Pxxp motif investing

pxxp motif investing

Pex13p is a peroxisomal membrane protein containing an SH3, which typically requires the PxxP motif for its binding partners, as observed in. ABSTRACT A common focus among molecular and cellular biologists is the identification of proteins that interact with each other. In accordance, mutating PxxP motif prevents Rig-I from inhibiting AKT activation, cyto- kine-stimulated myeloid progenitor proliferation. WALLY YACHTS BETTER PLACE REALTY

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Serine phosphorylation-independent downregulation of cell-surface CD4 by nef. The negative effect of human immunodeficiency virus type 1 Nef on cell surface CD4 expression is not species specific and requires the cytoplasmic domain of CD4. The HIV Nef protein: facts and hypotheses. Res Virol. On the HIV nef gene product. Requirement of human immunodeficiency virus type 1 nef for in vivo replication and pathogenicity. Importance of the nef gene for maintenance of high virus loads and for development of AIDS.

Lack of a negative influence on viral growth by the nef gene of human immunodeficiency virus type 1. The envelope glycoprotein of the human immunodeficiency virus binds to the immunoglobulin-like domain of CD4. Vpu-induced degradation of CD4: requirement for specific amino acid residues in the cytoplasmic domain of CD4.

Mutational analysis of the human immunodeficiency virus: the orf-B region down-regulates virus replication. Signalling through SH2 and SH3 domains. Trends Cell Biol. The noncatalytic src homology region 2 segment of abl tyrosine kinase binds to tyrosine-phosphorylated cellular proteins with high affinity. The human immunodeficiency virus-1 nef gene product: a positive factor for viral infection and replication in primary lymphocytes and macrophages.

Advanced mammalian gene transfer: high titre retroviral vectors with multiple drug selection markers and a complementary helper-free packaging cell line. Nucleic Acids Res. SHan abundant protein domain in search of a function. FEBS Lett. Regulation of src family tyrosine kinases in lymphocytes.

Trends Biochem Sci. Human immunodeficiency virus type 1 negative factor is a transcriptional silencer. SH2 and SH3 domains. A large fraction of these motifs can be assigned to structurally conserved types of class I and class II sequences. These sequences may serve as leads for the development of peptidomimics that specifically target these organisms. Received October 22, ; revised January 6, ; accepted February 2, Edited by Alan Fersht Introduction The assignment of biological function to new proteins remains a formidable problem.

Integration of proteins into biochemical and signaling pathways is an essential requisite for understanding each protein. Although we now have genomic information on a variety of organisms, our understanding of the biological function s of most new proteins remains limited. Rapid protein sequence divergence often makes sequence comparisons difficult, leading to a failure in detecting evolutionary conservation of function Florens et al. Further, genomic and structural information may be insufficient in assigning all the biochemical attributes to a protein, given that multiple cellular functions may be associated with the same protein fold.

Aside from a primary biochemical role, many proteins have additional functional attributes that are utilized in networking with cellular proteins. The amino acid proline attains paramount importance in many protein—protein interactions Sudol, ; Kay et al. These structurally conserved domains are ubiquitous in biological systems, including in a bacterium such as the Mycobacterium Ponting et al.

Most proteins known to interact with SH3 domains contain at least one copy of the motif PxxP. Analysis of phage display libraries have demonstrated that individual SH3 domains have distinct specificities for potential ligands and can discern subtle differences in the ligand primary structure Sparks et al.

Much of this specificity comes from amino acids flanking the core PxxP motif Sparks et al. We reasoned that dissecting the proteomes for the presence of PxxP sequences would open new vistas in understanding sets of protein—protein interactions and signaling pathways. We therefore performed extensive in silico sieving of the complete proteomes of two pathogenic organisms, P.

We defined a set of PxxP motifs that have been experimentally verified to bind to SH3 domains Cesareni et al. Our results indicate an abundance of class I and class II PxxP motifs in the proteomes of two major pathogenic organisms and three higher eukaryotic organisms.

Our analyses have also identified shared motifs in the proteomes of M. We propose a novel strategy of drug target selection where multiple proteins in the cell can be simultaneously inhibited using peptidomimics that target common PxxP motifs. In line with this strategy, we have identified several motifs that are highly conserved in the cytoplasmic the erythrocyte cytoplasm domains of P. These PxxP motifs are absent from the human proteome. Methods The proteomes should harbor a specific number of PxxP motifs depending on the average size of the protein and the size of the proteome.

To address this issue, we used the simple probability concept. We calculated the probability of the occurrence of a particular motif in any random sequence by the multiplication rule of probability. This calculation is based on the ATGC content of each genome studied and on codon degeneracy. To find the expected number of these motifs in the entire proteome, the above value A is multiplied by the total number of proteins in the proteome. Occurrences of each motif in the five proteomes were determined and expected distributions were computed.

This allowed us to calculate the difference between observed and expected values. The observed and expected frequencies along logarithmic values of respective motif probabilities are represented graphically in Figure 1. Since the probability values are very low and therefore difficult to represent graphically, their logarithmic values are presented logarithm to base Simple Unix and PERL scripts were used to automate the motif searches using data from public access genomic and proteomic databases.

Results An abundance of PxxP motifs in various proteomes We identified all proteins with at least one occurrence of the PxxP motif in the proteomes of human, mouse, S. The resulting motifs were delineated into classes and subclasses keeping in view published nomenclatures Rickles et al. A large fraction of the diversity observed in SH3 I domains is represented in the SH3 repertoire of Saccharomyces cerevisiae Cesareni et al. Therefore, we selected the SH3 domain containing proteins of S.

We followed the PxxP motif nomenclature published recently Cesareni et al. All other atypical PxxP motifs are grouped under Class X. The various subclasses have been defined based on highly probable consensus motifs which have also been experimentally verified for binding to different SH3 domains Kay et al.

We used the consensus sequences for various classes and subclasses as queries and filtered out the hits for each proteome. The number of PXXP motifs in each proteome was plotted as a percentage of total number of proteins Figure 2 a. The P. The M. Surprisingly, the S. These data reveal the abundance of PXXP motifs in proteins from evolutionary distant species. Based on the P. The data indicate that PxxP motifs are prevalent in cytoplasmic, nuclear and surface proteins.

This wide occurrence across diverse functional classes in the five proteomes indicates evolutionary conservation of protein—protein networks centered on PxxP sequences. Functional significance of PxxP classes and subclasses The number of major classes of PxxP motifs in each organism was plotted as a percentage of total number of PxxP motifs in that respective organism Figure 2 b and Table IV.