Proteins and their 3 D Structure
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1 Structural BioInformatics Laboratory: SBI Proteins and their 3 D Structure Embrapa Informática Agropecuária Cidade Universitária - UNICAMP Campinas, SP
2 Sequence Structure Function Role Blast Lexical STING Sintactic SMS Semantic Microarray Image Analysing Pragmatic Gene Anotation Gene Comparison Function Descriptors Structure Descriptors Gene Expression Networks Proteomics
3 Bringing Genome Into Three Dimensions Old protein map Parallels that help us to see the problem better
4 Structure/function descriptors in JPD
5 Data/information deluge and flavors of Bioinformatics
6 Datalibrary 2003 (february) nucleotide sequences, bp 112 Published-complete genomes 590 Genomes being done Protein Sequences Protein Structures Plasmodium falciparum genes, bp Genes in Homo sapiens, bp, genes in Xyllela fastidiosa, Bases, 2775 proteins Publications in PubMedline
7 Datalibrary 2003 (October) 29,189,427 nucleotide sequences (~40 x 10 9 bp) Published-complete genomes: Virus: 1421; Archaea:16; Bacteria:135; Eucariots: 9 +4 vertebrates+7 plants 590 Genomes being done 1,139,154 Protein Sequences 22,700 Protein Structures (PDB) 480 genes in Mycoplasma genitalium: 580,000 bp 35,000 Genes in Homo sapiens (3.164 x 10 9 bp) 27,936 genes in Xyllela fastidiosa, Bases, >10,000,000 Publications in PubMedline
8 The high throughputs...
9 Structural Bioinformatics Ancient Chinese Hindu Babylonian Egyptian Maya Roman Modern Arabic MCMLVI 1956 Parallels that help us to see the problem better
10 SMS and Protein Dossier Drug Target DB Onde atuamos? Sequenciamento de Genomas Genômica Estrutural Livro da vida Structural DB anotação Descritores de estrutura Estrutura-Funcão Busca por novos efetores Drug Discovery Mutational and dynamic studies Interação proteína-ligante (matching DB) Docking
11 Final goal: complement Genome Track SMS and Protein Dossier Drug Target DB Complete Genome Sequence Homology Modeling Small molecules Database Local PDB files Fingerprint Fingerprint 2D Contour map surface matching Ligand-binding site 2-D information (for search ) Protein-binding site 2-D information (for search) Mutational and dynamic studies Protein/Ligand interaction (matching DB) Docking
12 Structural Bioinformatics 1. Sequence similarity search 2. Sequence alignments 3. Structure alignment 4. Secondary structure prediction 5. Structure modeling (homology modeling) 6. Structure prediction (threding) 7. Characterization of structure 8. Relationship: sequence-structure-function 9. Function modifiers 10.Compiling the list of pairs: structure and its function modifier
13 Structural Bioinformatics Sequence similarity search Sequence alignment Parallels that help us to see the problem better
14 Structural Bioinformatics AKWHGGAFWPPH WAAGAHWPHAQD Parallels that help us to see the problem better
15 Bringing Genome Into Three Dimensions Functional Genomics Milestone: How well function can be inherited from similar sequences? From sequence to function: desires and problems
16 Data/information deluge and flavors of Bioinformatics
17 High Throughputs help increase a picture resolution: 1. Genomic sequencing 2. Protein crystalization 3. Synchrotron crystallography 4. NMR 5. Mass spectrometry 6. Mutageneses experiments 7. Screening 8. Chemical synthesis
18 High Throughputs help increase a picture resolution: 1.What do we get? 2.A big puzzle with great many peaces!!!
19 Next Step in Genomics Transcriptomics involves large-scale analysis of messenger RNAs (molecules that are transcribed from active genes) to follow when, where, and under what conditions genes are expressed. Proteomics the study of protein expression and function can bring researchers closer than gene expression studies to what s actually happening in the cell. Structural genomics initiatives are being launched worldwide to generate the 3-D structures of one or more proteins from each protein family, thus offering clues to function and biological targets for drug design. Knockout studies are one experimental method for understanding the function of DNA sequences and the proteins they encode. Researchers inactivate genes in living organisms and monitor any changes that could reveal the function of specific genes. Comparative genomics analyzing DNA sequence patterns of humans and well-studied model organisms side-by-side has become one of the most powerful strategies for identifying human genes and interpreting their function.
20 Structural Bioinformatics From gene to functional protein Parallels that help us to see the problem better
21 Structural Bioinformatics
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23 Structural Bioinformatics
24 Structural Bioinformatics
25 Structural Bioinformatics
26 Structural Bioinformatics
27 Structural Bioinformatics Sequence alignment Parallels that help us to see the problem better
28 Scoring Matrices Instead of using points at match/mismatch, we may use scoring matrix For DNA/RNA match=1, mismatch = 0 dotplot is now converted into diagram of numbers and best alignment corresponds to this diagonal with greatest numerical value T G A C T G A C
29 A R N D C Q E G H I L K M F P S T W Y V A R N D C Q E G H I L K M F P S T W Y V
30 Dotplot with scores Two proteins aligned produce score dotplot from which one can calculate optimal alignment H E A G A W G H E E P A W H E A E
31 Simple alignment Graphical presentation of alignment CGCTTCGGACGAAATCGCATCAGCATACGATCGCATGCCGGGCGGGATAAC CGAAATCGCATCAGCATACGATCGCATGC
32 Alignment with gaps Simple alignment does not always function well: CGCTTCGGACGAAATCGCATCAGCATACGATCGCATGCCGGGCGGGATAAC CGCTTCGGACGAAATCGCATCA-GCATACGATCGCATGCCGGGCGGGATAA CGAAATCGCATCACGCATACGATCGCATGC In many cases where two sequences do not coincide/align perfectly, it is necessary to introduce gaps.
33 Structural Bioinformatics Structure elements Parallels that help us to see the problem better
34 STING Millennium Suite: Analysing structure of proteins and their complexes - What do we know about structure and its relationship with function? What are the building blocks of microfactories, better known as PROTEINS? What is the structural hierarchi in proteins?
35 STING Millennium Suite: Analysing structure of proteins and their complexes - Secondary structure elements: Helix Turn Sheet Coil
36 STING Millennium Suite: Analysing structure of proteins and their complexes - Peptide bond and other types of intimate amino acid contacts
37 STING Millennium Suite: Analysing structure of proteins and their complexes -
38 Analysing structure of proteins and their complexes - STING Millennium Suite: Proper structural parameters: dihedral angles and Ramachandran plot
39 Analysing structure of proteins and their complexes STING Millennium Suite: Types of intimate amino acid contacts: Hydrogen Bonds
40 Analysing structure of proteins and their complexes Diamond STING Suite: Types of intimate amino acid contacts: Hydrogen Bonds
41 Analysing structure of proteins and their complexes STING Millennium Suite: Proper structural parameters: dihedral angles and Ramachandran plot
42 Analysing structure of proteins and their complexes - SMS way Alpha Helix
43 Ramachandran Plot
44 Analysing structure of proteins and their complexes - SMS way Collagen Helix
45 Analysing structure of proteins and their complexes - SMS way 1. antiparallela C. Struttura Extended a foglietto sheet - antiparallel ripiegato
46 Analysing structure of proteins and their complexes - SMS way Extended sheet - parallel
47 Analysing structure of proteins and their complexes - SMS way Beta Turn
48 Analysing structure of proteins and their complexes - SMS way Type II turn
49 Structural Bioinformatics Protein types Parallels that help us to see the problem better
50 1. mioglobin Analysing structure of proteins and their complexes - SMS way 2. flavodoxin 3. immunoglobulin lgg: domain C H 2
51 α-helix superhelix 3nm 1,5 nm A. α-cheratin 10nm 1. protofilament Structural Proteins 1. Triple Helix 2. Typical Sequence 1. 3-D presentation 3. Triple Helix (view from above) Collagen 2. Front view C. Silk fiber
52 1. monomer: cartoon Globular Proteins 1. dimer 2. monomer: van der Waals presentation C. Tertiary structure 2. complex Zn 2+ hexamer D. Quaternary Structure
53 Membrane protein secondary structure prediction phpspholipid glycoprotein glycolipid Extracellular cell side External protein Integral membrane proteins Citoplasmic side
54 Residuo K-D GES Ile Val Leu Phe Cys Met Ala 1,8 1.6 Tyr Gly Thr Ser Trp Pro His Asp Glu Asn Gln Lys Arg Table 2. Hydrophobicity scale by Kyte & Doolittle (1982) (K-D) and by Goldman, Engelman & Steitz (Engelman et al., 1986) (GES).
55 Structural Bioinformatics Structure modelling Parallels that help us to see the problem better
56 Probably non-globular Protein 15% As yet unobserved folds 20% Sequence-based fold Recognition 50% Full threading methods 15% Figure 5 Hypothentical applicability of diferent categories of fold-recognition methods to the open Reading Frames of small bacterial genomes. At present sequance-based fold recognition (e.g. GenTHREADER) is successful for aroud 50% of the ORFs. Structures of a further 15% of ORFs can probably be assigned. By full threading methods such as THREADER, and the reamaining 35% cannot currently be recognized either because the fold has not yet observed, or because the ORF encodes a non-globular protein (e.g. atransmembrane protein).
57 Unannotated regions PDB match region Transmembrane or Low complexity region Pie Chart of structural assignments to the proteome of the bacterium Mycoplasma genitalium. Almost half of the amino acids (49%) in the Mycoplasma genitalium proteins have a structural annotation. In this case, the structural anotation was taken from the SUPERFAMILY database(version 1.59, September 2002), described in Section Roughty one fifth of the proteome is predicted to be a transmembrane helix or low complexity region by therelevant computer programs. The remaining 30% of the proteome is unassigned.
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59 Structural Bioinformatics Structure alignment Parallels that help us to see the problem better
60
61 Structural Bioinformatics Function modifiers: drugs Parallels that help us to see the problem better
62 Molecular Geometry and 3D Matching Formato PDB Definições de Superfície Molecular Pockets e Cavities Fingerprints Matching Docking
63 Final goal: complement Genome Track SMS and Protein Dossier Drug Target DB Complete Genome Sequence Homology Modeling Small molecules Database Local PDB files Fingerprint Fingerprint 2D Contour map surface matching Ligand-binding site 2-D information (for search ) Protein-binding site 2-D information (for search) Mutational and dynamic studies Protein/Ligand interaction (matching DB) Docking
64 Hundreds of targets Now.. millions of compounds
65 Structural Bioinformatics
66 Structural Bioinformatics
67 Structural Bioinformatics
68 Structural Bioinformatics
69 Leaving Surface: below the hood...
70 Structural Bioinformatics AKWHGGAFWPPH ARWHGGWPHAQE WAAGAHWPHAQD Intermediary sequence - problem solved!
Structural bioinformatics
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