Protein binding peptide

Wilson, D. S., Keefe, A. D., and Szostak, J. W. (2001) The use of mRNA display to select high-affinity protein-binding peptides. Proc. Natl. Acad. Sci. USA 98, 3750-3755. 

G protein-binding peptides reveal mechanistic insights and "hotspots" for chemical intervention... 

In the defense mechanisms of the immnne system, helper T cell activation is essential for the initiation of a protective immnne response to pathogens and tumors. HLA-DR, the predommant isotype of the human class II major histocompatibility complex (MHC), plays a central role in helper T cell selection and activation. HLA-DR proteins bind peptide fragments derived from protein antigens and display them on the surface of antigen-presenting cells (APC) for interaction with antigen-specific receptors of T lymphocytes. 

Z2. Zhu, W., Williams, R. S., and Kodadek, T., A CDC6 protein-binding peptide selected using a bacterial two-hybrid-like system is a cell cycle inhibitor. J. Biol. Chem. 275, 32098-32105 (2000). 

Class 1 and class II MHC molecules bind peptide antigens and present them at the cell surface for interaction with receptors on T cells. The extracellular portion of these molecules consists of a peptide-binding domain formed by two helical regions on top of an eight-stranded antiparallel p sheet, separated from the membrane by two lower domains with immunoglobulin folds. These domains are differently disposed between the two protein subunits in class I and class II molecules. 

Nonrepetitive but well-defined structures of this type form many important features of enzyme active sites. In some cases, a particular arrangement of coil structure providing a specific type of functional site recurs in several functionally related proteins. The peptide loop that binds iron-sulfur clusters in both ferredoxin and high potential iron protein is one example. Another is the central loop portion of the E—F hand structure that binds a calcium ion in several calcium-binding proteins, including calmodulin, carp parvalbumin, troponin C, and the intestinal calcium-binding protein. This loop, shown in Figure 6.26, connects two short a-helices. The calcium ion nestles into the pocket formed by this structure. 

Penicillin Binding Protein Pentasaccharide Peptide Mass Fingerprint Peptide YY Peptidoglycans Peptidyl Transferase Center Peptidyl-Dipeptidase PERI... 

Allaire M, Chernaia MM, Malcolm BA, James MN (1994) Picomaviral 3C cysteine proteinases have a fold similar to chymotrypsin-Kke serine proteinases. Nature 369 72-76 Altman MD, Nalivaika EA, Prabu-Jeyabalan M, Schiffer CA, Tidor B (2008) Computational design and experimental study of tighter binding peptides to an inactivated mutant of HIV-1 protease. Proteins 70 678-694... 

There have been notable successes in the replacement of individual peptide residues by peptoid monomers with retention of in vitro activity and enhancement of specificity. Unfortunately, attempts to completely transform those bioactive peptides that function via specific peptide-protein binding events into entirely pep-toid-based ohgomers have so far proven successful only at short chain lengths (e.g. [23]). It remains to be seen whether any general strategy can be developed in... 

The method utilizing ID NMR is simple and eonvenient. Henee the NMR method diseussed here ean be applied to the systematie investigation of the membrane irug inter-aetions, elosely related to the vital function in biomembranes. It is expected that the application can be extended to the lipid-peptide interaction and protein uptake. We are now applying the method to apolipoprotein binding with lipid bilayers and emulsions. Preferential protein binding sites in membranes can be specified by NMR on the molecular level. 

One of the first practical applications for these fluorescent labelled heparins was to examine the heparin binding behavior of different proteins and peptides under study in our laboratories. To this end we used a modification of the dot-blot assay described by Hirose and colleagues (13). F-D labelled heparin (-1 fluorescein/heparin) was radiolabelled with 125Iodine using iodobeads, to a specific activity of approximately 0.5 x 106 cpm/pg. Solutions of proteins with known heparin-binding capacities were dotted on nitrocellulose paper. A series of replicates... 

Methods for quantifying both the transcellular diffusion and concurrent metabolism of drugs and the unusual transcellular diffusion of membrane-interactive molecules coupled with the influence of protein binding are described in detail. To demonstrate the utility of cultured cell monolayers as a tool for basic science investigations, a subsection is devoted to the elucidation of rate-determining steps and factors in the passive diffusion of peptides across biological membranes. The chapter concludes with a discussion on the judicious use of in vitro cell monolayer results to predict in vivo results. 

The most common second messenger activated by protein/peptide hormones and catecholamines is cyclic adenosine monophosphate (cAMP). The pathway by which cAMP is formed and alters cellular function is illustrated in Figure 10.1. The process begins when the hormone binds to its receptor. These receptors are quite large and span the plasma membrane. On the cytoplasmic surface of the membrane, the receptor is associated with a G protein that serves as the transducer molecule. In other words, the G protein acts as an intermediary between the receptor and the second messengers that will alter cellular activity. These proteins are referred to as G proteins because they bind with guanosine nucleotides. In an unstimulated cell, the inactive G protein binds guanosine diphosphate (GDP). When the hormone... 

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