BCB 444/544

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BCB 444/544

• Lecture 20
• Protein Structure Basics,
• Visualization, Classification Comparison
• 20_Oct08

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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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BCB 544 - Extra Required Reading

• Assigned Mon Sept 24
• BCB 544 Extra Required Reading Assignment
• for 544 Extra HW1 Task 2
• Pollard KS, ., Haussler D. (2006) An RNA gene
  expressed during cortical development evolved
  rapidly in humans. Nature 443 167-172.
• http//www.nature.com/nature/journal/v443/n7108/ab
  s/nature05113.html
• doi10.1038/nature05113
• PDF available on class website - under Required
  Reading Link

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BCB 544 Projects (Optional for BCB 444)

• For a better idea about what's involved in the
  Team Projects, please look over last year's
  expectations for projects http//www.public.iasta
  te.edu/f2007.com_s.544/project.htm
• Criteria for evaluation of projects (oral
  presentations) are summarized here
• http//www.public.iastate.edu/7Ef2007.com_s.544/h
  omework/HW7.pdf

Please note wrong URL (instead of that shown
above) was included in originally posted
544ExtraHW1 corrected version is posted now
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Assignments Announcements - 1

• Students registered for BCB 444 Two Grading
  Options
• 1) Take Final Exam per original Grading Policies
• 2) Instead of taking Final Exam - you may
  participate in a Team Research Project
• If you choose 2, please do 3 things
• Contact Drena (in person)
• Send email to Michael Terribilini
  (terrible_at_iastate.edu)
• Complete 544 Extra HW1 - Task 1.1 by noon on Mon
  Oct 1

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Assignments Announcements - 2

• BCB 444s (Standard)
• 200 pts Midterm Exams 100 points each
• 200 Homework Laboratory assignments 200
  points
• 100 Final Exam
• 500 pts Total for BCB 444
• BCB 444p (Project)
• 200 pts Midterm Exams 100 points each
• 200 Homework Laboratory assignments 200
  points
• 190 Team Research Project
• 590 pts Total for BCB 444p
• BCB 544 200 pts Midterm Exams 100 points
  each
• 200 Homework Laboratory assignments
• 100 Final Exam
• 200 Discussion Questions Team Research
  Projects
• 700 pts Total for BCB 544

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Assignments Announcements 3

• ALL HomeWork 3
• Due Mon Oct 8 (Today) 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
  (not Monday)
• 444 "Project-instead-of-Final" students should
  also submit
• HW544Extra 1
• Due Task 1.1 - Mon Oct 8 (Today) by noon
• Due Task 1.2 - Fri Oct 12 by 5 PM (not Monday)
• Task 2 NOT required!

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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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Amino Acids

• Each of 20 different amino acids has different
  "R-Group" or side chain attached to Ca

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Peptide Bond is Rigid and Planar
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Certain Side-chain Configurations are
Energetically Favored (Rotamers)
Ramachandran plot "Allowable" psi phi angles
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Glycine is Smallest Amino Acid R group H atom

• Glycine residues increase backbone flexibility
  because they have no R group

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Proline is Cyclic

• Proline residues reduce flexibility of
  polypeptide chain
• Proline cis-trans isomerization is often a
  rate-limiting step in protein folding
• Recent work suggests it also may also regulate
  ligand binding in native proteins Andreotti
  (BBMB)

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Cysteines can Form Disulfide (S-S) Bonds

• Disulfide bonds (covalent) stabilize
• 3-D structures
• In eukaryotes, disulfide bonds are often found
  in secreted proteins or extracellular domains

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Globular Proteins Have a Compact Hydrophobic
Core

• Packing of hydrophobic side chains into interior
  is main driving force for folding
• Problem? Polypeptide backbone is highly polar
  (hydrophilic) due to polar -NH and CO in each
  peptide unit (which are charged at neutral pH7,
  found in biological systems) these polar groups
  must be neutralized
• Solution? Form regular secondary structures,
• e.g., ?-helix, b-sheet- both stabilized by
  H-bonds

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Exterior Surface of Globular Proteins is
Generally Hydrophilic

• Hydrophobic core formed by packed secondary
  structural elements provides compact, stable core
• "Functional groups" of protein are attached to
  this framework exterior has more flexible
  regions (loops) and polar/charged residues
• Hydrophobic "patches" on protein surface are
  often involved in protein-protein interactions

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Protein Secondary Structures

• ??Helices
• ??Sheets
• Loops
• Coils

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??Helix Stabilized by H-bonds Between every
4th Residue in Backbone
C black O red N blue H white
Look Charges on backbone are "neutralized" by
hydrogen bonds (H-bonds) - red fuzzy vertical
bonds
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Types of ??Helices

• "Standard" ??helix 3.6 residues per turn
• H-bonds between C0 of residue n
• and N-H of residue n 4
• (this neutralizes backbone chgs)
• Helix ends are polar almost always on surface of
  protein
• Other types of helices?
• n 5 ? helix
• n 3 310 helix

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??Helix R-Groups are on Outside
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Certain Amino Acids are "Preferred" Others
are Rare in ??Helices

• Ala, Glu, Leu, Met good helix formers
• Pro, Gly Tyr, Ser very poor
• Amino acid composition distribution varies,
  depending on on location of helix in 3-D structure

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?-Sheets - also Stabilized by H-bonds Between
Backbone Atoms
Anti-parallel
Parallel
?-Sheets R-Groups are Above Below "Plane"
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Coils

• Regions of 2' structure that are not helices,
  sheets, or recognizable turns
• Intrinsically disordered regions appear to play
  important functional roles

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?Loops Turns

• Connect helices and sheets
• Vary in length 3-D configurations
• Are located on surface of structure
• Are more "tolerant" of mutations
• Are more flexible, can adopt multiple
  conformations
• Tend to have charged and polar amino acids
• Are frequently components of active sites
• Some fall into distinct structural families
  (e.g., hairpin loops, reverse turns)

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Globular Proteins are Built from Recurring
Structural Patterns

• Structural Motifs supersecondary structures
  combinations of 2' structural elements
• Domains combinations of motifs
• Independently folding unit (foldon)
• Functional unit

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Simple Motifs Combine to Form Domains
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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 with 2 sheets
  forming sandwich
• 3) a????Domains
• Mainly parallel sheets with intervening helices,
  also 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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?-Domain Structures 4-Helix Bundles
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?-Sheets Up-and-Down Sheets Barrels
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a?? Domains Leucine-rich Motifs can Form
Horseshoes
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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)

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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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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