1. 10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification1 BCB 444/544 Lecture 20 Protein Structure Basics, Visualization, Classification & Comparison #20_Oct08

2. 10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification2 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)

3. 10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification3 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

4. 10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification4 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 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

5. 10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification5 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: 1)Contact Drena (in person) 2)Send email to Michael Terribilini (terrible@iastate.edu)terrible@iastate.edu 3)Complete 544 Extra HW#1 - Task 1.1 by noon on Mon Oct 1

6. 10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification6 Assignments & Announcements - #2 BCB 444s (Standard): 200 ptsMidterm Exams = 100 points each 200 Homework & Laboratory assignments = 200 points 100 Final Exam 500 ptsTotal for BCB 444 BCB 444p (Project): 200 ptsMidterm Exams = 100 points each 200 Homework & Laboratory assignments = 200 points 190 Team Research Project 590 ptsTotal for BCB 444p BCB 544: 200 pts Midterm Exams = 100 points each 200 Homework & Laboratory assignments 100 Final Exam 200Discussion Questions & Team Research Projects 700 ptsTotal for BCB 544

7. 10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification7 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!

8. 10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification8 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)

9. 10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification9 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. 10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification10 Amino Acids Each of 20 different amino acids has different "R-Group" or side chain attached to C 

11. 10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification11 Peptide Bond is Rigid and Planar

12. 10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification12 Certain Side-chain Configurations are Energetically Favored (Rotamers) Ramachandran plot: "Allowable" psi & phi angles

13. 10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification13 Glycine is Smallest Amino Acid R group = H atom Glycine residues increase backbone flexibility because they have no R group

14. 10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification14 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)

15. 10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification15 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

16. 10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification16 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

17. 10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification17 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

18. 10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification18 Protein Secondary Structures  Helices  Sheets Loops Coils

19. 10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification19  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

20. 10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification20 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 = 3 10 helix

21. 10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification21  Helix: R-Groups are on Outside

22. 10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification22 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

23. 10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification23  -Sheets - also Stabilized by H-bonds Between Backbone Atoms Anti-parallelParallel  -Sheets: R-Groups are Above & Below "Plane"

24. 10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification24 Coils Regions of 2' structure that are not helices, sheets, or recognizable turns Intrinsically disordered regions appear to play important functional roles

25. 10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification25  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)

26. 10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification26 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

27. 10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification27 Simple Motifs Combine to Form Domains

28. 10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification28 6 Main Classes of Protein Structure 1)  -Domains Bundles of helices connected by loops 2)  -Domains Mainly antiparallel sheets, usually with 2 sheets forming sandwich 3)  Domains Mainly parallel sheets with intervening helices, also mixed sheets 4)  Domains Mainly segregated helices and sheets 5) Multidomain (  Containing domains from more than one class 6 ) Membrane & cell-surface proteins

29. 10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification29  -Domain Structures: 4-Helix Bundles

30. 10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification30  -Sheets: Up-and-Down Sheets & Barrels

31. 10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification31  Domains: Leucine-rich Motifs can Form Horseshoes

32. 10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification32 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 http://www.ebi.ac.uk/msd Especially good for interactions & binding sites

33. 10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification33 PDB (RCSB) - recently "remediated" http://www.rcsb.org/pdb http://www.rcsb.org/pdb

34. 10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification34 Structure at NCBI http://www.ncbi.nlm.nih.gov/Structure http://www.ncbi.nlm.nih.gov/Structure

35. 10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification35 MMDB at NCBI http://www.ncbi.nlm.nih.gov/Structure/MMDB/mmdb.shtml http://www.ncbi.nlm.nih.gov/Structure/MMDB/mmdb.shtml

36. 10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification36 MM 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)

37. 10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification37 MStructure MSD: Molecular Structure Database http://www.ebi.ac.uk/msd/ http://www.ebi.ac.uk/msd/

38. 10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification38 wwPDB: World Wide PDB http://www.wwpdb.org

39. 10/8/07BCB 444/544 F07 ISU Dobbs #20 - Protein Structure Basics & Classification39 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