Identification of hub proteins from sequence

Identification of hub proteins from sequence is a challenge in molecular biology. Therefore, it is of interest to predict protein hubs in networks. We describe the prediction of protein "hub" using physiochemical, thermodynamic and conformational properties of amino acid residues in sequence. We have used twenty sequence based features to identify hub behaviour. Linear discriminant analysis and normalised Bayesian approach were utilized for identifying hub proteins solely using these sequence features in E. coli/H. sapiens datasets with accuracies of 99.5/98.6, 87.8/89.6 and 90.1/92.6, respectively.     

Evolutionary and physiological importance of hub proteins

It has been claimed that proteins with more interaction partners (hubs) are both physiologically more important (i.e., less dispensable) and, owing to an assumed high density of binding sites, slow evolving. Not all analyses, however, support these results, probably because of biased and less-than reliable global protein interaction data. Here we provide the first examination of these issues using a comprehensive literature-curated dataset of well-substantiated protein interactions in Saccharomyces cerevisiae. Whereas use of less reliable yeast two-hybrid data alone can reject the possibility that local connectivity correlates with measures of dispensability, in higher quality datasets a relatively robust correlation is observed. In contrast, local connectivity does not correlate with the rate of protein evolution even in reliable datasets. This perhaps surprising lack of correlation with evolutionary rate appears in part to arise from the fact that hub proteins do not have a higher density of residues associated with binding. However, hub proteins do have at least one other set of unusual features, namely rapid turnover and regulation, as manifest in high mRNA decay rates and a large number of phosphorylation sites. This, we suggest, is an adaptation to minimize unwanted activation of pathways that might be mediated by adventitious binding to hubs, were they to actively persist longer than required at any given time point. We conclude that hub proteins are more important for cellular growth rate and under tight regulation but are not slow evolving.     

How geneticists can help reporters to get their story right

Many geneticists are disgruntled with the coverage of genetics in the mass media, yet geneticists themselves have a part to play in improving that coverage. This article aims to help geneticists to do so by explaining the forces that shape science news. It provides some specific options for reducing hype, countering genetic determinism and preventing the use of genetics to reinforce discriminatory messages, slants that many reporters are inclined to give to their articles.     

Toxin entry: how bacterial proteins get into mammalian cells

Certain bacteria secrete protein toxins that catalytically modify and disrupt essential processes in mammalian cells, often leading to cell death. As the substrates modified by these toxins are located in the mammalian cell cytosol, a catalytically active toxin polypeptide must reach this compartment in order to act. The toxins bind to receptors on the surface of susceptible cells and enter them by endocytic uptake. Endocytosed toxins initially accumulate in endosomes, where some of these proteins take advantage of the acidic environment within these organelles to form, or contribute to the formation of, protein-conducting channels through which the catalytic polypeptide is able to translocate into the cytosol. Other toxins are unable to respond to low pH in this way and must undergo intracellular vesicular transport to reach a compartment where pre-existing protein-conducting channels occur and can be exploited for membrane translocation — the endoplasmic reticulum. In this way, cell entry by this second group of toxins demonstrates that the secretory pathway of mammalian cells is completely reversible.     

Enzymatic conversion of proteins to glycoproteins by lipid-linked saccharides: A study of potential exogenous acceptor proteins

Previous studies have shown that a membrane preparation from hen oviduct catalyzes transfer of oligosaccharide from oligosaccharide-P-P-dolichol to denatured RNase and α-lactalbumin. To gain further insight into the structural requirements of a protein that allow it to serve as a substrate for glycosylation, the acceptor ability of a variety of other modified proteins containing the tripeptide sequence -ASN-X-(SER/THR)- has been investigated. Of 7 proteins tested, 2 (ovine prolactin and rabbit muscle triosephosphate isomerase) could be enzymatically glycosylated by a particulate preparation from hen oviduct. The remaining 5 proteins, assayed as either S-carboxy-methylated or S-aminoethylated derivatives, were inactive as carbohydrate acceptors. However, cyanogen bromide treatment of 2 of the inactive proteins, bovine catalase and concanavalin A from jack bean, yielded peptide fragments which served as substrates for glycosylation. These results suggests that for some proteins, disruption of the tertiary structure is sufficient to allow attachment of carbohydrate. Other denatured proteins may possess additional restrictions imposed by their secondary structure. In certain cases, these restrictions are removed when the polypeptide chain is fragmented.     

Exploring the evolutionary rate differences of party hub and date hub proteins in Saccharomyces cerevisiae protein-protein interaction network

Evolutionary rates of party hub and date hub proteins of Saccharomyces cerevisiae are analyzed under the perspective of ordered/disordered ness of proteins and the three dimensional structural context such as the solvent accessibility of the amino acid residues. Our results suggest that the lowering of evolutionary rate of the party hub proteins than the date hub proteins is solely contributed by the ordered regions of the corresponding proteins. Moreover the slower evolutionary rate of the party hub proteins than the date hub counterparts can be attributed to the presence of buried amino acid residues. Thus, our work endeavors further into the understanding of the evolutionary rate differences of the two different types of hub proteins of S. cerevisiae.     

Motor proteins: kinesin can replace Myosin

Directional transport of specific cargos is tuned to specific molecular motors and specific cytoskeletal tracks. Myosin V transports its cargo on actin cables, whereas kinesin or dynein transport their cargo on microtubules. A recent study shows that an engineered kinesin can substitute for myosin V and its cargo-specific transport and subsequent cellular functions.     

Molecular motors: strategies to get along

The majority of active transport in the cell is driven by three classes of molecular motors: the kinesin and dynein families that move toward the plus-end and minus-end of microtubules, respectively, and the unconventional myosin motors that move along actin filaments. Each class of motor has different properties, but in the cell they often function together. In this review we summarize what is known about their single-molecule properties and the possibilities for regulation of such properties. In view of new results on cytoplasmic dynein, we attempt to rationalize how these different classes of motors might work together as part of the intracellular transport machinery. We propose that kinesin and myosin are robust and highly efficient transporters, but with somewhat limited room for regulation of function. Because cytoplasmic dynein is less efficient and robust, to achieve function comparable to the other motors it requires a number of accessory proteins as well as multiple dyneins functioning together. This necessity for additional factors, as well as dynein's inherent complexity, in principle allows for greatly increased control of function by taking the factors away either singly or in combination. Thus, dynein's contribution relative to the other motors can be dynamically tuned, allowing the motors to function together differently in a variety of situations.     

UV-light-induced conversion and aggregation of prion proteins

Increasing evidence suggests a central role for oxidative stress in the pathology of prion diseases, a group of fatal neurodegenerative disorders associated with structural conversion of the prion protein (PrP). Because UV-light-induced protein damage is mediated by direct photo-oxidation and radical reactions, we investigated the structural consequences of UVB radiation on recombinant murine and human prion proteins at pH 7.4 and pH 5.0. As revealed by circular dichroism and dynamic light scattering measurements, the observed PrP aggregation follows two independent pathways: (i) complete unfolding of the protein structure associated with rapid precipitation or (ii) specific structural conversion into distinct soluble β-oligomers. The choice of pathway was directly attributed to the chromophoric properties of the PrP species and the susceptibility to oxidation. Regarding size, the oligomers characterized in this study share a high degree of identity with oligomeric species formed after structural destabilization induced by other triggers, which significantly strengthens the theory that partly unfolded intermediates represent initial precursor molecules directing the pathway of PrP aggregation. Moreover, we identified the first suitable photo-trigger capable of inducing refolding of PrP, which has an important biotechnological impact in terms of analyzing the conversion process on small time scales.     

Antiapoptotic herpesvirus Bcl-2 homologs escape caspase-mediated conversion to proapoptotic proteins

The antiapoptotic Bcl-2 and Bcl-x(L) proteins of mammals are converted into potent proapoptotic factors when they are cleaved by caspases, a family of apoptosis-inducing proteases (E. H.-Y. Cheng, D. G. Kirsch, R. J. Clem, R. Ravi, M. B. Kastan, A. Bedi, K. Ueno, and J. M. Hardwick, Science 278:1966-1968, 1997; R. J. Clem, E. H.-Y. Cheng, C. L. Karp, D. G. Kirsch, K. Ueno, A. Takahashi, M. B. Kastan, D. E. Griffin, W. C. Earnshaw, M. A. Veliuona, and J. M. Hardwick, Proc. Natl. Acad. Sci. USA 95:554-559, 1998). Gamma herpesviruses also encode homologs of the Bcl-2 family. All tested herpesvirus Bcl-2 homologs possess antiapoptotic activity, including the more distantly related homologs encoded by murine gammaherpesvirus 68 (gammaHV68) and bovine herpesvirus 4 (BHV4), as described here. To determine if viral Bcl-2 proteins can be converted into death factors, similar to their cellular counterparts, five herpesvirus Bcl-2 homologs from five different viruses were tested for their susceptibility to caspases. Only the viral Bcl-2 protein encoded by gammaHV68 was susceptible to caspase digestion. However, unlike the caspase cleavage products of cellular Bcl-2, Bcl-x(L), and Bid, which are potent inducers of apoptosis, the cleavage product of gammaHV68 Bcl-2 lacked proapoptotic activity. KSBcl-2, encoded by the Kaposi's sarcoma-associated herpesvirus, was the only viral Bcl-2 homolog that was capable of killing cells when expressed as an N-terminal truncation. However, because KSBcl-2 was not cleavable by caspases, the latent proapoptotic activity of KSBcl-2 apparently cannot be released. The Bcl-2 homologs encoded by herpesvirus saimiri, Epstein-Barr virus, and BHV4 were not cleaved by apoptotic cell extracts and did not possess latent proapoptotic activities. Thus, herpesvirus Bcl-2 homologs escape negative regulation by retaining their antiapoptotic activities and/or failing to be converted into proapoptotic proteins by caspases during programmed cell death.