SnugDock: Paratope Structural Optimization during Antibody-Antigen Docking Compensates for Errors in Antibody Homology Models

High resolution structures of antibody-antigen complexes are useful for analyzing the binding interface and to make rational choices for antibody engineering. When a crystallographic structure of a complex is unavailable, the structure must be predicted using computational tools. In this work, we illustrate a novel approach, named SnugDock, to predict high-resolution antibody-antigen complex structures by simultaneously structurally optimizing the antibody-antigen rigid-body positions, the relative orientation of the antibody light and heavy chains, and the conformations of the six complementarity determining region loops. This approach is especially useful when the crystal structure of the antibody is not available, requiring allowances for inaccuracies in an antibody homology model which would otherwise frustrate rigid-backbone docking predictions. Local docking using SnugDock with the lowest-energy RosettaAntibody homology model produced more accurate predictions than standard rigid-body docking. SnugDock can be combined with ensemble docking to mimic conformer selection and induced fit resulting in increased sampling of diverse antibody conformations. The combined algorithm produced four medium (Critical Assessment of PRediction of Interactions-CAPRI rating) and seven acceptable lowest-interface-energy predictions in a test set of fifteen complexes. Structural analysis shows that diverse paratope conformations are sampled, but docked paratope backbones are not necessarily closer to the crystal structure conformations than the starting homology models. The accuracy of SnugDock predictions suggests a new genre of general docking algorithms with flexible binding interfaces targeted towards making homology models useful for further high-resolution predictions

Structure-Based Design of Supercharged, Highly Thermoresistant Antibodies

Mutation of surface residues to charged amino acids increases resistance to aggregation and can enable reversible unfolding. We have developed a protocol using the Rosetta computational design package that “supercharges” proteins while considering the energetic implications of each mutation. Using a homology model, a single-chain variable fragment antibody was designed that has a markedly enhanced resistance to thermal inactivation and displays an unanticipated ≈30-fold improvement in affinity. Such supercharged antibodies should prove useful for assays in resource-limited settings and for developing reagents with improved shelf lives

Conflict and Catastrophe MedicineA Practical Guide /

XXXII, 964 p. 100 illus., 86 illus. in color.onli

Bis(imino)pyridine Cobalt-Catalyzed Dehydrogenative Silylation of Alkenes: Scope, Mechanism, and Origins of Selective Allylsilane Formation

The aryl-substituted bis­(imino)­pyridine cobalt methyl complex, (^MesPDI)­CoCH₃ (^MesPDI = 2,6-(2,4,6-Me₃C₆H₂-NCMe)₂C₅H₃N), promotes the catalytic dehydrogenative silylation of linear α-olefins to selectively form the corresponding allyl­silanes with commercially relevant tertiary silanes such as (Me₃SiO)₂MeSiH and (EtO)₃SiH. Dehydrogenative silylation of internal olefins such as <i>cis</i>- and <i>trans</i>-4-octene also exclusively produces the allyl­silane with the silicon located at the terminus of the hydrocarbon chain, resulting in a highly selective base-metal-catalyzed method for the remote functionalization of C–H bonds with retention of unsaturation. The cobalt-catalyzed reactions also enable inexpensive α-olefins to serve as functional equivalents of the more valuable α, ω-dienes and offer a unique method for the cross-linking of silicone fluids with well-defined carbon spacers. Stoichiometric experiments and deuterium labeling studies support activation of the cobalt alkyl precursor to form a putative cobalt silyl, which undergoes 2,1-insertion of the alkene followed by selective β-hydrogen elimination from the carbon distal from the large tertiary silyl group and accounts for the observed selectivity for allyl­silane formation

Community-Wide Assessment of Protein-Interface Modeling Suggests Improvements to Design Methodology.

International audienceThe CAPRI (Critical Assessment of Predicted Interactions) and CASP (Critical Assessment of protein Structure Prediction) experiments have demonstrated the power of community-wide tests of methodology in assessing the current state of the art and spurring progress in the very challenging areas of protein docking and structure prediction. We sought to bring the power of community-wide experiments to bear on a very challenging protein design problem that provides a complementary but equally fundamental test of current understanding of protein-binding thermodynamics. We have generated a number of designed protein-protein interfaces with very favorable computed binding energies but which do not appear to be formed in experiments, suggesting that there may be important physical chemistry missing in the energy calculations. A total of 28 research groups took up the challenge of determining what is missing: we provided structures of 87 designed complexes and 120 naturally occurring complexes and asked participants to identify energetic contributions and/or structural features that distinguish between the two sets. The community found that electrostatics and solvation terms partially distinguish the designs from the natural complexes, largely due to the nonpolar character of the designed interactions. Beyond this polarity difference, the community found that the designed binding surfaces were, on average, structurally less embedded in the designed monomers, suggesting that backbone conformational rigidity at the designed surface is important for realization of the designed function. These results can be used to improve computational design strategies, but there is still much to be learned; for example, one designed complex, which does form in experiments, was classified by all metrics as a nonbinder