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Community-wide blind prediction experiments such as CAPRI and CASP provide an objective measure of the current state of predictive methodology. Here we describe a community-wide assessment of methods to predict the effects of mutations on protein-protein interactions. Twenty-two groups predicted the effects of comprehensive saturation mutagenesis for two designed influenza hemagglutinin binders and the results were compared with experimental yeast display enrichment data obtained using deep sequencing. The most successful methods explicitly considered the effects of mutation on monomer stability in addition to binding affinity, carried out explicit side-chain sampling and backbone relaxation, evaluated packing, electrostatic, and solvation effects, and correctly identified around a third of the beneficial mutations. Much room for improvement remains for even the best techniques, and large-scale fitness landscapes should continue to provide an excellent test bed for continued evaluation of both existing and new prediction methodologies.

Oligomeric proteins are more abundant in nature than monomeric proteins, and involved in all biological processes. In the absence of an experimental structure, their subunits can be modeled from their sequence like monomeric proteins, but reliable procedures to build the oligomeric assembly are scarce. Template-based methods, which start from known protein structures, are commonly applied to model subunits. We present a method to model homodimers that relies on a structural alignment of the subunits, and test it on a set of 511 target structures recently released by the Protein Data Bank, taking as templates the earlier released structures of 3108 homodimeric proteins (H-set), and 2691 monomeric proteins that form dimer-like assemblies in crystals (M-set). The structural alignment identifies a H-set template for 97% of the targets, and in half of the cases, it yields a correct model of the dimer geometry and residue-residue contacts in the target. It also identifies a M-set template for most of the targets, and some of the crystal dimers are very similar to the target homodimers. The procedure efficiently detects homology at low levels of sequence identities, and points to erroneous quaternary structures in the Protein Data Bank. The high coverage of the target set suggests that the content of the Protein Data Bank already approaches the structural diversity of protein assemblies in nature, and that template-based methods should become the choice method for modeling oligomeric as well as monomeric proteins.

International audience

International audience; Dans cet article, nous décrivons l'interaction protéine-protéine dans le cadre du modèle de l'énergie stochastique (Random Energy Model) de la physique statistique. Nous simulons en amarrant les deux protéines partenaires, le processus d'association de deux protéines formant un complexe. Nous obtenons les spectres d'énergie d'un jeu de complexes protéine-protéine de structure tridimensionnelle connue en effectuant l'amarrage dans des orientations aléatoires et en calculant un score pour les complexes modèles ainsi générés. Nous utilisons une représentation très simplifiée de la structure où chaque acide aminé est remplacé par sa cellule de Voronoï, et nous appliquons le programme d'apprentissage par algorithme génétique ROGER à un ensemble de paramètres mesurés sur cette représentation, afin de dériver une fonction de score appropriée. En considérant les scores obtenus comme des énergies d'interaction, nous obtenons le spectre d'énergie de chaque complexe. Il s'approche d'une distribution gaussienne qui nous permet de calculer des paramètres physiques comme la température de transition vitreuse et la température de transition spécifique du système.

International audience; The protein product of the YGR205w gene of Saccharomyces cerevisiae was targeted as part of our yeast structural genomics project. YGR205w codes for a small (290 amino acids) protein with unknown structure and function. The only recognizable sequence feature is the presence of a Walker A motif (P loop) indicating a possible nucleotide binding/converting function. We determined the three-dimensional crystal structure of Se-methionine substituted protein using multiple anomalous diffraction. The structure revealed a well known mononucleotide fold and strong resemblance to the structure of small metabolite phosphorylating enzymes such as pantothenate and phosphoribulo kinase. Biochemical experiments show that YGR205w binds specifically ATP and, less tightly, ADP. The structure also revealed the presence of two bound sulphate ions, occupying opposite niches in a canyon that corresponds to the active site of the protein. One sulphate is bound to the P-loop in a position that corresponds to the position of ␤-phosphate in mononucleotide protein ATP complex, suggesting the protein is indeed a kinase. The nature of the phosphate accepting substrate remains to be determined.