1. Protein Structure Basics Presented by Alison Fraser, Christine Lee, Pradhuman Jhala, Corban Rivera

2. Importance of Proteins Muscle structure depends on protein-protein interactions Muscle structure depends on protein-protein interactions Transport across membranes involves protein- solute interactions Transport across membranes involves protein- solute interactions Nerve activity requires transmitter substance- protein interactions Nerve activity requires transmitter substance- protein interactions Immune protection requires antibody-antigen interactions Immune protection requires antibody-antigen interactions

3. Overview Primary Structure Primary Structure Secondary Structure Secondary Structure Tertiary Structure Tertiary Structure Quaternary Structure Quaternary Structure

4. Primary Structure Polypeptide chains  Amino Acids Polypeptide chains  Amino Acids Largest polypeptide chain approx has 5000AA but most have less than 2000AA Largest polypeptide chain approx has 5000AA but most have less than 2000AA Amino Acid Basic Structure H 2 N-CH-COOH Amino Acid Basic Structure H 2 N-CH-COOH Arrangement of the 20 amino acids in the polypeptide is the amino acid sequence which composes the primary structure of the protein Arrangement of the 20 amino acids in the polypeptide is the amino acid sequence which composes the primary structure of the protein National Genome Research Institute genome.gov

5. http://www.people.virginia.edu/~rjh9u/aminacid.html 20 Amino Acids Nonpolar, hydrophobic Polar, uncharged Polar, charged

6. Amino Acid Classification A Venn diagram showing the relationship of the 20 naturally occurring amino acids to a selection of physio-chemical properties thought to be important in the determination of protein structure.

7. Stereochemistry Configuration of amino acids in proteins Configuration of amino acids in proteins The CORN Law The CORN Law

8. Bond Formation Linking two amino acids together Linking two amino acids together Definitions (N-terminal, C-terminal, polypeptide backbone, amino acid residue, side chains) Definitions (N-terminal, C-terminal, polypeptide backbone, amino acid residue, side chains) http://web.mit.edu/esgbio/www/lm/proteins/peptidebond.html

9. Primary Structure What is a native protein? What is a native protein? Protein conformation & problem of protein folding Protein conformation & problem of protein folding  Hydrophobic, hydrophilic  Charge  Chaperones

10. Special Purpose Amino Acids Proline Proline Cysteine Cysteine

11. Introduction Introduction Peptide bond geometry Peptide bond geometry Ramachandran plot Ramachandran plot Structures Structures Protein Secondary Structure

12. Regular local structures formed by single strands of peptide chain due to constraints on backbone conformation

13. Peptide Bond http://cmgm.stanford.edu/biochem/biochem201/Slides/

14. Peptide Bond Resonance Resonance C-N bond length of the peptide is 10% shorter than that found in usual C-N amine bonds C-N bond length of the peptide is 10% shorter than that found in usual C-N amine bonds Peptide bond planer Peptide bond planer ω, angle around peptide bond, ω, angle around peptide bond, 0 0 for cis, 180 0 for trans

15. Ramachandran Plot http://hykim.chungbuk.ac.kr/lectures/biochem/4-5/fig6-9(L).jpg

16. Alpha Helix http://cmgm.stanford.edu/biochem/biochem201/Slides/

17. Alpha Helix Left-handed Right-handed http://www.rtc.riken.go.jp

18. Alpha Structure Features 3.6 residues per turn 3.6 residues per turn 5.4 angstroms in length per turn 5.4 angstroms in length per turn carboxyl group of residue i hydrogen bonds to amino group of residue i+4 carboxyl group of residue i hydrogen bonds to amino group of residue i+4

19. Helix Structures Φ ψ H Bond R/t A/t Φ ψ H Bond R/t A/t Alpha -57.8 -47 i, i + 4 3.6 13 3-10 Helix -49 -26 i, i + 3 3.0 10 Pi Helix -57 -80 i, i + 5 4.4 16 http://broccoli.mfn.ki.se

20. More Helix Structures TypeΦψcomments Collagen-51153Fibrous proteins Three left handed helicies Collagen-51153Fibrous proteins Three left handed helicies (GlyXY)n, X Y = Pro / Lys Type II helices-79150left-handed helicies formed by polyglycine Type II helices-79150left-handed helicies formed by polyglycine

21. Beta Sheet http://www.rothamsted.bbsrc.ac.uk/notebook/courses/guide/images/sheet.gif

22. Beta Sheet Features Sheets can be made up of any number of strands Sheets can be made up of any number of strands Orientation and hydrogen bonding pattern of strands gives rise to flat or twisted sheets Orientation and hydrogen bonding pattern of strands gives rise to flat or twisted sheets Parallel sheets buried inside, while Antiparallel sheets occurs on the surface Parallel sheets buried inside, while Antiparallel sheets occurs on the surface

23. More Beta Structures Beta Bulge chymotrypsin (1CHG.PDB) involving residues 33 and 41-42 Anti parallel Beta Twist pancreatic trypsin inhibitor (5PTI) 0 to 30 degrees per residue Distortion of tetrahedral N atom http://broccoli.mfn.ki.se

24. Beta turns i + 1 Pro i + 2 Pro or Gly i + 3 Gly http://rayl0.bio.uci.edu/~mjhsieh/sstour/image/betaturn.png

26. Interactions Covalent bonds Covalent bonds Disulphide bond (2.2 0 A) between two Cys residues Disulphide bond (2.2 0 A) between two Cys residues Non-covalent bonds Non-covalent bonds Long range electrostatic interaction Short range (4 0 A) van der Waals interaction Hydrogen bond (3 0 A)

27. Tertiary Protein Structure Defines the three dimensional conformation of an entire peptide chain in space Defines the three dimensional conformation of an entire peptide chain in space Determined by the primary structure Determined by the primary structure Modular in nature Modular in nature

28. Aspects which determine tertiary structure Covalent disulfide bonds from between closely aligned cysteine residues form the unique Amino Acid cystine. Covalent disulfide bonds from between closely aligned cysteine residues form the unique Amino Acid cystine. Nearly all of the polar, hydrophilic R groups are located in the surface, where they may interact with water Nearly all of the polar, hydrophilic R groups are located in the surface, where they may interact with water The nonpolar, hydropobic R groups are usually located inside the molecule The nonpolar, hydropobic R groups are usually located inside the molecule

29. Motifs and Domains Motif – a small structural domain that can be recognized in a variety of proteins Motif – a small structural domain that can be recognized in a variety of proteins Domain – Portion of a protein that has a tertiary structure of its own. In larger proteins each domain is connected to other domains by short flexible regions of polypeptide. Domain – Portion of a protein that has a tertiary structure of its own. In larger proteins each domain is connected to other domains by short flexible regions of polypeptide.

35. Modular Nature of Protiens Epidermal Growth Factor (EGF) domain is a module present in several different proteins illustrated here in orange. Epidermal Growth Factor (EGF) domain is a module present in several different proteins illustrated here in orange. Each color represents a different domain Each color represents a different domain

36. Domain Shuffling Occurs in evolution Occurs in evolution New proteins arise by joining of preexisting protein domain or modules. New proteins arise by joining of preexisting protein domain or modules.

37. Quaternary Structure Not all proteins have a quaternary structure Not all proteins have a quaternary structure A composite of multiple poly-peptide chains is called an oligomer or multimeric A composite of multiple poly-peptide chains is called an oligomer or multimeric Hemoglobin is an example of a tetramer Hemoglobin is an example of a tetramer Globular vs. Fibrous Globular vs. Fibrous

38. Protein Folding Protein folding constitutes the process by which a poly-peptide chain reduces its free energy by taking a secondary, tertiary, and possibly a quaternary structure Protein folding constitutes the process by which a poly-peptide chain reduces its free energy by taking a secondary, tertiary, and possibly a quaternary structure

39. Thermodynamics Proteins follow spontaneous reactions to reach the conformation of lowest free energy Proteins follow spontaneous reactions to reach the conformation of lowest free energy Reaction spontaneity is modeled by the equation ΔG= ΔH-TΔS Reaction spontaneity is modeled by the equation ΔG= ΔH-TΔS

40. Molecular Visualization Goal: Clear visualization of molecular structure Goal: Clear visualization of molecular structure Different visualization modes elucidate different molecular properties Different visualization modes elucidate different molecular properties Some representations include Ribbons, SpaceFill and Backbone Some representations include Ribbons, SpaceFill and Backbone