Download Protein Structure Basics & Classification: Lecture 20 in BCB 444/544 Fall 07 - Prof. Drena and more Lab Reports Bioinformatics in PDF only on Docsity!
Classification
BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification 10/8/07 1
BCB 444/
Lecture 20
Protein Structure Basics,
Visualization, Classification & Comparison
#20_Oct
BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification 10/8/07 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) BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification 10/8/07 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/nature
- PDF available on class website - under Required Reading Link BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification 10/8/07 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 included in originally posted 544ExtraHW#1; corrected version is posted now BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification 10/8/07 5
Assignments & Announcements -
Students registered for BCB 444: Two Grading Options
- Take Final Exam per original Grading Policies
- 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 BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification 10/8/07 6
Assignments & Announcements -
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
Classification
BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification 10/8/07 7
Assignments & Announcements
ALL: HomeWork # Due: Mon Oct 8 (Today) by 5 PM
- HW544: HW544Extra # √ 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 #
- 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! BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification 10/8/07 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) BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification 10/8/07 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! BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification 10/8/07 10
Amino Acids
- Each of 20 different amino acids has different "R-Group" or side chain attached to Cα BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification 10/8/07 11
Peptide Bond is Rigid and Planar
BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification 10/8/07 12 Certain Side-chain Configurations are Energetically Favored (Rotamers) Ramachandran plot: "Allowable" psi & phi angles
Classification
BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification 10/8/07 19
α−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 BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification 10/8/07 20
Types of α−Helices
"Standard" α−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 = π helix n + 3 = 310 helix BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification 10/8/07 21
α−Helix: R-Groups are on Outside
BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification 10/8/07 22
Certain Amino Acids are "Preferred" &
Others are Rare in α−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 BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification 10/8/07 23
β-Sheets - also Stabilized by H-bonds
Between Backbone Atoms
Anti-parallel Parallel
β-Sheets: R-Groups are Above & Below "Plane"
BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification 10/8/07 24
Coils
- Regions of 2' structure that are not helices, sheets, or recognizable turns
- Intrinsically disordered regions appear to play important functional roles
Classification
BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification 10/8/07 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) BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification 10/8/07 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 BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification 10/8/07 27
Simple Motifs Combine to Form Domains
BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification 10/8/07 28
6 Main Classes of Protein Structure
1 ) α-Domains Bundles of helices connected by loops
- β-Domains Mainly antiparallel sheets, usually with 2 sheets forming sandwich 3 ) α/β Domains Mainly parallel sheets with intervening helices, also mixed sheets 4 ) α+β Domains Mainly segregated helices and sheets
- Multidomain (α & β) Containing domains from more than one class 6 ) Membrane & cell-surface proteins BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification 10/8/07 29
α-Domain Structures: 4-Helix Bundles
BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification 10/8/07 30
β-Sheets: Up-and-Down Sheets & Barrels
Classification
BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification 10/8/07 37
MSD: MMolecular SStructuretructure Database
http://www.ebi.ac.uk/msd/ BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification 10/8/07 38
wwPDB: World Wide PDB
http://www.wwpdb.org BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification 10/8/07 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
