VAP-1 as drug target in inflammation : structural features determining ligand interactions

Vascular adhesion protein-1 (VAP-1), which belongs to the copper amine oxidases (CAOs), is a validated drug target in inflammatory diseases. Inhibition of VAP-1 blocks the leukocyte trafficking to sites of inflammation and alleviates inflammatory reactions. In this study, a novel set of potent pyridazinone inhibitors is presented together with their X-ray structure complexes with VAP-1. The crystal structure of serum VAP-1 (sVAP-1) revealed an imidazole binding site in the active site channel and, analogously, the pyridazinone inhibitors were designed to bind into the channel. This is the first time human VAP-1 has been crystallized with a reversible inhibitor and the structures reveal detailed information of the binding mode on the atomic level. Similarly to some earlier studied inhibitors of human VAP-1, the designed pyridazinone inhibitors bind rodent VAP-1 with a lower affinity than human VAP-1. Therefore, we made homology models of rodent VAP-1 and compared human and rodent enzymes to determine differences that might affect the inhibitor binding. The comparison of the crystal structures of the human VAP-1 and the mouse VAP-1 homology model revealed key differences important for the species specific binding properties. In general, the channel in mouse VAP-1 is more narrow and polar than the channel in human VAP-1, which is wider and more hydrophobic. The differences are located in the channel leading to the active site, as well as, in the entrance to the active site channel. The information obtained from these studies is of great importance for the development and design of drugs blocking the activity of human VAP-1, as rodents are often used for in vivo testing of candidate drugs. In order to gain more insight into the selective binding properties of the different CAOs in one species a comprehensive evolutionary study of mammalian CAOs was performed. We found that CAOs can be classified into sub-families according to the residues X1 and X2 of the Thr/Ser-X1-X2-Asn-Tyr-Asp active site motif. In the phylogenetic tree, CAOs group into diamine oxidase, retina specific amine oxidase and VAP-1/serum amine oxidase clades based on the residue in the position X2. We also found that VAP-1 and SAO can be further differentiated based on the residue in the position X1. This is the first large-scale comparison of CAO sequences, which explains some of the reasons for the unique substrate specificities within the CAO family.

Structural and Mechanistic Studies of Phosphoserine Aminotransferase

Phosphoserine aminotrasferase (PSAT: EC 2.6.1.52) is a vitamin B6-dependent enzyme and a member of the subgroup IV in the aminotransferase superfamily. Here, X-ray crystallography was used to determine the structure of PSAT from Bacillus alcalophilus with pyridoxamine 5′-phosphate (PMP) at high resolution (1.57 Å). In addition, analysis of active residues and their conformational changes was performed. The structure is of good quality as indicated, for example, by the last recorded Rwork and Rfree numbers (0.1331 and 0.1495, respectively). The enzyme was initially crystallized in the presence of substrate L-glutamate with the idea to produce the enzyme-substrate complex. However, the structure determination revealed no glutamate bound at the active site. Instead, the Schiff base between Lys196 and PLP appeared broken, resulting in the formation of PMP owing to the excess of the donor substrate used during co-crystallization. Structural comparison with the free PSAT enzyme and the PSAR-PSER complex showed that the aromatic ring of the co-factor remains in almost the same place in all structures. A flexible nearby loop in the active site was found in the same position as in the free PSAT structure while in the PSAT-PSER structure it moves inwards to interact with PSER. B-factors comparison in all three structures (PSAT-PMP complex, free PSAT, and PSAT-PSER complex) showed elevated loop flexibility in the absence of the substrate, indicating that loop flexibility plays an important role during substrate binding. The reported structure provides mechanistic details into the reaction mechanism of PSAT and may help in understanding better the role of various parts in the structure towards the design of novel compounds as potential disruptors of PSAT function. This may lead to the development of new drugs which could target the human and bacterial PSAT active site.

Chassis frame design of a mobile platform equipped with robotic arms

The overall objective of the thesis is to design a robot chassis frame which is a bearing structure of a vehicle supporting all mechanical components and providing structure and stability. Various techniques and scientific principles were used to design a chassis frame.Design principles were applied throughout the process. By using Solid-Works software,virtual models was made for chassis frame. Chassis frame of overall dimension 1597* 800*950 mm3 was designed. Center of mass lieson 1/3 of the length from front wheel at height 338mm in the symmetry plane. Overall weight of the chassis frame is 80.12kg. Manufacturing drawing is also provided. Additionally,structural analysis was done in FEMAP which gives the busting result for chassis design by taking into consideration stress and deflection on different kind of loading resembling real life case. On the basis of simulated result, selected material was verified. Resulting design is expected to perform its intended function without failure. As a suggestion for further research, additional fatigue analysis and proper dynamic analysis can be conducted to make the study more robust.

Organisational purchasing of service design – Agency and client perspectives

There has been an increase in the interest in service design, as companies have become more customer-centric and their focus has shifted to customer experiences. The actual organisational purchasing of service design has been given little attention, until recent years. The purpose of this study is to explore the purchasing of service design from the perspectives of sellers (service design agencies) and buying clients (business organisations). In order to understand the phenomenon, also agencies and clients’ approaches to service design discipline, purchasing processes, challenges related to purchasing and ways of facilitating the purchasing are explored. The research follows qualitative research method and utilises abductive reasoning. A proposition framework was formed by combining services marketing, design and organisational buying behaviour literatures, and was tested against real-life business cases. Empirical data was gathered by interviewing eight service design agency representatives and five client representatives in Finland. The results of semi-structural interviews were analysed by finding repetitive themes. The proposition framework was updated according to interview findings. There were both similarities and differences in service design agencies and clients’ approaches to service design. Service design represents a strategic activity to both parties, and it helps in clients’ business development and in discovering opportunities. It is an ideology; a way of thinking and working. The driving force for purchasing service design seemed to be something else than service design itself. Projects have been bought for 1) change and innovation related development, 2) channel related development or for 3) customer experience related development. Seven purchasing challenge themes were recognised: 1) poor or differing service design understanding, 2) selling of service design, 3) varying expectations, 4) difficulty of pre-evaluation, 5) buyers and buying companies, 6) project process and nature and 7) unclear project results. These all can be considered to cause challenges in organisational service design purchasing. Challenges can be caused by either participant, the agency or the client, and take place at any point of the purchasing process. Some of the challenges could be considered as barriers to purchasing or they play a role in an unsuccessful service project – and therefore, result in an unsuccessful organisational purchase. Purchasing could be facilitated in various ways by either participant; some ways are more attitude based, others actionable improvements. Thesis’s theoretical and managerial findings can be utilised to both improve the selling and purchasing of service design services.

Examining human-centered design practice in the mobile apps era

Human-Centered Design (HCD) is a well-recognized approach to the design of interactive computing systems that supports everyday and professional lives of people. To that end, the HCD approach put central emphasis on the explicit understanding of users and context of use by involving users throughout the entire design and development process. With mobile computing, the diversity of users as well as the variety in the spatial, temporal, and social settings of the context of use has notably expanded, which affect the effort of interaction designers to understand users and context of use. The emergence of the mobile apps era in 2008 as a result of structural changes in the mobile industry and the profound enhanced capabilities of mobile devices, further intensify the embeddedness of technology in the daily life of people and the challenges that interaction designers face to cost-efficiently understand users and context of use. Supporting interaction designers in this challenge requires understanding of their existing practice, rationality, and work environment. The main objective of this dissertation is to contribute to interaction design theories by generating understanding on the HCD practice of mobile systems in the mobile apps era, as well as to explain the rationality of interaction designers in attending to users and context of use. To achieve that, a literature study is carried out, followed by a mixed-methods research that combines multiple qualitative interview studies and a quantitative questionnaire study. The dissertation contributes new insights regarding the evolving HCD practice at an important time of transition from stationary computing to mobile computing. Firstly, a gap is identified between interaction design as practiced in research and in the industry regarding the involvement of users in context; whereas the utilization of field evaluations, i.e. in real-life environments, has become more common in academic projects, interaction designers in the industry still rely, by large, on lab evaluations. Secondly, the findings indicate on new aspects that can explain this gap and the rationality of interaction designers in the industry in attending to users and context; essentially, the professional-client relationship was found to inhibit the involvement of users, while the mental distance between practitioners and users as well as the perceived innovativeness of the designed system are suggested in explaining the inclination to study users in situ. Thirdly, the research contributes the first explanatory model on the relation between the organizational context and HCD; essentially, innovation-focused organizational strategies greatly affect the cost-effective usage of data on users and context of use. Last, the findings suggest a change in the nature of HCD in the mobile apps era, at least with universal consumer systems; evidently, the central attention on the explicit understanding of users and context of use shifts from an early requirements phase and continual activities during design and development to follow-up activities. That is, the main effort to understand users is by collecting data on their actual usage of the system, either before or after the system is deployed. The findings inform both researchers and practitioners in interaction design. In particular, the dissertation suggest on action research as a useful approach to support interaction designers and further inform theories on interaction design. With regard to the interaction design practice, the dissertation highlights strategies that encourage a more cost-effective user- and context-informed interaction design process. With the continual embeddedness of computing into people’s life, e.g. with wearable devices and connected car systems, the dissertation provides a timely and valuable view on the evolving humancentered design.