Protein Structure Prediction 11/11/05

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1 11/11/05 Protein Structure Prediction & Modeling Bioinformatics Seminars Nov 11 Fri 12:10 BCB Seminar in E164 Lago Building Supertrees Using Distances Steve Willson, Dept of Mathematics 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 11/11/05 D Dobbs ISU - BCB 444/544X: Protein Structure Prediction 1 11/11/05 D Dobbs ISU - BCB 444/544X: Protein Structure Prediction 2 Protein Structure & Function: Analysis & Prediction Mon Protein structure: basics; classification,databases, visualization Wed Protein structure databases - cont. Thurs Lab Protein structure databases Visualization software Secondary structure prediction Reading Assignment (for Mon-Fri) Mount Bioinformatics Chp 10 Protein classification & structure prediction pp Ck Errata: Fri Protein structure prediction Protein-nucleic acid interactions 11/11/05 D Dobbs ISU - BCB 444/544X: Protein Structure Prediction 3 11/11/05 D Dobbs ISU - BCB 444/544X: Protein Structure Prediction 4 Required: BCB 544 Additional Reading Gene Prediction: Burge & Karlin 1997 JMB 268:78 Optional: Prediction of complete gene structures in human genomic DNA Structure Prediction: Schueler-Furman Baker 2005 Science 310:638 Progress in modeling of protein structures and interactions Review last lecture: Protein Structure: Databases, Classification & Visualization 11/11/05 D Dobbs ISU - BCB 444/544X: Protein Structure Prediction 5 11/11/05 D Dobbs ISU - BCB 444/544X: Protein Structure Prediction 6 D Dobbs ISU - BCB 444/544X 1

2 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 11/11/05 D Dobbs ISU - BCB 444/544X: Protein Structure Prediction 7 11/11/05 D Dobbs ISU - BCB 444/544X: Protein Structure Prediction 8 Protein structure databases PDB Protein Data Bank MMDB (RCSB) - THE protein structure database Molecular Modeling Database (NCBI Entrez) - has "added" value Protein structure classification SCOP = Structural Classification of Proteins Levels reflect both evolutionary and structural relationships CATH = Classification by Class, Architecture, Topology & Homology MSD Molecular Structure Database Especially good for interactions, binding sites DALI/FSSP (recently moved to EBI & reorganized) fully automated structure alignments DALI server DALI Database (fold classification) 11/11/05 D Dobbs ISU - BCB 444/544X: Protein Structure Prediction 9 11/11/05 D Dobbs ISU - BCB 444/544X: Protein Structure Prediction 10 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 11/11/05 D Dobbs ISU - BCB 444/544X: Protein Structure Prediction 11 Protein structure visualization Superb interactive structure visualization software by Jane & Dave Richardson, Duke University KINIMAGE Fantastic research tools for structure analysis & refinement 11/11/05 D Dobbs ISU - BCB 444/544X: Protein Structure Prediction 12 D Dobbs ISU - BCB 444/544X 2

3 RCSB PDB - Beta site MMDB 11/11/05 D Dobbs ISU - BCB 444/544X: Protein Structure Prediction 13 11/11/05 D Dobbs ISU - BCB 444/544X: Protein Structure Prediction 14 Cn3D Cn3D : Displaying 2' Structures 11/11/05 D Dobbs ISU - BCB 444/544X: Protein Structure Prediction 15 11/11/05 D Dobbs ISU - BCB 444/544X: Protein Structure Prediction 16 Cn3D: Structural Alignments SCOP - Structure Classification 11/11/05 D Dobbs ISU - BCB 444/544X: Protein Structure Prediction 17 11/11/05 D Dobbs ISU - BCB 444/544X: Protein Structure Prediction 18 D Dobbs ISU - BCB 444/544X 3

4 6 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 CATH - Structure Classification 11/11/05 D Dobbs ISU - BCB 444/544X: Protein Structure Prediction 19 11/11/05 D Dobbs ISU - BCB 444/544X: Protein Structure Prediction 20 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? 11/11/05 D Dobbs ISU - BCB 444/544X: Protein Structure Prediction 21 11/11/05 D Dobbs ISU - BCB 444/544X: Protein Structure Prediction 22 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 11/11/05 D Dobbs ISU - BCB 444/544X: Protein Structure Prediction 23 11/11/05 D Dobbs ISU - BCB 444/544X: Protein Structure Prediction 24 D Dobbs ISU - BCB 444/544X 4

5 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 11/11/05 D Dobbs ISU - BCB 444/544X: Protein Structure Prediction 25 11/11/05 D Dobbs ISU - BCB 444/544X: Protein Structure Prediction 26 New today: Protein Structure Prediction Secondary structure (text focuses on this - I won't) Tertiary structure (let's do this instead!) Deciphering the Protein Folding Code Protein Structure Prediction or "Protein Folding" Problem given the amino acid sequence of a protein, predict its 3-dimensional structure (fold) "Inverse Folding" Problem given a protein fold, identify every amino acid sequence that can adopt its 3-dimensional structure 11/11/05 D Dobbs ISU - BCB 444/544X: Protein Structure Prediction 27 11/11/05 D Dobbs ISU - BCB 444/544X: Protein Structure Prediction 28 Protein Structure Determination? High-resolution structure determination X-ray crystallography (<1A ) Nuclear magnetic resonance (NMR) (~1-2.5A ) Lower-resolution structure determination Cryo-EM (electron-microscropy) ~10-15A Theoretical Models? Highly variable - now, some equiv to X-ray! Tertiary Structure Prediction Fold or tertiary structure prediction problem can be formulated as a search for minimum energy conformation search space is defined by psi/phi angles of backbone and side-chain rotamers search space is enormous even for small proteins! number of local minima increases exponentially of the number of residues Computationally it is an exceedingly difficult problem! 11/11/05 D Dobbs ISU - BCB 444/544X: Protein Structure Prediction 29 11/11/05 D Dobbs ISU - BCB 444/544X: Protein Structure Prediction 30 D Dobbs ISU - BCB 444/544X 5

6 Ab Initio Prediction 1. Develop energy function bond energy bond angle energy dihedral angle energy van der Waals energy electrostatic energy 2. Calculate structure by minimizing energy function (usually Molecular Dynamics or Monte Carlo methods) Ab initio prediction - not practical in general Computationally? very expensive Accuracy? Usually poor for all but short peptides (but see Baker review!) Two primary methods Comparative Modeling 1) Homology modeling 2) Threading (fold recognition) Note: both rely on availability of experimentally determined structures that are "homologous" or at least structurally very similar to target Provide folded structure only Provides both folding pathway & folded structure 11/11/05 D Dobbs ISU - BCB 444/544X: Protein Structure Prediction 31 11/11/05 D Dobbs ISU - BCB 444/544X: Protein Structure Prediction 32 Homology Modeling 1. Identify homologous protein sequences PSI-BLAST multiple sequence alignment (MSA) 2. Among those with available structures, choose closest sequence match for template 3. Build model by placing residues into corresponding positions of homologous structure models & refine by "tweaking" Homology modeling - works "well" Computationally? not very expensive Accuracy? higher sequence identity better model Requires >30% sequence identity Threading - Fold Recognition Identify best fit between target sequence & template structure 1. Develop energy function 2. Develop template library 3. Align target sequence with each template & score 4. Determine best score (1D to 3D alignment) 5. Build refine structure as in homology modeling Threading - works "sometimes" Computationally? Can be expensive or cheap, depends on energy function & whether "all atom" or "backbone only" threading Accuracy? in theory, should not depend on sequence identity (should depend on quality of template library & "luck") But, usually higher sequence identity better model 11/11/05 D Dobbs ISU - BCB 444/544X: Protein Structure Prediction 33 11/11/05 D Dobbs ISU - BCB 444/544X: Protein Structure Prediction 34 Threading - a "local" example Threading Goals & Issues Target Sequence ALKKGF HFDTSE Find correct sequence-structure alignment of a target sequence with its native-like fold in PDB Structure Templates 1. Align target sequence with template structures (fold library) from the Protein Data Bank (PDB) 2. Calculate energy (score) to evaluate goodness of fit between target sequence & template structure 3. Rank models based on energy scores Structure database - must be complete: no decent model if no good template in library! Sequence-structure alignment algorithm: Bad alignment Bad score! Energy function (scoring scheme): must distinguish correct sequence-fold alignment from incorrect sequence-fold alignments must distinguish correct fold from close decoys Prediction reliability assessment - how determine whether predicted structure is correct (or even close?) 11/11/05 D Dobbs ISU - BCB 444/544X: Protein Structure Prediction 35 11/11/05 D Dobbs ISU - BCB 444/544X: Protein Structure Prediction 36 D Dobbs ISU - BCB 444/544X 6

7 Threading Structure database Build a template database (e.g., ASTRAL domain library derived from PDB) Threading - Energy function Two main methods (and combinations of these) Structural profile (environmental) physico-chemical properties of aa s Contact potential (statistical) based on contact statistics from PDB (Miyazawa & Jernigan - Jernigan now at ISU) Supplement with additional decoys, e.g., generated using ab initio approach such as Rosetta (Baker) 11/11/05 D Dobbs ISU - BCB 444/544X: Protein Structure Prediction 37 11/11/05 D Dobbs ISU - BCB 444/544X: Protein Structure Prediction 38 Protein Threading typical energy function MTYKLILNGKTKGETTTEAVDAATAEKVFQYANDNGVDGEWTYTE What is "probability" that two specific residues are in contact? Total energy: E_p + E_s + E_g How well does a specific residue fit structural environment? Alignment gap penalty? Find a sequence-structure alignment that minimizing the energy function A Rapid Threading Approach for Protein Structure Prediction Kai-Ming Ho, Physics Haibo Cao Yungok Ihm Zhong Gao James Morris Cai-zhuang Wang Drena Dobbs, GDCB Jae-Hyung Lee Michael Terribilini Jeff Sander 11/11/05 D Dobbs ISU - BCB 444/544X: Protein Structure Prediction 39 11/11/05 D Dobbs ISU - BCB 444/544X: Protein Structure Prediction 40 Performance Evaluation? "Blind Test" Typical Results: well, actually, BEST Results: HO = #1 ranked CASP prediction for this target CASP5 Competition (Critical Assessment of Protein Structure Prediction) Target 174 PDB ID = 1MG7 Predicted Structure Given: Amino acid sequence Goal: Predict 3-D structure T174_1 (before experimental results published) Actual Structure T174_2 11/11/05 D Dobbs ISU - BCB 444/544X: Protein Structure Prediction 41 D Dobbs ISU - BCB 444/544X 7

8 Overall Performance in CASP5 Contest (M. Levitt, Stanford) FR Fold Recognition (targets manually assessed by Nick Grishin) Rank Z-Score Ngood Npred NgNW NpNW Group-name Ginalski Skolnick Kolinski Baker BIOINFO.PL Shortle BAKER-ROBETTA Brooks Ho-Kai-Ming Jones-NewFold FR NgNW - number of good predictions without weighting for multiple models FR NpNW - number of total predictions without weighting for multiple models D Dobbs ISU - BCB 444/544X 8