Current Protein and Peptide Science - Volume 9, Issue 1, 2008

This article gives an overview of recent progress in protein-protein docking and it identifies several directions for future research. Recent results from the CAPRI blind docking experiments show that docking algorithms are steadily improving in both reliability and accuracy. Current docking algorithms employ a range of efficient search and scoring strategies, including e.g. fast Fourier transform correlations, geometric hashin Read More

Host cell entry by influenza and other enveloped viruses is well characterized, however, the manner in which non-enveloped viruses deliver their genome across host cell membranes in the absence of membrane fusion remains unresolved. The discovery of short, membrane altering, amphipathic or hydrophobic sequences in several non-enveloped virus capsid proteins such as the γ (gamma) peptide of nodaviruses an Read More

The network paradigm is based on the derivation of emerging properties of studied systems by their representation as oriented graphs: any system is traced back to a set of nodes (its constituent elements) linked by edges (arcs) correspondent to the relations existing between the nodes. This allows for a straightforward quantitative formalization of systems by means of the computation of mathematical descriptors of such gra Read More

Lantibiotics are a diverse family of bacterially synthesized antimicrobial peptides produced by gram-positive bacteria. They usually have a broad spectrum of targets, often including closely related strains. The production of lantibiotics must thus be coupled with a mechanism by which the producing strain can protect itself from the lethal action of its own antimicrobial compound. This mechanism is referred to as immunity. Read More

In living cells, membrane proteins are essential to signal transduction, nutrient use, and energy exchange between the cell and environment. Due to challenges in protein expression, purification and crystallization, deposition of membrane protein structures in the Protein Data Bank lags far behind existing structures for soluble proteins. This review describes recent advances in solution NMR allowing the study of a select set o Read More

Protein and peptide sequences contain clues for functional prediction. A challenge is to predict sequences that show low or no homology to proteins or peptides of known function. A machine learning method, support vector machines (SVM), has recently been explored for predicting functional class of proteins and peptides from sequence-derived properties irrespective of sequence similarity, which has shown impressive perfor Read More

A group of serine peptidases, the prolyl oligopeptidase family, cannot hydrolyze proteins and peptides containing more than 30 residues. The crystal structure of prolyl oligopeptidase (POP) has shown that the enzyme is composed of a peptidase domain with an α/β hydrolase fold and a seven-bladed β-propeller domain. This domain covers the catalytic triad and excludes large, structured peptides from the active site. Th Read More