Protein-protein interactions are of great importance to a number of essential biological processes including cell cycle regulation, cell-cell interactions, DNA replication, transcription and translation. Thus, an understanding of protein-protein interactions is critical for understanding many facets of cell function. Unfortunately, the tools and methods currently in use to identify and study protein-protein interactions focus largely on high affinity, stable interactions. However, the majority of the protein-protein interactions involved in regulatory processes have weak affinities and are transient in nature. Therefore, it is important to develop new biotechnology capable of detecting weak and/or transient protein-protein interactions in vivo. Here, we describe four new methods that allow for the identification and study of weak and/or transient protein-protein interactions in vivo. First, we developed a rapid method to convert Escherichia coli orthogonal tRNA/synthetase pairs into an orthogonal system for mammalian cells in order to site-specifically incorporate unnatural amino acids into any gene of interest using stop codon suppression. This method will allow the expression and purification of proteins that carry normally transient post-translational modifications. Second, we successfully employed site-specific unnatural amino acid incorporation to chemically cross-link a known homodimer, Sortase A, in vivo. Third, we developed a novel tetracycline repressor-based mammalian two-hybrid system and successfully detected homo- and hetero-dimers that are known to have weak binding constants. Finally, a synthetic antibody (termed a synbody) that binds weakly to the SH3 domain of the proto-oncogene Abelson tyrosine kinase was developed. The synbody can potentially be used as a first generation drug and/or biomarker. We hope that the methods developed in this dissertation will enable the scientific community to better understand weak/transient protein-protein interactions in vivo. / text

published_or_final_version / Chemistry / Doctoral / Doctor of Philosophy

Tight junctions, as zones of close contact between epithelial and endothelial cells, form a physical barrier as one of the first host defense strategies that prevent the intrusion of pathogens across epithelia and endothelia. Recently, an interaction between the Severe Acute Respiratory Syndrome-Coronavirus (SARS-CoV) envelope protein (E) and PALS1, a member of the CRB tight junction complex, was identified in the Virus-Host Interaction group at HKU-Pasteur Research Centre (Teoh et al, 2010). In this report, I present in vitro data which helps to better understand how this protein-protein interaction could interfere with the formation and maintenance of tight junctions at the apical domain of epithelial cells. In previous research, the interaction between E and PALS1 was identified through a yeast two-hybrid screen and confirmed in vitro. A PDZ-binding motif (PBM) was identified at the C-terminal end of E, which interacts with the PDZ domain of PALS1. The objective of my research was to further enhance the knowledge of this interaction by studying the effect of E expression on PALS1 localization and tight junction structure in epithelial cells. I have shown that expression of E is associated with a partial relocalization of PALS1 to the Golgi compartment. Also, I discovered that when wild-type E, E(wt), was expressed in the MDCKII cell model, the time required for tight junction formation was extended to 6-8 hours, while normal cells only required two hours. Interestingly, expression of the E protein with a deletion of the PBM, E(ΔPBM) did not affect the timing of tight junction formation. This finding indicates that the PBM plays a critical role in the process of alteration of tight junctions mediated by E, most likely through its interaction with PALS1. Furthermore, the localization pattern of E was altered when its PBM was deleted. In the MDCKII model, E(wt) located, as expected, at membranes of the Golgi compartment, whereas E(ΔPBM) had a diffused distribution in the cytosol. This observation suggests that the PBM acts as a localization signal for the E protein to the Golgi region, which is the assembly site of the virus. Finally, to examine the role of the PBM in the context of the whole virus, I participated in the production of SARS-CoV recombinant viruses, with mutations in the PBM of E. Though this work is still in progress, the use of these viruses should help to delineate the role of E PBM in SARS-CoV induced pathogenesis in vitro and ultimately in vivo. / published_or_final_version / Pathology / Master / Master of Philosophy

The functional aspects of proteins are largely dictated by highly selective protein- protein and protein-ligand interactions, even in situations of high structural homology, where electrostatic factors are the major contributors to selectivity. The vibrational Stark effect (VSE) allows us to measure electrostatic fields in complex environments, such as proteins, by the introduction of a vibrational chromophore whose vibrational absorption energy is linearly sensitive to changes in the local electrostatic field. The works presented here seek to computationally quantify electrostatic fields measured via VSE, with the eventual goal of being able to quantitatively predict electrostatic fields, and therefore Stark shifts, for any given protein-interaction. This is done using extensive molecular dynamics in the Amber03 and AMOEBA force fields to generate large ensembles the GTPase Rap1a docked to RalGDS and [superscript p]²¹Ras docked to RalGDS. We discuss how side chain orientations contribute to the differential binding of different mutations of Rap1a binding to RalGDS, where it was found that a hydrogen-bonding pocket is disrupted by the mutation of position 31 from lysine to glutamic acid. We then show that multi-dimensional umbrella sampling of the probe orientations yields a wider range of accessible structures, increasing the quality of the ensembles generated. A large variety of methods for calculating electrostatic fields are presented, with Poisson- Boltzmann electrostatics yielding the most consistent, reliable results. Finally, we explore using AMOEBA for both ensemble-generation as well as the electrostatic description of atoms for field calculations, where early results suggest that the electrostatic field due to the induce dipole moment of the probe is responsible for predicting qualitatively correct Stark shifts.

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R1162 is a broad-host range, mobilizable plasmid conferring resistance to streptomycin and sulfonamides. Efficient conjugative mobilization of R1162 requires three plasmid-encoded proteins: MobA, MobB and MobC. MobA binds plasmid DNA at the origin of transfer (oriT), nicks the subsequently transferred strand and ligates the ends of the strand after transfer into the recipient. The N-terminal region of this protein carries out this DNA processing. The C-terminal half is a primase required to initiate DNA synthesis at two single-stranded priming sites sites, oriL and oriR, during vegetative plasmid replication. The primase region of MobA is not necessary for DNA processing by the N-terminal part of the protein, however its role in strand replacement during conjugation is not clearly defined. This study demonstrates that R1162 can undergo multiple rounds of transfer from a single plasmid molecule. The presence of oriL increases the frequency of second-round transfer, presumably due to initiation of replacement strand synthesis at this site by R1162 primase in the donor. Priming at oriR by the primase region of MobA is required for efficient replacement strand synthesis in the recipient when the plasmid is transferred to Salmonella. When the plasmid is transferred into E. coli, the plasmid-encoded priming system is not required for strand replacement in the recipient, presumably due to a host-encoded mechanism capable of priming the transferred strand. Transport of MobA through the R751 conjugative pore was also investigated. The two domains of MobA can be transported to recipient cells independently of each other. However, MobB is required for the transport of either fragment. Two sites, named the R-site and the P-site, are located in the relaxase and primase domains of MobA, respectively, and make up part of the signals required for MobA transport. Unlike previously described type IV transport signals, domain structure is required for the MobA transport signals to be active. / text

Microarray technology has revolutionized the field of molecular biology by offering an efficient and cost effective platform for the simultaneous quantification of thousands of genes or even entire genomes in a single experiment. Unlike southern blotting, which is restricted to the measurement of one gene at-a-time, microarrays offer biologists with the opportunity to carry out genome-wide experiments in order to help them gain a systems level understanding of cell regulation and control. The application of bioinformatics in the milieu of gene expression analysis has attracted a great deal of attention in the recent past due to specific algorithms and software solutions that attempt to illustrate complex multidimensional microarray data in a biologically coherent fashion so that it can be understood by the biologist. This has given rise to some exciting prospects for deciphering microarray data, by helping us refine our comprehension pertinent to the underlying physiological dynamics of disease. Although much progress is being made in the development of specialized bioinformatics software pipelines with the purpose of decoding large volumes of gene expression data in the context of systems biology, several loopholes exist. Perhaps most notable of these loopholes is the fact that there is an increasing demand for software solutions that specialize in automating the comparison of multiple gene expression profiles, derived from microarray experiments sharing a common biological theme. This is no doubt an important challenge, since common genes across different biological conditions having similar expression patterns are likely to be involved in the same biological process and hence, may share the same regulatory signatures. The potential benefits of this in refining our understanding of the physiology of disease are undeniable. The research presented in this thesis provides a systematic walkthrough of a series of software pipelines developed for the purpose of streamlining gene expression analysis in a systems biology context. Firstly, we present BiSAn, a software tool that deciphers expression data from the perspective of transcriptional regulation. Following this, we present Genome Interaction Analyzer (GIA), which analyzes microarray data in the integrative framework of transcription factor binding sites, protein-protein interactions and molecular pathways. The final contribution is a software pipeline called MicroPath, which analyzes multiple sets of gene expression profiles and attempts to extract common regulatory signatures that may be implicating the biological question.

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Το επιστημονικό ενδιαφέρον της παρούσας διδακτορικής διατριβής εστιάζεται στο ρόλο του κυτταροσκελετού της δεσμίνης (desmin), της μυοειδικής πρωτεΐνης, μέλος της οικογένειας των ενδιάμεσων ινιδίων, στη διατήρηση και τη λειτουργία του καρδιακού μυός. H καταστολή της έκφρασης της δεσμίνης σε μύες με τη χρησιμοποίηση της γονιδιακής στόχευσης, έδειξε πως η έκφραση της δεσμίνης είναι απαραίτητη για τη διατήρηση της λειτουργικής και δομικής ακεραιότητας του καρδιακού μυός. Μύες που δεν εκφράζουν δεσμίνη αναπτύσσουν διατατική καρδιομυοπάθεια, που χαρακτηρίζεται από ανωμαλίες σε υποκυτταρικά οργανίδια, όπως είναι τα μιτοχόνδρια, εκτεταμένη ίνωση και εναπόθεση ασβεστίου, με επακόλουθο τον κυτταρικό θάνατο, και τελικά την καρδιακή ανεπάρκεια. Πιο συγκεκριμένα σε μια προσπάθεια διερεύνησης της βιολογικής δράσης της δεσμίνης, μελετήθηκαν οι πρωτεϊνικές αλληλεπιδράσεις αυτού του μορίου. Η ανεύρεση μορίων με τα οποία η δεσμίνη αλληλεπιδρά μπορεί να δώσει σημαντικές πληροφορίες για τη βιολογικής της δράση και να βοηθήσει στην κατανόηση της παθολογίας που παρατηρείται σε επίμυς όπου έχει κατασταλεί η έκφρασή της (διαγονιδιακό μοντέλο διατατικής καρδιομυοπάθειας που έχει δημιουργηθεί από το εργαστήριό μας, des-/-) ή σε ασθενείς με καρδιομυοπάθειες εξαιτίας μεταλλαγών στο μόριο της δεσμίνης. Για το σκοπό αυτό εφαρμόστηκε η μέθοδος του διυβριδικού συστήματος ζύμης (Yeast two-hybrid), όπου χρησιμοποιήθηκε τμήμα του μορίου της δεσμίνης (το αμινο-τελικό άκρο), με το οποίο ‘σαρώθηκε’ (screening) μια cDNA καρδιακή βιβλιοθήκη, και βρέθηκε ένας αριθμός δυνητικών αλληλεπιδράσεων. Η σάρωση αποκάλυψε την αλληλεπίδραση της δεσμίνης με ένα νέο μόριο, τη Myospryn, μια μυοειδική πρωτεΐνη 413 kDa, μέλος της οικογένειας των TRIM-like πρωτεϊνών. Η πρωτεΐνη myospryn βρέθηκε αρχικά να αλληλεπιδρά με την πρωτεΐνη dysbindin, η οποία εμπλέκεται σε διαδικασίες διαμετακίνησης πρωτεϊνών, κυστιδίων και βιοσύνθεσης οργανιδίων, και αποτελεί συστατικό ενός πρωτεϊνικού συμπλόκου υπεύθυνου για τη βιογένεση λυσοσωμάτων και λυσοσωματικά συσχετιζόμενων οργανιδίων, γνωστό ως Biogenesis of Lysosome Related Organelles (BLOC-1). Η πρόσδεση της δεσμίνης με τη myospryn επαληθεύτηκε με in vitro μεθόδους (GST pull down assay, Co-immunoprecipitation). H ανάλυση ανοσοαποτύπωσης (western blot) απεκάλυψε ότι το ανοσολογικό σύμπλοκο που κατακρημνίζεται με χρήση αντισωμάτων δεσμίνης περιέχει, εκτός της myospryn, και δυο τουλάχιστον υπομονάδες του πρωτεϊνικού συμπλόκου BLOC-1, dysbindin και pallidin. Πειράματα με το δι-υβριδικό σύστημα ζύμης απεκάλυψαν την ακριβή περιοχή αλληλεπίδρασης των δύο πρωτεϊνών, και η οποία περιλαμβάνει τα αα58-103 του αμινο-τελικού άκρου της δεσμίνης και τα τελευταία 24αα του καρβόξυ-τελικού άκρου του μορίου της myospryn, που αντιστοιχούν στο SPRY τμήμα του TRIM-like μοτίβου της οικογένειας των πρωτεϊνών στην οποία ανήκει η myospryn. Πειράματα ανοσοφθορισμού σε απομονωμένα καρδιομυοκύτταρα απεκάλυψαν ότι η myospryn τοπολογείται στην περιφέρεια του πυρήνα, σε στενή γειτνίαση με τις μεμβράνες του ενδοπλασματικού δικτύου, και στο σημείο αυτό αλληλο-επικαλύπτεται με τη δεσμίνη, η οποία σχηματίζει ένα δίκτυο ινιδίων που διατρέχει όλο το μήκος του κυττάρου. Στον ενήλικο καρδιακό ιστό, η myospryn βρίσκεται κυρίως στους εμβόλιμους δίσκους, καθώς και στο επίπεδο της πλασματικής μεμβράνης, του σαρκολείματος, όπου και αλληλοεπικαλύπτεται με τη δεσμίνη. Η αλληλο-επικάλυψη των δυο πρωτεϊνών είναι έντονη στο επίπεδο των εμβόλιμων δίσκων. Δείχθηκε πως η myospryn άλληλο-επικαλύπτεται με τα λυσοσώματα καθώς και ότι η δεσμίνη είναι απαραίτητη τόσο για τη σωστή τοπολόγηση της myospryn, όσο και για αυτήν των λυσοσωμάτων. Τέλος, με πειράματα καταστολής τηw έκφρασης της myospryn, αποκαλύφθηκε πως η παρουσία της myospryn είναι απαραίτητη προκειμένου η δεσμίνη να μπορεί να ανοσοκατακρημνίσει τις υπομονάδες του BLOC-1, dysbindin και pallidin Τέλος, στην προσπάθεια χαρακτηρισμού του λειτουργικού ρόλου της myospryn συμπεριλήφθηκε η χρησιμοποίηση του μοντέλου του D. rerio (zebrafish). Χρησιμοποιώντας την τεχνολογία των antisense morpholinos, ήταν δυνατή η παρεμπόδιση της έκφρασης της myospryn και η μελέτη των επιπτώσεων στην ανάπτυξη και λειτουργία του καρδιακού ιστού. Η καταστολή της έκφρασης της myospryn είχε ως αποτέλεσμα σοβαρές δομικές και λειτουργικές ανωμαλίες στο καρδιακό σύστημα ατόμων Danio rerio, καταδεικνύοντας την σπουδαιότητα αυτού του μορίου στην ανάπτυξη του καρδιακού συστήματος του D.rerio. Συμπερασματικά η παρούσα διδακτορική διατριβή διαπραγματεύεται τις πρωτεϊνικές αλληλεπιδράσεις της μυοειδικής πρωτεΐνης δεσμίνης, αποκαλύπτοντας νέους ρυθμιστικούς ρόλους για το μόριο αυτό. / The scientific interest of this PhD thesis is mainly the role of desmin cytoskeleton (the muscle-specific intermediate filament) in myocyte maintenance and function. The ablation of desmin expression in mice by gene targeting demonstrated that desmin expression is crucial for maintanance of healthy muscle. Mice null for desmin develop dilated cardiomyopathy characterized by mitochondrial abnormalities, extensive cardiomyocyte death, fibrosis, calcification and eventually heart failure. Study of desmin protein interactions could facilitate our understanding of the molecular mechanisms responsible for the observed pathology. To that end, we have performed a yeast two-hybrid screening of a cardiac cDNA library We showed that the desmin amino-terminal domain [Naa(1 -103)] binds to a 413kDa TRIM-like protein, myospryn, originally identified as the muscle-specific partner of dysbindin, a component of the Biogenesis of Lysosome Related Organelles Complex 1 (BLOC-1). Binding of desmin with myospryn was confirmed with GST pull down assays and co-immunoprecipitation experiments. Western blot analysis revealed that the complex immunoprecipitated by desmin antibodies, in addition to myospryn contained the BLOC-1 components dysbindin and pallidin. Deletion analysis revealed that only the [Naa(1 -103)] fragment of desmin binds to myospryn carboxyl terminus and that this association takes place through the 24aa long C-terminal end of the SPRY domain of myospryn. Using an antibody against the COOH terminus of myospryn, we demonstrated that myospryn co-localizes with desmin at the periphery of the nucleus, in close proximity to the endoplasmic reticulum, of mouse neonatal cardiomyocytes. In adult heart muscle, the two proteins co localize, predominantly, at intercalated discs and costameres. We also showed that myospryn colocalizes with lysosomes. Using desmin null hearts, we demonstrated that desmin is required for both the proper perinuclear localization of myospryn, as well as the proper positioning of lysosomes, thus suggesting a potential role of desmin IFs in lysosomes and lysosome-related organelle biogenesis and/or positioning. siRNAs experiments for myospryn knock down revealed that when myospryn is absent, desmin is not able to immunoprecipitate BLOC-1 subunits. Additionally, the in vivo role of myospryn was examined using the model of D. rerio. Using a splice morpholino for knocking down myospryn transcript, we examined the effects on zebrafish heart development and function caused by the absence of myospryn, where it was shown that myospryn is essential for the early heart development in D.rerio. In summary, this work reveals the association of desmin with a novel molecule, myospryn, and it sheds light on novel regulatory role for this member of intermediate filament family.