Local energetic frustration conservation in protein families and superfamilies.

Energetic local frustration offers a biophysical perspective to interpret the effects of sequence variability on protein families. Here we present a methodology to analyze local frustration patterns within protein families and superfamilies that allows us to uncover constraints related to stability and function, and identify differential frustration patterns in families with a common ancestry. We analyze these signals in very well studied protein families such as PDZ, SH3, ɑ and ß globins and RAS families. Recent advances in protein structure prediction make it possible to analyze a vast majority of the protein space. An automatic and unsupervised proteome-wide analysis on the SARS-CoV-2 virus demonstrates the potential of our approach to enhance our understanding of the natural phenotypic diversity of protein families beyond single protein instances. We apply our method to modify biophysical properties of natural proteins based on their family properties, as well as perform unsupervised analysis of large datasets to shed light on the physicochemical signatures of poorly characterized proteins such as the ones belonging to emergent pathogens.

Assessing the accuracy of contact and distance predictions in CASP14.

We present the results of the assessment of the intramolecular residue-residue contact and distance predictions from groups participating in the 14th round of the CASP experiment. The performance of contact prediction methods was evaluated with the measures used in previous CASPs, while distance predictions were assessed based on a new protocol, which considers individual distance pairs as well as the whole predicted distance matrix, using a graph-based framework. The results of the evaluation indicate that predictions by the tFold framework, TripletRes and DeepPotential were the most accurate in both categories. With regards to progress in method performance, the results of the assessment in contact prediction did not reveal any discernible difference when compared to CASP13. Arguably, this could be due to CASP14 FM targets being more challenging than ever before.

Trivial and nontrivial error sources account for misidentification of protein partners in mutual information approaches.

The problem of finding the correct set of partners for a given pair of interacting protein families based on multi-sequence alignments (MSAs) has received great attention over the years. Recently, the native contacts of two interacting proteins were shown to store the strongest mutual information (MI) signal to discriminate MSA concatenations with the largest fraction of correct pairings. Although that signal might be of practical relevance in the search for an effective heuristic to solve the problem, the number of MSA concatenations with near-native MI is large, imposing severe limitations. Here, a Genetic Algorithm that explores possible MSA concatenations according to a MI maximization criteria is shown to find degenerate solutions with two error sources, arising from mismatches among (i) similar and (ii) non-similar sequences. If mistakes made among similar sequences are disregarded, type-(i) solutions are found to resolve correct pairings at best true positive (TP) rates of 70%-far above the very same estimates in type-(ii) solutions. A machine learning classification algorithm helps to show further that differences between optimized solutions based on TP rates are not artificial and may have biological meaning associated with the three-dimensional distribution of the MI signal. Type-(i) solutions may therefore correspond to reliable results for predictive purposes, found here to be more likely obtained via MI maximization across protein systems having a minimum critical number of amino acid contacts on their interaction surfaces (N > 200).

Unraveling the molecular basis of host cell receptor usage in SARS-CoV-2 and other human pathogenic ß-CoVs.

The recent emergence of the novel SARS-CoV-2 in China and its rapid spread in the human population has led to a public health crisis worldwide. Like in SARS-CoV, horseshoe bats currently represent the most likely candidate animal source for SARS-CoV-2. Yet, the specific mechanisms of cross-species transmission and adaptation to the human host remain unknown. Here we show that the unsupervised analysis of conservation patterns across the ß-CoV spike protein family, using sequence information alone, can provide valuable insights on the molecular basis of the specificity of ß-CoVs to different host cell receptors. More precisely, our results indicate that host cell receptor usage is encoded in the amino acid sequences of different CoV spike proteins in the form of a set of specificity determining positions (SDPs). Furthermore, by integrating structural data, in silico mutagenesis and coevolution analysis we could elucidate the role of SDPs in mediating ACE2 binding across the Sarbecovirus lineage, either by engaging the receptor through direct intermolecular interactions or by affecting the local environment of the receptor binding motif. Finally, by the analysis of coevolving mutations across a paired MSA we were able to identify key intermolecular contacts occurring at the spike-ACE2 interface. These results show that effective mining of the evolutionary records held in the sequence of the spike protein family can help tracing the molecular mechanisms behind the evolution and host-receptor adaptation of circulating and future novel ß-CoVs.

Impacto psicossocial do isolamento durante pandemia de covid-19 na população brasileira: análise transversal preliminar / Psychosocial impact of COVID-19 self-isolation on the Brazilian population: a preliminary cross-sectional analysis

Resumo Este artigo trata de uma pesquisa quantitativa, descritiva e analítica da população brasileira em isolamento social (IS) durante pandemia do novo coronavírus, com o objetivo de identificar preditores de estresse psicossocial com dados recolhidos por questionário on-line nas redes sociais em abril de 2020. Do total de 3.836 pessoas participantes, prevaleceram: mulheres (2.821; 73,5%); faixa etária de 30 a 39 anos (1.101; 28,7%); com pós-graduação (2075;54,1%); estando em IS (3.447; 89,9%). Houve diferença significativa pelo fato de as pessoas estarem em IS: sentir medo de serem infectadas pelo coronavírus (p<0,001); preocupação se alguém precisava sair de casa (p<0,001); rotina modificada após o IS, destacando "entretanto conseguiram se adaptar à nova realidade", comparado aos que "tiveram a rotina alterada sem conseguir se adaptar" (p<0,001); tristeza ou preocupação, fazendo outras atividades como exercício físico, práticas religiosas, atividades lúdicas (p<0,001); e não pensaram numa solução para esse problema (p<0,001); além de mudança no padrão de sono (p=0,006). Os achados revelam a necessidade de discussão ampliada dos determinantes sociais da saúde, que devem envolver não só a doença, mas levar em consideração as relações sociais, as manifestações culturais e a economia, que podem impactar a saúde mental das pessoas.

Abstract This is a quantitative, descriptive, and analytical study of the Brazilian population in social isolation (SI) during the novel coronavirus pandemic whose aim was to identify predictive factors for psychosocial stress using data collected by a social media-based online questionnaire administered in April 2020. Among the 3,836 participants, most were women (2,821; 73.5%), aged from 30 to 39 years (1,101; 28.7%), with post-graduate education (2,075;54.1%), and in SI (3,447; 89.9%). We found significant differences between individuals who were in SI and those who were not regarding: feeling afraid of being infected by the coronavirus (p<0.001) and worried if someone had to leave the house (p<0.001); changes in routine after self-isolating in those who managed to adapt to the new reality compared to those who could not adapt (p<0.001); feeling sad and worried while doing other activities, such as physical exercise, religious practices, or recreational activities (p<0.001); inability to imagine a solution to this problem (p<0.001), and changes in sleep pattern (p=0.006). Our findings indicate the need for further discussions about the social determinants of health, addressing not only the disease per se, but also social relations, cultural manifestations, and the economy, which may impact people's mental health.

Perfil do serviço de terapia periodontal básica na estratégia saúde da família / Profile of the periodontal basic therapy service in the health care strategy

O presente estudo objetivou analisar o perfil do Serviço de Terapia Periodontal Básica (TPB) na Estratégia Saúde da Família (ESF) da Microrregião de Saúde de Acaraú, Ceará, Brasil. Baseado em informações colhidas através de questionário semi-estruturado junto aos Cirurgiões-Dentistas (CDs) das ESF que lá atuam. A maioria dos profissionais relatou realizar o diagnóstico dos pacientes com necessidade de TPB através de exame clínico e sondagem, informação controversa ao verificar-se que 87,5% dos CDS relatam a falta de materiais e instrumentais específicos como sondas periodontais como fator que dificulta a conduta em TPB. As principais necessidades dos pacientes candidatos a TPB são controle de placa e cálculo dental, assim como as condutas de tratamento mais realizadas pelos CDs da ESF são raspagens e instrução de higiene oral. Os encaminhamentos ao Centro de Especialidades Odontológicas são nos casos de doença periodontal e necessidades de cirurgias periodontais. Com relação à capacitação, os CDs se interessaram, por treinamento sobre o uso de antibióticos em periodontia (84%), lesões gengivais não-induzidas por placa bacteriana (78%) e abscessos do periodonto (72%). Na conduta clínica, os profissionais relataram maior dificuldade na prescrição de medicamentos (53%). Na simulação dos casos clínicos, em sua maioria, os CDs demonstraram conhecimento teórico sobre diagnóstico, fatores etiológicos e tratamentos periodontais. (AU)

The aim of this study was to evaluate the profile of Basic Periodontal Therapy (BPT) at "Family Health Strategy (FHS)" in the Acaraú, state of Ceará, Brazil. It was based on the information collected from a questionnaire answered by the dentists that work in the FHS of that region. Most part of the professionals reported that the diagnosis of patients that need Basic Periodontal Therapy (BPT)is made through oral exam and probing. That information disagrees with the fact that 87,5% of the professionals reported lack of specific materials, such as periodontal probe, avoiding a proper diagnosis. The main needs of a patient with BPT are plaque and tartar control as well as dental scaling and oral hygiene instructions are the most common treatments. The patients are screened to "Center of Dental Specialties" when they present periodontal disease or when periodontal surgery are indicated. The dentists have interest on learning about antibiotics that are prescribed to patients with periodontal diseases (84%), gingival lesions that are not caused by bacterial plaque (78%) and abscesses (72%). The professionals also reported that they think is more difficult to prescribed drugs (53%). The dentists also answered questions about a fictitious case. The test revealed that they have more knowledge about diagnosis, etiology e periodontal treatments (AU)

Coevolutive, evolutive and stochastic information in protein-protein interactions.

Here, we investigate the contributions of coevolutive, evolutive and stochastic information in determining protein-protein interactions (PPIs) based on primary sequences of two interacting protein families A and B. Specifically, under the assumption that coevolutive information is imprinted on the interacting amino acids of two proteins in contrast to other (evolutive and stochastic) sources spread over their sequences, we dissect those contributions in terms of compensatory mutations at physically-coupled and uncoupled amino acids of A and B. We find that physically-coupled amino-acids at short range distances store the largest per-contact mutual information content, with a significant fraction of that content resulting from coevolutive sources alone. The information stored in coupled amino acids is shown further to discriminate multi-sequence alignments (MSAs) with the largest expectation fraction of PPI matches - a conclusion that holds against various definitions of intermolecular contacts and binding modes. When compared to the informational content resulting from evolution at long-range interactions, the mutual information in physically-coupled amino-acids is the strongest signal to distinguish PPIs derived from cospeciation and likely, the unique indication in case of molecular coevolution in independent genomes as the evolutive information must vanish for uncorrelated proteins.

Therapeutical effects of vaccine from Trypanosoma cruzi amastigote surface protein 2 by simultaneous inoculation with live parasites.

The aim of this study was to evaluate the efficacy of vaccine using replication-deficient human recombinant Type 5 replication-defective adenoviruses (AdHu5) carrying sequences of the amastigote surface protein 2 (ASP2) (AdASP2) in mice infected with the Trypanosoma cruzi ( T cruzi) Y strain. A total of 16 A/Sn mice female were distributed into four groups, as follows (n = 4 per group): Group 1 - Control Group (CTRL); Group 2 - Infected Group (TC): animals were infected by subcutaneous route with 150 bloodstream trypomastigotes of T cruzi Y strain; Group 3 - Immunized Group (AdASP-2): animals were immunized by intramuscular injection (im) route with 50 µL of AdSP-2 (2 × 10 8 plaque forming units [pfu]/cam) at day 0; Group 4-Immunized and Infected Group (AdASP-2+TC): animals were immunized by im route with 50 µL of ASP-2 (2 × 10 8 pfu/cam) and infected by T cruzi at the same day (day 0). It was observed a significant decrease of nests in the group that was immunized with AdASP-2 and infected on the same day. Tumor necrosis factor alpha (TNF-α) and inducible nitric oxide synthase (iNOS) gene expressions showed a significant increase in the AdASP-2+TC group when compared to TC group, but it was noted that Cyclooxygenase-2 (Cox-2) was increased in TC group when compared to AdASP-2+TC group. Increase of matrix metalloproteinases-2 (MMP-2) and decrease of MMP-9 immunoexpression in the AdASP-2+TC group was noticed as well. Oxidative DNA damage was present in myocardium for AdASP-2+TC group as a result of 8-hydroxydeoxyguanosine immunoexpression. Taken together, our results highlighted an increased oxidative stress, MMP-2 activity and inflammatory host response promoted by AdASP-2 against T cruzi infection.

Therapeutic effects of vaccine derived from amastigote surface protein-2 (ASP-2) against Chagas disease in mouse liver.

This study investigated the efficacy of the vaccine in liver of mice infected with the Trypanosoma cruzi (T. cruzi) and immunized with AdASP-2. For this purpose, histopathological analysis and gene expression of COX-2, TNF-alpha, TNFR, iNOS, cytochrome C, caspase-3, TLR4, IL-6 and IL10 were evaluated. The following groups were used in this study: Group 1 - Control Group (CTRL) animals received AdßGal vehicle; Group 2 - Infected Group (TC) animals were infected with T. cruzi; Group 3 - Immunized Group (AdASP-2): animals were immunized by AdASP-2 vaccine; Group 4 - Immunized and Infected Group (AdASP-2+TC) animals were infected with T. cruzi and immunized by AdSP-2 vaccine. A significant decrease of amastigote nests was noticed in the group of animals that were immunized with AdASP-2 and infected on the same day. COX-2 and TNF-alpha gene expressions increased in TC group, whereas TNF-alpha decreased in the TC+AdASP-2 group. TNFR expression was high in AdASP-2+TC group. iNOS expression was high for all experimental groups whereas cytochrome C decreased for all experimental groups. Caspase 3 increased in TC and TC+AdASP-2 groups. The gene expression of TLR4 and IL-10 showed an increase in AdASP-2+TC group. Finally, hepatic fibrosis was noticed to TC and AdASP-2 + TC groups. Taken together, our results demonstrated that vaccination with AdASP-2 was effective against the acute phase of experimental Chagas disease as a result of a more powerful and rapid immune response closely related to expression of some inflammatory genes, such as iNOS, TNF-alpha, TLR 4, and IL-10.

CD8(+) T cell-mediated immunity during Trypanosoma cruzi infection: a path for vaccine development?

MHC-restricted CD8(+) T cells are important during infection with the intracellular protozoan parasite Trypanosoma cruzi, the causative agent of Chagas disease. Experimental studies performed in the past 25 years have elucidated a number of features related to the immune response mediated by these T cells, which are important for establishing the parasite/host equilibrium leading to chronic infection. CD8(+) T cells are specific for highly immunodominant antigens expressed by members of the trans-sialidase family. After infection, their activation is delayed, and the cells display a high proliferative activity associated with high apoptotic rates. Although they participate in parasite control and elimination, they are unable to clear the infection due to their low fitness, allowing the parasite to establish the chronic phase when these cells then play an active role in the induction of heart immunopathology. Vaccination with a number of subunit recombinant vaccines aimed at eliciting specific CD8(+) T cells can reverse this path, thereby generating a productive immune response that will lead to the control of infection, reduction of symptoms, and reduction of disease transmission. Due to these attributes, activation of CD8(+) T lymphocytes may constitute a path for the development of a veterinarian or human vaccine.