| Titre : | Discovery and Characterization of a set of Ligand Binding Research on Prophyrin Proteins Binding Structural Motifs Structural Motifs in Pathogenesis-Related Proteins; A Structural Bioinformatics study Towords Unravelling Essentials in Protein Structure-Function Relationships |
| Auteurs : | Belkhiri Kheira, Auteur ; Abdelkrim Rachedi, Directeur de thèse |
| Type de document : | texte imprimé |
| Editeur : | Dr. Moulay Tahar Université Saida, Faculté des Sciences Naturelles et de la Vie, 2024/2025 |
| Format : | 79 p / 29 CM |
| Accompagnement : | CD |
| Langues: | Anglais |
| Langues originales: | Anglais |
| Catégories : | |
| Mots-clés: | Pathogenesis-Related proteins ; PR-proteins ; Plant Immunity ; Structural Bioinformatics ; Structural & Functional Motifs ; Ligand Binding Environment ; Amino Acids ; Residues ; Databases ; SSFS |
| Résumé : |
This project seeks to explore more the basis behind structure-function relationship in the
biological context of macromolecules; the proteins related to plant biology as in the case of this study. Furthermore, the study draws attention to results that would touch upon distant evolutionary relations across species. The understanding of the structure-function relationship is important for deeper studies of the biological function of proteins, and macromolecules in general, in both health and disease situations. One way to undertake this kind of study is to analyse the protein structures involved in selected biological functions and examine their ligand-binding environments. In this project, a set of 3D structures of Pathogenesis-Related proteins (PR-proteins), representing 115 full chains from 62 Protein Databank (PDB) entries from different source organisms or species, has been studied in terms of their binding site environments and a significant number of bound ligands. The study implemented structural bioinformatics tools developed at the Department of Biology, University of Saida. Recognized public databases relevant to protein data like the UniProt and the Protein Databank (PDB) have been used as main sources of the data. Methods including data mining, data parsing and extraction, molecular graphical software (RasMol), and a locally developed bioinformatics software, namely the Structure, Sequence and Function Server (SSFS), have been used to carry out the study in this project. The study resulted in the identification and construction of a set of PR-protein structural and functional binding motifs that have been classified into seven (7) structural classes, including: loops only, α-helix only, β-strand only, α & β only, loops & α-helices, loops & β-strands, and loops & α-helices & β-strands. These motifs have been characterised and analysed based on their binding site residue content and properties. They are associated with a number of vital biological functions that fall under the theme of plant immunity. The data and analysis pertaining to this project have been stored in a flat-file database to be made accessible for querying and exploration by scientists in the field. |
| Note de contenu : |
List of Abbreviations .............................................................................................. I
List of Figures ...................................................................................................... IV List of Tables ....................................................................................................... VI General Introduction .............................................................................................. 1 Chapitre 1: Literature review Literature review .................................................................................................... 5 I.Introduction .................................................................................................. 5 II.Strategies of plant pathogens ....................................................................... 5 III.Definition of an immune system .................................................................. 5 III.1 How Plant Defence against Pathogens? ....................................................... 6 III.1.1 Structural defence mechanisms ................................................................. 6 III-1-2- Biochemical defence mechanisms: ........................................................... 7 III. Notion of proteins......................................................................................... 8 IV.1 What are proteins? ........................................................................................ 9 VI.1.1 Amino acids ................................................................................................ 9 IV.2. Structural and Functional Properties of Proteins ........................................ 11 IV.2.1. Structural Properties of Proteins .............................................................. 11 IV.2.1.1. Primary Structure.................................................................................. 11 IV.2.1.2. Secondary Structure............................................................................. 12 IV.2.1.3. Tertiary Structure.................................................................................. 14 IV.2.1.4. Quaternary Structure ............................................................................ 15 VI. The relationship between the levels of structure in proteins ......................... 16 VI.1. What is the functional properties of a protein? .......................................... 16 VI.2. Structure-function Relationship.................................................................. 17 VII. An overview of plant immunity ................................................................... 17VII.1. What is Pathogenesis-Related (PR) Proteins? ....................................... 19 VII.2. Classification of Pathogenesis Related Proteins .................................... 20 VII.3. Functional characterization and mode of action .................................... 21 VII.4. PR-proteins activation as a defense response ........................................ 23 VII.5. Biochemical characteristics. Cellular and tissue localization. ............... 25 VIII. Proteins and Structural Motifs ................................................................. 26 VIII.1. Protein Sequence Motifs ....................................................................... 26 VIII.1.1. Helix-turn-helix motif:....................................................................... 26 VIII.1.2. Zinc finger motif ................................................................................ 27 VIII.1.3 Coiled-coil motif ................................................................................. 28 VIII.2. Protein Structural Motifs: ................................................................... 28 VIII.2.1. α-Helices ............................................................................................ 28 VIII.2.2. β-Sheets.............................................................................................. 29 VIII.2.3. Loops ................................................................................................. 30 IX. Methods for experimentally determining protein structures ...................... 30 IX.1. x-Ray Crystallography ........................................................................... 31 Principles .......................................................................................................... 31 IX.2. Nuclear Magnetic Resonance Spectroscopy of Proteins ........................ 31 Principles .......................................................................................................... 31 IX.3. Cryo-electron microscopy ....................................................................... 32 X. Use of Bioinformatics Tools in Different Spheres of Life Sciences ........... 33 X.1. What is bioinformatics? ............................................................................ 33 X.2. DNA and Protein Sequence Databases ..................................................... 33 X.3. Databases used in this work ...................................................................... 34 X.3.1. UniProt ................................................................................................... 34 X.3.2. Protein Data Bank (PDB) ...................................................................... 34 X.3.3. PDB Members........................................................................................ 35X.3.3.1. Protein Data Bank (RCSB) ................................................................... 35 X.3.3.2, Protein Data Bank Europe (PDBe) ....................................................... 35 X.3.3.3. Protein Data Bank Japan (PDBj) ........................................................... 36 Chapitre 2: Materials and methods Materials and methods ......................................................................................... 38 Introduction:......................................................................................................... 38 I.1.Protein structures (PDB entries): .................................................................... 39 II. Extraction and process data in a CSV format and data Minning:................... 43 II.1.Binding Details and download data in a CSV file: ...................................... 44 II.2. Data of the ligand binding details: ............................................................... 46 II.3. Binding Motifs Construction and Representation: ...................................... 49 II.3. Graphical Represntation of the Motifs :....................................................... 49 II.3.1. binding details general view representation : ........................................... 51 III.Flat-Files Database creation: .......................................................................... 52 IV. World Wide Web Database : ......................................................................... 54 Chapitre 3 : Results and Discussion Results and Discussion ........................................................................................ 56 I. Introduction ...................................................................................................... 56 II. Pathogenesis Related Proteins Binding Structural Motifs: ............................. 56 III. Binding details: .............................................................................................. 57 IV. Structural types of motifs and classification: ................................................ 58 V. Binding residues sequences of the motifs: ..................................................... 63 VI. Classification of motifs per ligands: .............................................................. 68 VI.1. Motifs Structure and Evolutionary Relationship:....................................... 70 VI.2. Motifs Structural Arrangement and Function relationship: ....................... 70 VII. Graphical Representation of Binding Motifs: .............................................. 71 VII. 1. HEM group binding motif mostly α- + β-structure: ................................ 71VII.2. CS binding motif mostly α- + β-structure: ................................................ 73 General conclusion .............................................................................................. 76 References ............................................................................................................ 79 |
Exemplaires
| Code-barres | Cote | Support | Localisation | Section | Disponibilité |
|---|---|---|---|---|---|
| aucun exemplaire |
Documents numériques (1)
BUC-M 000483 Adobe Acrobat PDF |
