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.

Kinetic target-guided synthesis (TGS) and in situ click chemistry are among unconventional discovery strategies having the potential to streamline the development of protein-protein interaction modulators (PPIMs). In kinetic TGS and in situ click chemistry, the target is directly involved in the assembly of its own potent, bidentate ligand from a pool of reactive fragments. Herein, we report the use and validation of kinetic TGS based on the sulfo-click reaction between thio acids and sulfonyl azides as a screening and synthesis platform for the identification of high-quality PPIMs. Starting from a randomly designed library consisting of nine thio acids and nine sulfonyl azides leading to eighty one potential acylsulfonamides, the target protein, Bcl-XL selectively assembled four PPIMs, acylsulfonamides SZ4TA2, SZ7TA2, SZ9TA1, and SZ9TA5, which have been shown to modulate Bcl-XL/BH3 interactions. To further investigate the Bcl-XL templation effect, control experiments were carried out using two mutants of Bcl-XL. In one mutant, phenylalanine Phe131 and aspartic acid Asp133, which are critical for the BH3 domain binding, have been substituted by alanines, while arginine Arg139, a residue identified to play a crucial role in the binding of ABT-737, a BH3 mimetic, has been replaced by an alanine in the other mutant. Incubation of these mutants with the reactive fragments and subsequent LC/MS-SIM analysis confirmed that these building block combinations yield the corresponding acylsulfonamides at the BH3 binding site, the actual "hot spot" of Bcl-XL. These results validate kinetic TGS using the sulfo-click reaction as a valuable tool for the straightforward identification of high-quality PPIMs. Protein-protein interactions of the Bcl-2 family have been extensively investigated and the anti-apoptotic proteins (Bcl-2, Bcl-XL, and Mcl-1) have been validated as crucial targets for the discovery of potential anti-cancer agents. At the outset, Bcl-2 and Bcl-XL were considered to play an important role in the regulation of apoptosis. Accordingly, several small molecule inhibitors targeting Bcl-2 and/or Bcl-XL proteins were primarily designed. A series of acylsulfonamides targeting these proteins were reported by Abbott laboratories, ABT-737 and ABT-263 being the most potent candidates. Remarkably, these molecules were found to exhibit weaker binding affinities against Mcl-1, another anti-apoptotic protein. Further experimental evidence suggests that, inhibitors targeting Mcl-1 selectively or in combination with other anti-apoptotic proteins would lead to desired therapeutic effect. As a result, numerous small molecules displaying activity against Mcl-1 have been identified so far. Specifically, acylsulfonamides derived from structure activity relationship by interligand nuclear overhauser effect (SAR by ILOEs), a fragment-based approach, have been recently reported with binding affinities in the nanomolar range. In the meantime, we have reported that the kinetic TGS approach can also be applied to identify acylsulfonamides as PPIMs targeting Bcl-XL. Taken together, structurally novel acylsulfonamides can be potentially discovered as Mcl-1 inhibitors using the kinetic TGS approach. Thus, a library of thirty one sulfonyl azides and ten thio acids providing three hundred and ten potential products was screened against Mcl-1 and the kinetic TGS hits were identified. Subsequently, control experiments involving Bim BH3 peptide were conducted to confirm that the fragments are assembled at the binding site of the protein. The kinetic TGS hits were then synthesized and subjected to the fluorescence polarization assay. Gratifyingly, activities in single digit micromolar range were detected, demonstrating that the sulfo-click kinetic TGS approach can also be used for screening and identification of acylsulfonamides as PPIMs targeting Mcl-1. The amide bond serves as one of nature's most fundamental functional group and is observed in a large number of organic and biological molecules. Traditionally, the amide functionality is introduced in a molecule through coupling of an amine and an activated carboxylic acid. Recently, various alternative methods have been reported wherein, the aldehydes or alcohols are oxidized using transition metal catalysts and are treated with amines to transform into the corresponding amides. These transformations however, require specially designed catalysts, long reaction times and high temperatures. We herein describe a practical and efficient amidation reaction involving aromatic aldehydes and various azides under mild basic conditions. A broad spectrum of functional groups was tolerated, demonstrating the scope of the reaction. Consequently, the amides were synthesized in moderate to excellent yields, presenting an attractive alternative to the currently available synthetic methods.

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.

Η ακρίβεια και η πιστότητα της διαδικασίας διπλασιασμού του γονιδιώματος είναι μείζωνος σημασίας για την κυτταρική επιβίωση. Τυχόν ανωμαλίες όπως μεταλλάξεις ή χρωμοσωμικές ανωμαλίες είναι δυνατόν να οδηγήσουν στην εμφάνιση κακοήθειας ή σε πρόωρο κυτταρικό θάνατο. Τα παραπάνω συνηγορούν στη μεγάλη σημασία που έχει η άρτια λειτουργία και ρύθμιση του κυτταρικού κύκλου. Δύο πρωτεϊνες, οι geminin και cdt1, κατέχουν πολύ σημαντικό ρόλο κατά τη διαδικασία ρύθμισης του κυτταρικού κύκλου. Πιο συγκεκριμένα, η cdt1 αποτελεί έναν βασικό παράγοντα αδειοδότησης της αντιγραφής. Δρα συνεργατικά με την πρωτεϊνη Cdc6 προκειμένου να γίνει η πρόσδεση του εξαμερούς συμπλόκου MCM2-7 στο προ-αντιγραφικό σύμπλοκο (pre-RC), διασφαλίζοντας με τον τρόπο αυτό τις απαραίτητες συνθήκες για τη διαδικασία αδειοδότησης της αντιγραφής (Maiorano D. et al., 2000). Η geminin συνιστά τον φυσικό αναστολέα της cdt1 στα μετάζωα. Προσδένεται ισχυρά στην τελευταία μετά την έναρξη της σύνθεσης του DNA, παρεμποδίζοντας με αυτόν τον τρόπο την επαναπρόσδεσή της στο προ-αντιγραφικό σύμπλοκο (Tada S. et al., 2001; Wohlschlegel J.A. et al., 2000). Η διαδικασία αδειοδότησης της αντιγραφής παρουσιάζει ανωμαλίες σε περιπτώσεις καρκινικών κυττάρων. Πιο συγκεκριμένα, έχει δειχθεί σταθερή υπερέκφραση της cdt1 σε καρκινικές κυτταρικές σειρές, τόσο σε πρωτεϊνικό όσο και σε μεταγραφικό επίπεδο (Xouri G. et al., 2004). Παρομοίως, αυξημένη έκφραση της cdt1 έχει παρατηρηθεί και σε περιπτώσεις καρκίνου του παχέος εντέρου καθώς και πρώιμου καρκίνου του πνεύμονα, στον άνθρωπο (Bravou V. et al., 2005; Karakaidos P. et al., 2004). Τα παραπάνω αποτελέσματα έχουν προκύψει κατόπιν μελέτης, η οποία πραγματοποιήθηκε στο εργαστήριό μας. Αναφορικά με τη geminin, αυξημένα επίπεδα έκφρασής της έχουν συσχετιστεί με καρκινώματα παχέος εντέρου καθώς και με τη διαίρεση κακοηθών κυττάρων, γενικότερα (Gonzalez M.A. et al., 2005; Wohlschlegel J.A. et al., 2002). Επιπροσθέτως, η geminin βρίσκει εφαρμογή ως ανεξάρτητος δείκτης σε περιπτώσεις επιθετικού καρκίνου του μαστού (Gonzalez M.A. et al., 2004). Βασιζόμενοι στα παραπάνω, θεωρούμε ότι το σύμπλοκο geminin-cdt1 συνιστά έναν ιδανικό στόχο για το σχεδιασμό νέων αντικαρκινικών φαρμάκων. Το πρώτο βήμα προς αυτήν την κατεύθυνση αποτελεί ο μαζικός έλεγχος συνθετικών συστατικών, τα οποία να έχουν την ικανότητα διάσπασης του συμπλόκου. Ενδεχόμενη εύρεση τέτοιων συνθετικών συστατικών καθώς και μετέπειτα φυσικοχημική βελτιστοποίησή τους είναι δυνατόν να οδηγήσει στη δημιουργία ενός νέου αντικαρκινικού φαρμάκου. Η ολοκλήρωση της χαρτογράφησης του ανθρώπινου γονιδιώματος συνέβαλε στην ταυτοποίηση νέων πρωτεϊνικών μορίων στόχων, τα οποία εμπλέκονται στο μοριακό μηχανισμό διαφόρων ασθενειών. Με βάση τις εξελίξεις των τελευταίων χρόνων στον τομέα της φαρμακοβιομηχανίας, η αξιοποίηση αυτής της γνώσης συνδέεται με το μαζικό έλεγχο συνθετικών συστατικών έναντι αυτών των μορίων στόχων. Απώτερο στόχο αποτελεί η αναγνώριση κατάλληλων συνθετικών συστατικών τα οποία θα έχουν την ικανότητα να αλληλεπιδρούν με το μόριο-στόχος και κατ’επέκταση να μεταβάλλουν τον τρόπο λειτουργίας του, προκειμένου να έχουμε το επιθυμητό φαρμακολογικό αποτέλεσμα. Αποφασιστικής σημασίας στην παραπάνω διαδικασία, αποτελεί η σωστή επιλογή της κατάλληλης μεθόδου μαζικού ελέγχου των νέων υποψήφιων φαρμάκων – συνθετικών συστατικών – έναντι του μορίου στόχου. Στην παρούσα διπλωματική, επιλέχθηκε προς εφαρμογή η μέθοδος FRET. Ένα από τα βασικά της πλεονεκτήματα είναι η υψηλή αναλογία ‘σήματος-θορύβου’ που εμφανίζει καθώς και η υψηλή ποιότητα των δεδομένων που παρέχει. Αν και αποτελεί μία σχετικά καινούρια τεχνική, εντούτοις αποτελεί μία από τις πιο βασικές μεθόδους της σύγχρονης φαρμακοβιομηχανίας λόγω της αξιοπιστίας που την χαρακτηρίζει και επιπλέον της συμβατότητάς της με αυτοματοποιημένες τεχνικές. Ασφαλώς, απαραίτητη προϋπόθεση για την εφαρμογή της συγκεκριμένης μεθόδου αποτελεί η απομόνωση της υπό μελέτη πρωτεϊνης. Η έκφραση του πρωτεϊνικού συμπλόκου geminin-cdt1 πραγματοποιήθηκε με τη χρήση βακτηριακών συστημάτων έκφρασης ετερόλογων πρωτεϊνών. Επίσης, ο καθαρισμός του συμπλόκου υπήρξε επιτυχής και βασίστηκε στην εφαρμογή των τεχνικών της χρωματογραφίας συγγένειας και της χρωματογραφίας διήθησης σε πηκτή. Το επόμενο βήμα ήταν να διαπιστώσουμε εάν η μέθοδος FRET καθιστά δυνατή την ανίχνευση σχηματισμού του συμπλόκου. Πράγματι, κάτι τέτοιο ήταν εφικτό καθώς σε συγκέντρωση 60-80nM του συμπλόκου, παρατηρήθηκε αύξηση του σήματος σχεδόν κατά πέντε φορές υψηλότερα από το επίπεδο “θορύβου”. Το αποτέλεσμα αυτό είναι ιδιαίτερα σημαντικό καθώς συνεπάγεται ότι με τη συγκεκριμένη μέθοδο είναι εφικτός ο μαζικός έλεγχος συνθετικών συστατικών, τα οποία θα έχουν την ικανότητα διάσπασης του συμπλόκου. Οι λόγοι που συντελούν στην καταλληλότητα της μεθόδου για αυτό το σκοπό έγκεινται αφενός στην ευαισθησία την οποία εμφανίζει (αύξηση του σήματος μέχρι και πέντε φορές) και αφετέρου στην ειδικότητα και την αξιοπιστία της, όπως έχει δειχθεί και με τα αντίστοιχα πειράματα. Σημαντικό επίσης πλεονέκτημα αποτελεί και η μικρή σχετικά ποσότητα πρωτεϊνης (60-80nM), η οποία απαιτείται. Σύμφωνα με τα δεδομένα που έχουν προκύψει από την παρούσα διπλωματική , το FRET assay συνιστά μία ιδανική μέθοδο για την πραγματοποίηση μαζικού ελέγχου συνθετικών συστατικών, τα οποία θα έχουν την ικανότητα διάσπασης του συμπλόκου geminin-cdt1. Δεδομένης της πολύ ισχυρής αλληλεπίδρασης του συγκεκριμένου συμπλόκου, πραγματοποιήθηκαν μεταλλαγές σε τρία υψηλά συντηρημένα κατάλοιπα της cdt1, τα οποία κατέχουν κυρίαρχο ρόλο στην αλληλεπίδραση με τη geminin, σύμφωνα με κρυσταλλογραφικά δεδομένα (Lee C. et al., 2004). Οι μεταλλαγές αυτές ενδέχεται να συμβάλλουν σε ένα πολύ πιο εύκολα διασπάσιμο σύμπλοκο, γεγονός που μπορεί να οδηγήσει στην ευκολότερη και γρηγορότερη ταυτοποίηση υποψήφιων συνθετικών συστατικών. / The accurate and timely duplication of the genome is vital for cell survival. Mutations rearrangements or loss of chromosomes can be detrimental to a single cell as well as to the whole organism, causing malignant cell growth or death. Origins of replication are licensed by a multi-subunit complex (pre-replicative complex: pre-RC) during G1 (Lei M & Tye B.K., 2001). Pre-RC assembly is an ordered, sequential process in which the Origin Recognition Complex (ORC) first binds to each replication origin and then recruits two other proteins: Cdc6 and Cdt1 (Bell S.P. & Dutta A., 2002). These two proteins function synergistically to load the six mini-chromosome maintenance helicase proteins (MCM2-7) onto the pre-RC, establishing the conditions for DNA licensing (Maiorano D. et al., 2000). The prevention of ectopically induced re-replication is accomplished by functionally redundant mechanisms, including sequestration of MCM by Crm1 (Yamaguchi R. & Newport J., 2003), inactivation and export from the nucleus of Cdc6 (Delmolino L.M. et al., 2001; Jiang W. et al., 1999; Pelizon C. et al., 2000) and degradation of Cdt1 (Nishitani H. et al., 2001). Metazoans, have evolved an additional system for preventing re-replication: Geminin, which was originally identified in Xenopus as essential factor to exit from mitosis (McGarry T.J. & Kirschner M.W., 1998), binds tightly to Cdt1 and prevents Cdt1 assembly onto pre-RC (Tada S. et al., 2001; Wohlschlegel J.A. et al., 2000). Licensing system members are misregulated in cancer cells and differential expression of licensing components could be used for the diagnosis and prognosis of cancer (Shreeram S. & Blow J.J., 2003). Over-expression of Cdt1 can predispose cells to a malignant transformation. It has been shown that Cdt1 is consistently over-expressed in cancer cell lines at both the protein and RNA level (Xouri G. et al., 2004). Moreover, Cdt1 protein is highly expressed in cases of human colon cancer and primary human lung carcinomas (Bravou V. et al., 2005; Karakaidos P. et al., 2004). Similarly, Geminin is also over-expressed in colon carcinomas and its expression levels were directly related to the cellular proliferation index in proliferating malignant cells (Gonzalez M.A. et al., 2005; Wohlschlegel J.A. et al., 2002). Furthermore, expression of Geminin is considered as an independent indicator of adverse prognosis in cases of invasive breast cancer (Gonzalez M.A. et al., 2004). Given the crucial role of the Geminin-Cdt1 complex in cell cycle regulation and cancer, this complex could serve as target for the discovery and development of novel anti-cancer drugs. This requires the screening of compounds that are capable of disrupting the geminin-cdt1 complex. For that purpose we performed a HTP (high-throughput)-compatible assay, called FRET-assay. The acronym FRET stands for Fluorescence Resonance Energy transfer. The principle of the assay is based on the radiationless transfer of energy from an excited donor fluorophore (Europium Cryptate) to a suitable acceptor fluorophore (XL665). The first step was the expression and purification of the geminin-cdt1 complex. The complex was expressed by using E. coli bacterial cells and purified by metal affinity chromatography on a Ni+2 column. As soon as the complex was ready to use, we next tried to investigate whether the formation of the complex was detectable by using the FRET assay. Indeed, at the complex concentration of 60nM and 80nM, the signal was about 5 times above background. This was a first indication that the Geminin-Cdt1 complex can be used successfully for energy transfer based assays. Given the very high binding affinity of the two proteins (Lee C. et al., 2004), it could be quite unlikely to find a compound that can disrupt the complex. To overcome that obstacle, three single mutations were made at the highly conserved Geminin-contacting residues of hCdt1, Y170, F173 and L176. The mutation of these residues to alanine can possibly provide a more easily disruptable complex, which could be of importance concerning the faster and easier identification of any candidate compounds. Our data suggest that hGeminin-Cdt1 complex can be considered as a promising target for compound screening. Given the high importance of Geminin-Cdt1 balance for maintaining genomic stability integrity and that both proteins have been correlated with cases of cancer, that screening could hopefully lead to the discovery and development of lead compounds towards anti-cancer drugs.

sHSPs maintain partially denaturing substrates in a soluble sHSP-substrate complex. The heterogeneous interaction between sHSPs and substrate within the complex has prevented a detailed study of the mechanism of sHSP substrate protection. Here, purified sHSPs and heat sensitive substrates were used to investigate the mechanism of sHSP chaperone action. Results presented provide new insights into how sHSPs recognize substrates, the architecture of the sHSP-substrate complex and factors contributing to chaperone efficiency.Direct evidence defining the role of the sHSP N-terminal arm and alpha crystallin domain in sHSP-substrate interactions is limited. A photoactivatable probe was site- specifically incorporated into PsHsp18.1, and cross-linking to substrate in sHSP-substrate complexes was quantified. The structurally flexible N-terminal arm of PsHsp18.1 makes strong contacts with both substrates tested, however differences in interaction were seen in the conserved alpha crystallin domain. Regions on the sHSP showing the strongest cross-links to substrates are buried within the dodecamer, supporting the model that the sHSP oligomer undergoes rearrangement or dissociation prior to substrate interactions.The arrangement of sHSPs and substrates whithin the complex is poorly defined. Limited proteolysis and chemical modification was combined with mass spectrometry to probe the sHSP-substrate complex using multiple sHSPs and substrates. This analysis reveals that a similar partially-denatured form of substrate is protected in the complex irrespective of sHSP identity. Further, sHSP in the complex is protected from proteolysis for a longer time compared to free sHSP. These data suggest that sHSPs and substrate are distributed both internally and on the periphery of the sHSP-substrate complex.Exact properties of the sHSP N-terminal arm contributing to protection are poorly defined. A molecular dynamics (MD) study was designed to test the hypothesis that the N-terminal arm could assume multiple conformations that can readily interact with denaturing substrates. Preliminary data suggest that at increased temperatures amino acids in the N-terminal arm form specific clusters which could act as substrate interaction sites. MD simulations, mutagenesis and altering the kinetics of substrate aggregation suggest that the conformational space occupied by the N-terminal arm at increased temperatures, along with flexibility and rate of substrate aggregation contribute to differences in chaperone efficiency.

Presented in this dissertation are studies on the gas-phase structural features of peptides and peptide fragment ions using mass spectrometry (MS), hydrogen/deuterium (H/D) exchange, infrared multiphoton dissociation (IRMPD) spectroscopy, and computational modeling. Additional studies are presented on the mechanism of hydrogen/deuterium exchange using a model amino acid system. The application of chemical cross-linking to investigate the interaction between two proteins, LexA and RecA, is also presented. Gas-phase structural features can be probed using a number of techniques, and several of the studies presented in this dissertation involve the use of gas-phase H/D exchange. Although the basic mechanism for exchange has been determined, the factors that affect the rate and extent of exchange are not well understood. A computational modeling study of the exchange behavior of asparagine and its methyl ester demonstrated that exchange will occur preferentially at sites of more similar basicity. The distinctive exchange behavior of a model histidine-containing pentapeptide, HAAAA, prompted further studies into the structural features that result in five fast exchanging hydrogens and one slower exchange. Peptide analogues were used to identify the sites of exchange, and IRMPD spectroscopy combined with computational modeling indicated that exchange may occur because interaction with water at those sites results in lower energy structures compared to the other sites. Structural studies were also performed to determine whether the b₂⁺ ion from HAAAA is an oxazolone or diketopiperazine. Although the IRMPD spectrum matched that of a diketopiperazine, H/D exchange and fragmentation studies revealed the presence of both a diketopiperazine and oxazolone structure. Protein-protein interactions perform a vital role in regulating cellular processes. Despite extensive mutational analysis, the binding interaction between LexA and RecA, two proteins involved in the SOS response, is unclear. Chemical cross-linking experiments were undertaken to help target future mutational studies, and these studies identified two possible interactions. The first potential binding interaction is located in the cleft of RecA, and the second interaction may be caused by a LexA dimer binding across the RecA helical groove. The presence of two different binding interactions suggests that LexA may have redundant binding modes for RecA interaction.

The interactions between protein-protein, protein-nucleic acid, and protein-small molecules are central to biological processes and are key for the design of new therapeutics. Rapid and easy to implement methodologies are needed that enable the interrogation of these interactions in a complex cellular context. Towards this goal, I have utilized the concept of split-protein reassembly, also called protein complementation, for the creation of a variety of sensor architectures that enable the interrogation of protein-nucleic acid, protein-protein, and protein-small molecule interactions. Utilizing the enzymatic split-reporter β-lactamase and existing zinc finger design strategies we applied our recently developed technology termed SEquence-Enabled Reassembly (SEER) towards the creation of a sensor capable of the specific detection of the CryIA transgene. Additionally, the split β-lactamase reporter was utilized for the sitespecific determination of DNA methylation at cytosine residues that is involved in epigenetic regulation. This method, dubbed mCpG-SEER, enabled the direct detection of femtomole levels of dsDNA methylation in sequence specific manner. In a separate endeavor, we have developed and optimized the first cell-free split-reporter systems for GFP, split β-lactamase, and firefly luciferase for the successful dsDNA-dependent reassembly of the various reporters. Our cell free in vitro translation systems eliminates previous bottlenecks encountered in split-reporter technologies such as laborious transfection/cell culture or protein purification. Capitalizing on the ease of use and speed afforded by this new technology we describe the sensitive detection of protein-protein, protein-nucleic acid, and protein-small molecule interactions and inhibitors thereof. In a related area, we have applied this rapid cell-free split-firefly luciferase assay to the specific interrogation of a large class of helix-receptor protein-protein interactions. We have built a panel consisting of the clinically relevant Bcl-2 family of proteins, hDM2, hDM4, and p53 and interrogated the specificity of helix-receptor interactions as well as the specificity of peptide and small-molecule inhibitors of these interactions. Finally, we describe the further applications of our cell-free technology to the development of a large number of general split-firefly luciferase sensors for the detection of ssRNA sequences, the detection of native proteins, the evaluation of protease activity, and interrogation of enzyme-inhibitor interactions. The new methodologies provided in this study provides a general and enabling methodology for the rapid interrogation of a wide variety of biomolecular interactions and their antagonists without the limitations imposed by current in vitro and in vivo approaches.

Da eine Vielzahl von Proteininteraktionen innerhalb zellulärer Organismen an der Grenzfläche zu Membranen stattfindet, ist die Untersuchung dieser Prozesse von gro-ßem wissenschaftlichem Interesse. Ziel dieser Arbeit war es Modellsysteme basierend auf artifiziellen Membranen zu entwickeln, mit deren Hilfe die Untersuchung ausge-wählter Proteininteraktionen ermöglicht werden konnte. Im ersten Abschnitt dieser Arbeit (Kapitel 4-6) wurde ein Biosensorassay basierend auf festköperunterstützten Membranen entwickelt, der die Quantifizierung der Interaktion von C-Polycystin-2 (cPC2) mit seinen Interaktionspartnern C-Polycystin-1 (cPC1) und PIGEA14 mittels der Quarzmikrowaagetechnik ermöglichte. Aufgrund der Tatsache, dass die Affinität von cPC2 zu cPC1 in Anwesenheit von Ca2+ dreifach höher war, wurde eine Ca2+ abhängige Trimerisierung von cPC2 postuliert. Die Unterschiede der ermittelten kinetischen Koeffizienten führten zur Entwicklung eines Bindunsgmodells, welches die dreistufige Adsorption von cPC2 an cPC1 in Abwesenheit bzw. einstufige Adsorption in Anwesenheit von Ca2+ implizierte. Im Falle der Interaktion von cPC2 mit PIGEA14 wurde die Abhänigkeit der cPC2 Bindung von der Pseudophosphorylie-rung des Proteins an Ser812 untersucht. Es wurde festgestellt, dass die Affinität der pseudophosphorylierten Mutante cPC2S812D zu PIGEA14 zweifach niedriger war, als die von cPC2wt. Im zweiten Abschnitt der Arbeit (Kapitel 7 und 8) wurde die spezifische Wechselwir-kung von filamentösem Aktin (F-Aktin) mit festkörperunterstützten und porenüber-spannenden Membranen untersucht. Die kontrollierte Anbindung von F-Aktin in und auf porösen Aluminiumoxidfilmen konnte mit Hilfe verschiedener Funktionalisie-rungsstrategien erzielt werden. Der Einfluss eines F-Aktin Netzwerks auf die Span-nung und viskoelastischen Eigenschaften porenüberspannender Membranen wurde mittels kraftmikroskopischer Studien untersucht. Es wurde nachgewiesen, dass der Einfluss von gebundenem F-Aktin auf die Membranspannung gering war, aber erst durch die F-Aktin Adhäsion viskoelastische Membraneigenschaften induziert wurden.

A modified yeast one-hybrid (MY1H) system has been developed for in vivo investigation of simultaneous protein-protein and protein:DNA interactions. The traditional yeast one-hybrid assay (Y1H) permits examination of one expressed protein targeting one DNA site, whereas our MY1H allows coexpression of two different proteins and examination of their activity at the DNA target. This single-plasmid based MY1H was validated by use of the DNA-binding protein p53 and its inhibitory partners, large T antigen (LTAg) and 53BP2. The MY1H system could be used to examine proteins that contribute inhibitory, repressive, coactivational or bridging functions to the protein under investigation, as well as potential extension toward library screening for identification of novel accessory proteins. After development and validation of the MY1H with the p53/LTAg/53BP2 system, we applied the MY1H system to investigate the DNA binding activities of heterodimeric proteins, the bHLH/PAS domains of AhR and Arnt that target the xenobiotic response element (XRE). The AhR/Arnt:XRE interaction, which served as our positive control for heterodimeric protein binding of the XRE DNA site, showed negative signals in initial MY1H experiments. These false negative observations were turned into true positives by increasing the number of DNA target sites upstream of the reporter genes and increasing the number of activator domains fused to the two monomers. This methodology may help trouble-shooting false negatives stemming from unproductive transcription in yeast genetic assays, which can be a common problem. In the study of XRE-binding proteins, two bHLHZ-like hybrid proteins, AhRJunD and ArntFos were designed and coexpressed in the MY1H and yeast two-hybrid (Y2H) systems; these proteins comprise the bHLH domains of AhR and Arnt fused to the leucine zipper (LZ) elements from bZIP proteins JunD and Fos, respectively. The in vivo assays revealed that in the absence of the XRE DNA site, heterodimers and homodimers formed, but in the presence of the nonpalindromic XRE, only heterodimers bound to the XRE and activated reporter transcription. The present results provide valuable information on DNA-mediated protein heterodimerization and specific DNA binding, as well as the relationship between protein structure and DNA-binding function.

A modified yeast one-hybrid (MY1H) system has been developed for in vivo investigation of simultaneous protein-protein and protein:DNA interactions. The traditional yeast one-hybrid assay (Y1H) permits examination of one expressed protein targeting one DNA site, whereas our MY1H allows coexpression of two different proteins and examination of their activity at the DNA target. This single-plasmid based MY1H was validated by use of the DNA-binding protein p53 and its inhibitory partners, large T antigen (LTAg) and 53BP2. The MY1H system could be used to examine proteins that contribute inhibitory, repressive, coactivational or bridging functions to the protein under investigation, as well as potential extension toward library screening for identification of novel accessory proteins. After development and validation of the MY1H with the p53/LTAg/53BP2 system, we applied the MY1H system to investigate the DNA binding activities of heterodimeric proteins, the bHLH/PAS domains of AhR and Arnt that target the xenobiotic response element (XRE). The AhR/Arnt:XRE interaction, which served as our positive control for heterodimeric protein binding of the XRE DNA site, showed negative signals in initial MY1H experiments. These false negative observations were turned into true positives by increasing the number of DNA target sites upstream of the reporter genes and increasing the number of activator domains fused to the two monomers. This methodology may help trouble-shooting false negatives stemming from unproductive transcription in yeast genetic assays, which can be a common problem. In the study of XRE-binding proteins, two bHLHZ-like hybrid proteins, AhRJunD and ArntFos were designed and coexpressed in the MY1H and yeast two-hybrid (Y2H) systems; these proteins comprise the bHLH domains of AhR and Arnt fused to the leucine zipper (LZ) elements from bZIP proteins JunD and Fos, respectively. The in vivo assays revealed that in the absence of the XRE DNA site, heterodimers and homodimers formed, but in the presence of the nonpalindromic XRE, only heterodimers bound to the XRE and activated reporter transcription. The present results provide valuable information on DNA-mediated protein heterodimerization and specific DNA binding, as well as the relationship between protein structure and DNA-binding function.