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The spike protein of SARS-CoV-2 is critical to viral infection of host cells which ultimately results in COVID-19. In this study we analyze the behavior of dihedral (phi and psi) angles of the spike protein over time from molecular dynamics and identify that the oscillations of these dihedral angles are dominated by a few discrete, relatively low frequencies in the 23-63 MHz range with 42.96875 MHz being the most prevalent frequency sampled by the oscillations. We further observe that upon tallying the populations of each individual frequency for all residues along the frequency spectrum, there is a regular alternation between high and low population counts along the increasing frequency values in the spectrum. This alternation of the counts becomes less pronounced and ultimately stabilizes as the frequency values increase. These observations thus suggest a regularity and propensity in the spike protein’s dihedral angles to avoid similar oscillation population counts between vicinal frequencies. We also observe that for amino acids that are least abundant in the S protein, there are certain frequencies at which the dihedral angles never oscillate, in contrast to relatively abundant amino acids that ultimately cover the entire spectrum. This suggests that the frequency components of dihedral angle oscillations may also be a function of position in the primary structure: the more positions an amino acid is found in, the more frequencies it can sample. Lastly, certain residues identified in the literature as constituting the inside of a druggable pocket of the spike protein, as well as other residues identified as allosteric sites, are observed in our data to have distinctive time domain profiles. This motivates us to propose residues from our dynamic data, with similar time domain profiles, which may be of potential interest to the vaccine and drug design communities, for further investigation. Thus our findings indicate that there is a particular frequency domain profile for the spike protein, hidden within the time domain data, and this information, perhaps with the suggested residues, might provide additional insight into therapeutic development strategies for COVID-19 and beyond.

Desde 1983, bajo el lema «Construyendo aquí y ahora el mundo que queremos», las ferias de consumo familiar constituyen una de las instancias de funcionamiento del Organismo de Integración Cooperativa Cecosesola, Central Cooperativa Regional (CCR), asociada a la Central Cooperativa Nacional de Venezuela (Ceconave).Sus 550 trabajadores–asociados– son el centro operativo de una cadena agroalimentaria, conformada en red que integra aguas arriba unos 600 proveedores de hortalizas frescas y víveres de varios estados del país que, abastecen el 40% de la población de Barquisimeto, unas 100.000familias beneficiarias. Sus precios son menores en un 50% en promedio al de los supermercados privados, gracias a una institucionalidad tejida desde lo cotidiano sobre criterios de confianza en y entre sus proveedores y los trabajadores-asociados. Como activista del cooperativismo impulsado por Ceconave y como académico, el autor conoce las Ferias desde antes de su puesta en marcha. Este artículo constituye una visión holística de Cecosesola y de sus Ferias, con forma de monografía descriptiva y analítica construida sobre visitas periódicas y entrevistas a los actores como fuentes primarias, y observaciones participantes fortalecidas con análisis de escritos de los propios actores, así como de consultores y otros investigadores interesados en esta experiencia.El documento se teje a partir de precisiones teóricas sobre el cooperativismo, el estado Lara como territorio base de las ferias y el surgimiento de una cultura participativa como eje transversal de Cecosesola y de las Ferias. En él se analiza la organización y funcionamiento autogestionario de estas últimas, su cadena de valor y el papel de sus actores, con énfasis en los criterios de comercio justo, las reuniones y decisiones consensuadas, los fondos como mecanismos de solidaridad y las ferias como mercado seguro para los productores. Finalmente reflexiona sobre la transformación cultural e institucional lograda y presenta un resumen de los impactos de las ferias a manera de balance social. Since 1983 and with the slogan «Building here and now the world we want», the family consumption fairs is one of the operating instances of the Organismo de Integración Cooperativa Cecosesola, a Regional Cooperative Center (CCR) associated with the Central Cooperativa Nacional de Venezuela (Central Cooperativa Nacional de Venezuela-Ceconave). Integrated by 550 workers-associates, they are the operational center of an agri-food chain that united in a network that integrates about 600 suppliers of fresh vegetables and food from several states of the country supplying 40% of the population of Barquisimeto, some 100,000 beneficiary families. Their prices are lower by 50% on average than private supermarkets, thanks to an institutional framework established on criteria of trust and other factors in and between its suppliers and its workers/associates. As an activist of the cooperativism promoted by Ceconave and as an academic, the author has known the Fairs before their constitution. This article in itself is based on a holistic vision of Cecosesola and its fairs. It is a descriptive and analytical monograph built on periodic visits and interviews with the actors as primary sources and participant observations strengthened with the analysis of the writings of the actors themselves, consultants, and other researchers interested in this experience. The document is grounded on theoretical considerations about cooperativism and the Lara State as the base territory of the fairs, and the emergence of participatory culture as a transversal axis of Cecosesola and the fairs. It analyzes the organization and their selfmanagement, their food value chains, as well the role of their actors, with emphasis on fair trade criteria, meetings and consensus decisions, funds as solidarity mechanisms, and fairs as a safe market for producers. Finally, a reflection on the cultural and institutional transformation achieved was carried out, and a summary of the impacts of the fairs as a social balance was presented. Depuis 1983, sous le slogan «Construire le monde que nous voulons ici et maintenant», les salons de la consommation familiale constituent l’une des instances opérationnelles de l’Organismo de IntegraciónCooperativa CECOSESOLA (anciennement Central Cooperativa de Servicios de Lara-Cecosesola, un centre coopératif régional - CCR), associé à la Central CooperativaNacional de Venezuela (CECONAVE). Ses 550 travailleurs –associés– constituent le centre opérationnel d’une chaîne agroalimentaire constituée d’un réseau, qui intègre en amont quelque 600 fournisseurs de légumes frais et d’aliments de divers États vénézuéliens qui approvisionnent environ 40 % de la population de Barquisimeto (capitale de Lara), avec quelque 100.000 familles bénéficiaires. Leurs prix sont inférieurs de 50 % en moyenne à ceux des supermarchés privés, grâce à un cadre institutionnel construit au quotidien, sur des critères de confiance dans et entre leurs fournisseurs et les salariés-associés. Militante du coopérativisme promu par la Ceconave et universitaire, l’auteur connaît les Foires bien avant leur lancement. Cet article est une vision holistique de CECOSESOLA et de ses Foires, de type descriptif et analytique, construite à partir de visites périodiques et d’entretiens avec les acteurs comme sources primaires, ainsi que d’observations participantes renforcées par l’analyse des écrits des acteurs eux-mêmes, ainsi que des consultants et autres chercheurs intéressés par une telle expérience. Le document est enrichi avec de détails théoriques sur le coopérativisme, l’État de Lara comme territoire de base des Foires et l’émergence d’une culture participative comme axe transversal de CECOSESOLA et de ses Foires. De même, il analyse l’organisation et l’autogestion de ceux-ci, leur chaîne de valeur et le rôle de leurs acteurs, en mettant l’accent sur les critères du commerce équitable, les rencontres et décisions consensuelles, les fonds comme mécanismes de solidarité, et les foires comme marché sûr pour les producteurs. Enfin, il présente uneréflexion sur la transformation culturelle et institutionnelle réalisée ainsi qu’une synthèse des principaux impacts des foires en tant qu’équilibre social. Desde 1983, sob o lema «Construindo aqui e agora o mundo que queremos», as feiras de consumo familiar constituem uma das instâncias de funcionamento do Organismo de Integração Cooperativa CECOSESOLA (anteriormente denominada Central Cooperativa de Serviços de Lara-Cecosesola, uma central cooperativa regional-CCR), associada à Central Cooperativa Nacional de Venezuela (CECONAVE). Seus 550 trabalhadores-associados constituem o centro operacional de uma cadeia agroalimentar conformada em rede, que integra águas acima, uns 600 fornecedores de hortaliças frescas e víveres de diferentes estados venezuelanos, os quais abastecem aproximadamente 40% da população de Barquisimeto (capital do estado Lara), com umas 100.000 famílias beneficiárias. Os preços praticados são 50% inferiores aos dos supermercados privados, graças a uma institucionalidade construída a partir do cotidiano e de critérios de confiança estabelecidos entre os fornecedores e os trabalhadores associados. Como ativista do cooperativismo impulsionado por Ceconave e como acadêmico, o autor conhece as Feiras desde antes de sua posta em marcha. Este artigo adota uma visão holística e de tipo descritivo e analítico de Cecosesola e de suas feiras, a qual é construída, enquanto fonte primária de informação, a partir de visitas periódicas e entrevistas junto a atores, ademais de observação participante acrescidas de análises escritas elaboradas pelos próprios atores, bem como de consultores e outros pesquisadores interessados nesta experiência. O documento é tecido a partir de aprofundamento sobre a questão do cooperativismo, do estado de Lara enquanto território base das Feiras e do surgimento de uma cultura participativa como eixo transversal de Cecosesola e de suas Feiras. Além disso, analisa a organização e seu funcionamento autogestionado, incluindo as particularidades desta cadeia de valor, o papel de seus atores, com ênfase nos critérios de comércio justo, as reuniões e decisões e seus consensos, os fundos como mecanismos de solidariedade, bem como o papel das feiras como mercado seguro para os produtores. Por fim, propõe uma reflexão sobre a transformação cultural e institucional lograda, bem como um resumo dos principais impactos das feiras à guisa de oferecer um balanço social. 55-80 agroalimentaria@ula.ve / ciaal.ula@gmail.com oscarbastidas@unete.com.ve Semestral http://erevistas.saber.ula.ve/agroalimentaria

Monitoring and strategic response to variants in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) represent a considerable challenge in the current pandemic and for future viral outbreaks. Mutations/deletions of the virion’s prefusion Spike protein may have significant impact on vaccines and therapeutics that utilize this key structural protein in their mitigation strategies. In this study, we have demonstrated how dominant energetic landscape mappings (“glue points”) based on ab inito all-atom force fields coupled with phylogenetic sequence alignment information can identify key residue mutations and deletions associated with variants. We also found several examples of excellent homology of stabilizing residue glue points across the lineages of betacoronavirus Spike proteins that we have called “sequence homologous glue points.” SARS-CoV-2 demonstrates the least number of stabilizing glue points associated with interchain interactions among Down-state protomers across lineages. Additionally, we computationally studied variants among the trimeric Spike protein of SARS-CoV-2 using all-atom molecular dynamics to ascertain structural and energetic changes among variants. We examined both a theoretically based triple mutant and the UK or B.1.1.7 variant. For the theoretical triple mutant, we demonstrated through alanine substitutions that three key residues could cause the transition of Down-to-Up protomer states, where the transition is characterized by the “arm” length of the receptor-binding domain (RBD) rather than the hinge angle. For the B.1.1.7 variant, we demonstrated the critical importance of mutations D614G and N501Y on the structure and binding, respectively, of the Spike protein. We note that these same two key mutations are also found in the South African B.1.351 variant. IMPORTANCE Viral variants represent a major challenge to monitoring viral outbreaks and formulating strategic health care responses. Variants represent transmitting viruses that have specific mutations and deletions associated with their genome. In the case of SARS-CoV-2 and other related viruses (betacoronaviruses), many of these mutations and deletions are associated with the Spike protein that the virus uses to infect cells. Here, we have analyzed both SARS-CoV-2 variants and related viruses, such as Middle Eastern respiratory syndrome coronavirus (MERS-CoV), in order to understand not only differences, but also key similarities between them. Understanding similarities can be as important as differences in determining key functional features of a class of viruses, such as the betacoronaviruses. We have used both phylogenetic analysis, which traces genetic similarities and differences, along with independent biophysics analysis, which adds function or behavior, in order to determine possible functional differences and hence possible transmission and infection differences among variants and lineages.

Monitoring and strategic response to variants in SARS-CoV-2 represents a considerable challenge in the current pandemic, as well as potentially future viral outbreaks of similar magnitude. In particular mutations and deletions involving the virion’s prefusion Spike protein have significant potential impact on vaccines and therapeutics that utilize this key structural viral protein in their mitigation strategies. In this study, we have demonstrated how dominant energetic landscape mappings (“glue points”) coupled with sequence alignment information can potentially identify or flag key residue mutations and deletions associated with variants. Surprisingly, we also found excellent homology of stabilizing residue glue points across the lineage of β coronavirus Spike proteins, and we have termed this as “sequence homologous glue points”. In general, these flagged residue mutations and/or deletions are then computationally studied in detail using all-atom biocomputational molecular dynamics over approximately one microsecond in order to ascertain structural and energetic changes in the Spike protein associated variants. Specifically, we examined both a theoretically-based triple mutant and the so-called UK or B.1.1.7 variant. For the theoretical triple mutant, we demonstrated through Alanine mutations, which help “unglue” key residue-residue interactions, that these three key stabilizing residues could cause the transition of Down to Up protomer states, where the Up protomer state allows binding of the prefusion Spike protein to hACE2 host cell receptors, whereas the Down state is believed inaccessible. Thus, we are able to demonstrate the importance of glue point residue identification in the overall stability of the prefusion Spike protein. For the B.1.1.7 variant, we demonstrated the critical importance of D614G and N5017 on the structure and binding, respectively, of the Spike protein. Notably, we had previously identified D614 as a key glue point in the inter-protomer stabilization of the Spike protein prior to the emergence of its mutation. The mutant D614G is a structure breaking Glycine mutation demonstrating a relatively more distal Down state RBD and a more stable conformation in general. In addition, we demonstrate that the mutation N501Y may significantly increase the Spike protein binding to hACE2 cell receptors through its interaction with Y41 of hACE2 forming a potentially strong hydrophobic residue binding pair. We note that these two key mutations, D614G and N501Y, are also found in the so-called South African (SA; B.1.351) variant of SARS-CoV-2. Future studies along these lines are, therefore, aimed at mapping glue points to residue mutations and deletions of associated prefusion Spike protein variants in order to help identify and analyze possible “variants of interest” and optimize efforts aimed at the mitigation of this current and future virions.

The SARS-CoV-2 virion responsible for the current world-wide pandemic COVID-19 has a characteristic Spike protein (S) on its surface that embellishes both a prefusion state and fusion state. The prefusion Spike protein (S) is a large trimeric protein where each protomer may be in a so-called Up state or Down state, depending on the configuration of its receptor binding domain (RBD) within its distal, prefusion S1 domain. The Up state is believed to allow binding of the virion to ACE-2 receptors on human epithelial cells, whereas the Down state is believed to be relatively inactive or reduced in its binding behavior. We have performed detailed all-atom, dominant energy landscape mappings for noncovalent interactions (charge, partial charge, and van der Waals) of the SARS-CoV-2 Spike protein in its static prefusion state based on two recent and independent experimental structure publications. We included both interchain interactions and intrachain (domain) interactions in our mappings in order to determine any telling differences (different so-called “glue” points) between residues in the Up and Down state protomers. The S2 proximal, fusion domain demonstrated no appreciable energetic differences between Up and Down protomers, including interchain as well as each protomer’s intrachain, S1-S2 interactions. However, the S1 domain interactions across neighboring protomers, which include the RBD-NTD cross chain interactions, showed significant energetic differences between Up-Down and Down-Down neighboring protomers. This included, for example, a key RBD residue ARG357 in the Up-Down interaction and a three residue sequence ALA520-PRO521-ALA522, associated with a turn structure in the RBD of the Up state protomer, acting as a stabilizing interaction with the NTD of its neighbor protomer. Additionally, our intra chain dominant energy mappings within each protomer, identified a significant “glue” point or possible “latch” for the Down state protomer between the S1 subdomain, SD1, and the RBD domain of the same protomer that was completely missing in the Up state protomer analysis. Ironically, this dominant energetic interaction in the Down state protomer involved the backbone atoms of the same three residue sequence ALA520-PRO521-ALA522 of the RBD with the amino acid R-group of GLN564 in the SD1 domain. Thus, this same three residue sequence acts as a stabilizer of the RBD in the Up conformation through its interactions with its neighboring NTD chain and a kind of latch in the Down state conformation through its interactions with its own SD1 domain. The dominant interaction energy residues identified here are also conserved across reported variations of SARS-CoV-2, as well as the closely related virions SARS-Cov and the bat corona virus RatG13. We conducted preliminary molecular dynamics simulations across 0.1 μ seconds to see if this latch provided structural stability and indeed found that a single point mutation (Q564G) resulted in the latch releasing transforming the protomer from the Down to the Up state conformation. Full trimeric Spike protein studies of the same mutation across all protomers, however, did not exhibit latch release demonstrating the critical importance of interchain interactions across the S1 domain, including RBD-NTD neighboring chain interactions. Therapies aimed at disrupting these noncovalent interactions could be a viable route for the physico-chemical mitigation of this deadly virion.

The SARS-Cov-2 virion responsible for the current world-wide pandemic Covid-19 has a characteristic Spike protein (S) on its surface that embellishes both a prefusion state and fusion state. The prefusion Spike protein (S) is a large trimeric protein where each protomer may be in a so-called Up state or Down state, depending on the configuration of its receptor binding domain (RBD). The Up state is believed to allow binding of the virion to ACE-2 receptors on human epithelial cells, whereas the Down state is believed to be relatively inactive or reduced in its binding behavior. We have performed detailed all-atom, dominant energy landscape mappings for noncovalent interactions (charge, partial charge, and van der Waals) of the SARS-Cov-2 Spike protein in its static prefusion state based on recent structural information. We included both interchain interactions and intrachain (domain) interactions in our mappings in order to determine any telling differences (different so-called “glue” points) between residues in the Up and Down state protomers. In general, the S2 or fusion machinery domain of S is relatively rigid with strong noncovalent interactions facilitated by helical secondary structures, whereas the S1 domain, which contains the RBD and N-terminal domain (NTD), is relatively more flexible and characterized by beta strand structural motifs. The S2 domain demonstrated no appreciable energetic differences between Up and Down protomers, including interchain as well as each protomer’s intrachain, S1-S2 interactions. However, the S1 domain interactions across neighboring protomers, which include the RBD-NTD cross chain interactions, showed significant energetic differences between Up-Down and Down-Down neighboring protomers. Surprisingly, the Up-Down, RBD-NTD interactions were overall stronger and more numerous than the Down-Down cross chain interactions, including the appearance of the three residue sequence ALA520-PRO521-ALA522 associated with a turn structure in the RBD of the Up state protomer. Additionally, our intrachain dominant energy mappings within each protomer, identified a significant “glue” point or possible “latch” for the Down state protomer between the S1 subdomain, SD1, and the RBD domain of the same protomer that was completely missing in the Up state protomer analysis. Ironically, this dominant energetic interaction in the Down state protomer involved the backbone atoms of the same three residue sequence ALA520-PRO521-ALA522 of the RBD with the R-group of GLN564 in the SD1 domain. Thus, this same three residue sequence acts as a stabilizer of the RBD in the Up conformation through its interactions with its neighboring NTD chain and a kind of latch in the Down state conformation through its interactions with its own SD1 domain. The dominant interaction energy residues identified here are also conserved across reported variations of SARS-Cov-2, as well as the closely related virions SARS-Cov and the bat corona virus RatG13. To help verify the potential latch for the Down state protomer, we conducted some preliminary molecular dynamic simulations that effectively turn off this specific latch glue point via a single point mutation of GLN564. Interestingly, the single point mutation lead to the latch releasing in less than a few nanoseconds, but the latch remained fixed in the wild state protomer for up to 0.1 microseconds that were simulated. Many more detailed studies are needed to understand the dynamics of the Up and Down states of the Spike protein, including the stabilizing chain-chain interactions and the mechanisms of transition from Down to Up state protomers. Nonetheless, static dominant energy landscape mappings and preliminary molecular dynamic studies given here may represent a useful starting point for more detailed dynamic analyses and hopefully an improved understanding of the structure-function relationship of this highly complex protein associated with COVID-19.