Secondary Structure Protein

I. Protein Structure A. Primary 1. Peptide Bond a. 2. Planar, strong, f/y angles Determination a. Sequence determination; CHEMICAL b. Sequence determination; PHYSICAL i. i. aa composition; Divide & conquer; Edman degradation Tandem Mass Spectrometry for proteins c. Sequence determination; BIOLOGICAL i. d. Genome sequenced; need partial sequence Determination of Disulfide bonds B. Secondary 1. 2. Conformational structure; Levinthal paradox Pauling & Corey’s predictions a. b. c. d. 3. C. a-Helix b-sheets/strands Connections between b-strands Connections between a-helices; angle not important Super secondary structure Tertiary 1. 2. 3. 4. 5. Picturing and classifications Topology Domains Intrinsically disordered Stability Secondary Structure 1 Protein Structure-Secondary β Sheets- antiparallel Using his rules, Pauling predicted two basic structures: a-helix b-sheet, which he called a “back-and-forth” structure Protein Structure-Secondary β Sheets- antiparallel 1 Right handed (2.07) 2 Dimensions -it’s a sheet Almost fully extended: -3.4 Å rise/residue -2 residues/repeat à Pitch is 6.8 Å -length variable 3 Conformational angles - f = – 139° - y = + 135° 4 Electrostatics -H-bonds all satisfied (as predicted) -no polarity 2 Protein Structure-Secondary β Sheets- parallel Pauling did not predict a b-sheet made of b-strands going the same direction. Protein Structure-Secondary β Sheets N C ~ C 6.8 N 3 Protein Structure-Secondary β Sheets f Structure y Rise (Dist/residue) (Å) Residues/ Repeat Pitch (Distance/ repeat) Diameter (Å) (Å) a-helix -57 -47 1.5 3.6 5.4 5.0 Anti- ⇌ b-sheet -139 +135 3.4 2 6.8 - Parallel ⥤ b-sheet -119 +113 3.2 2 6.4 - Protein Structure-Secondary β Sheets 5 R-groups -alternate and point away from sheet ~ 6.8 4 Protein Structure-Secondary β Sheet: Space Filling Model Concanavalin A PDBid 2CNA Protein Structure-Secondary The b Sheet: Propensities Like: -prefer large, bulky groups -Val, Ile, Leu, Tyr, Trp, Phe Don’t Like: -Pro (same reason) -Glu/Asp/Lys (full charges too close) -Gly (same reason) 5 Protein Structure-Secondary The β Sheet: examples Globular Proteins Neuraminidase • 6 x 4-stranded β Sheets: make a funnel to active site • right-handed twist Protein Structure-Secondary The β Sheet: examples Fibrous Proteins: Silk fibroin (b-keratin) Silk all parallel b-sheet Sequence repeats: (GAGAGSGAAG(SGAGAG)8Y)X (x>10) - Gly is every-other residue, and Ala as well - Recall the alternating R-groups - Therefore, Gly is all on one side of sheet, and Ala on the other side of sheet 6 Protein Structure-Secondary The β Sheet: examples Silk fibroin (bkeratin) Silk's tensile strength is comparable to that of steel and about half as strong as Kevlar Protein Structure-Secondary β Sheets 85% G, A, S 7 Protein Structure-Secondary ~ ~ 6.8 Å 6.4 Å Protein Structure-Secondary a-helix b-sheet 8 Protein Structure-Secondary Purple=polar Gold=hydrophobic Recall that b-sheets require strands from different parts of the same polymer, so…. How are the connected? Oxy-Myoglobin and Concanavalin A PDBids 1A6M and 2CNA See “Protein Structure Videos” (First link) Protein Structure-Secondary Reverse Turns in Polypeptide Chains y = 0° i+3 f = + 80° N C i+2 f = – 90° f = – 139° Also called b-turn, b-bend, or hairpin y = – 30° y = +135° C i+1 f = – 60-65° i N y = +120° 9 Protein Structure-Secondary Structure f y Rise (Dist/resid ue) (Å) Residues/Re peat (Distance/repeat) Pitch (Å) Diameter (Å) a-helix -57 -47 1.5 3.6 5.4 5.0 Anti- ⇌ b-sheet -139 +135 3.4 2 6.8 - Parallel ⥤ b-sheet -119 +113 3.2 2 6.4 - 4 0 - 4 0 - b-turn-Type I i+1 -60 -30 - i+2 -90 0 - b-turn-Type II i+1 -60 120 - i+2 80 0 - Start and stop with same angles Protein Structure-Secondary Reverse Turns in Polypeptide Chains: Propensities Often Asn (satisfy H-bonding) Often Gly (f = – 65°) Often Pro -Pro-Asn- -Pro-Gly- 10 Protein Structure-Secondary Turns in Polypeptide Chains often use cis-Pro Protein Structure-Secondary Reverse Turns are used for anti-parallel sheets, but how do parallel strands find each other to make a sheet? 11 Protein Structure-Secondary These strands are not straight as we saw, and this twist helps the conformation of these loops. Summary These loops are very often not just random conformations, but form a-helices Protein Structure-Secondary What is happening? • Different pieces of 2° structure are mixing together. • These are called “Motifs” or Super-secondary Structures • What are the structures and names of some of the most common motifs? • bab • Rossmann Fold • b-hairpin • aa • Greek key • b-meander • b-barrel • ab-barrel 12 Protein Structure-Supersecondary Short turn bab b-hairpin Long turn Take a b-hairpin, which is an antiparallel bsheet, but the topology of the strands is not sequential aa babab=Rossmann Fold aa with different sized loops Protein Structure-Supersecondary Short turn bab b-hairpin aa Long turn Take a b-hairpin, which is an antiparallel bsheet, but the topology of the strands is not sequential babab=Rossmann Fold aa with different sized loops 13 Protein Structure-Supersecondary Due to the right-handed twist in the b-strands, as you add more strands, the structure comes back on itself to form “barrels” b-meander (b)8 Greek Key (b)8 (ab)8-Barrel 4 (bab) motifs connected by 4 a-helices Protein Structure-Supersecondary Due to the right-handed twist in the b-strands, as you add more strands the structure comes back on itself to form “barrels” b-meander (b)8 Greek Key (b)8 (b-barrel) (ab)8-Barrel 4 (bab) motifs connected by 4 a-helices 14 I. Protein Structure A. Primary 1. Peptide Bond a. 2. Planar, strong, f/y angles Determination a. Sequence determination; CHEMICAL b. Sequence determination; PHYSICAL i. i. aa composition; Divide & conquer; Edman degradation Tandem Mass Spectrometry for proteins c. Sequence determination; BIOLOGICAL i. d. Genome sequenced; need partial sequence Determination of Disulfide bonds B. Secondary 1. 2. Conformational structure; Levinthal paradox Pauling & Corey’s predictions a. b. c. d. 3. C. a-Helix b-sheets/strands Connections between b-strands Connections between a-helices; angle not important Super secondary structure Tertiary 1. 2. 3. 4. 5. Picturing and classifications Topology Domains Intrinsically disordered Stability Tertiary Structure 15 Bovine Carboxypeptidase A Carboxypeptidase A PDBid 3CPA Protein Structure-Tertiary Picturing protein structure Space-fill Backbone trace Ribbon Triose-phosphate Isomerase (TIM) 16 Protein Structure-Tertiary Picturing protein structure Ribbon Surface contour Ribbon with Spaceside-chains filling Sperm-whale Myoglobin (Mb) Protein Structure-Tertiary Protein Classification: α, β, α/β, or barrels By Topology Cytochrome b562 PDBid 256B Human immunoglobulin fragment PDBid 7FAB Dogfish lactate dehydrogenase PDBid 6LDH 17