International Protein

PIR-International Protein Sequence Database Redundant protein sequence database... 

WC Barker, JS Garavelli, DH Haft, LT Hunt, CR Marzec, BC Orcutt, GY Snmvasarao, LSL Yeh, RS Ledley, HW Mewes, F Pfeiffer, A Tsugita. The PIR-International protein sequence database. Nucleic Acids Res 26 27-32, 1998. 

An assay that produces multiple biological readouts. Most commonly used in relation to the mathematical analysis of an image acquired using an automated microscope whereby analysis algorithms quantify cellular parameters (e.g., number, motility, neurite outgrowth, size, shape) and subcellular events (e.g., receptor internalization, protein translocation, protein expression nuclei shape). 

An important point to note here and elsewhere in the description of cell activity is that the particular nature of calcium biochemistry, including the availability of the element and its necessary rejection from the prokaryote cell, when linked to stimulated input and interaction with specific internal proteins of selected properties, made it uniquely suitable for the function as an elementary ionic fast in/out messenger. It was then capable of signalling to cell changes once cell size and organisation increased beyond the elementary level of a cell with one small, rapidly... 

PIR (http //pir.georgetown.edu/), Protein Information Resource, located at Georgetown University Medical Center, which has provided the first international Protein Sequence Database. 

Protein information resource (Barker et al., 1999) was established in 1984 by the National Biomedical Research Foundation (NBRF) as a successor to the original NBRF Protein Sequence Database, developed over 20 years by the late Margaret O. Dayhoff and published as the Atlas of Protein Sequence and Structure (Dayhoff et al., 1965 Dayhoff, 1979). Since 1988 the database has been maintained by PIR-Intemational, a collaboration between the NBRF, the Munich Information Center for Protein Sequences (MIPS), and the Japan International Protein Information Database (JIPID). 

Selected entries from Methods in Enzymology [vol, page(s)] Databases and Resources Information services of European Bioinformatics Institute, 266, 3 TDB new databases for biological discovery, 266, 27 PIR-international protein sequence database, 266, 41 superfamily classification in PIR-international protein sequence database, 266, 59 gene classification artificial neural system, 266, 71 blocks database and its applications, 266, 88 indexing and using sequence databases, 266, 105 SRS information retrieval system for molecular biology data banks, 266, 114. 

Intracellular antigens could be modified internal proteins, which are continuously removed by the cell, the structure altered and attached to MHC I. This takes place in the rough endoplasmic reticulum. The protein/pep tide-hapten fragments are then presented to the external surface of the cell membrane as a complex with the MHC I. Then cytotoxic T cells (CD8+) accept the protein/peptide and destroy the cell. This mechanism gives rise to a type IV response. 

Cells which lost part of or all internal protein via osmotic shock techniques (e.g. hemolysis). 

Frequently, with gradient gels an internal protein marker is selected because the dye front has become diffuse or has run off the bottom of the gel. 

Authier, F., B.I. Posner, and J.J. Bergeron. 1996. Endosomal proteolysis of internalized proteins. FEBS Lett. 389 55-60. 

There are different classes of protein sequence databases. Primary and secondary databases are used to address different aspects of sequence analysis. Composite databases amalgamate a variety of different primary sources to facilitate sequence searching efficiently. The primary structure (amino acid sequence) of a protein is stored in primary databases as linear alphabets that represent the constituent residues. The secondary structure of a protein corresponding to region of local regularity (e.g., a-helices, /1-strands, and turns), which in sequence alignments are often apparent as conserved motifs, is stored in secondary databases as patterns. The tertiary structure of a protein derived from the packing of its secondary structural elements which may form folds and domains is stored in structure databases as sets of atomic coordinates. Some of the most important protein sequence databases are PIR (Protein Information Resource), SWISS-PROT (at EBI and ExPASy), MIPS (Munich Information Center for Protein Sequences), JIPID (Japanese International Protein Sequence Database), and TrEMBL (at EBI). ... 

The PIR Protein Sequence Database (Barker et al., 2001 Wu et al., 2002) developed at the National Biomedical Research Foundation (NBRF) has been maintained by PIR-International Protein Sequence Database (PSD), which is the largest publicly distributed and freely available protein sequence database. The consortium includes PIR at the NBRF, MIPS, and JIPID. PIR-International provides online access at http //pir.georgetown.edu to numerous sequence and auxiliary databases. These include PSD (annotated and classified protein sequences), PATCHX (sequences not yet in PSD), ARCHIVE (sequences as originally reported... 

The Munich Information Center for Protein Sequences (MIPS) (Mewes et al., 2000) collects and processes sequence data for the PIR-International Protein Sequence Database project. Access to the database is provided through its Web server, http //www.mips.biochem.mpg.de/. The implementation of PrIAn (Protein Input and Annotation) data input has greatly increased database entries of PIR-International. 

The Protein Information Resources (PIR) (Wu et al., 2002) of NBRF in collaboration with MIPS and JIPID produces the annotated protein sequence database in the PIR-MIPS International Protein Sequence Database (PSD). The PSD is a comprehensive annotated and nonredundant protein sequence database. Its annotation includes concurrent cross-references to other sequence, structure, genomic and citatation databases, as well as functional descriptions and structural features. The PIR-International database is accessible at the PIR site, http //pir, georgetown.edu, and at the MIPS site, http //www.mips.biochem.mpg.de. 

Active transport mechanisms exist in the gastrointestinal tract and other epithelial sites, for the absorption of di- and tri-peptides. As described above, a greater understanding of the molecular specificity of this carrier could provide important leads for the delivery of peptides. Proteins and large peptides may be transported across cells via endocytic processes. Transcytosis is achieved if the endocytic vesicles can reach the basal membrane without fusion with lysosomes. However, various studies have shown that in the majority of cases the internalized protein is degraded, indicating that the transcytotic pathway is a minor one and most of the endocytosed protein is subject to lysosomal degradation. 

Fernandez, J., DeMott, M., Atherton, D., and Mische, S. (1992). Internal protein sequence analysis enzymatic digestion for less than 10 micrograms of protein bound to polyvinylidene difluoride or nitrocellulose membranes. Anal. Biochem. 201, 255-264. 

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