hi!
Does anyone know references for well established parameters for Mn2+ or Zn2+ ions for Amber force fields?
Thanks in advance!

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Cited By

Projects

Projects (2)
Project
This is a long term project on Food Science and Technology, whose central aim is using computational molecular modelling tools to study, clarify and understand, at the atomic level, how the structure, dynamics and interactions among food biomolecules impact their techno-functionalities and/or bioactivities. It involves the colaboration of several researchers, as well as the participation of various MSc and PhD candidates advised or co-advised by me. Not exhaustively, the themes addressed include: (1) elucidation and understanting of interaction modes between food proteins and small ligand molecules (docking approaches); (2) elucidation and understanting of dynamic behavior of food proteins structures, at different temperatures, and subjected to varying pH and specific ions in aqueous media or adsorbed on interfaces (molecular dynamics approaches); (3) elucidation and understanting of dynamic behavior of food polysaccharides, at different temperatures, and subjected to varying pH and specific ions in aqueous media (molecular dynamics approaches).
Project
The main goal of this project is to shed light upon the molecular recognition kinetics and dynamics through the ligand pespective, by using computational approaches.