bcb 444/544
DESCRIPTION
BCB 444/544. Lecture 22 Secondary Structure Prediction Tertiary Structure Prediction #22_Oct10. Required Reading ( before lecture). Mon Oct 8 - Lecture 20 Protein Secondary Structure Prediction Chp 14 - pp 200 - 213 Wed Oct 10 - Lecture 21 Protein Tertiary Structure Prediction - PowerPoint PPT PresentationTRANSCRIPT
10/12/07BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction
BCB 444/544
Lecture 22
Secondary Structure Prediction
Tertiary Structure Prediction
#22_Oct10
10/12/07BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction
Mon Oct 8 - Lecture 20
Protein Secondary Structure Prediction
• Chp 14 - pp 200 - 213
Wed Oct 10 - Lecture 21
Protein Tertiary Structure Prediction
• Chp 15 - pp 214 - 230
Thurs Oct 11 & Fri Oct 12 - Lab 7 & Lecture 22
Protein Tertiary Structure Prediction
• Chp 15 - pp 214 - 230
Required Reading (before lecture)
10/12/07BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction
Assignments & Announcements
ALL: HomeWork #3 √Due: Mon Oct 8 by 5 PM
• HW544: HW544Extra #1
√Due: Task 1.1 - 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 1.1 - Mon Oct 8 by noon
• Due: Task 1.2 - Fri Oct 12 by 5 PM <Task 2 NOT required for BCB444 students>
10/12/07BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction
New Reading & Homework Assignment
ALL: HomeWork #4 (posted online today)Due: Fri Oct 19 by 5 PM (one week from today)
Read: Ginalski et al.(2005) Practical Lessons from Protein Structure Prediction, Nucleic Acids Res. 33:1874-91. http://nar.oxfordjournals.org/cgi/content/full/33/6/1874 (PDF posted on website)
• Although somewhat dated, this paper provides a nice overview of protein structure prediction methods and evaluation of predicted structures.
• Your assignment is to write a summary of this paper - for details
see HW#4 posted online & sent by email on Fri Oct 12
10/12/07BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction
Seminars this Week - (yesterday)
BCB List of URLs for Seminars related to Bioinformatics:http://www.bcb.iastate.edu/seminars/index.html
• Oct 11 Thurs
• Dr. Klaus Schulten (Univ of Illinois) - Baker Center Seminar
The Computational Microscope 2:10 PM in E164
Lagomarcino http://www.bioinformatics.iastate.edu/seminars/abstracts/2007_2008/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
http://www.cs.iastate.edu/~colloq/new/gusfield.shtml
10/12/07BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction
Seminars this Week - Fri (today)
BCB List of URLs for Seminars related to Bioinformatics:http://www.bcb.iastate.edu/seminars/index.html
• Oct 12 Fri • Dr. Edward Yu (Physics/BBMB, ISU) - BCB Faculty Seminar
TBA: "Structural Biology" (see URL below) 2:10 PM in 102
Sci http://webdev.its.iastate.edu/webnews/data/site_gdcb_dept_seminars/30/webnewsfilefield_abstract/Dr.-Ed-Yu.pdf
• Dr. Srinivas Aluru (ECprE, ISU) - GDCB Seminar
Consensus Genetic Maps: A Graph Theoretic Approach 4:10 PM in 1414
MBBhttp://webdev.its.iastate.edu/webnews/data/
site_gdcb_dept_seminars/35/webnewsfilefield_abstract/Dr.-Srinivas-Aluru.pdf
10/12/07BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction
Chp 12 - Protein Structure Basics
SECTION V STRUCTURAL BIOINFORMATICS
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)
10/12/07BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction
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: http://en.wikipedia.org/wiki/Protein_structure
1. 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)
• http://www.uweb.engr.washington.edu/research/tutorials/SPM.pdf
• Circular Dichroism (CD), several other spectroscopic methods
10/12/07BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction
"Best" Resolution of Protein Structures
• High-resolution methods• X-ray crystallography (< 1A)• NMR (~1 - 2.5A)
• Lower-resolution methods• Cryo-EM (~10-15A)
• Theoretical Models? • Usually low resolution, at present, but• Highly variable - & a few ~crystal data
Baker & Sali (2000)Pevsner Fig 9.36
10/12/07BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction
Chp 13 - Protein Structure Visualization, Comparison & Classification
SECTION V STRUCTURAL BIOINFORMATICS
Xiong: Chp 13
Protein Structure Visualization, Comparison & Classification
• Protein Structural Visualization• Protein Structure Comparison - later• Protein Structure Classification
10/12/07BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction
Protein Structure Classification
• SCOP = Structural Classification of Proteins
Levels reflect both evolutionary and structural relationships
http://scop.mrc-lmb.cam.ac.uk/scop
• CATH = Classification by Class, Architecture,Topology & Homologyhttp://cathwww.biochem.ucl.ac.uk/latest/
• DALI - (recently moved to EBI & reorganized)
DALI Database (fold classification)http://ekhidna.biocenter.helsinki.fi/dali/start
Each method has strengths & weaknesses….
10/12/07BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction
Chp 14 - Secondary Structure Prediction
SECTION V STRUCTURAL BIOINFORMATICS
Xiong: Chp 14
Protein Secondary Structure Prediction
• Secondary Structure Prediction for Globular Proteins
• Secondary Structure Prediction for Transmembrane Proteins
• Coiled-Coil Prediction
10/12/07BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction
Secondary Structure Prediction
Has become highly accurate in recent years (>85%)
• Usually 3 (or 4) state predictions:
• H = -helix• E = -strand• C = coil (or loop)• (T = turn)
10/12/07BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction
Secondary Structure Prediction Methods
• 1st Generation methods
Ab initio - used relatively small dataset of structures availableChou-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 availableGOR II, III, IV, SOPM, GOR V, FDM
• 3rd Generation methodsHomology-based & Neural network based
PHD, PSIPRED, SSPRO, PROF, HMMSTR, CDM
• Meta-Servers combine several different methods
Consensus & Ensemble basedJPRED, PredictProtein, Proteus
10/12/07BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction
Secondary Structure Prediction Servers
Prediction Evaluation?
• Q3 score - % of residues correctly predicted (3-state)
in cross-validation experiments
Best results? Meta-servers
• http://expasy.org/tools/ (scroll for 2' structure prediction)
• http://www.russell.embl-heidelberg.de/gtsp/secstrucpred.html
• JPred www.compbio.dundee.ac.uk/~www-jpred
• PredictProtein http://www.predictprotein.org/ Rost, Columbia
Best "individual" programs? ??
• CDM http://gor.bb.iastate.edu/cdm/ Sen…Jernigan, ISU
• FDM (not available separately as server) Cheng…
Jernigan, ISU
• GOR V http://gor.bb.iastate.edu/ Kloczkowsky…Jernigan, ISU
10/12/07BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction
• 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 sequence-similar 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: http://gor.bb.iastate.edu/cdm/
Consensus Data Mining (CDM)
10/12/07BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction
Where Find "Actual" Secondary Structure? In the PDB
10/12/07BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction
How Does Predicted Secondary Structure Compare?
e.g., from CMD
Query MAATAAEAVASGSGEPREEAGALGPAWDESQLRSYSFPTRPIPRLSQSDPRAEELIENEEGOR V CCCCHHHHHHHHCCHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHCCCCFDM CCCCCCCCCCCCCCCCCEECCCCCCCCCHHHCCCCCCEECCCCCCCCCCHHHHHHHHCCCCDM CCCCHHHHHHCCCCCCCEECCCCCCCCCHHHCCCCCCEECCCCCCCCCCHHHHHHHHCCC
DSSPAuthor
10/12/07BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction
Secondary Structure Prediction: for Different Types of Proteins/Domains
For Complete proteins:
Globular Proteins - use methods previously described
Transmembrane (TM) 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…
10/12/07BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction
SS Prediction 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:
- helical
- barrel
10/12/07BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction
SS Prediction for TM -Helices
-Helical TM domains:• Helices are 17-25 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
10/12/07BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction
SS Prediction for TM -Helices
-Helical TM domains:• Helices are 17-25 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
10/12/07BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction
SS Prediction for TM -Barrels
-Barrel TM domains: • -strands are amphipathic (partly hydrophobic, partly
hydrophilic)
• Strands are 10 - 22 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 ?
10/12/07BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction
Prediction of Coiled-Coil Domains
Coiled-coils• Superhelical protein motifs or domains, with two or more
interacting -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
10/12/07BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction
Chp 15 - Tertiary Structure Prediction
SECTION V STRUCTURAL BIOINFORMATICS
Xiong: Chp 15
Protein Tertiary Structure Prediction
• Methods• Homology Modeling• Threading and Fold Recognition• Ab Initio Protein Structural Prediction• CASP
10/12/07BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction
Structural Genomics - Status & Goal
~ 20,000 "traditional" genes in human genome (recall, this is fewer than earlier estimate of
30,000)
~ 2,000 proteins in a typical cell> 4.9 million sequences in UniProt (Oct 2007)> 46,000 protein structures in the PDB (Oct 2007)
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
10/12/07BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction
Structural Genomics Projects
TargetDB: database of structural genomics targetshttp://targetdb.pdb.org
10/12/07BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction
Protein Sequence & Structure: Analysis
• Diamond STING Millennium - Many useful structure analysis tools, including Protein Dossier http://trantor.bioc.columbia.edu/SMS/
• SwissProt (UniProt)Protein knowledgebasehttp://us.expasy.org/sprot
• InterProSequence analysis toolshttp://www.ebi.ac.uk/interpro
10/12/07BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction
Protein Structure Prediction or Protein Folding Problem
"Major unsolved problem in molecular biology"
In cells: spontaneousassisted by enzymesassisted by chaperones
In vitro: many proteins can fold to their "native" states spontaneously & without assistance
but, many do not!
10/12/07BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction
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 that 3-dimensional structure
10/12/07BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction
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 2 Major Protein Folding Problems:
1- Determination of folding pathway 2- Prediction of tertiary structure from
sequence
Both still largely unsolved problems
10/12/07BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction
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 & rearrangement of some 2' structures
Native state? - assumed to be lowest free energy - may be an ensemble of structures
10/12/07BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction
Protein Dynamics
• Protein in native state is NOT static
• Function of many proteins requires 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 ~ 2 H-bonds!)
• Folding involves changes in both entropy & enthalpy
10/12/07BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction
Difficulty of Tertiary Structure Prediction
Folding 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 with number of residues
Computationally it is an exceedingly difficult problem!
10/12/07BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction
From Thursday's Lab:
• Homology Modeling - using SWISS-MODEL• http://swissmodel.expasy.org//SWISS-MODEL.html
• Threading - using 3-D JURY (BioinfoBank, a METAserver)• http://meta.bioinfo.pl/submit_wizard.pl
• Be sure to take a look at CASP contest:• http://predictioncenter.gc.ucdavis.edu/
• CASP7 contest in 2006 • http://www.predictioncenter.org/casp7/Casp7.html