Potential Autoimmunity Resulting from Molecular Mimicry between SARS-CoV-2 Spike and Human Proteins.

Molecular mimicry between viral antigens and host proteins can produce cross-reacting antibodies leading to autoimmunity. The coronavirus SARS-CoV-2 causes COVID-19, a disease curiously resulting in varied symptoms and outcomes, ranging from asymptomatic to fatal. Autoimmunity due to cross-reacting antibodies resulting from molecular mimicry between viral antigens and host proteins may provide an explanation. Thus, we computationally investigated molecular mimicry between SARS-CoV-2 Spike and known epitopes. We discovered molecular mimicry hotspots in Spike and highlight two examples with tentative high autoimmune potential and implications for understanding COVID-19 complications. We show that a TQLPP motif in Spike and thrombopoietin shares similar antibody binding properties. Antibodies cross-reacting with thrombopoietin may induce thrombocytopenia, a condition observed in COVID-19 patients. Another motif, ELDKY, is shared in multiple human proteins, such as PRKG1 involved in platelet activation and calcium regulation, and tropomyosin, which is linked to cardiac disease. Antibodies cross-reacting with PRKG1 and tropomyosin may cause known COVID-19 complications such as blood-clotting disorders and cardiac disease, respectively. Our findings illuminate COVID-19 pathogenesis and highlight the importance of considering autoimmune potential when developing therapeutic interventions to reduce adverse reactions.

An Easy Protocol for Evolutionary Analysis of Intrinsically Disordered Proteins.

We present an easy protocol for evolutionary analysis of proteins, with an emphasis on studying the evolutionary dynamics of disordered regions. Using the p53 protein family as an example, we provide a guide for finding homologous sequences in a database and refining a dataset before constructing the evolutionary context by building a phylogenetic tree. We show how a multiple sequence alignment and phylogeny for a protein family can be further partitioned into smaller datasets in order to investigate the changes in disorder content across the phylogeny. Based on the evolutionary context, we also investigate site-specific conservation of disorder. Last, we address how to evaluate the evolutionary dynamics of disorder-to-order transitions.

Exploring Evolutionary Constraints in the Proteomes of Zika, Dengue, and Other Flaviviruses to Find Fitness-Critical Sites.

Dengue virus (DENV) challenges vaccine design due to antibody-dependent enhancement (ADE) and evidence suggests that Zika virus (ZIKV) experiences ADE with DENV and West Nile virus (WNV) antibodies. Thus, multiple flaviviruses must be considered when developing novel therapies against ZIKV. We analyzed 42 flavivirus polyproteins in their evolutionary context to identify motifs conserved in sequence with low real-time and evolutionary conformational flexibility, thought to be fitness-critical sites. We also analyzed evolutionary rate-shifts between clades for insight on vector specificity. For mosquito-borne flaviviruses, two conserved motifs were identified within the RNA-dependent RNA polymerase (RdRP), critical for flavivirus genome replication. Clade-specific motifs were identified for the ZIKV+DENV and WNV clades, many of which were also in RdRP. Six sites in motifs for WNV experienced significant evolutionary rate-shifts, suggesting their importance for functional divergence. Overall, some of these motifs are prime candidates as broadly neutralizing antiviral drug targets across different mosquito-borne flaviviruses.

Evolution of intrinsic disorder in eukaryotic proteins.

Conformational flexibility conferred though regions of intrinsic structural disorder allows proteins to behave as dynamic molecules. While it is well-known that intrinsically disordered regions can undergo disorder-to-order transitions in real-time as part of their function, we also are beginning to learn more about the dynamics of disorder-to-order transitions along evolutionary time-scales. Intrinsically disordered regions endow proteins with functional promiscuity, which is further enhanced by the ability of some of these regions to undergo real-time disorder-to-order transitions. Disorder content affects gene retention after whole genome duplication, but it is not necessarily conserved. Altered patterns of disorder resulting from evolutionary disorder-to-order transitions indicate that disorder evolves to modify function through refining stability, regulation, and interactions. Here, we review the evolution of intrinsically disordered regions in eukaryotic proteins. We discuss the interplay between secondary structure and disorder on evolutionary time-scales, the importance of disorder for eukaryotic proteome expansion and functional divergence, and the evolutionary dynamics of disorder.

Functional Diversification after Gene Duplication: Paralog Specific Regions of Structural Disorder and Phosphorylation in p53, p63, and p73.

Conformational and functional flexibility promote protein evolvability. High evolvability allows related proteins to functionally diverge and perhaps to neostructuralize. p53 is a multifunctional protein frequently referred to as the Guardian of the Genome-a hub for e.g. incoming and outgoing signals in apoptosis and DNA repair. p53 has been found to be structurally disordered, an extreme form of conformational flexibility. Here, p53, and its paralogs p63 and p73, were studied for further insights into the evolutionary dynamics of structural disorder, secondary structure, and phosphorylation. This study is focused on the post gene duplication phase for the p53 family in vertebrates, but also visits the origin of the protein family and the early domain loss and gain events. Functional divergence, measured by rapid evolutionary dynamics of protein domains, structural properties, and phosphorylation propensity, is inferred across vertebrate p53 proteins, in p63 and p73 from fish, and between the three paralogs. In particular, structurally disordered regions are redistributed among paralogs, but within clades redistribution of structural disorder also appears to be an ongoing process. Despite its deemed importance as the Guardian of the Genome, p53 is indeed a protein with high evolvability as seen not only in rearranged structural disorder, but also in fluctuating domain sequence signatures among lineages.