Institute of Fundamental Technological Research
Polish Academy of Sciences

Staff

Rodrigo Azevedo Moreira da Silva, PhD

Department of Biosystems and Soft Matter (ZBiMM)
Division of Modelling in Biology and Medicine (PMBM)
position: assistant professor
telephone: (+48) 22 826 12 81 ext.: 326
room: 221
e-mail:


Recent publications
1.  Moreira R., Vargas Guzman H., Boopathi S., Baker J.L., Poma Bernaola A., Characterization of structural and energetic differences between conformations of the SARS-CoV-2 spike protein, Materials, ISSN: 1996-1944, DOI: 10.3390/ma13235362, Vol.13, No.23, pp.5362-1-14, 2020

Abstract:
The novel coronavirus disease 2019 (COVID-19) pandemic has disrupted modern societies and their economies. The resurgence in COVID-19 cases as part of the second wave is observed across Europe and the Americas. The scientific response has enabled a complete structural characterization of the Severe Acute Respiratory Syndrome—novel Coronavirus 2 (SARS-CoV-2). Among the most relevant proteins required by the novel coronavirus to facilitate the cell entry mechanism is the spike protein. This protein possesses a receptor-binding domain (RBD) that binds the cellular angiotensin-converting enzyme 2 (ACE2) and then triggers the fusion of viral and host cell membranes. In this regard, a comprehensive characterization of the structural stability of the spike protein is a crucial step to find new therapeutics to interrupt the process of recognition. On the other hand, it has been suggested that the participation of more than one RBD is a possible mechanism to enhance cell entry. Here, we discuss the protein structural stability based on the computational determination of the dynamic contact map and the energetic difference of the spike protein conformations via the mapping of the hydration free energy by the Poisson–Boltzmann method. We expect our result to foster the discussion of the number of RBD involved during recognition and the repurposing of new drugs to disable the recognition by discovering new hotspots for drug targets apart from the flexible loop in the RBD that binds the ACE2.

Keywords:
COVID-19, SARS-CoV-2, spike protein, RBD, structural stability, large conformational changes, protein complexes, free energy, molecular dynamics, dynamics contact analysis

Affiliations:
Moreira R. - IPPT PAN
Vargas Guzman H. - Max-Planck-Institute for Polymer Research (DE)
Boopathi S. - other affiliation
Baker J.L. - other affiliation
Poma Bernaola A. - IPPT PAN
2.  Moreira R., Chwastyk M., Baker J.L., Vargas Guzman H.A., Poma A., Quantitative determination of mechanical stability in the novel coronavirus spike protein, NANOSCALE, ISSN: 2040-3364, DOI: 10.1039/D0NR03969A, Vol.12, No.31, pp.16409-16413, 2020

Abstract:
We report on the novel observation about the gain in mechanical stability of the SARS-CoV-2 (CoV2) spike (S) protein in comparison with SARS-CoV from 2002 (CoV1). Our findings have several biological implications in the subfamily of coronaviruses, as they suggest that the receptor binding domain (RBD) (~200 amino acids) plays a fundamental role as a damping element of the massive viral particle's motion prior to cell-recognition, while also facilitating viral attachment, fusion and entry. The mechanical stability via pulling of the RBD is 250 pN and 200 pN for CoV2 and CoV1 respectively, and the additional stability observed for CoV2 (~50 pN) might play a role in the increasing spread of COVID-19.

Affiliations:
Moreira R. - IPPT PAN
Chwastyk M. - Institute of Physics, Polish Academy of Sciences (PL)
Baker J.L. - other affiliation
Vargas Guzman H.A. - Max-Planck-Institute for Polymer Research (DE)
Poma A. - IPPT PAN
3.  Braga L.S., Azevedo Moreira R., Soares Leal D.H., Ramalho T.C., Quantification of molecular orbitals based on projection operators: methodological development and applications to basicity prediction of organic compounds in the gas phase, Chemical Physics Letters, ISSN: 0009-2614, DOI: 10.1016/j.cplett.2019.04.023, Vol.726, pp.87-92, 2019

Abstract:
Basicity is an important parameter with impact on biological systems and technological problems. The HOMO-LUMO and FERMO theoretical approaches can describe the acid-base behavior of compounds as amines, carboxylic acids and alcohols. In this work, a method was developed using the localization degree ГFERMO parameter based on projection operators to quantify the localization of molecular orbitals. This new method was employed for the analysis of the protonation reaction of 30 organic compounds. The quantitative data from our findings were able to reproduce experimental data, pointing out that the FERMO approach could better describe the acid-base behavior of the investigated compounds.

Keywords:
molecular orbital, HOMO-LUMO, FERMO, Acid-base behaviour, Localization degree, ГFERMO

Affiliations:
Braga L.S. - Federal University of Lavras (BR)
Azevedo Moreira R. - other affiliation
Soares Leal D.H. - Federal University of Espirito Santo (BR)
Ramalho T.C. - Federal University of Lavras (BR)
4.  Azevedo Moreira R., Energy Gaps of Polyradicals from an Effective and Transferable Hamiltonian with through-Bond Interactions, Journal of Chemical Theory and Computation, ISSN: 1549-9618, DOI: 10.1021/acs.jctc.7b00930, Vol.14, No.1, pp.1-8, 2018

Abstract:
Current model Hamiltonians and ab initio manybody quantum treatments of π-conjugated polyradicals formed from hydrocarbons produce divergent results because of numerical complexity and large size of the basis-function set used. We propose an alternative, three-term Hamiltonian, to describe these various polyradicals that simplifies considerably the computational cost while providing a physical interpretation for all three terms and a high degree of model universality. The essential feature of this Hamiltonian is a term, not present in previous models, describing the three-sited through-bond interaction that governs the noninteracting spin-up and spin-down sectors. A computation of the lowest energy gaps and spin configurations for the smaller polyradicals demonstrates the efficacy of the model and its potential in applications in revealing electrical conductivity and ferromagnetism of the more complicated substituted polyradicals.

Affiliations:
Azevedo Moreira R. - other affiliation
5.  Azevedo Moreira R., de Melo C.P., Entanglement and Electronic Correlation in Polycyclic Aromatic Molecules, Brazilian Journal of Physics, ISSN: 0103-9733, DOI: 10.1007/s13538-017-0535-7, Vol.47, No.6, pp.575-582, 2017

Abstract:
Based on the diagonalization of an effective Hamiltonian, we investigate the role of electronic correlation on the aromatic behavior of polycyclic aromatic hydrocarbons (PAHs). We show that for benzene and several examples of PAHs, a singular change in the electronic distribution happens at a relatively narrow range of the Coulomb interaction strength; in each case, the CC bond distribution pattern agrees with the known chemical behavior of the corresponding compound. We explore the link between electronic correlation and information entropy and show that several signatures of fluctuations in the one-particle entropy occur at the same range of values of the Coulomb parameter that correspond to a realistic bond-order distribution of the PAHs. These results indicate that the singular stability of the electronic distribution of aromatic compounds is associated with an optimum range of correlation effects, which can be understood in terms of the entanglement of the two sub-lattices of alternating carbon atoms and the presence of a localization transition of the overall electronic density.

Keywords:
Aromatic compounds, Model Hamiltonian, Exact diagonalization, Electronic correlation, Information entropy

Affiliations:
Azevedo Moreira R. - other affiliation
de Melo C.P. - Universidade Federal de Pernambuco (BR)
6.  Azevedo Moreira R., de Melo C.P., On the separability of the extended molecule: Constructing the best localized molecular orbitals for an organic molecule bridging two model electrodes, JOURNAL OF CHEMICAL PHYSICS, ISSN: 0021-9606, DOI: 10.1063/1.4894845, Vol.141, pp.124712-1-10, 2014

Abstract:
Based on a quantum chemical valence formalism that allows the rigorous construction of best-localized molecular orbitals on specific parts of an extended system, we examined the separability of individual components of model systems relevant to the description of electron transport in molecular devices. We started by examining how to construct the maximally localized electronic density at the tip of a realistic model of a gold electrode. By varying the number of gold atoms included in the local region where to project the total electronic density, we quantitatively assess how many molecular orbitals are entirely localized in that region. We then considered a 1,4-benzene-di-thiol molecule connected to two model gold electrodes and examined how to localize the electronic density of the total system in the extended molecule, a fractional entity comprising the organic molecule plus an increasing number of the closest metal atoms. We were able to identify in a rigorous manner the existence of three physically different electronic populations, each one corresponding to a distinct set of molecular orbitals. First, there are those entirely localized in the extended molecule, then there is a second group of those completely distributed in the gold atoms external to that region, and, finally, there are those delocalized over the entire system. This latter group can be associated to the shared electronic population between the extended molecule and the rest of the system. We suggest that the treatment here presented could be useful in the theoretical analysis of the electronic transport in nanodevices whenever the use of localized molecular states are required by the physics of the specific problem, such as in cases of weak coupling and super-exchange limits.

Affiliations:
Azevedo Moreira R. - other affiliation
de Melo C.P. - Universidade Federal de Pernambuco (BR)

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