BCB 444/544
Lecture 22
 Secondary Structure Prediction
Tertiary Structure Prediction
#22_Oct10
BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction
10/12/07
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
• Chp 15 - pp 214 - 230
Thurs Oct 11 & Fri Oct 12 - Lab 7 & Lecture 22
Protein Tertiary Structure Prediction
• Chp 15 - pp 214 - 230
BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction
10/12/07
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>
BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction
10/12/07
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
BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction
10/12/07
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
BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction
10/12/07
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/webne
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
http://webdev.its.iastate.edu/webnews/data/site_gdcb_dept_seminars/35/web
newsfilefield_abstract/Dr.-Srinivas-Aluru.pdf
BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction
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Chp 12 - Protein Structure Basics
SECTION V
STRUCTURAL BIOINFORMATICS
Xiong: Chp 12 Protein Structure Basics
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•
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Amino Acids
Peptide Bond Formation
Dihedral Angles
Hierarchy
Secondary Structures
Tertiary Structures
• Determination of Protein 3-Dimensional Structure
• Protein Structure DataBank (PDB)
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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
3. Other methods (usually lower resolution, at present):
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Electron Paramagnetic Resonance (EPR - also called ESR, EMR)
Electron microscopy (EM)
Cryo-EM
Scanning Probe Microscopies (AFM - Atomic Force Microscopy)
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•
http://www.uweb.engr.washington.edu/research/tutorials/SPM.pdf
Circular Dichroism (CD), several other spectroscopic methods
BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction
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"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
Pevsner
Fig 9.36
Baker & Sali (2000)
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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
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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 & Homology
http://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….
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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
BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction
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Secondary Structure Prediction
Has become highly accurate in recent years (>85%)
• Usually 3 (or 4) state predictions:
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H = -helix
E = -strand
C = coil (or loop)
(T = turn)
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Secondary Structure Prediction Methods
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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)
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2nd Generation methods
based on much larger datasets of structures now available
GOR II, III, IV, SOPM, GOR V, FDM
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3rd Generation methods
Homology-based & Neural network based
PHD, PSIPRED, SSPRO, PROF, HMMSTR, CDM
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Meta-Servers
combine several different methods
Consensus & Ensemble based
JPRED, PredictProtein, Proteus
BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction
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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/
• FDM
(not available separately as server)
• GOR V
Sen…Jernigan, ISU
Cheng…Jernigan, ISU
http://gor.bb.iastate.edu/ Kloczkowsky…Jernigan, ISU
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Consensus Data Mining (CDM)
• 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: http://gor.bb.iastate.edu/cdm/
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Where Find "Actual" Secondary Structure?
In the PDB
BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction
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How Does Predicted Secondary Structure
Compare?
e.g., from CMD
DSSP
Author
Query
GOR V
FDM
CDM
MAATAAEAVASGSGEPREEAGALGPAWDESQLRSYSFPTRPIPRLSQSDPRAEELIEN
CCCCHHHHHHHHCCHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHH
CCCCCCCCCCCCCCCCCEECCCCCCCCCHHHCCCCCCEECCCCCCCCCCHHHHH
CCCCHHHHHHCCCCCCCEECCCCCCCCCHHHCCCCCCEECCCCCCCCCCHHHHH
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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…
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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
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SS Prediction for TM -Helices
-Helical TM domains:
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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
BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction
10/12/07
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
BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction
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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 ?
BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction
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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
BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction
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Chp 15 - Tertiary Structure Prediction
SECTION V
STRUCTURAL BIOINFORMATICS
Xiong: Chp 15
Protein Tertiary Structure Prediction
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Methods
Homology Modeling
Threading and Fold Recognition
Ab Initio Protein Structural Prediction
CASP
BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction
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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
BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction
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Structural Genomics Projects
TargetDB: database of structural genomics targets
http://targetdb.pdb.org
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Protein Sequence & Structure: Analysis
• Diamond STING Millennium - Many useful structure analysis
tools, including Protein Dossier
http://trantor.bioc.columbia.edu/SMS/
• SwissProt (UniProt)
Protein knowledgebase
http://us.expasy.org/sprot
• InterPro
Sequence analysis tools
http://www.ebi.ac.uk/interpro
BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction
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Protein Structure Prediction
or Protein Folding Problem
"Major unsolved problem in molecular biology"
In cells:
spontaneous
assisted by enzymes
assisted by chaperones
In vitro:
many proteins can fold to their "native"
states spontaneously & without assistance
but, many do not!
BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction
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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
BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction
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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
BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction
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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
BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction
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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
BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction
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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!
BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction
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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
BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction
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