BCB 444544

1
BCB 444/544

• Lecture 21
• Protein Structure Visualization, Classification
  Comparison
• Secondary Structure Prediction
• 21_Oct10

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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

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Assignments Announcements

• ALL HomeWork 3
• vDue Mon Oct 8 by 5 PM
• HW544 HW544Extra 1
• vDue 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
• vDue Task 1.1 - Mon Oct 8 by noon
• Due Task 1.2 - Fri Oct 12 by 5 PM
• ltTask 2 NOT required for BCB444 studentsgt

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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? 210 PM in E164
  Lagomarcino http//www.bioinformatics.iastate.edu/
  seminars/abstracts/2007_2008/Klaus_Schulten_Semina
  r.pdf
• Dr. Dan Gusfield (UC Davis) - Computer Science
  Colloquium ReCombinatorics Combinatorial
  Algorithms for Studying History of Recombination
  in Populations 330 PM in Howe Hall Auditorium
• http//www.cs.iastate.edu/colloq/new/gusfield.sh
  tml

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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) 210 PM in 102 Sci
  http//webdev.its.iastate.edu/web
  news/data/site_gdcb_dept_seminars/30/webnewsfilefi
  eld_abstract/Dr.-Ed-Yu.pdf
• Dr. Srinivas Aluru (ECprE, ISU) - GDCB Seminar
• Consensus Genetic Maps A Graph Theoretic
  Approach
• 410 PM in 1414 MBB
• http//webdev.its.iastate.edu/webnews/data/site_gd
  cb_dept_seminars/35/webnewsfilefield_abstract/Dr.-
  Srinivas-Aluru.pdf

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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)

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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!

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6 Main Classes of Protein Structure

• 1) a-Domains
• Bundles of helices connected by loops
• 2) ?-Domains
• Mainly antiparallel sheets, usually 2 sheets
  forming sandwich
• 3) a????Domains
• Mainly parallel sheets with intervening helices,
  mixed sheets
• 4) ?a????Domains
• Mainly segregated helices and sheets
• 5) Multidomain (a? ? ???
• Containing domains from more than one class
• 6) Membrane cell-surface proteins

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Protein Structure Databases

• PDB - Protein Data Bank
• http//www.rcsb.org/pdb/
• (RCSB) - THE protein structure database
• MMDB - Molecular Modeling Database
• http//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

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PDB (RCSB) - recently "remediated"
http//www.rcsb.org/pdb
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Structure at NCBI http//www.ncbi.nlm.nih.gov/Str
ucture
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MMDB at NCBI http//www.ncbi.nlm.nih.gov/
Structure/MMDB/mmdb.shtml
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MMDB Molecular Modeling 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/vastsea
  rch.html

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MSD Molecular Structure Database http//www.ebi.
ac.uk/msd/
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wwPDB World Wide PDB http//www.wwpdb.org
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Experimental Determination of 3D Structure

• 2 Major Methods to obtain high-resolution
  structures
• X-ray Crystallography (most PDB structures)
• Nuclear Magnetic Resonance (NMR) Spectroscopy
• Note Advantages Limitations of each method
• (See your lecture notes textbook)
• For more info http//en.wikipedia.org/wiki/Pro
  tein_structure
• 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/tutor
  ials/SPM.pdf
• Circular Dichroism (CD), several other
  spectroscopic methods

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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
• Protein Structure Classification

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Protein Structure Visualization

• RASMOL decendents PyMol, MolMol
• http//www.umass.edu/microbio/rasmol/index2.htm
• Cn3D - esp. good for structural alignments
• http//www.biosino.org/mirror/www.ncbi.nlm.nih.go
  v/Structure/cn3d/
• CHIME (Protein Explorer)
• http//www.umass.edu/microbio/chime/getchime.htm
• MolviZ.Org
• http//www.umass.edu/microbio/chime
• Deep View Swiss-PDB Viewer
• http//www.expasy.org/spdbv

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PyMol http//pymol.sourceforge.net/
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Cn3D http//www.ncbi.nlm.nih.gov/Structure/CN3
D/cn3d.shtml
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Cn3D Displaying 3' Structures
Chloroquine
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Cn3D Structural Alignments
NADH
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Protein Explorer (Chime)http//www.umass.edu/micr
obio/chime/pe_beta/pe/protexpl/frntdoor.htm
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Protein Structure Comparison Methods
We will skip this for now

• 3 Basic Approaches for Aligning Structures
• Intermolecular -
• Intramolecular -
• Combined -
• DALI/FSSP (most commonly used)
• Fully automated structure alignments
• DALI server http//www.ebi.ac.uk/dali/index.html
• DALI Database (fold classification) http//ek
  hidna.biocenter.helsinki.fi/dali/start

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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.b
  iochem.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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SCOP - Structure Classification http//scop.mrc-l
mb.cam.ac.uk/scop/
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CATH - Structure Classification
http//www.cathdb.info/latest/index.html
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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

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Secondary Structure Prediction

• Has become highly accurate in recent years (gt85)
• Usually 3 (or 4) state predictions
• H ?-helix
• E ?-strand
• C coil (or loop)
• (T turn)

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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
  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

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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/secstru
  cpred.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/
  SenJernigan, ISU
• GOR V http//gor.bb.iastate.edu/
  KloczkowskyJernigan, 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 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/

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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

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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
• 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

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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 ?

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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

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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