The MoVIN server for the analysis of protein interaction networks

<p>Abstract</p> <p>Background</p> <p>Protein-protein interactions are at the basis of most cellular processes and crucial for many bio-technological applications. During the last few years the development of high-throughput technologies has produced several large-scale protein-protein interaction data sets for various organisms. It is important to develop tools for dissecting their content and analyse the information they embed by data-integration and computational methods.</p> <p>Results</p> <p>Interactions can be mediated by the presence of specific features, such as motifs, surface patches and domains. The co-occurrence of these features on proteins interacting with the same protein can indicate mutually exclusive interactions and, therefore, can be used for inferring the involvement of the proteins in common biological processes.</p> <p>We present here a publicly available server that allows the user to investigate protein interaction data in light of other biological information, such as their sequences, presence of specific domains, process and component ontologies. The server can be effectively used to construct a high-confidence set of mutually exclusive interactions by identifying similar features in groups of proteins sharing a common interaction partner. As an example, we describe here the identification of common motifs, function, cellular localization and domains in different datasets of yeast interactions.</p> <p>Conclusions</p> <p>The server can be used to analyse user-supplied datasets, it contains pre-processed data for four yeast Protein Protein interaction datasets and the results of their statistical analysis. These show that the presence of common motifs in proteins interacting with the same partner is a valuable source of information, it can be used to investigate the properties of the interacting proteins and provides information that can be effectively integrated with other sources. As more experimental interaction data become available, this tool will become more and more useful to gain a more detailed picture of the interactome.</p

Detecting Mutually Exclusive Interactions in Protein-Protein Interaction Maps

Comprehensive protein interaction maps can complement genetic and biochemical experiments and allow the formulation of new hypotheses to be tested in the system of interest. The computational analysis of the maps may help to focus on interesting cases and thereby to appropriately prioritize the validation experiments. We show here that, by automatically comparing and analyzing structurally similar regions of proteins of known structure interacting with a common partner, it is possible to identify mutually exclusive interactions present in the maps with a sensitivity of 70% and a specificity higher than 85% and that, in about three fourth of the correctly identified complexes, we also correctly recognize at least one residue (five on average) belonging to the interaction interface. Given the present and continuously increasing number of proteins of known structure, the requirement of the knowledge of the structure of the interacting proteins does not substantially impact on the coverage of our strategy that can be estimated to be around 25%. We also introduce here the Estrella server that embodies this strategy, is designed for users interested in validating specific hypotheses about the functional role of a protein-protein interaction and it also allows access to pre-computed data for seven organisms

FunClust: a web server for the identification of structural motifs in a set of non-homologous protein structures

The occurrence of very similar structural motifs brought about by different parts of non homologous proteins is often indicative of a common function. Indeed, relatively small local structures can mediate binding to a common partner, be it a protein, a nucleic acid, a cofactor or a substrate. While it is relatively easy to identify short amino acid or nucleotide sequence motifs in a given set of proteins or genes, and many methods do exist for this purpose, much more challenging is the identification of common local substructures, especially if they are formed by non consecutive residues in the sequence

The Effects of Acetylenic Tricyclic Bis-(Cyano Enone) on Cell Migration

Although cancer survival rates have significantly improved over the past few decades, the improvements are primarily due to early diagnosis and inhibiting cancer growth. Limited progress has been made in the treatment of cancer metastasis, which contributes to 90% of cancer related deaths, and therapeutic agents targeting the various aspects of metastasis are lacking. One potential approach is to utilize small pharmacological compounds to inhibit tumour cell motility, as a strategy against tumour cell migration, invasion, and metastasis. The acetylenic tricyclic bis-(cyano enone), TBE-31, has been shown to be a promising chemopreventative compound. However, its effects on cell migration are unknown. This thesis focuses on deciphering the molecular mechanisms TBE-31 utilizes to inhibit cell migration. I demonstrated that TBE-31 binds with cysteine 374 of actin, inhibits actin polymerization and stress fiber formation. These findings were applied to a model of epithelial-to-mesenchymal transition, a precursor event to metastasis, where I determined TBE-31 was able to inhibit the crucial rearrangement of cortical actin to form actin stress fibers, which prime tumour cells for migration. In addition to the actin cytoskeleton, I demonstrated that TBE-31 alters microtubule dynamics and organization. Microtubule-dependent trafficking was also shown to be disrupted by TBE-31, and the localization of the polarity proteins Rac1, IQGAP and Tiam1 were altered from the leading edge of migrating cells. Lastly, TBE-31 was shown to inhibit Rat2 and NIH3T3 fibroblast as well as H1299 non-small cell lung cancer tumour cell migration. Taken together, my work provides novel insights on the underlying mechanisms by which TBE-31 utilizes to inhibit cell migration and provide important knowledge for developing therapeutic compounds that target tumour cell motility in metastasis

Characterisation of the 3'-UTR of the COL5A1 gene: implication for musculoskeletal soft tissue injuries

COL5A1 encodes the α1 chain of type V collagen, a minor fibrillar collagen that is an important regulator of collagen fibril assembly. A polymorphism (rs12722, C/T) within the 3'-untranslated region (UTR) of COL5A1 is associated with chronic Achilles tendinopathy (TEN) and other soft tissue injuries as well as exercise-related phenotypes. These phenotypes are directly or indirectly associated with the mechanical properties of musculoskeletal soft tissue. It has therefore been hypothesised that variants in the COL5A1 gene, specifically the 3'-UTR, regulate synthesis of the α1(V) chain and type V collagen production. Type V collagen levels in turn regulate fibril architecture and structure and, thereby, mechanical properties of musculoskeletal soft tissues. Although the 3'-UTR of many eukaryotic genes have been shown to play an important regulatory role, the function of the COL5A1 3'-UTR is currently unknown. Aim. The primary aim of this thesis was therefore to determine whether the COL5A1 3'-UTR was functional and to identify functional differences between the COL5A1 3'-UTR cloned from participants with TEN and healthy asymptomatic control individuals. The secondary aim was to start mapping the functional regions within the 3'-UTR, focusing on regions which are potentially responsible for contributing to the tendinopathic phenotype

FAM49 - A novel regulator of the protrusive behaviour and motility of cells

Most eukaryotic cell motility relies on plasma membrane protrusions, which depend on the actin cytoskeleton and its tight regulation. The SCAR/WAVE complex, a pentameric assembly comprising SCAR/WAVE, Nap1, CYFIP/Pir121, Abi and HSPC300, is a key driver of actin-based protrusions such as pseudopods. SCAR/WAVE is thought to activate the Arp2/3 complex, a crucial actin nucleator, after being itself activated by upstream signals such as active Rac1. Despite recent progress on the study of the SCAR/WAVE complex, its regulation is still incompletely understood, with Nap1’s role being particularly enigmatic. Upon screening for potential Nap1 binding partners in the social amoeba Dictyostelium discoideum – a well established model organism in the study of the actin cytoskeleton and cell motility – we found FAM49, a ~36 kDa protein of unknown function which is highly conserved in Metazoa (animals) and evolutionarily closer species such as D. discoideum. Interestingly, D. discoideum’s FAM49 and its homologs contain a DUF1394 domain, which is also predicted in CYFIP/Pir121 proteins and most likely involved in their direct binding to active Rac1, which in turn contributes to SCAR/WAVE’s activation. FAM49’s unknown role, apparent high degree of conservation and potential connections to SCAR/WAVE and Rac1 persuaded us to start investigating its function and biological relevance in D. discoideum, leading to the work presented in this thesis. Several pieces of our data collectively support a function for FAM49 in modulating the protrusive behaviour, and ultimately motility, of D. discoideum cells, as well as a regulatory link between FAM49 and Rac1. FAM49’s involvement in protrusion regulation was first hinted at by our observation that GFP-tagged FAM49 is enriched in pseudopods. The possibility of a link with Rac1 was then strengthened by two additional observations: first, pseudopodial GFP-FAM49 is substantially co-enriched with active Rac, both showing fairly comparable spatio-temporal accumulation dynamics; second, when dominant-active (G12V) Rac1 is expressed in cells, it triggers the recruitment and persistent accumulation of GFP-FAM49 at the plasma membrane, where both become highly co-enriched. We subsequently determined that fam49 KO cells differ from wild-type cells in the way they protrude and move, as assessed in under-agarose chemotaxis assays. In particular, our data indicate that fam49 KO cells tend to display a lower degree of global protrusive activity, their protrusions extend more slowly and are less discrete, and the cells end up moving at lower speeds and with higher directional persistence. This phenotype was substantially rescued by FAM49 re-expression. While re-expressing FAM49 in fam49 KO cells we generated putative FAM49 overexpressor cells; compared to wild-type cells, they displayed atypically thin pseudopods and what seemed to be an excessively dynamic, and perhaps less coordinated, protrusive behaviour. Additional data in our study suggest that pseudopods made by fam49 KO cells are still driven by SCAR/WAVE, which is clearly not being replaced by WASP (as is now known to be the case in D. discoideum cells lacking a functional SCAR/WAVE complex). Nonetheless, the peculiar dynamics of those pseudopods imply that SCAR/WAVE’s activity is regulated differently when FAM49 is lost, though it remains to be determined how. This thesis is the first report of a dedicated study on FAM49 and lays the foundation for future research on it

Biopsychosocial-Spiritual Factors Impacting African American Patients' Cardiac Rehabilitation Referral and Participation

African Americans carry a heavier burden of cardiovascular risk factors and have higher rates of death from coronary heart disease than any other racial/ethnic group in the United States, yet they are also less likely to be referred to, participate in, or benefit from Cardiac Rehabilitation (CR). In order to investigate the demographic and biopsychosocial-spiritual factors impacting African American patients' referral to and participation in CR, three research articles were completed: (a) a systematic review of the literature regarding this topic; (b) a descriptive phenomenological study designed to explore the lived experience of seven African American patients recovering from cardiac events and/or surgeries; and (c) a policy brief synthesizing the findings from a systematic review of the literature and a mixed methods study to offer policy-, programmatic-, and individual-level recommendations to best support African American patients' recovery from cardiac events and/or experiences. The systematic review demonstrated a paucity of studies on the demographic and biopsychosocial-spiritual factors impacting African American patients' CR referral and attendance. The studies that were identified demonstrated that, among African American patients, there was a lower likelihood for CR referral, a higher likelihood of enrolling in CR with more cardiovascular risk factors, and a lower likelihood of CR participation and completion due to factors related to low socioeconomic status. The phenomenological study resulted in six emergent themes relevant to the lived experience of seven African Americans (4 men and 3 women) who had experienced a cardiac event and/or surgery: (a) Participants valued medical providers' involvement during treatment and recovery; (b) Social support and participants' need for it changed post-event/surgery; (c) Participants' pre- and post-event/surgery experiences affected health outcomes; (d) Participants' sense of agency affected their life perspectives and health behaviors; (e) Participants experienced inconsistent referral to and utilization of CR; and (f) Participants' investment in faith was intensified or maintained. The policy brief emphasized the role of patients' education and income levels in their likelihood to attend CR. Recommendations for improving cardiac outcomes for African American patients in the rural Southeast included systematizing orders for CR on discharge paperwork, assessing and accounting for patients' levels of social support and spiritual resources, and coaching medical providers to reinforce treatment recommendations in a way that is understandable to patients and opens up discussion regarding potential biopsychosocial-spiritual barriers to implementing these recommendations.  Ph.D