Current Protein and Peptide Science - Volume 10, Issue 3, 2009

The myelin basic protein (MBP) family comprises a variety of developmentally-regulated members arising from different transcription start sites, differential splicing, and post-translational modifications. The “classic” isoforms of MBP include the 18.5 kDa form, which predominates in adult human myelin and facilitates compaction of the mature myelin sheath in the central nervous system, thereby maintaining its structural i Read More

Computational protein tertiary structure prediction has made significant progress over the last decade due to the advancement of techniques and the growth of sequence and structure databases. However, it is still not very easy to predict the accuracy of a given predicted structure. Predicting the accuracy, or quality assessment of a prediction model, is crucial for a practical use of the model such as biochemical experimental d Read More

The Helmholtz free energy, F and the entropy, S are related thermodynamic quantities with a special importance in structural biology. We describe the difficulties in calculating these quantities and review recent methodological developments. Because protein flexibility is essential for function and ligand binding, we discuss the related problems involved in the definition, simulation, and free energy calculation of microstates (su Read More

Large volumes of protein sequence and structure data acquired by proteomic studies led to the development of computational bioinformatic techniques that made possible the functional annotation and structural characterization of proteins based on their primary structure. It has become evident from genome-wide analyses that many proteins in eukaryotic cells are either completely disordered or contain long unstructure Read More

Template based protein structure prediction (commonly referred to as homology or comparative modeling) uses knowledge of solved structures to model a protein sequence's native or true fold. First, a parent structure is found and then a template structure is built by mapping the target sequence onto the parent structure. This putative structure is refined using a combination of backbone moves, side-chain packing, and l Read More

Major Histo-Compatibility (MHC) class I molecules are major agents of the mammalian adaptive immune system. Class I molecules bind short antigenic peptides with a length of 8-10 residues in the Endoplasmatic Reticulum (ER) and after transport to the cell surface the peptides are presented to T-lymphocytes. The binding site of class I molecules is formed by a deep cleft between two α-helices at top of an extended Read More