The conjugation of a small organic molecule to synthetic polypeptides from a designed set has been shown to give rise to binders with high affinity and selectivity for the phosphorylated model proteins α-casein and β-casein but not for ovoalbumin. The small organic molecule that was used for this purpose is comprised of two di-(2-picolyl)amine groups assembled on a dimethylphenyl scaffold, and is capable of complexing two Zn2+ ions to form chelates that bind the phosphate ion. The designed polypeptides used for binder construction have no precedence in nature and do not show any prior selectivity favouring any single protein. The polypeptide conjugate binders showed high affinity towards the model protein α-casein, the binder molecule 4C15L8-PP1 bound α-casein with a dissociation constant KD of 17 nM, although the di-(2-picolyl) amine based chelate in the presence of Zn2+ bound phosphate ion with dissociation constants in the low mM range. The observed affinity is due to interactions between the Zn2+ chelate and the phosphate groups of α-casein and also to interactions between the polypeptide scaffold and α-casein. The binder was found to selectively extract α-casein from buffer, bovine milk and human serum spiked with α-casein. The flexible construction of the binder permits for flexible modifications like attachment of fluorophores for titrations and quantifications. The binders were shown to efficiently capture α-casein from human serum when immobilized on solid support in a continuous flow system and to release the captured α-casein upon a simple change of pH using 0.1% acqueous trifluoroacetica acid. The developed technology brings new opportunities in investigating posttranslational phosphorylation events that are involved in signaling cascades and triggering many biologically relevant functions. A new chemical linker technology has also been developed for the purpose of conjugating biomolecules taking advantage of amino groups for the conjugation. By combining two esters with different reactivities, separated by an aliphatic chain, a molecular tool was developed that allows for controlled conjugation of biomolecules. The two esters react at different rates and can therefore be separated and allowed to react under different conditions in each step, thereby allowing for selective linkage formation between the subunits. The size of the spacer can be varied by selecting the appropriate dicarboxylic acid. The developed technology was shown to provide specificity in heteroconjugate formation in the assembly of a variety of heteroconjugates where polypeptides were combined with other peptides, carbohydrates and proteins.

With growing environmental concerns, efforts are made to replace petroleum based products with renewable alternatives. This is particularly evident in the packaging industry, where replacing synthetic polymers with renewable materials is of considerable interest. Materials for food packaging need to give protection, acting as a barrier against substances that can adversely affect the food quality such as water and oxygen. In this work, barrier dispersion coatings based on starch were used to produce coated papers which act as barrier against water and oxygen. However, since starch is both a hydrophilic and hygroscopic material, this barrier material becomes problematic to use at high relative humidity. In order to reduce this problem and improve the barrier properties enabling starch based barrier materials to be used in food packaging applications, two approaches were studied. Citric acid was utilized as a cross-linker of the starch and it was found to reduce the moisture sorption, the molecular movement and swelling at high relative humidity. It was seen that cross-linking and hydrolysis due to the low pH both affected the barrier properties significantly, but in opposing directions. By controlling these two reactions it was seen that this could lead to reduced gas permeability. It was also seen that cross-linking of starch by citric acid occurs at low temperatures, 70 °C at pH as high as 6.5. Starch nano-composites were produced by incorporating montmorillonite, to the barrier dispersion to improve the barrier properties. It was seen that the suspension viscosity was reduced by poly(ethylene glycol) and citric acid adsorption on the montmorillonite particles. Also, a tendency for improved barrier properties with reduced aggregate volume fraction and reduced swelling was observed. It was also seen that up scaling this formulation to pilot scale was possible and that promising results were achieved. / Baksidestext With growing environmental concerns, efforts are made to replace petroleum based materials with renewable alternatives such as starch. In this work, dispersions based on starch were used to produce coated papers which act as barrier against substances that can adversely affect the food quality such as water and oxygen. However, since starch is both a hydrophilic and hygroscopic material, this barrier material becomes problematic to use at high relative humidity. Citric acid was utilized as cross-linker for starch and it was found to reduce the moisture sorption, diffusion and swelling at high relative humidity. Both cross-linking and hydrolysis due to the low pH affected the barrier properties significantly, but in opposing directions. By controlling these two reactions it was possible to achieve reduced gas permeability. Starch nano-composites were produced by incorporating montmorillonite clay, to the barrier dispersion. It was seen that the suspension viscosity was reduced by poly(ethylene glycol) and citric acid adsorption on the clay. Also, a tendency for improved barrier properties with reduced aggregate volume fraction and reduced swelling was observed. It was also seen that up scaling this formulation to pilot scale was possible and promising results were achieved. / Renewable Functional Barriers

With widespread use of the Internet, data is often shared between organizations in B2B health care networks. Integrating data across all sources in a health care network would be useful to public health surveillance and provide a complete view of how the overall network is performing. Because of the lack of standardization for a common data model across organizations, matching identities between different locations in order to link and aggregate records is difficult. Moreover, privacy legislation controls the use of personal information, and health care data is very sensitive in nature so the protection of data privacy and prevention of personal health information leaks is more important than ever. Throughout the process of integrating data sets from different organizations, consent (explicitly or implicitly) and/or permission to use must be in place, data sets must be de-identified, and identity must be protected. Furthermore, one must ensure that combining data sets from different data sources into a single consolidated data set does not create data that may be potentially re-identified even when only summary data records are created. In this thesis, we propose new privacy preserving data integration protocols for public health surveillance, identify a set of privacy preserving data integration patterns, and propose a supporting framework that combines a methodology and architecture with which to implement these protocols in practice. Our work is validated with two real world case studies that were developed in partnership with two different public health surveillance organizations.

This collection of work explores conflict and connection. The poems are shorter, but they are no less conflicted about human nature and our own desires to be good, while struggling with less-good desires. My construction of progressive imagery has changed from Confessional to a sensory connectivity of situation and feel. Breaking the collection into parts allows for grouping according to speaker relationship and voice.

Reading from paper-based materials has been a major way for people to acquire knowledge. However, paper-based materials are constricted in presenting abstract and complex knowledge or concepts. Recent development of smartphone makes it a device not only for interpersonal communication, but also for accessing rich digital resources over the Internet. Because both paper-based materials and smartphone are mobile and portable, we can make use of the networking capability of smartphone to access digital materials from the Internet to enrich conventional paper-based reading activities such that students¡¦ reading comprehension can be enhanced. The present study came up with an innovative paper-based reading system integrated with digital materials delivered from the smartphone. QR codes were employed to automatically link the content of the print material with relevant digital resources. Also, questions were given to students along the reading process to scaffold the reading activity in order to help students comprehend the essence of the reading pieces. A quasi-experimental design was used to evaluate the effectiveness of the learning system in improving students¡¦ reading comprehension. The results suggested that whether or not using QR code to automate linking digital and print materials does not significantly influence student reading comprehension; however, using questions to scaffold the reading process significantly improves students¡¦ reading comprehension. The survey conducted in the experiment suggested that most of the students agreed that the integrated learning system benefits English reading comprehension. The implication of the results and suggestions to system design and future studies were then addressed.

In the present project I propose to describe the design, development and implementation of mobile application TaggingCreaditor. TaggingCreaditor, as its name suggests, is a tool that allows the creation and edition of content for collaborative location-based mobile games, i.e., for the called 'Tagging games', whose physical elements are identified with tags such as a QR code or RFID code tags. The application has been developed for both desktop computers and mobile devices. In this paper the editor for the mobile devices will be presented. Mobile technologies play an increasingly important role in our lives, so that it is reasonable that new ideas come up to take advantage of this technology. An interesting example is the collaborative location-based mobile games that have the great advantage that they can be used for both entertainment and learning. Examples of collaborative location-based games are MuseumScrabble or CityScrabble, of which a study will be carried out prior to the design of the content editor. The problem is that there are plenty of locations where you can play many of the existing location-based games, but we do not have a generic tool that facilitates the creation of content. This is what comes to solving TaggingCreaditor: creating content for these games so that any developer can operate his game at any location in the world. Even, a school teacher could use this tool to create content for their students in a museum to which they will visit. Therefore, this application could be considered as a useful supporting utility for collaborative location-based mobile games such as MuseumScrabble or CityScrabble mentioned before. Among the highlights and strengths of the application, we find that it is a generic and collaboration tool. First, the application is designed with the idea that it can be used by a large number of mobile location-based games, so it is a generic tool. And, secondly, the content editor has the advantage of being collaborative, allowing multiple users to create content for their own games in parallel in the same database. I would like to finish remarking the utility that a generic editor may have for the location-based games, allowing to create content of any subject for whatever the game is and in any place of the world. I also would like to highlight that the editor can be improved in a lot of different ways, for instance, an interesting improvement could be the multi-user support so that each user can create their own games without using the same database that other users. / Η παρούσα εργασία περιγράφει το σχεδιασμό, την ανάπτυξη και την υλοποίηση της εφαρμογής ΤaggingCreaditor για κινητές συσκευές. To TaggingCreaditor όπως αποκαλύπτει και το όνομα του είναι ένα εργαλείο για την παραγωγή και επεξεργασία περιεχομένου για συνεργατικά χωρο-ευαίσθητα παιχνίδια με κινητές συσκευές, όπως για παράδειγμα τα “Tagging games” όπου τα φυσικά αντικείμενα αναγνωρίζονται μέσω της σάρωσης QR ή RFID ετικετών. Η εφαρμογή αναπτύχθηκε για χρήση σε σταθερό υπολογιστή αλλά και σε κινητές συσκευές. Σε αυτή τη διπλωματική εργασία θα παρουσιαστεί η εφαρμογή που αφορά στην παραγωγή και επεξεργασία περιεχομένου για κινητές συσκευές. Οι κινητές τεχνολογίες διαδραματίζουν όλο ένα και σημαντικότερο ρόλο στη ζωή μας, με αποτέλεσμα πολλές νέες ιδέες να προκύπτουν λαμβάνοντας υπόψην τα πλεονεκτήματα αυτών των τεχνολογιών. Ενδιαφέρον είναι το παράδειγμα των συνεργατικών χωρο-ευαίσθητων παιχνιδιών τα οποία μπορούν να χρησιμοποιηθούν παράλληλα για ψυχαγωγία και μάθηση. Τέτοια παραδείγματα αποτελούν τα παιχνίδια MuseumScrable και CityScrable, στα οποία έχει γίνει εκτενής μελέτη πριν το σχεδιασμό του TaggingCreaditor. Τα υπάρχοντα χωρο-ευαίσθητα παιχνίδια μπορούν να παιχτούν σε πολλούς χώρους ωστόσο δεν υπάρχει ένα εργαλείο γενικής εφαρμογής το οποίο να διευκολύνει στην δημιουργία περιεχομένου για τα παιχνίδια αυτά. Αυτό το κενό έρχεται καλύψει η παρούσα διπλωματική εργασία με το σχεδιασμό και την ανάπτυξη του εργαλείου TaggingCreaditor. To εργαλείο αυτό αναπτύχθηκε για την παραγωγή και επεξεργασία περιεχομένου για χωρο-ευαίσθητα παιχνίδια έτσι ώστε κάθε σχεδιαστής παιχνιδιού να μπορεί να σχεδιάσει παιχνίδια για να παιχτούν σε οποιαδήποτε περιοχή του κόσμου. Για παράδειγμα, ένας δάσκαλος θα μπορούσε να σχεδιάσει ένα παιχνίδι και να παράξει περιεχόμενο για αυτό ώστε να παιχτεί από τους μαθητές του κατά την διάρκεια μιας επικείμενης επίσκεψης σε ένα μουσείο. Επιπρόσθετα, αυτό το εργαλείο θα μπορούσε να αποτελεί υποστηρικτική λειτουργία για τα υπάρχοντα συνεργατικά χωρο-ευαίσθητα παιχνίδια όπως τα MuseumScrable και CityScrable. Ανάμεσα στα κυριότερα σημεία και δυνατότητες αυτής της εφαρμογής, είναι το γεγονός ότι το TaggingCreaditor είναι ένα συνεργατικό και γενικής εφαρμογής εργαλείο. Κατά πρώτον, ο σχεδιασμός έγινε έτσι ώστε πολλοί χρήστες να μπορούν συνεργατικά και παράλληλα να παράγουν και να επεξεργάζονται το περιεχόμενο των παιχνιδιών τους, χρησιμοποιώντας μια κοινή βάση δεδομένων. Κατά δεύτερον, η εφαρμογή αυτή σχεδιάστηκε με το σκεπτικό πως θα μπορεί να χρησιμοποιηθεί για την παραγωγή και επεξεργασία του περιεχομένου ενός μεγάλου αριθμού χωροευαίσθητων παιχνιδιών, κάτι που κάνει το συγκεκριμένο εργαλείο να είναι εργαλείο γενικής εφαρμογής. Θα ήθελα να κλείσω τονίζοντας την χρησιμότητα που μπορεί να έχει ένα τέτοιο εργαλείο γενικής εφαρμογής για τα χωρο-ευαίσθητα παιχνίδια, επιτρέποντας την δημιουργία και επεξεργασία περιεχομένου γύρω από οποιαδήποτε θεματική ενότητα, για οποιοδήποτε παιχνίδι και σε οποιαδήποτε περιοχή του κόσμου αυτό παίζεται. Θα ήθελα επίσης να τονίσω πως το συγκεκριμένο εργαλείο μπορεί να βελτιωθεί με πολλούς διαφορετικούς τρόπους όπως για παράδειγμα να μπορεί να υποστηρίζει πολλούς χρήστες οι οποίοι όμως δεν θα χρησιμοποιούν κοινή βάση δεδομένων για την παραγωγή και επεξεργασία του περιεχομένου των παιχνιδιών τους.

Nowadays, mobile games and applications have turned around in essential elements in the current society. But, at the same time that world does not stop (society, tendencies, ... it changes daily), mobile games and applications should update and modify their contents. Thus, content providers play an important role and turn around important. The Human Computer Interaction (HCI) group from University of Patras, have developed some mobile games with a playful and educative scope, and also its content editors. But, could be possible stopping developing one editor for each game and make one in common? even could we extend it to other games not developed by the HCI group? This will be our purpose during this document. Trying to create a content editor despite the fact of the differences of the games, logic, user interface and other many aspects which differ them. Therefore, the content provider should be able to create, edit or update the information or content without changing the performance of the games. For carrying this out, first of all we should analyze which things the games have in common and then, to get an abstraction. This abstraction should work for all the games although they have incompatible properties among them. Then, for this kind of properties, we should add somehow a visibility parameter. By this way, that properties will be invisible for games which do not use them. Hence, this common content editor should be able to add, modify and delete objects of the games which have been developed and can be played everywhere in the whole world. / Η παρούσα εργασία περιγράφει το σχεδιασμό, την ανάπτυξη και την υλοποίηση της εφαρμογής ΤaggingCreaditor για χρήση σε σταθερό υπολογιστή. To TaggingCreaditor όπως αποκαλύπτει και το όνομα του είναι ένα εργαλείο για την παραγωγή και επεξεργασία περιεχομένου για συνεργατικά χωρο-ευαίσθητα παιχνίδια με κινητές συσκευές, όπως για παράδειγμα τα “Tagging games” όπου τα φυσικά αντικείμενα αναγνωρίζονται μέσω της σάρωσης QR ή RFID ετικετών. Η εφαρμογή αναπτύχθηκε για χρήση σε σταθερό υπολογιστή αλλά και σε κινητές συσκευές. Σε αυτή τη διπλωματική εργασία θα παρουσιαστεί η εφαρμογή που αφορά στην παραγωγή και επεξεργασία περιεχομένου για χρήση σε σταθερό υπολογιστή. Ενδιαφέρον είναι το παράδειγμα των συνεργατικών χωρο-ευαίσθητων παιχνιδιών τα οποία μπορούν να χρησιμοποιηθούν παράλληλα για ψυχαγωγία και μάθηση. Τέτοια παραδείγματα αποτελούν τα παιχνίδια MuseumScrable και CityScrable, στα οποία έχει γίνει εκτενής μελέτη πριν το σχεδιασμό του TaggingCreaditor. Τα υπάρχοντα χωρο-ευαίσθητα παιχνίδια μπορούν να παιχτούν σε πολλούς χώρους ωστόσο δεν υπάρχει ένα εργαλείο γενικής εφαρμογής το οποίο να διευκολύνει στην δημιουργία περιεχομένου για τα παιχνίδια αυτά. Αυτό το κενό έρχεται καλύψει η παρούσα διπλωματική εργασία με το σχεδιασμό και την ανάπτυξη του εργαλείου TaggingCreaditor. To εργαλείο αυτό αναπτύχθηκε για την παραγωγή και επεξεργασία περιεχομένου για χωρο-ευαίσθητα παιχνίδια έτσι ώστε κάθε σχεδιαστής παιχνιδιού να μπορεί να σχεδιάσει παιχνίδια για να παιχτούν σε οποιαδήποτε περιοχή του κόσμου. Για παράδειγμα, ένας δάσκαλος θα μπορούσε να σχεδιάσει ένα παιχνίδι και να παράξει περιεχόμενο για αυτό ώστε να παιχτεί από τους μαθητές του κατά την διάρκεια μιας επικείμενης επίσκεψης σε ένα μουσείο. Επιπρόσθετα, αυτό το εργαλείο θα μπορούσε να αποτελεί υποστηρικτική λειτουργία για τα υπάρχοντα συνεργατικά χωρο-ευαίσθητα παιχνίδια όπως τα MuseumScrable και CityScrable. Ανάμεσα στα κυριότερα σημεία και δυνατότητες αυτής της εφαρμογής, είναι το γεγονός ότι το TaggingCreaditor είναι ένα συνεργατικό και γενικής εφαρμογής εργαλείο. Κατά πρώτον, ο σχεδιασμός έγινε έτσι ώστε πολλοί χρήστες να μπορούν συνεργατικά και παράλληλα να παράγουν και να επεξεργάζονται το περιεχόμενο των παιχνιδιών τους, χρησιμοποιώντας μια κοινή βάση δεδομένων. Κατά δεύτερον, η εφαρμογή αυτή σχεδιάστηκε με το σκεπτικό πως θα μπορεί να χρησιμοποιηθεί για την παραγωγή και επεξεργασία του περιεχομένου ενός μεγάλου αριθμού χωρο-ευαίσθητων παιχνιδιών, κάτι που κάνει το συγκεκριμένο εργαλείο να είναι εργαλείο γενικής εφαρμογής. Θα ήθελα να κλείσω τονίζοντας την χρησιμότητα που μπορεί να έχει ένα τέτοιο εργαλείο γενικής εφαρμογής για τα χωρο-ευαίσθητα παιχνίδια, επιτρέποντας την δημιουργία και επεξεργασία περιεχομένου γύρω από οποιαδήποτε θεματική ενότητα, για οποιοδήποτε παιχνίδι και σε οποιαδήποτε περιοχή του κόσμου αυτό παίζεται. Θα ήθελα επίσης να τονίσω πως το συγκεκριμένο εργαλείο μπορεί να βελτιωθεί με πολλούς διαφορετικούς τρόπους όπως για παράδειγμα να μπορεί να υποστηρίζει πολλούς χρήστες οι οποίοι όμως δεν θα χρησιμοποιούν κοινή βάση δεδομένων για την παραγωγή και επεξεργασία του περιεχομένου των παιχνιδιών τους.

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.

A recent shift towards proteomics has seen many structural genomics initiatives set up for high-throughput structure determination using traditional methods of x-ray crystallography and NMR. The next step in the proteomic revolution focuses on the interplay of multi-protein complexes and transient protein-protein interactions, which are involved in many cellular functions. Greater understanding of protein-protein interactions will inevitably lead to better comprehension of the regulation of cellular process, which has implications in biomedical sciences and biotechnology. Even though many high-resolution initiatives focus on proteins and protein complexes, their structure-determination success rates are still low. An emerging approach uses chemical cross-linking and mass spectrometry to derive a set of sparse distance constrains, which can be used for building models of proteins and to map out residues in protein interaction interface based on partial structural information. This technique allows low-resolution identification of protein structures and their interactions in cases where traditional structure determination techniques did not produce results. Chemical cross-linkers have been successfully used for many years in identifying interacting proteins. However, recent advances in mass spectrometry have allowed the identification of exact insertion points of low-abundance cross-links and hence has opened up a new perspective on the use of cross-linkers in combination with computational structure prediction. For protein interaction studies, the approach uses chemical cross-linking information with molecular docking, so that the cross-links are treated as explicit constraints in the calculations. This study focuses on a low-cost and rapid approach to structure prediction, where partial structural information and distance constraints can be used to obtain the relative orientation of interacting proteins and domains, specifically as a rescue strategy where traditional high resolution structure determination methods were unsuccessful. This hybrid biochemical/bioinformatics approach was applied in the determination of structure of the latexin:carboxypeptidase A complex, and succeeded in achieving 4 Å rmsd compared to the crystal structure determined subsequently (Mouradov et al., 2006). Application of the bioinformatics/biochemical approach to multi-domain proteins was carried out on murine acyl-CoA thioesterase 7 (Acot7). X-ray crystallography provided structures of the two separate domains of Acot7, however the full length protein did not crystalise. Combining chemical cross-linking, mass spectrometry, molecular docking and homology modeling we were able to reconstruct how the two domains are arranged in the full length protein (Forwood et al., 2007). Limitations of this technique caused by the enormous complexity of the cross-linking reaction mixtures were identified and emphasized by analysing a large (four protein) complex of DNA polymerase III, where only one inter-protein cross-link was identified. A rapid and cost-effective method for identification of cross-linked peptides using a commercially available cross-linker was developed as part of the overall aim of streamlining the hybrid biochemical/bioinformatics in order for it to become a generally applicable technique for rapid protein structure characterisation (King et al., 2008). Finally an in-house software package was developed for assignment of cross-linked peptides based on m/z values.