10/10/07bcb 444/544 f07 isu dobbs #21 - protein secondary structure prediction1 bcb 444/544 lecture...

10/10/07BCB 444/544 F07 ISU Dobbs #21 - Protein Secondary Structure Prediction 1

BCB 444/544

Lecture 21

Protein Structure Visualization, Classification & Comparison

Secondary Structure Prediction

#21_Oct10


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


• Chp 15 - pp 214 - 230

Required Reading (before lecture)


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>


Seminars this Week - Thurs:

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


Seminars this Week - Fri:

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 MBB

http://webdev.its.iastate.edu/webnews/data/site_gdcb_dept_seminars/35/webnewsfilefield_abstract/Dr.-Srinivas-Aluru.pdf


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)


Protein Structure & Function

• 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!


6 Main Classes of Protein Structure

1) -Domains

Bundles of helices connected by loops

2) -DomainsMainly antiparallel sheets, usually 2 sheets forming

sandwich

3) DomainsMainly parallel sheets with intervening helices, mixed

sheets

4) Domains

Mainly segregated helices and sheets

5) Multidomain (Containing domains from more than one class

6) Membrane & cell-surface proteins


Protein Structure Databases

PDB - Protein Data Bank http://www.rcsb.org/pdb/ (RCSB) - THE protein structure database

MMDB - Molecular Modeling Databasehttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Structure

(NCBI Entrez) - has "added" value

MSD - Molecular Structure Database http://www.ebi.ac.uk/msd

Especially good for interactions & binding sites


PDB (RCSB) - recently "remediated" http://www.rcsb.org/pdb


Structure at NCBIhttp://www.ncbi.nlm.nih.gov/Structure


MMDB at NCBI http://www.ncbi.nlm.nih.gov/Structure/MMDB/mmdb.shtml


MMDB: MMolecular MModeling Data Base

• 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)

http://www.ncbi.nlm.nih.gov/Structure/VAST/vastsearch.html


MSD: MMolecular SStructuretructure Database

http://www.ebi.ac.uk/msd/


wwPDB: World Wide PDBhttp://www.wwpdb.org


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


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, MolMolhttp://www.umass.edu/microbio/rasmol/index2.htm

Cn3D - esp. good for structural alignmentshttp://www.biosino.org/mirror/www.ncbi.nlm.nih.gov/Structure/cn3d/

CHIME (Protein Explorer)http://www.umass.edu/microbio/chime/getchime.htm

MolviZ.Orghttp://www.umass.edu/microbio/chime

Deep View = Swiss-PDB Viewerhttp://www.expasy.org/spdbv


PyMol http://pymol.sourceforge.net/


Cn3D http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml


Cn3D : Displaying 3' Structures

Chloroquine


Cn3D: Structural Alignments

NADH


Protein Explorer (Chime)http://www.umass.edu/microbio/chime/pe_beta/pe/protexpl/frntdoor.htm


Protein Structure Comparison Methods

3 Basic Approaches for Aligning Structures:

1. Intermolecular -

2. Intramolecular -

3. Combined -

• DALI/FSSP (most commonly used)Fully automated structure alignments

1. DALI server http://www.ebi.ac.uk/dali/index.html2. DALI Database (fold classification)

http://ekhidna.biocenter.helsinki.fi/dali/start

We will skip this for now


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….


SCOP - Structure Classificationhttp://scop.mrc-lmb.cam.ac.uk/scop/

QuickTime™ and aTIFF (LZW) decompressor

are needed to see this picture.


CATH - Structure Classification http://www.cathdb.info/latest/index.html

QuickTime™ and aTIFF (LZW) decompressor

are needed to see this picture.


Chp 14 - Secondary Structure Prediction


Xiong: Chp 14

Protein Secondary Structure Prediction

• Secondary Structure Prediction for Globular Proteins

• Secondary Structure Prediction for Transmembrane Proteins

• Coiled-Coil 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)


Secondary Structure Prediction 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 availableGOR II, III, IV, SOPM

• 3rd Generation methodsHomology-based & Neural network based

PHD, PSIPRED, SSPRO, PROF, HMMSTR

• Meta-Serverscombine several different methods

Consensus & Ensemble basedJPRED, PredictProtein


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

• GOR V http://gor.bb.iastate.edu/ 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 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)


Secondary Structure Prediction: 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 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


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


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 ?


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


Chp 15 - Tertiary Structure Prediction


Xiong: Chp 15


• Methods• Homology Modeling• Threading and Fold Recognition• Ab Initio Protein Structural Prediction• CASP

10/10/07bcb 444/544 f07 isu dobbs #21 - protein secondary structure prediction1 bcb 444/544 lecture...

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