Tertiary motifs as building blocks for the design of protein‐binding peptides

Despite advances in protein engineering, the de novo design of small proteins or peptides that bind to a desired target remains a difficult task. Most computational methods search for binder structures in a library of candidate scaffolds, which can lead to designs with poor target complementarity and low success rates. Instead of choosing from pre‐defined scaffolds, we propose that custom peptide structures can be constructed to complement a target surface. Our method mines tertiary motifs (TERMs) from known structures to identify surface‐complementing fragments or “seeds.” We combine seeds that satisfy geometric overlap criteria to generate peptide backbones and score the backbones to identify the most likely binding structures. We found that TERM‐based seeds can describe known binding structures with high resolution: the vast majority of peptide binders from 486 peptide‐protein complexes can be covered by seeds generated from single‐chain structures. Furthermore, we demonstrate that known peptide structures can be reconstructed with high accuracy from peptide‐covering seeds. As a proof of concept, we used our method to design 100 peptide binders of TRAF6, seven of which were predicted by Rosetta to form higher‐quality interfaces than a native binder. The designed peptides interact with distinct sites on TRAF6, including the native peptide‐binding site. These results demonstrate that known peptide‐binding structures can be constructed from TERMs in single‐chain structures and suggest that TERM information can be applied to efficiently design novel target‐complementing binders.     

Thermal ecology and baseline energetic requirements of a large‐bodied ectotherm suggest resilience to climate change

1. Most studies on how rising temperatures will impact terrestrial ectotherms have focused on single populations or multiple sympatric species. Addressing the thermal and energetic implications of climatic variation on multiple allopatric populations of a species will help us better understand how a species may be impacted by altered climates.
2. We used eight years of thermal and behavioral data collected from four populations of Pacific rattlesnakes (Crotalus oreganus) living in climatically distinct habitat types (inland and coastal) to determine the field‐active and laboratory‐preferred body temperatures, thermoregulatory metrics, and maintenance energetic requirements of snakes from each population.
3. Physical models showed that thermal quality was best at coastal sites, but inland snakes thermoregulated more accurately despite being in more thermally constrained environments. Projected increases of 1 and 2°C in ambient temperature result in an increase in overall thermal quality at both coastal and inland sites.
4. Population differences in modeled standard metabolic rate estimates were driven by body size and not field‐active body temperature, with inland snakes requiring 1.6× more food annually than coastal snakes.
5. All snakes thermoregulated with high accuracy, suggesting that small increases in ambient temperature are unlikely to impact the maintenance energetic requirements of individual snakes and that some species of large‐bodied reptiles may be robust to modest thermal perturbations under conservative climate change predictions.

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The two kinds of free energy and the Bayesian revolution

The concept of free energy has its origins in 19th century thermodynamics, but has recently found its way into the behavioral and neural sciences, where it has been promoted for its wide applicability and has even been suggested as a fundamental principle of understanding intelligent behavior and brain function. We argue that there are essentially two different notions of free energy in current models of intelligent agency, that can both be considered as applications of Bayesian inference to the problem of action selection: one that appears when trading off accuracy and uncertainty based on a general maximum entropy principle, and one that formulates action selection in terms of minimizing an error measure that quantifies deviations of beliefs and policies from given reference models. The first approach provides a normative rule for action selection in the face of model uncertainty or when information processing capabilities are limited. The second approach directly aims to formulate the action selection problem as an inference problem in the context of Bayesian brain theories, also known as Active Inference in the literature. We elucidate the main ideas and discuss critical technical and conceptual issues revolving around these two notions of free energy that both claim to apply at all levels of decision-making, from the high-level deliberation of reasoning down to the low-level information processing of perception.     

Technoecological analysis of energy carriers for long‐haul transportation

Long‐haul transportation demand is predicted to increase in the future, resulting in higher carbon dioxide emissions. Different drivetrain technologies, such as hybrid or battery electric vehicles, electrified roads, liquefied natural gas and hydrogen, might offer solutions to this problem. To assess their ecological and economic impact, these concepts were simulated including a weight and cost model to estimate the total cost of ownership. An evolutionary algorithm optimizes each vehicle to find a concept specific optimal solution. A model calculates the minimum investment in infrastructure required to meet the energy demand for each concept. A well‐to‐wheel analysis takes into account upstream and on‐road carbon dioxide emissions, to compare fully electric vehicles with conventional combustion engines. Investment in new infrastructure is the biggest drawback of electrified road concepts, although they offer low CO₂ emissions. The diesel hybrid is the best compromise between carbon reduction and costs.     

Flexible docking of peptides to proteins using CABS‐dock

Molecular docking of peptides to proteins can be a useful tool in the exploration of the possible peptide binding sites and poses. CABS‐dock is a method for protein–peptide docking that features significant conformational flexibility of both the peptide and the protein molecules during the peptide search for a binding site. The CABS‐dock has been made available as a web server and a standalone package. The web server is an easy to use tool with a simple web interface. The standalone package is a command‐line program dedicated to professional users. It offers a number of advanced features, analysis tools and support for large‐sized systems. In this article, we outline the current status of the CABS‐dock method, its recent developments, applications, and challenges ahead.     

Genetic Predisposition and its Heredity in the Context of Increased Prevalence of Dermatophytoses

Mycopathologia - Dermatophytosis is a widespread disease with high prevalence and a substantial economic burden associated with costs of treatment. The pattern of this infectious disease covers a...     

SANS (USH1G) regulates pre-mRNA splicing by mediating the intra-nuclear transfer of tri-snRNP complexes

Splicing is catalyzed by the spliceosome, a compositionally dynamic complex assembled stepwise on pre-mRNA. We reveal links between splicing machinery components and the intrinsically disordered ciliopathy protein SANS. Pathogenic mutations in SANS/USH1G lead to Usher syndrome—the most common cause of deaf-blindness. Previously, SANS was shown to function only in the cytosol and primary cilia. Here, we have uncovered molecular links between SANS and pre-mRNA splicing catalyzed by the spliceosome in the nucleus. We show that SANS is found in Cajal bodies and nuclear speckles, where it interacts with components of spliceosomal sub-complexes such as SF3B1 and the large splicing cofactor SON but also with PRPFs and snRNAs related to the tri-snRNP complex. SANS is required for the transfer of tri-snRNPs between Cajal bodies and nuclear speckles for spliceosome assembly and may also participate in snRNP recycling back to Cajal bodies. SANS depletion alters the kinetics of spliceosome assembly, leading to accumulation of complex A. SANS deficiency and USH1G pathogenic mutations affects splicing of genes related to cell proliferation and human Usher syndrome. Thus, we provide the first evidence that splicing dysregulation may participate in the pathophysiology of Usher syndrome.