Europe is arguably in need of a more offensive approach towards theencouragement of entrepreneurship and research based product development.Several European initiatives have been initiated towards this aim, one ofwhich is the Knowledge and Innovation Communities (KICs); an initiativeultimately taken by the European Commission. The main purpose of the KICsis to foster innovation and commercialization in Europe by combining forcesof industry and university, much in line with the theory of the TripleHelix. This master’s thesis is a follow up report of a previously conductedRemotely Operated Vehicle (ROV) market analysis, which was a deliverable inthe OTS project; a KIC InnoEnergy initiated project, aiming towards productdevelopment within the ocean energy sector. The purpose of this thesis hasbeen to, on the one hand evaluate how such a multidisciplinary projectworks in practice, the consequences of its design and the coping of theseconsequences, and on the other hand to identify and map prerequisites for asituation regarding if, and how, the project should invite anotherparticipant from industry into a collaboration. Based on a qualitativeanalysis of seven interviews with representatives from both academia andindustry, the conclusions indicated that the structure and future of theOTS/ROV project is perceived as unclear, best remedied by strongermanagement, additional funding, and invitation of a new collaborator. Thedemands for such collaboration mainly include an explicit project plan fromthe external ROV supplier’s point of view, and the sharing of knowledge andequipment of the supplier from the internal members’ point of view.

This thesis addresses the opportunities and difficulties that can occur in the creation of an innovation arena concerning sustainable city solutions. A case study was conducted of the Stockholm Royal Seaport project and a model for the management of an innovation arena was created. Three critical factors were discovered which were commitment, collective risk taking and trust and their connection to the overall common vision for an innovation arena. Conclusions after analyzing the critical factors was that clear contracts needs to be established and that third party involvement in the process of searching, qualifying and coaching of involved actors can be helpful in the process of developing an innovation arena.

Knowledge production has changed considerably in the past few decades. This transformation has notably affected universities both as unique institutions and citadels of knowledge. These changes are being brought by a number of factors, such as the globalization of the economy, the rise of technologies based on generic forms of knowledge, and the ability of universities to hold and exploit patents. In both scale and intensity, these alterations have led policy makers to reflect more on how scientific and technological innovation can and should be enhanced by policy decisions that would improve university-industry and government cooperation. This new fusion of three complementary societal sectors has been described by sociologists as the triple helix. As an analytical and normative concept, the triple helix is derived from the changing role of government in different societies in relation to academia and industry. Its basis is the recognition that the interaction among university-industry-government as relatively independent, yet inter-dependent institutional spheres is critical to improving the conditions for innovation in a knowledge-based society. The study reveals that commercial research funding significantly affects the perceptions of university-industry collaboration and academic knowledge capitalization. The analysis showed that academic scientists who received commercial research funding have relatively positive views about university-industry relations than those who do not receive such funds. However, one cannot conclude that commercial activities of academic scientists are harming the core functions of the university or that intellectual autonomy is being surrendered to industrial partners. Based on the findings of the study, and the contours of the triple helix model, it is argued that the growth of university-industry-government collaboration is not necessarily pre-determined in favour of either private corporations or the state, nor is it necessarily at the expense of universities. It is further contended that the growing notion that academic capitalism is harming the core functions of the university is perhaps a bit simplistic in that the issue is more complex and multifaceted than usually acknowledged. <p>In light of the above, the study asserts that the future viability of policies encouraging universities to be entrepreneurial may, if approached strategically, be catalysts for the science-based knowledge economy. For that to be realistic there is the need to understand the university as a differentiated social system rather than a unified whole. This will avoid the situation whereby all university activities are subordinated under a homogenous policy of one size fits all. In the context of triple helix relations, conceptualizing the university as a differentiated social system means a deep-seated and continually growing purposeful specialization such as the adoption of an economic development function in addition to teaching, research and community engagement.

This work investigates pathways of conformational transitions in ubiquitous RNA structural motifs. In our lab, we have developed multi-scale structural datamining techniques for identification of three-dimensional structural patterns in high-resolution crystal structures of globular RNA. I have applied these techniques to identify variations in the conformations of RNA double-helices and tetraloops. The datamined structural information is used to propose reaction coordinates for conformational transitions involved in double-strand helix propagation and tetraloop folding in RNA. I have also presented an algorithm to identify stacked RNA bases. In this work, experimentally derived thermodynamic evaluation of the conformations has been used to as an additional parameter to add detail to RNA structural transitions. RNA conformational transitions help control processes in small systems such as riboswitches and in large systems such as ribosomes. Adopting functional conformations by globular RNA during a folding process also involves structural transitions. RNA double-helices and tetraloops are common, ubiquitous structural motifs in globular RNA that independently fold in to a thermodynamically stable conformation. Folding models for these motifs are proposed in this work with probable intermediates ordered along the reaction coordinates. We hypothesize that frequently observed structural states in crystals structures are analogous in conformation to stable thermodynamic â on-pathwayâ folded states. Conversely, we hypothesize that conformations that are rarely observed are improbable folding intermediates, i.e., these conformational states are â off-pathwayâ states. In general on-pathway states are assumed to be thermodynamically more stable than off-pathway states, with the exception of kinetic traps. Structural datamining shows that double helices in RNA may propagate by the â stack-ratchetâ mechanism proposed here instead of the commonly accepted zipper mechanism. Mechanistic models for RNA tetraloop folding have been proposed and validated with experimentally derived thermodynamic data. The extent of stacking between bases in RNA is variable, indicating that stacking may not be a two-state phenomenon. A novel algorithm to define and identify stacked bases at atomic resolution has also been presented in this work.

The p53 protein promotes tumor eradication upon activation, making it an attractive target in cancer therapies. A reported 50% of all human cancers display aberrant activation of the MDM2 oncoprotein, which directly promotes tumorgenesis by inactivating the transcriptional activity of wild type p53, and is commonly associated with drug, chemo, and radio therapy resistance. Previously reported crystallographic analysis of the p53/MDM2 complex infers that the p53 protein forms a 2.5 turn amphipathic alpha helix whose hydrophobic face interacts within a deep hydrophobic cleft in the NH2-terminal domain of the globular MDM2. This suggests that the synthesis of small molecular antagonists of p53/MDM2 binding interactions, capable of reactivating wild type p53 function, show a promising therapeutic strategy in pharmaceutical discovery. The use of alpha helix mimics for the disruption of p53/MDM2 binding interactions has been amply documented in the literature; however, these compounds contain hydrophobic scaffolds that limit their usefulness as potential drug candidates. Presented is the design, synthesis, and biological evaluation of novel non-peptidic, drug-like, small molecule inhibitors to target p53/MDM2 binding interactions. The mimetics are designed to bind to the NH2-terminal domain of MDM2 protein leaving p53 unbound and capable of activation. The inhibitor design is based on an alpha helix mimetic scaffold derived from functionalized piperazines, diketopiperazines, and/or pyrimides. The mimetics are designed to have a comparably higher degree of solubility and notably facile synthesis yet still maintain the desired spacial arrangements of hydrophobic side chains in the ith, ith+4, and ith+7 positions of a natural alpha helix. The small molecules are designed to act as antagonists of protein/protein interactions, tumor inhibitors, and potent p53 activators.

Many currently relevant diseases such as cancer arise from altered biological pathways that rely on protein-protein interactions. The proteins involved in these interactions contain certain functional domains that are responsible for the protein's biological activities. These domains consist of secondary structural elements such as α-helices and Β-sheets which are at the heart of the protein's biological activity. Therefore, designing drugs that inhibit protein-protein interactions by binding to these key secondary structural elements should provide an effective treatment for many diseases. Presented in this dissertation are the designs, syntheses, and biological evaluations for both novel α-helix and novel Β-sheet mimics. The α-helix mimics were designed to inhibit the interactions between the tumor suppressor protein p53 and its inhibitor protein, MDM2. We also targeted the interactions between the Bak/Bcl-xL proteins. Using the knowledge gained from Hamilton's 1,4-terphenylene scaffold, we designed our inhibitors to be non-peptidic small molecule α-helix mimics. These molecules were designed to bind to the NH2-terminal domain of MDM2 protein thus preventing it from binding to the p53 protein thereby allowing p53 to induce apoptosis. The α-helix mimetic scaffold is designed around a central functionalized pyridazine ring while maintaining the appropriate distances between the ith, ith+4, and ith+7 positions of a natural alpha helix. The Β-sheet mimics were designed as inhibitors for the integrin mediated extracellular matrix cell adhesion found in Multiple Myeloma. We have designed, synthesized, and incorporated novel Β-turns to induce the formation of Β-hairpins as well as to cyclize the peptides in order to increase their binding affinities and reduce proteolytic cleavage. Given that many protein-protein interactions occur through hydrophobic interactions; our primary Β-turn promoter was designed with the ability to alter the Β-hairpin's hydrophobicity depending on the sulfonyl group used in the turn. The synthesis of several different sulfonyl chlorides for use in our Β-turn promoter is included in this section. We have also provided a detailed structural analysis and characterization of these new cyclic peptides via NMR and CD spectrometry. Using standard 2D NMR methods, we have elucidated the 3D conformation of several peptides in solution. We have also studied the structure activity relationships (SAR) for these cyclic peptides and then correlated these results with those obtained from the NMR studies.

The fundamental process by which an alpha-helical membrane protein attains its ultimate structure has previously been depicted as two energetically distinct stages where (1) the transmembrane (TM) segments are first threaded into the membrane bilayer as stable alpha-helices; and then (2) laterally interact to form the correct tertiary and/or quaternary structures. Central to the second stage of this model is the presence of amino acid sequence motifs in the TM segments that provide interaction-compatible surfaces through which the TM alpha-helices interact. Although these ideas have proven to be pivotal to the progress of the membrane protein folding field, a growing number of examples indicates that a variety of additional factors work together to dictate the ultimate interaction fate of TM embedded segments. In this context, we expand on these factors and explore other properties that can modulate the association of TM alpha-helices. A peptide model of myelin proteolipid protein (PLP) TM4 is capable of TM helix-helix interactions in SDS and biological membranes. Increasing the side chain volumes of two disease relevant residues (Ala242 and A248) reduces peptide self-association, indicating that these sites mediate TM helix packing through van der Waals interactions. Examination of the PLP TM2 alpha-helix shows that it is also capable of self-association and that its dimeric state depends on the presence or absence of residues at its C-terminus. Specifically, this sensitivity was attributed to changes in local hydrophobicity; a decrease in hydrophobicity likely reduces detergent-peptide interactions, which disrupts peptide alpha-helicity and the effectiveness of a nearby interaction compatible surface. We take advantage of this finding to determine the feasibility of coupling helix-helix interactions to an external factor such as pH. Our results indicate that pH can indeed modulate the dimerization state of the TM2 peptide and does so through the change in protonation state of Glu88. Increasing our knowledge of the variables contributing to TM helix-helix interactions provides valuable insights into membrane protein folding and how mutations can compromise this process. This knowledge will allow us to expand our arsenal of approaches to counter membrane protein misassembly--and ultimately human disease.

The fundamental process by which an alpha-helical membrane protein attains its ultimate structure has previously been depicted as two energetically distinct stages where (1) the transmembrane (TM) segments are first threaded into the membrane bilayer as stable alpha-helices; and then (2) laterally interact to form the correct tertiary and/or quaternary structures. Central to the second stage of this model is the presence of amino acid sequence motifs in the TM segments that provide interaction-compatible surfaces through which the TM alpha-helices interact. Although these ideas have proven to be pivotal to the progress of the membrane protein folding field, a growing number of examples indicates that a variety of additional factors work together to dictate the ultimate interaction fate of TM embedded segments. In this context, we expand on these factors and explore other properties that can modulate the association of TM alpha-helices. A peptide model of myelin proteolipid protein (PLP) TM4 is capable of TM helix-helix interactions in SDS and biological membranes. Increasing the side chain volumes of two disease relevant residues (Ala242 and A248) reduces peptide self-association, indicating that these sites mediate TM helix packing through van der Waals interactions. Examination of the PLP TM2 alpha-helix shows that it is also capable of self-association and that its dimeric state depends on the presence or absence of residues at its C-terminus. Specifically, this sensitivity was attributed to changes in local hydrophobicity; a decrease in hydrophobicity likely reduces detergent-peptide interactions, which disrupts peptide alpha-helicity and the effectiveness of a nearby interaction compatible surface. We take advantage of this finding to determine the feasibility of coupling helix-helix interactions to an external factor such as pH. Our results indicate that pH can indeed modulate the dimerization state of the TM2 peptide and does so through the change in protonation state of Glu88. Increasing our knowledge of the variables contributing to TM helix-helix interactions provides valuable insights into membrane protein folding and how mutations can compromise this process. This knowledge will allow us to expand our arsenal of approaches to counter membrane protein misassembly--and ultimately human disease.

Historically, the paradigm of similarity of protein sequences implying common structure, function and ancestry was generalized based on studies of globular domains. The implications of sequence similarity among non-globular protein segments have not been studied to the same extent; nevertheless, homology considerations are silently extended for them. This appears especially detrimental in the case of transmembrane helices (TMs) and signal peptides (SPs) where sequence similarity is necessarily a consequence of physical requirements rather than common ancestry. Since the matching of SPs/TMs creates the illusion of matching hydrophobic cores, the inclusion of SPs/TMs into domain models can give rise to wrong annotations. More than 1001 domains among the 10,340 models of Pfam release 23 and 18 domains of SMART version 6 (out of 809) contain SP/TM regions. As expected, fragment mode HMM searches generate promiscuous hits limited to solely the SP/TM part among clearly unrelated proteins. More worryingly, this work shows explicit examples that the scores of clearly false-positive hits, even in globalmode searches, can be elevated into the significance range just by matching the hydrophobic runs. In the PIR iProClass database v3.74 using conservative criteria, this study finds that at least between 2.1% and 13.6% of its annotated Pfam hits appear unjustified for a set of validated domain models. Thus, false positive domain hits enforced by SP/TM regions can lead to dramatic annotation errors where the hit has nothing in common with the problematic domain model except the SP/TM region itself. A workflow of flagging problematic hits arising from SP/TM-containing models for critical reconsideration by annotation users is provided. While E-value guided extrapolation of protein domain annotation from libraries such as Pfam with the HMMER suite is indispensable for hypothesizing about the function of experimentally uncharacterized protein sequences, it can also complicate the annotation problem. In HMMER2, the E-value is computed from the score via a logistic function or via a domain model-specific extreme value distribution (EVD); the lower of the two is returned as E-value for the domain hit in the query sequence. We demonstrated that, for thousands of domain models, this treatment results in switching from the EVD to the statistical model with the logistic function when scores grow (for Pfam release 23, 99% in the global mode and 75% in the fragment mode). If the score corresponding to the breakpoint results in an E-value above a user-defined threshold (e.g., 0.1), a critical score region with conflicting E-values from the logistic function (below the threshold) and from EVD (above the threshold) does exist. Thus, this switch will affect E-value guided annotation decisions in an automated mode. To emphasize, switching in the fragment mode is of no practical relevance since it occurs only at E-values far below 0.1. Unfortunately, a critical score region does exist for 185 domain models in the hmmpfam and 1748 domain models in the hmmsearch global-search mode. For 145 out the respective 185 models, the critical score region is indeed populated by actual sequences. In total, 24.4% of their hits have a logistic function-derived E-value<0.1 when the EVD provides an E-value>0.1. Examples of false annotations are provided and the appropriateness of a logistic function as alternative to the EVD is critically discussed. This work shows that misguided E-value computation coupled with non-globular regions embedded in domain model library not only causes annotation errors in public databases but also limits the extrapolation power of protein function prediction tasks. So far, the preceding work has demonstrated that sequence homology considerations widely used to transfer functional annotation to uncharacterized protein sequences require special precautions in the case of non-globular sequence segments including membrane-spanning stretches from non-polar residues. We found that there are two types of transmembrane helices (TMs) in membrane-associated proteins. On the one hand, there are so-called simple TMs with elevated hydrophobicity, low sequence complexity and extraordinary enrichment in long aliphatic residues. They merely serve as membrane-anchoring device. In contrast, so-called complex TMs have lower hydrophobicity, higher sequence complexity and some functional residues. These TMs have additional roles besides membrane anchoring such as intramembrane complex formation, ligand binding or a catalytic role. Simple and complex TMs can occur both in single- and multi-membrane-spanning proteins essentially in any type of topology. Whereas simple TMs have the potential to confuse searches for sequence homologues and to generate unrelated hits with seemingly convincing statistical significance, complex TMs contain essential evolutionary information. For extending the homologyconcept onto membrane proteins, we provide a necessary quantitative criterion to distinguish simple TMs in query sequences prior to their usage in homology searches based on assessment of hydrophobicity and sequence complexity of the TM sequence segments. Theoretical insights from this work were applied to problems of function prediction for specific uncharacterized gene/protein sequences (for example, APMAP and ARXES) and for the functional classification of TM-containing proteins.

Thesis (doctoral)--Universität Bern, 1913. / Includes bibliographical references.