Domain, protein

The protein sequence database is also a text-numeric database with bibliographic links. It is the largest public domain protein sequence database. The current PIR-PSD release 75.04 (March, 2003) contains more than 280 000 entries of partial or complete protein sequences with information on functionalities of the protein, taxonomy (description of the biological source of the protein), sequence properties, experimental analyses, and bibliographic references. Queries can be started as a text-based search or a sequence similarity search. PIR-PSD contains annotated protein sequences with a superfamily/family classification. 

King, R D, M Saqi, R Sayle and M J E Sternberg 1997. DSC Public Domain Protein Secondary Structui e Prediction. Computer Applications in the Biosciences 13 473-474. 

Larger proteins usually have two or more stmctural units termed domains, each domain having stmctures similar to single-domain proteins. The interaction between individual domains is much less extensive than that within a single domain. In many cases each domain is responsible for carrying out a specific function. 

Boumann, U., et al. Three-dimensional structure of the alkaline protease of Pseudomonas aeruginosa, a two-domain protein with a calcium binding parallel beta roll motif. EMBO J. 12 3357-3364, 1993. 

Richmond and collaborators (Figure 12.30). The octamer (Figure 12.29) has surface landmarks that guide the course of the DNA around the octamer 146 bp of B-DNA in a flat, left-handed superhelical conformation make 1.65 turns around the histone core (Figure 12.30), which itself is a protein superhelix consisting of a spiral array of the four histone dimers. Histone 1, a three-domain protein, serves to seal the ends of the DNA turns to the nucleosome core and to organize the additional 40 to 60 bp of DNA that link consecutive nucleo-... 

Adaptor proteins are multi-domain proteins (Fig. 1) that interact with components of signaling pathways [1]. As a consequence of these interactions, adaptor proteins are able to regulate signaling events within the cell, providing spatiotemporal control and specificity, and influencing how a cell responds to a particular stimulus. 

Non-EF-hand Ca2+-binding proteins including the annexins, C2-domain proteins, and gelsolin, and the EF-hand Ca2+-binding proteins. 

The exocytotic release of neurotransmitters from synaptic vesicles underlies most information processing by the brain. Since classical neurotransmitters including monoamines, acetylcholine, GABA, and glutamate are synthesized in the cytoplasm, a mechanism is required for their accumulation in synaptic vesicles. Vesicular transporters are multitransmembrane domain proteins that mediate this process by coupling the movement of neurotransmitters to the proton electrochemical gradient across the vesicle membrane. 

Treacy, M. N He, X., and Rosenfeld, M. G. (1991). I-POU a POU-domain protein that inhibits neuron-specific gene activation. Nature 350 577-584. 

Figure 5.1. Yeast two-hybrid system. Interaction of proteins X and Y upstream of a reporter gene leads to transcriptional activation. Protein X is part of a fusion protein that binds to a site on DNA upstream of the reporter gene by means of a DNA binding domain. Protein Y is part of a fusion protein that contains a transcriptional activation domain. Interaction of proteins X and Y places the activation domain in the vicinity of the reporter gene and stimulates its transcription.

Yeates TO (2002) Structures of set domain proteins protein lysine methyltransferases make their mark. Cell 111 5-7... 

Trievel RC, Beach BM, Dirk LMA, Houtz RL, Hurley JH (2002) Structure and catalytic mechanism of a set domain protein methyltransferase. Cell 111 91—103... 

Kuchinke U, Grawe F, Knust E 1998 Control of spindle orientation in Drosophila by the Par-3-related PDZ-domain protein Bazooka. Curr Biol 8 1357—1365... 

Figure 3.9 MALDITOF mass spectrum showing over-expressed soluble core domain protein of cytochrome B5.

Figure 7.8 Regulation of IRP-1 and IRP-2. The two IRPs are shown as homologous four domain proteins that bind to IREs (left) In iron-replete cells, IRP-1 assembles a cubane Fe-S cluster that is liganded via cys-437, -503 and -506. Similar cysteines are conserved in IRP-2 (Cys-512, -578 and -581), but it is unresolved as to whether they also coordinate an Fe-S cluster, (right) In iron-replete cells, IRP-2 is targeted for destruction via a specific region (shaded in black), whereas IRP-1, with a 4Fe-4S cluster, is stable and active as a cytoplasmic aconitase. Multiple signals induce IRE-binding by IRP-1 with distinct kinetics. Whether or not NO and H2O2 induce IRP-1 by apoprotein formation remains to be addressed directly. From Hentze and Kuhn, 1996. Copyright (1996) National Academy of Sciences, USA.

Kasparkova, J. Zehnulova, J. Farrell, N. Brabec, V. DNA interstrand crosslinks of novel antitumor trinuclear platinum complex BBR. Conformation, recognition by HMG-domain proteins and nucleotide excision repair. J Biol Chem 2002, 277, 48076-48086. 

Protein-protein interactions between heterodimeric protein pairs that form only transient interactions can be detected, y-secre-tase is presenilin-1 (PS1) dependent [51-53]. PS1 is a 467-amino acid, 9-transmembrane domain protein. Over 100 documented single point mutations are known to cause autosomal-dominant familial AD (FAD) [54], in which the ratio of the more fibrilogenic variety of A ft (A/142) to the less fibrilogenic variety (A/140) is increased. Chinese hamster ovary (CHO) cells were stably transfected with human APP and either wild type or mutant PS1 [4, 55]. 

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