Prediction of functionally important residues in globular proteins from unusual central distances of amino acids

<p>Abstract</p> <p>Background</p> <p>Well-performing automated protein function recognition approaches usually comprise several complementary techniques. Beside constructing better consensus, their predictive power can be improved by either adding or refining independent modules that explore orthogonal features of proteins. In this work, we demonstrated how the exploration of global atomic distributions can be used to indicate functionally important residues.</p> <p>Results</p> <p>Using a set of carefully selected globular proteins, we parametrized continuous probability density functions describing preferred central distances of individual protein atoms. Relative preferred burials were estimated using mixture models of radial density functions dependent on the amino acid composition of a protein under consideration. The unexpectedness of extraordinary locations of atoms was evaluated in the information-theoretic manner and used directly for the identification of key amino acids. In the validation study, we tested capabilities of a tool built upon our approach, called SurpResi, by searching for binding sites interacting with ligands. The tool indicated multiple candidate sites achieving success rates comparable to several geometric methods. We also showed that the unexpectedness is a property of regions involved in protein-protein interactions, and thus can be used for the ranking of protein docking predictions. The computational approach implemented in this work is freely available via a Web interface at <url>http://www.bioinformatics.org/surpresi</url>.</p> <p>Conclusions</p> <p>Probabilistic analysis of atomic central distances in globular proteins is capable of capturing distinct orientational preferences of amino acids as resulting from different sizes, charges and hydrophobic characters of their side chains. When idealized spatial preferences can be inferred from the sole amino acid composition of a protein, residues located in hydrophobically unfavorable environments can be easily detected. Such residues turn out to be often directly involved in binding ligands or interfacing with other proteins.</p

BIOINFORMATICS ANALYSIS OF CYCLIN-DEPENDENT KINASE 5: INSIGHTS TO DRUG DISCOVERY

Ph.DDOCTOR OF PHILOSOPH

Expression of recombinant S-locus F-box-S2 protein and computational modeling of protein interaction at the self-incompatibility locus of Rosaceae

Philosophiae Doctor - PhDSelf-incompatibility (SI) is a major mechanism that prevents inbreeding in ow-ering plants, which was identi ed in Rosaceae, Solanaceae and Scrophulariace. In these families, SI is gametophytic and retains inter-speci c genetic variations by out-crossing promotion. Self-incompatibility is genetically controlled by an S- locus where both male (pollen) and female (pistil) S-determinants are encoded. The female determinant (SRNase) has been extensively studied, whereas its male counterpart (SLF/SFB) has only recently been characterized as a pollen-expressed protein, which encodes for an F-box domain. However, the exact mechanism of in- teraction between SLF/SFB and SRNase is still largely unclear in Rosaceae. This study takes a closer look at the mechanism of self-incompatibility to gain a clearer understanding of the ligand-receptor binding mechanism of SI using molecular evolutionary analysis, structure prediction and binding speci city characteriza- tion, the outcome of which, will translate into a guideline for future studies. The major aims of this study were to derive an evolutionary pattern for GSI in Rosaceae subfamilies and to further assess the collaborative non-self recognition in Malus domestica Borkh.. The evolutionary analysis suggests a di erence in the evolution- ary pattern of Prunoideae and Maloideae S-genes, hence proposing a di erence in their GSI systems. Furthermore, sites responsible for this divergence are identi ed as critical amino acids in GSI function. To maintain GSI it is expected that the S-genes must be linked and co-evolve as a genetic unit. The results of this study show that these genes have co-existed, while SRNase have experienced a higher rate of evolution compared to SLF, thus rejecting the co-evolution of these genes in Maloideae. Furthermore, positively selected sites of S-locus pistil and pollen genes were identi ed that are likely to be responsible for speci city determination. Di erent numbers of these sites are found for both S-genes, while SRNase holds a larger number of positively selected sites. Additionally a model of speci city is introduced that supports the collaborative non-self recognition in Malus GSI, while critical sites responsible for such speci city are proposed and mapped to the predicted ancestral tertiary structure of SRNase and SLF/SFB. The identi cation of regions determining pollen pistil speci city as well as proposing a Collaborative Non-self Recognition model for Malus domestica Borkh. provide greater in-sight into how pollen-pistil communication system works in Maloideae (Rosaceae subfamily)

9th International Conference on Business, Technology and Innovation 2020

Welcome to IC – UBT 2020 UBT Annual International Conference is the 9th international interdisciplinary peer reviewed conference which publishes works of the scientists as well as practitioners in the area where UBT is active in Education, Research and Development. The UBT aims to implement an integrated strategy to establish itself as an internationally competitive, research-intensive university, committed to the transfer of knowledge and the provision of a world-class education to the most talented students from all background. The main perspective of the conference is to connect the scientists and practitioners from different disciplines in the same place and make them be aware of the recent advancements in different research fields, and provide them with a unique forum to share their experiences. It is also the place to support the new academic staff for doing research and publish their work in international standard level. This conference consists of sub conferences in different fields like: Security Studies Sport, Health and Society Psychology Political Science Pharmaceutical and Natural Sciences Mechatronics, System Engineering and Robotics Medicine and Nursing Modern Music, Digital Production and Management Management, Business and Economics Language and Culture Law Journalism, Media and Communication Information Systems and Security Integrated Design Energy Efficiency Engineering Education and Development Dental Sciences Computer Science and Communication Engineering Civil Engineering, Infrastructure and Environment Architecture and Spatial Planning Agriculture, Food Science and Technology Art and Digital Media This conference is the major scientific event of the UBT. It is organizing annually and always in cooperation with the partner universities from the region and Europe. We have to thank all Authors, partners, sponsors and also the conference organizing team making this event a real international scientific event. Edmond Hajrizi, President of UBTUBT – Higher Education Institutio