FUNCTIONAL PREDICTION OF BIOACTIVE TOXINS IN SCORPION VENOM THROUGH BIOINFORMATICS TAN THIAM JOO , PAUL ( B. Appl. Sc. (Hons.), NUS ) A THESIS SUBMITTED FOR THE DEGREE OF DOCTOR OF PHILOSOPHY DEPARTMENT OF BIOCHEMISTRY NATIONAL UNIVERSITY OF SINGAPORE 2005 Functional prediction of bioactive toxins in scorpion venom through bioinformatics Acknowledgements Throughout my Ph.D. candidature, I have been accompanied and supported by friends and family members to complete this thesis. So it is with deep gratitude that I express my heartfelt appreciation to the following: Almighty God who has blessed me with gifts and talents to share with others. Professor Vladimir Brusic, my supervisor and mentor, whom I owe lots of gratitude. Through his guidance and advice, I have improved on my writing skill and learnt to be an independent researcher. It is also through his faith in me that I have realised my potential. Professor Shoba Ranganathan, my co-supervisor, for her valuable advices and support which motivated me to pursue Ph.D. Seng Hong, Fahad, ZongHong, Anitha and XuanLinh for their computing assistance in my research. Asif, Heiny, Stephanie and Wilson for their critique of my dissertation and companionship during lunch and at I2R. Judice, Chris, Yew Kwang and Lynn for their listening ears and encouragement during difficult times. Bernett, Lesheng, Vivek, Victor and Justin, my fellow post-graduate friends for their comradeship. My mother, Madam Soong Kim Song, for her perseverance in the face of adversity. My family especially my eldest sister, Anna, for their love, encouragement, prayers and support. My deepest and sincere gratitude, Paul Tan Thiam Joo November, 2005 I Functional prediction of bioactive toxins in scorpion venom through bioinformatics Table of Contents Acknowledgements.............................................................................................................. I Table of Contents…............................................................................................................II Summary…………........................................................................................................... VI List of Tables…….. ........................................................................................................VIII List of Figures……........................................................................................................... IX Part I: Chapter 1 Introduction .......................................................................................1 1.1 Research issues investigated in this thesis.............................................................. 6 1.2 Contribution of this thesis....................................................................................... 8 1.3 A summary of the thesis ......................................................................................... 9 Part I: Chapter 2 Literature review ............................................................................11 2.1 Use of bioinformatics to complement experimental studies................................. 12 2.2 Genome sequencing of venomous animals........................................................... 13 2.3 Sources of toxin data and related information...................................................... 14 2.3.1 GenBank and GenPept databases.......................................................................... 14 2.3.2 Swiss-Prot and TrEMBL databases ...................................................................... 15 2.3.3 Protein Data Bank (PDB)...................................................................................... 15 2.3.4 PubMed literature database................................................................................... 16 2.3.5 Issues on data collection, cleaning, annotation ..................................................... 16 2.4 Data warehouses of toxins .................................................................................... 18 2.5 Bioinformatic tools ............................................................................................... 18 2.6 Bioinformatic applications.................................................................................... 19 2.7 Prediction of structure and function of toxins....................................................... 20 II Functional prediction of bioactive toxins in scorpion venom through bioinformatics Chapter summary.............................................................................................................. 22 Part II: Chapter 3 Classification of scorpion toxin data ..............................................24 3.1 Classification of scorpion toxins........................................................................... 27 3.2 Data classification of scorpion toxin sequences ................................................... 29 3.3 Materials and Methods.......................................................................................... 30 3.3.1 Classification of sequences into groups by BLAST ............................................. 31 3.3.2 Data classification into subgroups by Clustal W .................................................. 34 3.3.2 Verification of groups and subgroups by MEGA 3.0 ........................................... 34 3.4 Results – Classification of scorpion toxin sequences ........................................... 36 3.5 Discussion and conclusions .................................................................................. 46 Chapter summary.............................................................................................................. 48 Part II: Chapter 4 Extraction of functional peptide motifs in scorpion toxins ……………… ...........................................................................................49 4.1 Materials and Methods.......................................................................................... 51 4.1.1 Scaling of binding affinities to a common scale in mutant toxin data.................. 52 4.1.2 Data analysis ......................................................................................................... 52 4.2 Results and discussion .......................................................................................... 53 4.2.1 Chloride channel motif.......................................................................................... 56 4.2.2 Sodium channels – β-excitatory motif .................................................................. 58 4.2.3 Sodium channels – β-mammal motif .................................................................... 60 4.2.4 Sodium channels – α-motif ................................................................................... 62 4.2.5 Sodium channels – α-like motif ............................................................................ 64 4.2.6 Potassium channel subtype – Ether-a-go-go-related K + channel motif ................ 66 4.2.7 Potassium channel subtype – Small conductance Ca 2+ -activated K + channel motif… .................................................................................................................. 67 III Functional prediction of bioactive toxins in scorpion venom through bioinformatics 4.2.8 Potassium channel subtypes – Large conductance Ca 2+ -activated K + channel and voltage-dependent K + channel motifs ............................................................ 68 4.3 Conclusion ............................................................................................................ 70 Chapter summary.............................................................................................................. 72 Part II: Chapter 5 Functional prediction of bioactive toxins in scorpion venom ......73 5.1 Prediction of functional properties of novel scorpion toxins by nearest neighbour analysis, sequence comparison and decision rules .............................. 75 5.2 Materials and Methods.......................................................................................... 76 5.2.1 Scorpion toxin data ............................................................................................... 76 5.2.2 Algorithm – nearest neighbour and rule-based..................................................... 77 5.3 Results – Accurate prediction of functional properties of novel scorpion toxins. 79 5.4 Discussion and conclusions .................................................................................. 89 Chapter summary.............................................................................................................. 91 Part III: Chapter 6 Implementation of scorpion toxin data warehouse …………………… ...........................................................................93 6.1 Data warehouse for information usage and knowledge discovery ....................... 95 6.2 Implementation of the data warehouse of scorpion toxins, SCORPION2............ 97 6.3 Materials and methods.......................................................................................... 97 6.3.1 Data collection of native and mutant scorpion toxin sequences and their 3D structures............................................................................................................... 98 6.3.2 Generation of homology models of scorpion toxins............................................. 99 6.3.3 Data cleaning....................................................................................................... 100 6.3.4 Data annotation