Improved prediction of site-rates from structure with averaging across homologs.

Variation in mutation rates at sites in proteins can largely be understood by the constraint that proteins must fold into stable structures. Models that calculate site-specific rates based on protein structure and a thermodynamic stability model have shown a significant but modest ability to predict empirical site-specific rates calculated from sequence. Models that use detailed atomistic models of protein energetics do not outperform simpler approaches using packing density.

Accurate prediction of protein assembly structure by combining AlphaFold and symmetrical docking.

AlphaFold can predict the structures of monomeric and multimeric proteins with high accuracy but has a limit on the number of chains and residues it can fold. Here we show that a combination of AlphaFold and all-atom symmetric docking simulations enables highly accurate prediction of the structure of complex symmetrical assemblies. We present a method to predict the structure of complexes with cubic - tetrahedral, octahedral and icosahedral - symmetry from sequence.

Facile Method for High-throughput Identification of Stabilizing Mutations.

Characterizing the effects of mutations on stability is critical for understanding the function and evolution of proteins and improving their biophysical properties. High throughput folding and abundance assays have been successfully used to characterize missense mutations associated with reduced stability. However, screening for increased thermodynamic stability is more challenging since such mutations are rarer and their impact on assay readout is more subtle.

A memetic algorithm enables efficient local and global all-atom protein-protein docking with backbone and side-chain flexibility.

Protein complex formation is encoded by specific interactions at the atomic scale, but the computational cost of modeling proteins at this level often requires use of simplified energy models and limited conformational flexibility. In particular, use of all-atom energy functions and backbone and side-chain flexibility results in rugged energy landscapes that are difficult to explore. In this study, we develop a protein-protein docking algorithm, EvoDOCK, that combines the strength of a differential evolution algorithm for efficient exploration of the global search space with the benefits of a local optimization method to refine detailed atomic interactions.

DnaK response to expression of protein mutants is dependent on translation rate and stability.

Chaperones play a central part in the quality control system in cells by clearing misfolded and aggregated proteins. The chaperone DnaK acts as a sensor for molecular stress by recognising short hydrophobic stretches of misfolded proteins. As the level of unfolded protein is a function of protein stability, we hypothesised that the level of DnaK response upon overexpression of recombinant proteins would be correlated to stability.

Amyloid β 42 fibril structure based on small-angle scattering.

Amyloid fibrils are associated with a number of neurodegenerative diseases, including fibrils of amyloid β42 peptide (Aβ42) in Alzheimer's disease. These fibrils are a source of toxicity to neuronal cells through surface-catalyzed generation of toxic oligomers. Detailed knowledge of the fibril structure may thus facilitate therapeutic development.

A thermodynamic model of protein structure evolution explains empirical amino acid substitution matrices.

Proteins evolve under a myriad of biophysical selection pressures that collectively control the patterns of amino acid substitutions. These evolutionary pressures are sufficiently consistent over time and across protein families to produce substitution patterns, summarized in global amino acid substitution matrices such as BLOSUM, JTT, WAG, and LG, which can be used to successfully detect homologs, infer phylogenies, and reconstruct ancestral sequences. Although the factors that govern the variation of amino acid substitution rates have received much attention, the influence of thermodynamic stability constraints remains unresolved.

An ultra-high affinity protein-protein interface displaying sequence-robustness.

Protein-protein interactions are crucial in biology and play roles in for example, the immune system, signaling pathways, and enzyme regulation. Ultra-high affinity interactions (K <0.1 nM) occur in these systems, however, structures and energetics behind stability of ultra-high affinity protein-protein complexes are not well understood.

ZEAL: protein structure alignment based on shape similarity.

Motivation: Most protein-structure superimposition tools consider only Cartesian coordinates. Yet, much of biology happens on the surface of proteins, which is why proteins with shared ancestry and similar function often have comparable surface shapes. Superposition of proteins based on surface shape can enable comparison of highly divergent proteins, identify convergent evolution and enable detailed comparison of surface features and binding sites.

Orientational Ambiguity in Septin Coiled Coils and its Structural Basis.

Septins are an example of subtle molecular recognition whereby different paralogues must correctly assemble into functional filaments important for essential cellular events such as cytokinesis. Most possess C-terminal domains capable of forming coiled coils which are believed to be involved in filament formation and bundling. Here, we report an integrated structural approach which aims to unravel their architectural diversity and in so doing provide direct structural information for the coiled-coil regions of five human septins.

Crystal Structure of Non-Structural Protein 10 from Severe Acute Respiratory Syndrome Coronavirus-2.

Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), causing Coronavirus Disease 19 (COVID-19), emerged at the end of 2019 and quickly spread to cause a global pandemic with severe socio-economic consequences. The early sequencing of its RNA genome revealed its high similarity to SARS, likely to have originated from bats. The SARS-CoV-2 non-structural protein 10 (nsp10) displays high sequence similarity with its SARS homologue, which binds to and stimulates the 3'-to-5' exoribonuclease and the 2'-O-methlytransferase activities of nsps 14 and 16, respectively.

Assembly of Capsids from Hepatitis B Virus Core Protein Progresses through Highly Populated Intermediates in the Presence and Absence of RNA.

The genetic material of viruses is protected by protein shells that are assembled from a large number of subunits in a process that is efficient and robust. Many of the mechanistic details underpinning efficient assembly of virus capsids are still unknown. The assembly mechanism of hepatitis B capsids has been intensively researched using a truncated core protein lacking the C-terminal domain responsible for binding genomic RNA.

Wnt5a is a TLR2/4-ligand that induces tolerance in human myeloid cells.

Innate immune responses are rapid, dynamic and highly regulated to avoid overt reactions. This regulation is executed by innate immune tolerance mechanisms that remain obscure. Wnt5a is a signalling protein mainly involved in developmental processes and cancer.

Bayesian inference of protein conformational ensembles from limited structural data.

Many proteins consist of folded domains connected by regions with higher flexibility. The details of the resulting conformational ensemble play a central role in controlling interactions between domains and with binding partners. Small-Angle Scattering (SAS) is well-suited to study the conformational states adopted by proteins in solution.

A Protein-Based Encapsulation System with Calcium-Controlled Cargo Loading and Detachment.

Protein-based encapsulation systems have a wide spectrum of applications in targeted delivery of cargo molecules and for chemical transformations in confined spaces. By engineering affinity between cargo and container proteins it has been possible to enable the efficient and specific encapsulation of target molecules. Missing in current approaches is the ability to turn off the interaction after encapsulation to enable the cargo to freely diffuse in the lumen of the container.

Computational assessment of folding energy landscapes in heterodimeric coiled coils.

The coiled coil structural motif consists of alpha helices supercoiling around each other to form staggered knobs-into-holes packing. Such structures are deceptively simple, especially as they often can be described with parametric equations, but are known to exist in various conformations. Even the simplest systems, consisting of 2 monomers, can assemble into a wide range of states.

Modeling the Structure of Helical Assemblies with Experimental Constraints in Rosetta.

Determining high-resolution structures of proteins with helical symmetry can be challenging due to limitations in experimental data. In such instances, structure-based protein simulations driven by experimental data can provide a valuable approach for building models of helical assemblies. This chapter describes how the Rosetta macromolecular package can be used to model homomeric protein assemblies with helical symmetry in a range of modeling scenarios including energy refinement, symmetrical docking, comparative modeling, and de novo structure prediction.

Correction: Thermal stability and structural changes in bacterial toxins responsible for food poisoning.

[This corrects the article DOI: 10.1371/journal.pone.

Thermal stability and structural changes in bacterial toxins responsible for food poisoning.

The staphylococcal enterotoxins (SEs) are secreted by the bacteria Staphylococcus aureus and are the most common causative agent in staphylococcal food poisoning. The staphylococcal enterotoxin A (SEA) has been associated with large staphylococcal food poisoning outbreaks, but newer identified SEs, like staphylococcal enterotoxin H (SEH) has recently been shown to be present at similar levels as SEA in food poisoning outbreaks. Thus, we set out to investigate the thermo-stability of the three-dimensional structures of SEA, SEH and staphylococcal enterotoxin E (SEE), since heat inactivation is a common method to inactivate toxins during food processing.

Mapping the Ca(2+) induced structural change in calreticulin.

Unlabelled: Calreticulin is a highly conserved multifunctional protein implicated in many different biological systems and has therefore been the subject of intensive research. It is primarily present in the endoplasmatic reticulum where its main functions are to regulate Ca(2+) homeostasis, act as a chaperone and stabilize the MHC class I peptide-loading complex. Although several high-resolution structures of calreticulin exist, these only cover three-quarters of the entire protein leaving the extended structures unsolved.

A De Novo Designed Coiled-Coil Peptide with a Reversible pH-Induced Oligomerization Switch.

Protein conformational switches have many useful applications but are difficult to design rationally. Here we demonstrate how the isoenergetic energy landscape of higher-order coiled coils can enable the formation of an oligomerization switch by insertion of a single destabilizing element into an otherwise stable computationally designed scaffold. We describe a de novo designed peptide that was discovered to switch between a parallel symmetric pentamer at pH 8 and a trimer of antiparallel dimers at pH 6.

Computational design of protein self-assembly.

Protein self-assembly is extensively used in nature to build functional biomolecules and provides a general approach to design molecular complexes with many intriguing applications. Although computational design of protein-protein interfaces remains difficult, much progress has recently been made in de novo design of protein assemblies with cyclic, helical, cubic, internal and lattice symmetries. Here, we discuss some of the underlying biophysical principles of self-assembly that influence the design problem and highlight methodological advances that have made self-assembly design a fruitful area of protein design.

Automated de novo phasing and model building of coiled-coil proteins.

Models generated by de novo structure prediction can be very useful starting points for molecular replacement for systems where suitable structural homologues cannot be readily identified. Protein-protein complexes and de novo-designed proteins are examples of systems that can be challenging to phase. In this study, the potential of de novo models of protein complexes for use as starting points for molecular replacement is investigated.