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In Silico Structure-Function, Specificity and Stability Studies of N-Terminal Nucleophile Hydrolase Enzymes

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In Silico Structure-Function, Specificity and Stability Studies of N-Terminal Nucleophile Hydrolase Enzymes IN SILICO STRUCTURE-FUNCTION, SPECIFICITY AND STABILITY STUDIES OF N-TERMINAL NUCLEOPHILE HYDROLASE ENZYMES THESIS SUBMITTED TO SAVITRIBAI PHULE PUNE UNIVERSITY FOR THE DEGREE OF DOCTOR OF PHILOSOPHY IN BIOTECHNOLOGY BY PRIYABRATA PANIGRAHI RESEARCH GUIDE Dr. C.G. SURESH DIVISION OF BIOCHEMICAL SCIENCES CSIR-NATIONAL CHEMICAL LABORATORY DR HOMI BHABHA ROAD, PUNE 411008 MAHARASHTRA, INDIA JUNE 2015 DECLARATION BY THE CANDIDATE I hereby declare that the thesis entitled “In silico structure-function, specificity and stability studies of N-terminal nucleophile hydrolase enzymes” submitted by me for the degree of Doctor of Philosophy is the record of work carried out by me during the period from July 2011 to June 2015 under the guidance of Dr. C.G. Suresh, Chief Scientist and has not formed the basis for the award of any degree, diploma, associateship, fellowship, titles in this or any other University or other institution of higher learning. I further declare that the material obtained from other sources has been duly acknowledged in the thesis. Priyabrata Panigrahi Division of Biochemical Sciences CSIR-National Chemical Laboratory Pune - 411 008 June 2015 Acknowledgement This thesis is the end of my journey towards obtaining Ph.D. It would not have been possible to accomplish this without the help, support and encouragement from many people including my well wishers, my friends and colleagues. I would like to express my thanks to everyone who have made this thesis possible and gave me an unforgettable experience. First and foremost, I would like to thank beloved BapDada and Brahmakumaris World Spiritual University for giving me inner strength and willpower to pursue this journey and also their staunch support during tough times. I am extremely thankful to Dr. C. G. Suresh, my research guide, for giving me complete freedom to execute my work. This work would not have been possible without his guidance, support and encouragement. I learnt not only the way he approaches to solve a problem but also influenced by his disciplined life and time management skills. I appreciate all his contributions of time, ideas to make my Ph.D. experience productive and stimulating. I would also like to thank Dr. Sureshkumar Ramasamy, for his critical suggestions in the work and constant encouragement in a very friendly manner. I am especially grateful to him for the cloning of PdPGA gene which was one of the turning points of my thesis where I step forward towards wetlab. Being from a pure computational background, entering to experimentation in the 3rd year of Ph.D. was one of the most-challenging periods for me. However due to the constant supports of my lab members, specifically Deepak and Ruchira, to whom I lovingly call ATH (Any Time Help) friends. Deepak was there throughout the wet lab experiments, without even bothering day or night, as well as his own work. Also the special thanks go to Ruby and Tulika, for their help in CD and Fluorescence experiments. I am especially grateful to Tejashree who helped me in maintaining the PdPGA clone. Coming to computational work, I enjoyed a lot working with Manas and Ranu. I thank Manas for his useful contributions in shaping all manuscripts and this thesis. As a part of this thesis, I had developed iRDP web server. With his useful discussions and brain-storming sessions, I could saw constant progress in iRDP web server development. Avinash Ghanate has an important contribution towards the development of the front end of the iRDP web server. I would like to thank Ranu for giving me moral support, encouragement and valuable discussion. I am grateful to my other lab members Urvashi, Nishant, Payal, Manu, Ameya, Deepanjan, Shridhar, Teju, Yashpal, Vijay and Aditi for providing a great working environment in the laboratory. Special thanks are due for my dearest friends Pandurang, Supriya, Rekha and Surabhi who gave a lot of moral support during tough times. I would like to acknowledge Dr. Asmita Prabhune, Dr. Sushama Gaikwad and Dr. Vaijayanti Kumar, for allowing me to use various instruments in their lab. I’m grateful to Dr. Vidya Gupta, Head, Division of Biochemical Sciences, CSIR-NCL, Pune and Dr. J.K. Pal, University of Pune, for being members of my evaluation committee. Their inputs have been invaluable to the progress of this work. I would like to thank Director, CSIR-National Chemical Laboratory (CSIR-NCL, Pune) for giving me the opportunity to work in this great institution. I would like to thank Council of Scientific & Industrial Research (CSIR) for the fellowship and CoESC for funding. Finally I would like to thank my parents and sister for their support and faith in me. Priyabrata Panigrahi Table of Contents ABBREVIATIONS…………………………………………………………………………………………i LIST OF TABLES………………………………………………………………………………………... iv LIST OF FIGURES………………………………………………………………………………………..vi ABSTRACT………………………………………………………………………………………………..1 Chapter 1 1.1 Enzyme-substrate interactions ................................................................................................................ 6 1.2 Substrate specificity of enzymes ............................................................................................................. 7 1.3 Enzyme classification ............................................................................................................................. 7 1.4 Enzyme kinetics ...................................................................................................................................... 8 1.5 Factors effecting enzyme activity ........................................................................................................... 9 1.6 Sequence, structure and substrate specificity relationship in enzymes ................................................. 11 1.7 Sequence, structure and stability relationship in enzymes .................................................................... 13 1.8 Ntn-hydrolase enzyme superfamily ...................................................................................................... 18 1.8.1 Self-processing cysteine-dependent Ntn-hydrolase enzyme superfamily (NtCn-hydrolases) ....... 26 1.8.1.1 Family C59 .............................................................................................................................. 26 1.8.1.2 Family C44 .............................................................................................................................. 28 1.8.1.3 Family C69 .............................................................................................................................. 29 1.8.1.4 Family C89 .............................................................................................................................. 29 1.8.1.5 Family C95 .............................................................................................................................. 30 1.8.1.6 Family C45 .............................................................................................................................. 30 1.8.2 Self-processing serine-dependent Ntn-hydrolase enzyme superfamily (NtSn-hydrolases) ........... 31 1.8.3 Self-processing threonine-dependent Ntn-hydrolase enzyme superfamily (NtTn-hydrolases) ..... 35 1.8.3.1 Family T1 ................................................................................................................................ 35 1.8.3.2 Family T2 ................................................................................................................................ 36 1.8.3.3 Family T3 ................................................................................................................................ 37 1.8.3.4 Family T5 ................................................................................................................................ 37 1.9 Scope of the thesis ................................................................................................................................ 38 1.9.1 Study of sequence-structure & specificity relationship in CGH family......................................... 38 1.9.1.1 Bile Salt Hydrolases, their physiological role and clinical importance .................................. 39 1.9.1.2 Penicillin V acylases, their physiological role and pharmaceutical importance ..................... 43 1.9.1.3 BSH and PVA: sequence and structural homology and difficulty in their distinction ............ 47 1.9.2 Study of sequence-structure & stability relationship through development of iRDP web server .. 48 1.9.3 Study of sequence-structure & stability relationship in PGA family. ............................................ 49 1.10 Tools and techniques used in this study. ............................................................................................. 53 Chapter 2 2.1 Introduction ........................................................................................................................................... 55 2.1.1 Difficulty in annotation of CGH enzymes as BSH/PVA and the need for an improved annotation method. ................................................................................................................................................... 56 2.2 Materials and Methods .......................................................................................................................... 58 2.2.1 Retrieval of CGH family members and phylogenetic analysis ...................................................... 58 2.2.2. Structure retrieval
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