10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification1 BCB 444/544...
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Transcript of 10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification1 BCB 444/544...
10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification 1
BCB 444/544
Lecture 20
Protein Structure Basics,Visualization, Classification &
Comparison
#20_Oct08
10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification 2
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)
10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification 3
BCB 544 - Extra Required Reading
Assigned Mon Sept 24
BCB 544 Extra Required Reading Assignment: for 544 Extra HW#1 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/abs/nature05113.html
doi:10.1038/nature05113 • PDF available on class website - under Required Reading
Link
10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification 4
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.iastate.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/homework/
HW7.pdf
Please note: wrong URL (instead of that shown above) was includedin originally posted 544ExtraHW#1; corrected version is posted now
10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification 5
Assignments & Announcements - #1
Students registered for BCB 444: Two Grading Options
1) Take Final Exam per original Grading Policies2) 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 ([email protected])• Complete 544 Extra HW#1 - Task 1.1 by noon on Mon
Oct 1
10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification 6
Assignments & Announcements - #2
BCB 444s (Standard):200 pts Midterm Exams = 100 points each 200 Homework & Laboratory assignments = 200 points100 Final Exam500 pts Total for BCB 444
BCB 444p (Project):
200 pts Midterm Exams = 100 points each 200 Homework & Laboratory assignments = 200 points190 Team Research Project590 pts Total for BCB 444p
BCB 544: 200 pts Midterm Exams = 100 points each 200 Homework & Laboratory assignments100 Final Exam 200 Discussion Questions & Team Research Projects 700 pts Total for BCB 544
10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification 7
Assignments & Announcements #3
ALL: HomeWork #3 Due: Mon Oct 8 (Today) 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 (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!
10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification 8
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)
10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification 9
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!
10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification 10
Amino Acids
• Each of 20 different amino acids has different "R-Group" or side chain attached to C
10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification 11
Peptide Bond is Rigid and Planar
10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification 12
Certain Side-chain Configurations are Energetically Favored (Rotamers)
Ramachandran plot: "Allowable" psi & phi angles
10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification 13
Glycine is Smallest Amino AcidR group = H atom
• Glycine residues increase backbone flexibility because they have no R group
10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification 14
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)
10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification 15
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
10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification 16
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 C=O in each peptide unit (which are charged at neutral pH=7, found in biological systems); these polar groups must be neutralized
• Solution? Form regular secondary structures, • e.g., -helix, -sheet- both stabilized by H-bonds
10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification 17
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
10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification 18
Protein Secondary Structures
• Helices
• Sheets
• Loops
• Coils
10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification 19
Helix: Stabilized by H-bonds Between
every ~ 4th Residue in Backbone
C = blackO = redN = blueH = white
Look: Charges on backbone are "neutralized" by hydrogen bonds (H-bonds) - red fuzzy vertical
bonds
10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification 20
Types of Helices
"Standard" helix: 3.6 residues per turn
H-bonds between C=0 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
10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification 21
Helix: R-Groups are on Outside
10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification 22
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
10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification 23
-Sheets - also Stabilized by H-bonds Between Backbone Atoms
Anti-parallel Parallel
-Sheets: R-Groups are Above & Below "Plane"
10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification 24
Coils
• Regions of 2' structure that are not helices, sheets, or recognizable turns
• Intrinsically disordered regions appear to play important functional roles
10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification 25
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)
10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification 26
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
10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification 27
Simple Motifs Combine to Form Domains
10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification 28
6 Main Classes of Protein Structure
1) -Domains
Bundles of helices connected by loops2) -Domains
Mainly antiparallel sheets, usually with 2 sheets forming sandwich
3) DomainsMainly parallel sheets with intervening
helices, also mixed sheets4) Domains
Mainly segregated helices and sheets
5) Multidomain (Containing domains from more than one class
6) Membrane & cell-surface proteins
10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification 29
-Domain Structures: 4-Helix Bundles
10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification 30
-Sheets: Up-and-Down Sheets & Barrels
10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification 31
Domains: Leucine-rich Motifs can Form Horseshoes
10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification 32
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
10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification 33
PDB (RCSB) - recently "remediated" http://www.rcsb.org/pdb
10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification 34
Structure at NCBIhttp://www.ncbi.nlm.nih.gov/Structure
10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification 35
MMDB at NCBI http://www.ncbi.nlm.nih.gov/Structure/MMDB/mmdb.shtml
10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification 36
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)
10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification 37
MSD: MMolecular SStructuretructure Database
http://www.ebi.ac.uk/msd/
10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification 38
wwPDB: World Wide PDBhttp://www.wwpdb.org
10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification 39
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