A forensic analysis of SARS-CoV-2 cases and COVID-19 mortality misreporting in the Brazilian population.

OBJECTIVE: The study aimed to investigate the misreporting number of positively tested individuals for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) succumbed or not to coronavirus disease 2019 (COVID-19) pandemic in Brazil at the city, state, and national scales using statistical forensic analysis. STUDY DESIGN: This is a register-based study over public health data collected, organized, and maintained by the Ministry of Health covering the Brazilian population. METHODS: We evaluated the Brazilian notifications of positively tested cases for SARS-CoV-2 who have succumbed or not to COVID-19 between February 26th to September 7th of 2020 at the city, state, and national scales for conformity to expected distribution provided by Benford's law (BL). RESULTS: Statistical analyzes demonstrated a significant rejection of SARS-CoV-2 notification cases at the city and the number of deaths by COVID-19 in all regional levels according to the hypothesis of conformity to BL. CONCLUSION: We demonstrated by BL, which has been widely applied to query the quality and reliability of different numerical data sources, the misreporting number of cases and deaths throughout the SARS-CoV-2 pandemic in Brazil. Therefore, we brought to light pieces of evidence that raise questions about the reliability of SARS-CoV-2 data in Brazil. This situation may have led to inconsistencies in public health policy actions, recommendations, and drastic humanitarian, social, and economic consequences such as the intensive unit care overload in some Brazilian regions.

Interaction of cyclic and linear Labaditin peptides with anionic and zwitterionic micelles.

Conformational changes of the cyclic (Lo) peptide Labaditin (VWTVWGTIAG) and its linear analogue (L1) promoted by presence of anionic sodium dodecyl sulfate (SDS) and zwitterionic L-α-Lysophosphatidylcholine (LPC) micelles were investigated. Results from λ(max) blue-shift of tryptophan fluorescence emission combined with Stern-Volmer constants values and molecular dynamics (MD) simulations indicated that L1 interacts with SDS micelles to a higher extent than does Lo. Further, the MD simulation demonstrated that both Lo and L1 interact similarly with LPC micelles, being preferentially located at the micelle/water interface. The peptide-micelle interaction elicits conformational changes in the peptides. Lo undergoes limited modifications and presents unordered structure in both LPC and SDS micelles. On the other hand, L1 displays a random-coil structure in aqueous medium, pH 7.0, and it acquires a ß-structure upon interaction with SDS and LPC, albeit with structural differences in each medium.

Structure and dynamics of the monomer of protein E of dengue virus type 2 with unprotonated histidine residues.

The surface of the dengue virus is composed of 180 copies of a multifunctional envelope glycoprotein that acts at several stages of viral infection. When the virus is in the endosome, these glycoproteins undergo major conformational rearrangements owing to the protonation of histidine side chains. This protonation allows for the formation of trimers, thereby triggering fusion between the viral and the host membranes. In this study, we examined the behavior of a monomer of this key protein containing unprotonated histidine side chains before the stage of trimer formation using explicit solvent molecular dynamics at various ionic strengths. The extended secondary structures, which contribute to protein stabilization, are smaller than those observed in a previous study involving monomers containing the protonated histidine. However, the structure of the monomer investigated herein is extremely stable under ionic strengths ranging from 0 to 225 mM. The results show that a protein surface frozen owing to interactions between charged groups is mainly responsible for this stabilization. Thus, focusing on binding sites and ligands that destabilize these properties can aid the search for dengue virus inhibitors.

Study of the antimicrobial peptide indolicidin and a mutant in micelle medium by molecular dynamics simulation.

The antimicrobial peptide indolicidin (IND) and the mutant CP10A in hydrated micelles were studied using molecular dynamics simulations in order to observe whether the molecular dynamics and experimental data could be sufficiently correlated and a detailed description of the interaction of the antimicrobial peptides with a model of the membrane provided by a hydrated micelle system could be obtained. In agreement with the experiments, the simulations showed that the peptides are located near the surface of the micelles. Peptide insertions agree with available experimental data, showing deeper insertion of the mutant compared with the peptide IND. Major insertion into the hydrophobic core of the micelle by all tryptophan and mutated residues of CP10A in relation to IND was observed. The charged residues of the terminus regions of both peptides present similar behavior, indicating that the major differences in the interactions with the micelles of the peptides IND and CP10A occur in the case of the hydrophobic residues.

The role of disulfide bridges in the 3-D structures of the antimicrobial peptides gomesin and protegrin-1: a molecular dynamics study.

Some antimicrobial peptides have a broad spectrum of action against many different kinds of microorganisms. Gomesin and protegrin-1 are examples of such antimicrobial peptides, and they were studied by molecular dynamics in this research. Both have a beta-hairpin conformation stabilized by two disulfide bridges and are active against gram-positive and gram-negative bacteria, as well as fungi. In this study, the role of the disulfide bridge in the maintenance of the tertiary peptide structure of protegrin-1 and gomesin is analyzed by the structural characteristics of these peptides and two of their respective variants, gomy4 and proty4, in which the four cysteines are replaced by four tyrosine residues. The absence of disulfide bridges in gomy4 and proty4 is compensated by overall reinforcement of the original hydrogen bonds and extra attractive interactions between the aromatic rings of the tyrosine residues. The net effects on the variants with respect to the corresponding natural peptides are: i) maintenance of the original beta-hairpin conformation, with great structural similarities between the mutant and the corresponding natural peptide; ii) combination of positive Phi and Psi Ramachandran angles within the hairpin head region with a qualitative change to a combination of positive (Phi) and negative (Psi) angles, and iii) significant increase in structural flexibility. Experimental facts about the antimicrobial activity of the gomesin and protegrin-1 variants have also been established here, in the hope that the detailed data provided in the present study may be useful for understanding the mechanism of action of these peptides.

Recognition of alpha-helix transmembrane domains with an amphipathy scale generated by molecular dynamics using only the primary sequence of proteins.

We recently developed an amphipathy scale, elaborated from molecular dynamics data that can be used for the identification of hydrophobic or hydrophilic regions in proteins. This amphipathy scale reflects side chain/water molecule interaction energies. We have now used this amphipathy scale to find candidates for transmembrane segments, by examining a large sample of membrane proteins with alpha-helix segments. The candidates were selected based on an amphipathy coefficient value range and the minimum number of residues in a segment. We compared our results with the transmembrane segments previously identified in the PDB_TM database by the TMDET algorithm. We expected that the hydrophobic segments would be identified using only the primary structures of the proteins and the amphipathy scale. However, some of these hydrophobic segments may pertain to hydrophobic pockets not included in transmembrane regions. We found that our amphipathy scale could identify alpha-helix transmembrane regions with a probability of success of 76% when all segments were included and 90% when all membrane proteins were included.

Recognition of alpha-helix transmembrane domains with an amphipathy scale generated by molecular dynamics using only the primary sequence of proteins

We recently developed an amphipathy scale, elaborated from molecular dynamics data that can be used for the identification of hydrophobic or hydrophilic regions in proteins. This amphipathy scale reflects side chain/water molecule interaction energies. We have now used this amphipathy scale to find candidates for transmembrane segments, by examining a large sample of membrane proteins with alpha-helix segments. The candidates were selected based on an amphipathy coefficient value range and the minimum number of residues in a segment. We compared our results with the transmembrane segments previously identified in the PDB_TM database by the TMDET algorithm. We expected that the hydrophobic segments would be identified using only the primary structures of the proteins and the amphipathy scale. However, some of these hydrophobic segments may pertain to hydrophobic pockets not included in transmembrane regions. We found that our amphipathy scale could identify alpha-helix transmembrane regions with a probability of success of 76% when all segments were included and 90% when all membrane proteins were included.

A new amphipathy scale I. Determination of the scale from molecular dynamics data.

Two new amphipathy scales elaborated from molecular dynamics data are presented. Their applications contribute for the identification of the hydrophobic or hydrophilic regions in proteins solely from the primary structure. The new amphipathy coefficients (AC) reflect the side chain/solvent molecules configurational energies. A polar (water) and an apolar solvent, CCl4, were used resulting in the two ACwater and ACCCl4 scales. These solvents were chosen to simulate the aqueous phases and the transmembrane ambients of cellular membranes where the membrane proteins act. The new amphipathy scales were compared with some previous scales determined by different methods, which were also compared between them, indicating more than 90% of the correlation coefficients are less than 0.9: the scales are strictly dependent on the methodologies used in their determination. The ACCCl4 scale is related with the size of side chain amino acids while ACwater is related with the hydrophobicity of side chain amino acids. The quality of the scales was confirmed by an example of application where ACwater was able to identify correctly the transmembrane, hydrophobic regions of a membrane protein. These results also indicate that water is an important factor responsible for the tertiary structure of membrane proteins.