BCB 444/544 Fall 07 Dobbs 1

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1 BCB 444/544 Lecture 21 Protein Structure Visualization, Classification & Comparison Secondary Structure #21_Oct10 Required Reading (before lecture) Mon Oct 8 - Lecture 20 Protein Secondary Structure Chp 14 - pp Wed Oct 10 - Lecture 21 Protein Tertiary Structure Chp 15 - pp Thurs Oct 11 & Fri Oct 12 - Lab 7 & Lecture 22 Protein Tertiary Structure Chp 15 - pp BCB 444/544 F07 ISU Dobbs #21 - Protein Secondary Structure 1 BCB 444/544 F07 ISU Dobbs #21 - Protein Secondary Structure 2 Assignments & Announcements Seminars this Week - Thurs: ALL: HomeWork #3 Due: Mon Oct 8 by 5 PM HW544: HW544Extra #1 Due: Task Mon Oct 1 by noon Due: Task 1.2 & Task 2 - Fri Oct 12 by 5 PM 444 "Project-instead-of-Final" students should also submit: HW544Extra #1 Due: Task Mon Oct 8 by noon Due: Task Fri Oct 12 by 5 PM <Task 2 NOT required for BCB444 students> BCB List of URLs for Seminars related to Bioinformatics: Oct 11 Thurs Dr. Klaus Schulten (Univ of Illinois) - Baker Center Seminar The Computational Microscope 2:10 PM in E164 Lagomarcino Klaus_Schulten_Seminar.pdf Dr. Dan Gusfield (UC Davis) - Computer Science Colloquium ReCombinatorics: Combinatorial Algorithms for Studying History of Recombination in Populations 3:30 PM in Howe Hall Auditorium BCB 444/544 F07 ISU Dobbs #21 - Protein Secondary Structure 3 BCB 444/544 F07 ISU Dobbs #21 - Protein Secondary Structure 4 Seminars this Week - Fri: Chp 12 - Protein Structure Basics BCB List of URLs for Seminars related to Bioinformatics: Oct 12 Fri Dr. Edward Yu (Physics/BBMB, ISU) - BCB Faculty Seminar TBA: "Structural Biology" (see URL below) 2:10 PM in 102 Sci wsfilefield_abstract/dr.-ed-yu.pdf Dr. Srinivas Aluru (ECprE, ISU) - GDCB Seminar Consensus Genetic Maps: A Graph Theoretic Approach 4:10 PM in 1414 MBB newsfilefield_abstract/dr.-srinivas-aluru.pdf Xiong: Chp 12 Protein Structure Basics Amino Acids Peptide Bond Formation Dihedral Angles Hierarchy Secondary Structures Tertiary Structures Determination of Protein 3-Dimensional Structure Protein Structure DataBank (PDB) BCB 444/544 F07 ISU Dobbs #21 - Protein Secondary Structure 5 BCB 444/544 F07 ISU Dobbs #21 - Protein Secondary Structure 6 BCB 444/544 Fall 07 Dobbs 1

2 Protein Structure & Function 6 Main Classes of Protein Structure Protein structure - primarily determined by sequence Protein function - primarily determined by structure Globular proteins: compact hydrophobic core & hydrophilic surface Membrane proteins: special hydrophobic surfaces Folded proteins are only marginally stable Some proteins do not assume a stable "fold" until they bind to something = Intrinsically disordered Predicting protein structure and function can be very hard -- & fun! 1) α-domains Bundles of helices connected by loops 2) β-domains Mainly antiparallel sheets, usually 2 sheets forming sandwich 3) α/β Domains Mainly parallel sheets with intervening helices, 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 BCB 444/544 F07 ISU Dobbs #21 - Protein Secondary Structure 7 BCB 444/544 F07 ISU Dobbs #21 - Protein Secondary Structure 8 Protein Structure Databases PDB (RCSB) - recently "remediated" PDB - Protein Data Bank (RCSB) - THE protein structure database MMDB - Molecular Modeling Database (NCBI Entrez) - has "added" value MSD - Molecular Structure Database Especially good for interactions & binding sites BCB 444/544 F07 ISU Dobbs #21 - Protein Secondary Structure 9 BCB 444/544 F07 ISU Dobbs #21 - Protein Secondary Structure 10 Structure at NCBI MMDB at NCBI BCB 444/544 F07 ISU Dobbs #21 - Protein Secondary Structure 11 BCB 444/544 F07 ISU Dobbs #21 - Protein Secondary Structure 12 BCB 444/544 Fall 07 Dobbs 2

3 MMDB: Molecular Modeling Data Base MSD: Molecular Structure Database Derived from PDB structure records "Value-added" to PDB records includes: Integration with other ENTREZ databases & tools Conversion to parseable ASN.1 data description language Data also available in mmcif & XML (also true for PDB now) Correction of numbering discrepancies in structure vs sequence Validation Explicit chemical graph information (covalent bonds) Integrated tool for identifying structural neighbors Vector Alignment Search Tool (VAST) BCB 444/544 F07 ISU Dobbs #21 - Protein Secondary Structure 13 BCB 444/544 F07 ISU Dobbs #21 - Protein Secondary Structure 14 wwpdb: World Wide PDB Experimental Determination of 3D Structure 2 Major Methods to obtain high-resolution structures 1. X-ray Crystallography (most PDB structures) 2. Nuclear Magnetic Resonance (NMR) Spectroscopy Note Advantages & Limitations of each method (See your lecture notes & textbook) For more info: 3. Other methods (usually lower resolution, at present): Electron Paramagnetic Resonance (EPR - also called ESR, EMR) Electron microscopy (EM) Cryo-EM Scanning Probe Microscopies (AFM - Atomic Force Microscopy) Circular Dichroism (CD), several other spectroscopic methods BCB 444/544 F07 ISU Dobbs #21 - Protein Secondary Structure 15 BCB 444/544 F07 ISU Dobbs #21 - Protein Secondary Structure 16 Chp 13 - Protein Structure Visualization, Comparison & Classification Xiong: Chp 13 Protein Structure Visualization, Comparison & Classification Protein Structural Visualization Protein Structure Comparison Protein Structure Classification Protein Structure Visualization RASMOL & decendents: PyMol, MolMol Cn3D - esp. good for structural alignments CHIME (Protein Explorer) MolviZ.Org Deep View = Swiss-PDB Viewer BCB 444/544 F07 ISU Dobbs #21 - Protein Secondary Structure 17 BCB 444/544 F07 ISU Dobbs #21 - Protein Secondary Structure 18 BCB 444/544 Fall 07 Dobbs 3

4 #21 - Protein Secondary Structure Cn3D PyMol BCB 444/544 F07 ISU Dobbs #21 - Protein Secondary Structure 19 BCB 444/544 F07 ISU Dobbs #21 - Protein Secondary Structure 20 Cn3D: Structural Alignments Cn3D : Displaying 3' Structures NADH Chloroquine BCB 444/544 F07 ISU Dobbs #21 - Protein Secondary Structure 21 BCB 444/544 F07 ISU Dobbs #21 - Protein Secondary Structure Protein Explorer (Chime) 22 Protein Structure Comparison Methods /frntdoor.htm We will skip this for now 3 Basic Approaches for Aligning Structures: 1. Intermolecular 2. Intramolecular 3. Combined DALI/FSSP (most commonly used) BCB 444/544 F07 ISU Dobbs #21 - Protein Secondary Structure BCB 444/544 Fall 07 Dobbs 23 Fully automated structure alignments DALI server DALI Database (fold classification) BCB 444/544 F07 ISU Dobbs #21 - Protein Secondary Structure 24 4

5 Protein Structure Classification SCOP - Structure Classification SCOP = Structural Classification of Proteins Levels reflect both evolutionary and structural relationships CATH = Classification by Class, Architecture,Topology & Homology DALI - (recently moved to EBI & reorganized) DALI Database (fold classification) Each method has strengths & weaknesses. BCB 444/544 F07 ISU Dobbs #21 - Protein Secondary Structure 25 BCB 444/544 F07 ISU Dobbs #21 - Protein Secondary Structure 26 CATH - Structure Classification Chp 14 - Secondary Structure Xiong: Chp 14 Protein Secondary Structure Secondary Structure for Globular Proteins Secondary Structure for Transmembrane Proteins Coiled-Coil BCB 444/544 F07 ISU Dobbs #21 - Protein Secondary Structure 27 BCB 444/544 F07 ISU Dobbs #21 - Protein Secondary Structure 28 Secondary Structure Has become highly accurate in recent years (>85%) Usually 3 (or 4) state predictions: H = α-helix E = β-strand C = coil (or loop) (T = turn) Secondary Structure Methods 1st Generation methods Ab initio - used relatively small dataset of structures available Chou-Fasman - based on amino acid propensities (3-state) GOR - also propensity-based (4-state) 2nd Generation methods based on much larger datasets of structures now available GOR II, III, IV, SOPM 3rd Generation methods Homology-based & Neural network based PHD, PSIPRED, SSPRO, PROF, HMMSTR Meta-Servers combine several different methods Consensus & Ensemble based JPRED, PredictProtein BCB 444/544 F07 ISU Dobbs #21 - Protein Secondary Structure 29 BCB 444/544 F07 ISU Dobbs #21 - Protein Secondary Structure 30 BCB 444/544 Fall 07 Dobbs 5

6 Secondary Structure Servers Consensus Data Mining (CDM) Evaluation? Q 3 score - % of residues correctly predicted (3-state) in cross-validation experiments Best results? Meta-servers (scroll for 2' structure prediction) JPred PredictProtein Best individual programs??? Rost, Columbia CDM Sen Jernigan, ISU GOR V Kloczkowsky Jernigan, ISU Developed by Jernigan Group at ISU Basic premise: combination of 2 complementary methods can enhance performance by harnessing distinct advantages of both methods; combines FDM & GOR V: FDM - Fragment Data Mining - exploits availability of sequencesimilar fragments in the PDB, which can lead to highly accurate prediction - much better than GOR V - for such fragments, but such fragments are not available for many cases GOR V - Garnier, Osguthorpe, Robson V - predicts secondary structure of less similar fragments with good performance; these are protein fragments for which FDM method cannot find suitable structures For references & additional details: BCB 444/544 F07 ISU Dobbs #21 - Protein Secondary Structure 31 BCB 444/544 F07 ISU Dobbs #21 - Protein Secondary Structure 32 Secondary Structure : for Different Types of Proteins/Domains For Complete proteins: Globular Proteins - use methods previously described Transmembrane (TMM) Proteins - use special methods (next slides) For Structural Domains: many under development: Coiled-Coil Domains (Protein interaction domains) Zinc Finger Domains (DNA binding domains), others SS for Transmembrane Proteins Transmembrane (TM) Proteins Only a few in the PDB - but ~ 30% of cellular proteins are membrane-associated! Hard to determine experimentally, so prediction important TM domains are relatively 'easy' to predict! Why? constraints due to hydrophobic environment 2 main classes of TM proteins: α- helical β- barrel BCB 444/544 F07 ISU Dobbs #21 - Protein Secondary Structure 33 BCB 444/544 F07 ISU Dobbs #21 - Protein Secondary Structure 34 SS for TM α-helices α-helical TM domains: Helices are amino acids long (span the membrane) Predominantly hydrophobic residues Helices oriented perpendicular to membrane Orientation can be predicted using "positive inside" rule Residues at cytosolic (inside or cytoplasmic) side of TM helix, near hydrophobic anchor are more positively charged than those on lumenal (inside an organelle in eukaryotes) or periplasmic side (space between inner & outer membrane in gram-negative bacteria) Alternating polar & hydrophobic residues provide clues to interactions among helices within membrane Servers? TMHMM or HMMTOP - 70% accuracy - confused by hydrophobic signal peptides (short hydrophobic sequences that target proteins to the endoplasmic reticulum, ER) Phobius - 94% accuracy - uses distinct HMM models for TM helices & signal peptide sequences SS for TM β-barrels β-barrel TM domains: β-strands are amphipathic (partly hydrophobic, partly hydrophilic) Strands are amino acids long Every 2nd residue is hydrophobic, facing lipid bilayer Other residues are hydrophilic, facing "pore" or opening Servers? Harder problem, fewer servers TBBPred - uses NN or SVM (more on these ML methods later) Accuracy? BCB 444/544 F07 ISU Dobbs #21 - Protein Secondary Structure 35 BCB 444/544 F07 ISU Dobbs #21 - Protein Secondary Structure 36 BCB 444/544 Fall 07 Dobbs 6

7 of Coiled-Coil Domains Coiled-coils Superhelical protein motifs or domains, with two or more interacting α-helices that form a "bundle" Often mediate inter-protein (& intra-protein) interactions 'Easy' to detect in primary sequence: Internal repeat of 7 residues (heptad) 1 & 4 = hydrophobic (facing helical interface) 2,3,5,6,7 = hydrophilic (exposed to solvent) Helical wheel representation - can be used manually detect these, based on amino acid sequence Servers? Coils, Multicoil - probability-based methods 2Zip - for Leucine zippers = special type of CC in TFs: characterized by Leu-rich motif: L-X(6)-L-X(6)-L-X(6)-L Chp 15 - Tertiary Structure Xiong: Chp 15 Protein Tertiary Structure Methods Homology Modeling Threading and Fold Recognition Ab Initio Protein Structural CASP BCB 444/544 F07 ISU Dobbs #21 - Protein Secondary Structure 37 BCB 444/544 F07 ISU Dobbs #21 - Protein Secondary Structure 38 BCB 444/544 Fall 07 Dobbs 7