Traditionally, computational protein design efforts have been directed at calculating a single sequence predicted to fold to a particular target structure. Recently, however, a number of conceptual generalizations have been pursued, ranging from the use of backbone flexibility, off-rotamer side chain flexibility, negative design, multi-body potentials, conformational free energy, and prediction of sequence profiles. Below I present our state-of-the-art research whose goal is to understand how protein sequences are optimized to be compatible with binding multiple partners with high affinity. – By Menachem Fromer.
In a first digest of 2009: two new Rosetta protocols – A new RosettaLigand – docking with full ligand and receptor flexibility, and an improved design protocol to recover native protein-protein interface sequences. Also a new structure of the NaK channel and analysis of its selectivity.
Carlos J. Camacho et al. study the relationship between peptide stabilities and their immunogenicity. They present a model system of several peptides corresponding to portions of murine HRS which are capable of inducing anti-protein antibodies of varying affinity and temporal persistence. On this system they show by molecular dynamics simulations, that sequences of the most immunogenic peptides correspond to highly ordered structural motifs in the parent protein. Competitive ELISAs provide direct evidence that these peptides share structural determinants with native protein. More interestingly they address the question of how can these less stable peptides induce the same immunogenic response. By Nir London
In this Bi-Weekly digest – relevant titles form current issues of molecular and computational biology literature, amongst featured titles: Surface Sites for Engineering Allosteric Control in Proteins and The RNA Polymerase ”Switch Region” Is a Target for Inhibitors. If you want to initiate in a public discussion on one of these, let us know in the comments.
In this weekly digest – relevant titles form current issues of Nature Structural and Molecular Biology, Bioinformatics, BMC Bioinformatics, Plos Computational Biology and Journal of Computational Biology. If you want to initiate in a public discussion on one of these, let us know in the comments.