PHYSICO: An UNIX based Standalone Procedure for Computation of Individual and Group Properties of Protein Sequences

In the genomic and proteomic era, efficient and automated analyses of sequence properties of protein have become an important task in bioinformatics. There are general public licensed (GPL) software tools to perform a part of the job. However, computations of mean properties of large number of orthologous sequences are not possible from the above mentioned GPL sets. Further, there is no GPL software or server which can calculate window dependent sequence properties for a large number of sequences in a single run. With a view to overcome above limitations, we have developed a standalone procedure i.e. PHYSICO, which performs various stages of computation in a single run based on the type of input provided either in RAW-FASTA or BLOCK-FASTA format and makes excel output for: a) Composition, Class composition, Mean molecular weight, Isoelectic point, Aliphatic index and GRAVY, b) column based compositions, variability and difference matrix, c) 25 kinds of window dependent sequence properties. The program is fast, efficient, error free and user friendly. Calculation of mean and standard deviation of homologous sequences sets, for comparison purpose when relevant, is another attribute of the program; a property seldom seen in existing GPL softwares.

Availability

PHYSICO is freely available for non-commercial/academic user in formal request to the corresponding author ni.ca.vinurub.hcetoib@eejrenabka     

2D-MH: A web-server for generating graphic representation of protein sequences based on the physicochemical properties of their constituent amino acids

Introduction of graphic representation for biological sequences can provide intuitive overall pictures as well as useful insights for performing large-scale analysis. Here, a new two-dimensional graph, called “2D-MH”, is proposed to represent protein sequences. It is formed by incorporating the information of the side-chain mass of each of the constituent amino acids and its hydrophobicity. The graphic curve thus generated is featured by (1) an one-to-one correspondence relation without circuit or degeneracy, (2) better reflecting the innate structure of the protein sequence, (3) clear visibility in displaying the similarity of protein sequences, (4) more sensitive for the mutation sites important for drug targeting, and (5) being able to be used as a metric for the “evolutionary distance” of a protein from one species to the other. It is anticipated that the presented graphic method may become a useful vehicle for large-scale analysis of the avalanche of protein sequences generated in the post-genomic age. As a web-server, 2D-MH is freely accessible at http://icpr.jci.jx.cn/bioinfo/pplot/2D-MH, by which one can easily generate the two-dimensional graphs for any number of protein sequences and compare the evolutionary distances between them.     

A model for Ca2+ oscillations stimulated by the type 5 metabotropic glutamate receptor: an unusual mechanism based on repetitive, reversible phosphorylation of the receptor

In parallel with experimental investigations, the molecular mechanisms responsible for Ca²⁺ oscillations have been much investigated with computational models. In the vast majority of cell-types, these oscillations rely on the biphasic regulation of the inositol 1,4,5-trisphosphate (InsP₃) receptor by cytosolic Ca²⁺. However, when Ca²⁺ oscillations are initiated by agonist stimulation of the type 5 metabotropic glutamate (mGlu5) receptor, oscillatory behaviour is tightly controlled by repetitive cycles of receptor phosphorylation/dephosphorylation leading to the periodic activation/deactivation of the G protein-activated signalling cascade downstream of this G protein-coupled receptor. We present a minimal model for mGlu5 receptor-induced Ca²⁺ oscillations, taking into account receptor phosphorylation by a protein kinase C isoenzyme sensitive to diacylglycerol but not to Ca²⁺. Depending on the density of receptors and the level of stimulation, the model reproduces Ca²⁺ oscillations based on either a ‘dynamic uncoupling’ mechanism or InsP₃ receptor dynamics. When based on the former mechanism, Ca²⁺ oscillation frequency is insensitive to the level of stimulation, while the level of receptor expression is a determinant of oscillation frequency. When investigating the conditions for the occurrence of oscillations, the model predicts that dynamic uncoupling likely relies on a steep relationship between the activity of PKC and the amount of phosphorylated mGlu5 receptor. Finally, we use the model to simulate the adaptation of the signalling pathway during periods of prolonged stimulation associated with receptor desensitization/internalization. The model suggests that the existence of both oscillatory mechanisms could allow for a significant lengthening of the repetitive Ca²⁺ responses under these conditions.     

Identification of an interaction between the TPalpha and TPbeta isoforms of the human thromboxane A2 receptor with protein kinase C-related kinase (PRK) 1: implications for prostate cancer

In humans, thromboxane (TX) A(2) signals through the TPα and TPβ isoforms of the TXA(2) receptor or TP. Here, the RhoA effector protein kinase C-related kinase (PRK) 1 was identified as an interactant of both TPα and ΤPβ involving common and unique sequences within their respective C-terminal (C)-tail domains and the kinase domain of PRK1 (PRK1(640-942)). Although the interaction with PRK1 is constitutive, agonist activation of TPα/TPβ did not regulate the complex per se but enhanced PRK1 activation leading to phosphorylation of its general substrate histone H1 in vitro. Altered PRK1 and TP expression and signaling are increasingly implicated in certain neoplasms, particularly in androgen-associated prostate carcinomas. Agonist activation of TPα/TPβ led to phosphorylation of histone H3 at Thr(11) (H3 Thr(11)), a previously recognized specific marker of androgen-induced chromatin remodeling, in the prostate LNCaP and PC-3 cell lines but not in primary vascular smooth muscle or endothelial cells. Moreover, this effect was augmented by dihydrotestosterone in androgen-responsive LNCaP but not in nonresponsive PC-3 cells. Furthermore, PRK1 was confirmed to constitutively interact with TPα/TPβ in both LNCaP and PC-3 cells, and targeted disruption of PRK1 impaired TPα/TPβ-mediated H3 Thr(11) phosphorylation in, and cell migration of, both prostate cell types. Collectively, considering the role of TXA(2) as a potent mediator of RhoA signaling, the identification of PRK1 as a bona fide interactant of TPα/TPβ, and leading to H3 Thr(11) phosphorylation to regulate cell migration, has broad functional significance such as within the vasculature and in neoplasms in which both PRK1 and the TPs are increasingly implicated.