Phage display peptide libraries are widely used in various protein-protein interaction studies to determine the immunological binding of proteins and epitope mapping of different targets. In the present study, the peptide library is used to identify the Fab binding epitope site of Tetanus Toxoid (TT). The peptides were screened against Fab by biopanning, using a random peptide 12mer phage displ...

The interaction of the trans-activation responsive (TAR) region of bovine immunodeficiency virus (BIV) RNA with the Tat peptide is known to play important role in viral replication. Despite being thoroughly studied through a structural point of view, the nature of binding between BIV TAR RNA and the BIV Tat peptide requires information related to its thermodynamics and the nature of hydration a...

SARS-CoV-2 infects human cells by binding its spike protein to the ACE2 receptor. Using a peptide biopanning strategy, authors have discovered small anti-ACE2 peptides that can effectively block SARS-CoV-2/ACE2 interaction. The be potentially used as prophylactic or therapeutic agents for and other ACE2-mediated viruses. This is reported Kun Cheng co-workers in article number 2100087.

MOTIVATION Algorithms for predicting peptide-MHC class II binding are typically similar, if not identical, to methods for predicting peptide-MHC class I binding despite known differences between the two scenarios. We investigate whether representing one of these differences, the greater range of peptide lengths binding MHC class II, improves the performance of these algorithms. RESULTS A non-...

The preparation of a pure, monoiodinated derivative of mast cell-degranulating peptide (MCD peptide), the mast cell-degranulating peptide from bee venom, has enabled us to identify binding sites in rat brain membranes that have a high affinity and specificity for this peptide. These binding sites are evenly distributed throughout the brain and copurify with synaptic membranes. Saturation-bindin...

Recent studies using solid-phase-binding assays and electron microscopy suggested the presence of a heparin-binding domain between the inner globule of a lateral short arm and the cross region of laminin. Using the information from the amino acid sequence of the B1 chain of laminin, several peptides were synthesized from areas with a low hydropathy index and a high density of lysines and/or arg...

The molecular chaperone 70-kDa heat-shock proteins (Hsp70s) play essential roles in maintaining protein homeostasis. Hsp110, an Hsp70 homolog, is highly efficient in preventing protein aggregation but lacks the hallmark folding activity seen in Hsp70s. To understand the mechanistic differences between these two chaperones, we first characterized the distinct peptide substrate binding properties...

We have solved the crystal structure of the MHCII molecule, IA(b), containing an antigenic variant of the major IA(b)-binding peptide derived from the MHCII IEalpha chain. The four MHC pockets at p1, p4, p6, and p9 that usually bind peptide side chains are largely empty because of alanines in the peptide at these positions. The complex is nevertheless very stable, apparently because of unique a...

(Constrained Optimization of Multi-state Energies by Tree Search): A provable and efficient protein design algorithm to optimize binding affinity and specificity with respect to sequence. Section A provides a highly simplified, " toy " example of a multistate protein design calculation to demonstrate the operation of comets. Section B provides details of the methods used to compute lower bounds...

TAP1/TAP2 complexes translocate peptides from the cytosol to the endoplasmic reticulum lumen to enable immune surveillance by CD8(+) T cells. Peptide transport is preceded by peptide binding to a cytosol-accessible surface of TAP1/TAP2 complexes, but the location of the TAP peptide-binding pocket remains unknown. Guided by the known contributions of polymorphic TAP variants to peptide selection...