Protein Structure Databases, cont. 11/09/05

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1 11/9/05 Protein Structure Databases (continued) Prediction & Modeling Bioinformatics Seminars Nov 10 Thurs 3:40 Com S Seminar in 223 Atanasoff Computational Epidemiology Armin R. Mikler, Univ. North Texas Nov 10 Thurs 4:10 EEOB Seminar in 210 Bessey Diversity and Evolution of Plant Immunity Genes: Insights from Molecular Population Genetics Peter Tiffin, Univ. of Minnesota CORRECTION: Bioinformatics Seminars Next week - Baker Center/BCB Seminars: (seminar abstracts available at above link) Nov 14 Mon 1:10 PM Doug Brutlag, Stanford Discovering transcription factor binding sites Nov 15 Tues 1:10 PM Ilya Vakser, Univ Kansas Modeling protein-protein interactions both seminars will be in Howe Hall Auditorium Protein Structure & Function: Analysis & Prediction Mon Protein structure: basics; classification,databases, visualization Wed Protein structure databases - cont. Thurs Lab Protein structure databases Protein structure analysis & prediction Fri Protein structure prediction Protein-nucleic acid interactions 3 4 Reading Assignment (for Mon-Fri) Mount Bioinformatics Chp 10 Protein classification & structure prediction pp Ck Errata: Review last lecture: Protein Structure: Basics Additional reading assignments for BCB 544: Gene Prediction: Burge & Karlin 1997 JMB 268:78 Prediction of complete gene structures in human genomic DNA Structure Prediction: Schueler-Furman Baker, Science 310:638 Progress in modeling of protein structures and interactions 5 6 D Dobbs ISU - BCB 444/544X 1

of 20 different amino acids has different "R-Group," side chain attached to Cα 7 8 Peptide bond is rigid

2 Protein Structure & Function Amino Acids Amino acids characteristics Structural classes & motifs Protein functions & functional families (not much - more on this later) Classification Databases Visualization Each of 20 different amino acids has different "R-Group," side chain attached to Cα 7 8 Peptide bond is rigid and planar Hydrophobic Amino Acids 9 10 Charged Amino Acids Polar Amino Acids D Dobbs ISU - BCB 444/544X 2

Certain side-chain configurations are energetically favored (rotamers) Glycine is smallest amino acid R group = H atom Ramachandran plot: "Allowable" psi & phi angles Glycine residues increase

protein folding Recent work suggests it also may also regulate ligand binding in native proteins -Andreotti 15 Cysteines can form disulfide bonds Disulfide bonds (covalent) stabilize 3-D structures

3 Certain side-chain configurations are energetically favored (rotamers) Glycine is smallest amino acid R group = H atom Ramachandran plot: "Allowable" psi & phi angles Glycine residues increase backbone flexibility because they have no R group Proline is cyclic Proline residues reduce flexibility of polypeptide chain Proline cis-trans isomerization is often a rate-limiting step in protein folding Recent work suggests it also may also regulate ligand binding in native proteins -Andreotti 15 Cysteines can form disulfide bonds Disulfide bonds (covalent) stabilize 3-D structures In eukaryotes, disulfide bonds are found only in secreted proteins or extracellular domains 16 Globular proteins have a compact hydrophobic core Packing of hydrophobic side chains into interior is main driving force for folding Problem? Polypeptide backbone is highly polar (hydrophilic) due to polar -NH and C=O in each peptide unit; these polar groups must be neutralized Solution? Form regular secondary structures, e.g., α-helix, β-sheet, stabilized by H-bonds Exterior surface of globular proteins is generally hydrophilic Hydrophobic core formed by packed secondary structural elements provides compact, stable core "Functional groups" of protein are attached to this framework; exterior has more flexible regions (loops) and polar/charged residues Hydrophobic "patches" on protein surface are often involved in protein-protein interactions D Dobbs ISU - BCB 444/544X 3

Protein Secondary Structures α Helices β Sheets Loops Coils α helix: stabilized by H-bonds between every ~ 4th residue in backbone C = black O = red N = blue 19 20 Certain amino acids are "preferred"

β-sheets - also stabilized by H-bonds between back bone atoms Anti-parallel Parallel 21 22 Connect helices and sheets Vary in length and 3-D configurations Are located on surface of structure Loops

4 Protein Secondary Structures α Helices β Sheets Loops Coils α helix: stabilized by H-bonds between every ~ 4th residue in backbone C = black O = red N = blue Certain amino acids are "preferred" & others are rare in α helices Ala, Glu, Leu, Met = good helix formers Pro, Gly Tyr, Ser = very poor Amino acid composition & distribution varies, depending on on location of helix in 3-D structure β-sheets - also stabilized by H-bonds between back bone atoms Anti-parallel Parallel Connect helices and sheets Vary in length and 3-D configurations Are located on surface of structure Loops Are more "tolerant" of mutations Are more flexible and can adopt multiple conformations Tend to have charged and polar amino acids Are frequently components of active sites Some fall into distinct structural families (e.g., hairpin loops, reverse turns) Coils Regions of 2' structure that are not helices, sheets, or recognizable turns Intrinsically disordered regions appear to play important functional roles D Dobbs ISU - BCB 444/544X 4

Globular proteins are built from recurring structural patterns Simple

combinations of 2' structural elements Domains = combinations of

main classes of protein structure 1) α Domains 2) β Domains 3) α/β

sheets, usually with 2 sheets forming sandwich Mainly parallel sheets

segregated helices and sheets 5) Multidomain (α & β) Containing

α-domain structures: 4-helix bundles 27 28 β-sheets: up-and-down

5 Globular proteins are built from recurring structural patterns Simple motifs combine to form domains Motifs or supersecondary structures = combinations of 2' structural elements Domains = combinations of motifs Independently folding unit (foldon) Functional unit main classes of protein structure 1) α Domains 2) β Domains 3) α/β Domains Bundles of helices connected by loops Mainly antiparallel sheets, usually with 2 sheets forming sandwich Mainly parallel sheets with intervening helices, also mixed sheets 4) α+β Domains Mainly segregated helices and sheets 5) Multidomain (α & β) Containing domains from more than one class 6) Membrane & cell-surface proteins α-domain structures: 4-helix bundles β-sheets: up-and-down sheets & barrels α/β-domains: leucine-rich motifs can form horseshoes D Dobbs ISU - BCB 444/544X 5

New today: Protein Structure Databases Classification Visualization Protein Structure Prediction Secondary structure Tertiary structure Protein sequence databases UniProt (SwissProt, PIR, EBI)

6 New today: Protein Structure Databases Classification Visualization Protein Structure Prediction Secondary structure Tertiary structure Protein sequence databases UniProt (SwissProt, PIR, EBI) NCBI Protein More on these later: protein function prediction Protein sequence & structure: analysis Diamond STING Millennium - many useful structure analysis tools, including Protein Dossier SwissProt (UniProt) protein knowledgebase InterPRO sequence analysis tools Protein structure databases PDB Protein Data Bank MMDB (RCSB) - THE protein structure database Molecular Modeling Database (NCBI Entrez) - has "added" value MSD Molecular Structure Database Especially good for interactions, binding sites Protein structure classification SCOP = Structural Classification of Proteins Levels reflect both evolutionary and structural relationships CATH = Classification by Class, Architecture, Topology & Homology DALI/FSSP (recently moved to EBI & reorganized) fully automated structure alignments DALI server DALI Database (fold classification) 35 Protein structure visualization Molecular Visualization Freeware: MolviZ.Org Protein Explorer RASMOL (& many decendents: Protein Explorer,PyMol, MolMol, etc.) CHIME Cn3D Deep View = Swiss-PDB Viewer 36 D Dobbs ISU - BCB 444/544X 6

7 Protein Structure Databases, cont. PDB (RCSB) RCSB PDB - Beta site MMDB D Dobbs ISU - BCB 444/544X NCBI Structure RCSB PDB - New Tutorial Cn3D

8 MMDB: Molecular Modeling Data Base Searching MMDB Derived PDB structure records Value added to PDB records including: Integration with other ENTREZ databases & tools Conversion to parseable ASN.1 data description language Correction of numbering discrepancies in structure vs sequence Validation Addition of explicit chemical graph information Structure neighbors determined by Vector Alignment Search Tool (VAST) 1CET MMDB Structure Summary Cn3D : Displaying 2' Structures BLAST neighbors VAST neighbors Cn3D viewer Chloroquine Cn3D : Displaying 3' Structures Cn3D: Structural Alignments Chloroquine NADH Chloroquine D Dobbs ISU - BCB 444/544X 8

Protein Explorer (RasMol/Chime) Protein Explorer 49 50 SCOP - Structure Classification CATH -

structures in the PDB Experimental determination of protein structure lags far behind sequence

Goal: Determine structures of "all" protein folds in nature, using combination of experimental

9 Protein Explorer (RasMol/Chime) Protein Explorer SCOP - Structure Classification CATH - Structure Classification Structural Genomics ~ 30,000 "traditional" genes in human genome (not counting:???) ~ 3,000 proteins in a typical cell > 2 million sequences in UniProt > 33,000 protein structures in the PDB Experimental determination of protein structure lags far behind sequence determination! Goal: Determine structures of "all" protein folds in nature, using combination of experimental structure determination methods (X-ray crystallography, NMR, mass spectrometry) & structure prediction Structural Genomics Projects TargetDB: database of structural genomics targets Protein Structure Prediction? D Dobbs ISU - BCB 444/544X 9

10 Protein Folding "Major unsolved problem in molecular biology" In cells: spontaneous assisted by enzymes assisted by chaperones Steps in Protein Folding 1- "Collapse"- driving force is burial of hydrophobic aa s (fast - msecs) 2- Molten globule - helices & sheets form, but "loose" (slow - secs) 3- "Final" native folded state - compaction, some 2' structures rearranged In vitro: many proteins fold spontaneously & many do not! Native state? - assumed to be lowest free energy - may be an ensemble of structures Protein Dynamics Protein in native state is NOT static Function of many proteins depends on conformational changes, sometimes large, sometimes small Globular proteins are inherently "unstable" (NOT evolved for maximum stability) Energy difference between native and denatured state is very small (5-15 kcal/mol) (this is equivalent to 1 or 2 H-bonds!) Folding involves changes in both entropy & enthalpy Protein Structure Prediction Structure is largely determined by sequence BUT: Similar sequences can assume different structures Dissimilar sequences can assume similar structures Many proteins are multi-functional Protein folding: determination of folding pathways prediction of tertiary structure still largely unsolved problems D Dobbs ISU - BCB 444/544X 10

Protein Folding Problem I400: Introduction to Bioinformatics

Protein Folding Problem I400: Introduction to Bioinformatics November 29, 2004 Protein biomolecule, macromolecule more than 50% of the dry weight of cells is proteins polymer of amino acids connected into