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Thesis Sci 2021 Abdulganiyyu Ibrahim A.Pdf A single AKH neuropeptide activating three different fly AKH-receptors: an insecticide study via computational methods. by Ibrahim A. Abdulganiyyu BSc (Hon) Chemistry Ibrahim A. Abdulganiyyu ow Thesis presented for the degree of Doctor of Philosophy in the Department of Chemistry University of Cape Town University of Cape T Supervisor: Prof. Graham E Jackson Co-Supervisor: Prof. Heather G. Marco NOVEMBER 30, 2020 The copyright of this thesis vests in the author. No quotation from it or information derived from it is to be published without full acknowledgement of the source. The thesis is to be used for private study or non- commercial research purposes only. Published by the University of Cape Town (UCT) in terms of the non-exclusive license granted to UCT by the author. University of Cape Town Table of Contents Table of Contents .................................................................................................................................... i DECLARATION ........................................................................................................................................ vi DEDICATION .......................................................................................................................................... vii ACKNOWLEDGEMENT .......................................................................................................................... viii Publications and conference contributions ............................................................................................ xi Publications ............................................................................................................................................ xi Conference contributions ....................................................................................................................... xi ABSTRACT .............................................................................................................................................. xii 1.0 Introduction: Background .............................................................................................. 1 1.2.0 Biology of Diptera (true flies) ......................................................................................... 4 1.3.0 Adipokinetic Hormones (AKHs) in Diptera ...................................................................... 6 1.4.0 G-protein coupled receptors (GPCRs) ............................................................................. 8 1.4.1 Secondary Structure and Function .................................................................................. 8 1.4.2 Classification of GPCRs .................................................................................................. 10 1.4.3 Adipokinetic hormone Receptor (AKHR) of the dipteran species studied in this thesis. ......................................... …………………………………………………………………………………………10 1.4.4 GPCRs class A activation ............................................................................................... 14 1.4.5 Signal transduction and G-proteins .............................................................................. 16 1.4.6 GPCRs structure ............................................................................................................ 16 1.4.7 GPCRs Three Dimensional (3D) Structures ................................................................... 20 1.4.8 Crystal structures of Beta2- adrenergic receptors (β2AR) and Rhodopsin ................... 20 1.4.9 Rhodopsin ..................................................................................................................... 21 1.4.10 Beta2-adrenergic receptor ............................................................................................ 22 1.5.0 Research Motivation and Statement of the Problem ................................................... 22 1.6.1 Aim ................................................................................................................................ 24 1.6.2 Specific objectives and expected significance of the research .................................... 24 1.7.0 Questions to be addressed in this work ....................................................................... 25 2.0 Construction of the Three-dimensional Structure of Phote-HrTH via NMR Restrained Molecular Dynamics……………..…………………………………………………………………………………………………………26 Summary…… ....................................................................................................................................... 26 2.1.1 Introduction .................................................................................................................. 27 2.1.2 Overview of some NMR structure elucidation programs. ............................................ 27 2.1.3 Brief information relating to chemical shifts ................................................................ 28 2.1.4 Chemical shift index (CSI) .............................................................................................. 32 i 2.1.5 Backbone angles (torsion angle) ................................................................................... 32 2.1.6 Scalar (spin-spin) couplings ........................................................................................... 33 2.1.7 Linewidth and signal: noise ratio .................................................................................. 34 2.1.8 Two-dimensional (2D) NMR- approaches TOCSY, NOESY, COSY and HSQC. ................ 34 Two-dimensional ................................................................................................................................... 34 2.1.9 Correlation spectroscopy (COSY) .................................................................................. 36 2.1.10 Total correlation spectroscopy (TOCSY)........................................................................ 36 2.1.11 Recognition of spin-systems (TOCSY) ........................................................................... 37 2.1.12 NOESY (Nuclear Over Hauser Effect Spectroscopy) and Sequential assignment of the spin systems ......................................... …………………………………………………………………………………………39 2.1.13 Heteronuclear single quantum coherence spectroscopy (HSQC) ................................. 41 2.1.14 Solvent suppression ...................................................................................................... 42 2.1.15 Structure calculation, the CcpNmr analysis-program ................................................... 42 2.1.16 Computational methods ............................................................................................... 44 2.1.17 Molecular mechanics (MM) .......................................................................................... 44 2.1.18 Force field...................................................................................................................... 44 2.1.19 Bonded Interactions ...................................................................................................... 45 2.1.20 Non-bonded interactions .............................................................................................. 46 2.1.21 Restraints and constraints ............................................................................................ 47 2.1.22 Minimization Energy (EM) ............................................................................................ 47 2.1.23 L-BFGS ........................................................................................................................... 48 2.1.24 Steepest descents ......................................................................................................... 48 2.1.25 Temperature and pressure coupling ............................................................................. 48 2.1.26 Simulated annealing (SA) .............................................................................................. 48 2.1.27 Molecular dynamics simulations .................................................................................. 49 2.1.28 Algorithms ..................................................................................................................... 49 2.1.29 Varlet algorithm (VA) .................................................................................................... 50 2.1.30 Leap-frog algorithms (LFA) ............................................................................................ 50 2.1.31 Periodic boundary conditions (PBC) ............................................................................. 51 2.1.31.1 Elucidating the solution structure of Phote-HrTH ........................................................ 52 2.1.31.2 Preparation of sample ................................................................................................... 52 2.1.32 NMR experiment ........................................................................................................... 52 2.1.33 Structure calculations ................................................................................................... 53 2.1.34 MD simulation ............................................................................................................... 53 2.1.35 Restrained molecular dynamics of Phote-HrTH ............................................................ 53 2.1.36 Simulation In water ......................................................................................................
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