The FoldX web server: an online force field

FoldX is an empirical force field that was developed for the rapid evaluation of the effect of mutations on the stability, folding and dynamics of proteins and nucleic acids. The core functionality of FoldX, namely the calculation of the free energy of a macromolecule based on its high-resolution 3D structure, is now publicly available through a web server at . The current release allows the calculation of the stability of a protein, calculation of the positions of the protons and the prediction of water bridges, prediction of metal binding sites and the analysis of the free energy of complex formation. Alanine scanning, the systematic truncation of side chains to alanine, is also included. In addition, some reporting functions have been added, and it is now possible to print both the atomic interaction networks that constitute the protein, print the structural and energetic details of the interactions per atom or per residue, as well as generate a general quality report of the pdb structure. This core functionality will be further extended as more FoldX applications are developed

SNPeffect: a database mapping molecular phenotypic effects of human non-synonymous coding SNPs

Single nucleotide polymorphisms (SNPs) are an increasingly important tool for genetic and biomedical research. However, the accumulated sequence information on allelic variation is not matched by an understanding of the effect of SNPs on the functional attributes or ‘molecular phenotype’ of a protein. Towards this aim we developed SNPeffect, an online resource of human non-synonymous coding SNPs (nsSNPs) mapping phenotypic effects of allelic variation in human genes. SNPeffect contains 31 659 nsSNPs from 12 480 human proteins. The current release of SNPeffect incorporates data on protein stability, integrity of functional sites, protein phosphorylation and glycosylation, subcellular localization, protein turnover rates, protein aggregation, amyloidosis and chaperone interaction. The SNP entries are accessible through both a search and browse interface and are linked to most major biological databases. The data can be displayed as detailed descriptions of individual SNPs or as an overview of all SNPs for a given protein. SNPeffect will be regularly updated and can be accessed at http://snpeffect.vib.be/

Quantifying information transfer by protein domains: Analysis of the Fyn SH2 domain structure

info:eu-repo/semantics/publishe

BriX: a database of protein building blocks for structural analysis, modeling and design

High-resolution structures of proteins remain the most valuable source for understanding their function in the cell and provide leads for drug design. Since the availability of sufficient protein structures to tackle complex problems such as modeling backbone moves or docking remains a problem, alternative approaches using small, recurrent protein fragments have been employed. Here we present two databases that provide a vast resource for implementing such fragment-based strategies. The BriX database contains fragments from over 7000 non-homologous proteins from the Astral collection, segmented in lengths from 4 to 14 residues and clustered according to structural similarity, summing up to a content of 2 million fragments per length. To overcome the lack of loops classified in BriX, we constructed the Loop BriX database of non-regular structure elements, clustered according to end-to-end distance between the regular residues flanking the loop. Both databases are available online (http://brix.crg.es) and can be accessed through a user-friendly web-interface. For high-throughput queries a web-based API is provided, as well as full database downloads. In addition, two exciting applications are provided as online services: (i) user-submitted structures can be covered on the fly with BriX classes, representing putative structural variation throughout the protein and (ii) gaps or low-confidence regions in these structures can be bridged with matching fragments

PepX: a structural database of non-redundant protein–peptide complexes

Although protein–peptide interactions are estimated to constitute up to 40% of all protein interactions, relatively little information is available for the structural details of these interactions. Peptide-mediated interactions are a prime target for drug design because they are predominantly present in signaling and regulatory networks. A reliable data set of nonredundant protein–peptide complexes is indispensable as a basis for modeling and design, but current data sets for protein–peptide interactions are often biased towards specific types of interactions or are limited to interactions with small ligands. In PepX (http://pepx.switchlab.org), we have designed an unbiased and exhaustive data set of all protein–peptide complexes available in the Protein Data Bank with peptide lengths up to 35 residues. In addition, these complexes have been clustered based on their binding interfaces rather than sequence homology, providing a set of structurally diverse protein–peptide interactions. The final data set contains 505 unique protein–peptide interface clusters from 1431 complexes. Thorough annotation of each complex with both biological and structural information facilitates searching for and browsing through individual complexes and clusters. Moreover, we provide an additional source of data for peptide design by annotating peptides with naturally occurring backbone variations using fragment clusters from the BriX database

How Protein Stability and New Functions Trade Off

Numerous studies have noted that the evolution of new enzymatic specificities is accompanied by loss of the protein's thermodynamic stability (ΔΔG), thus suggesting a tradeoff between the acquisition of new enzymatic functions and stability. However, since most mutations are destabilizing (ΔΔG>0), one should ask how destabilizing mutations that confer new or altered enzymatic functions relative to all other mutations are. We applied ΔΔG computations by FoldX to analyze the effects of 548 mutations that arose from the directed evolution of 22 different enzymes. The stability effects, location, and type of function-altering mutations were compared to ΔΔG changes arising from all possible point mutations in the same enzymes. We found that mutations that modulate enzymatic functions are mostly destabilizing (average ΔΔG = +0.9 kcal/mol), and are almost as destabilizing as the “average” mutation in these enzymes (+1.3 kcal/mol). Although their stability effects are not as dramatic as in key catalytic residues, mutations that modify the substrate binding pockets, and thus mediate new enzymatic specificities, place a larger stability burden than surface mutations that underline neutral, non-adaptive evolutionary changes. How are the destabilizing effects of functional mutations balanced to enable adaptation? Our analysis also indicated that many mutations that appear in directed evolution variants with no obvious role in the new function exert stabilizing effects that may compensate for the destabilizing effects of the crucial function-altering mutations. Thus, the evolution of new enzymatic activities, both in nature and in the laboratory, is dependent on the compensatory, stabilizing effect of apparently “silent” mutations in regions of the protein that are irrelevant to its function

Photopatterning of PDMS Films: Challenging the Reaction between Benzophenone and Silicone Functional Groups

International audienceDirect photopatterning of PDMS (Polydimethylsiloxane) through benzophenone photo-inhibition has received great interest in recent years. Indeed, the simplicity and versatility of this technique allows for easy processing of micro-canals, or local control of PDMS mechanical properties. Surprisingly, however, the chemical reactions between silicone hydride and/or silicone vinyl groups and benzophenone have only been assessed through qualitative methods (e.g., Attenuated total reflection fourier transform infrared). In this communication, the previously proposed reaction pathways are challenged, using nuclear magnetic resonance (NMR) spectroscopy and size exclusion chromatography (SEC) monitoring. A different mechanism depicting the role of benzophenone irradiation on the polyaddition reaction of silicone formulations is proposed, and a simplified procedure involving aromatic solvent is finally disclosed

How I met your elastomers: from network topology to mechanical behaviours of conventional silicone materials

International audienceSilicone elastomers are available in different formulations that are mainly discriminated by their crosslinking mechanisms. Different chemical networks lead to diverse mechanical behaviours. This work aims at comparing three types of conventional silicone elastomers, one Liquid Silicone Rubber (LSR), one High Consistency Rubber (HCR) and one, thermoplastic, hydrogen bonded cross-linked elastomer (TPE). Each one is studied and compared in terms of network microstructure versus mechanical behaviour

Architectured silicone elastomers for biomedical applications

International audienceSilicone rubber are currently used in biomedical applications. Nevertheless, they have an isotropic mechanical behavior. In order to mimic soft tissues, it is important to develop anisotropy in these materials. In this way a means to create heterogeneities in the degree of crosslinking is developed by UV irradiation. This method permit to create membranes with non-homogeneous mechanical properties

Influence of the microstructure of gums on the mechanical properties of silicone high consistency rubbers

International audienceThis paper is devoted to the characterization and processing of high molar mass vinyl-bearing polysiloxanes in high consistency silicone rubber (HCR) formulations. The molar masses of five different polydimethylsiloxane gums, bearing vinyl groups at the ends and along their chains, were evaluated by size exclusion chromatography and rheometry. Si-29 and H-1 NMR spectroscopy allowed the precise determination of the vinyl content and of the distribution in the different polymers. Typical HCRs formulated from these gums were heat-cured to process silicone rubbermaterials that were then tested mechanically. The macromolecular properties were correlated to the final material network structure. The amount of reactive vinyl moieties, rather than their distribution along or at the end of chains, is a key parameter to tailor the material mechanical properties