Three Dimensional Structure of Proteins Secondary Structure Biochem 4511 Figures Essentials of Biochemistry 3rd Ed OSU Custom Edition Principles of Biochemistry 5th Ed Moran et al Lehninger Principles of Biochemistry 5th Ed Nelson Cox Fundamentals of Biochemistry 2nd Ed Voet Voet Pratt Levels of Protein Structure Rules for Secondary Structure In 1950s Linus Pauling and Robert Corey proposed helices and sheets as stable secondary structural elements They described structures that were 1 Sterically allowed and favorable 2 Maximized the hydrogen bonding capacity of backbone amide nitrogens and carbonyl groups Restraints on Local Protein Structure Amide bonds are planar and primarily Restraints on Local Protein Structure Phi Psi In this figure 180 extended conformation C CO NH C CO NH C Free rotation is limited to the NH C and C CO bonds The angles around these bonds are known as dihedral or torsion angles Restraints on Local Protein Structure Some dihedral angles will be more favored than others Steric clash between backbone and side chain atoms Hydrogen Bonding 21 kJ mol 1 5 kcal mol 1 Right Handed Helix 57 47 3 6 residues per turn Pitch distance helix rises per turn of 5 4 Hydrogen bonding pattern C O of residue i and amide N H of residue i 4 Hydrogen bond distance 2 8 Amino Acids Helical propensity by frequency Sheet 139 135 119 113 Parallel Sheet Idealized geometry 119 113 Non linear H bonds Antiparallel Sheet Idealized geometry 139 135 H bonds line up Amino Acids Sheet Propensity Sheet sheet keeps large and branched side chains far apart minimizing steric clash Mixed Three Stranded Sheet N C N C C N Extended Sheets In three dimensions extended sheets are twisted Arrows indicate N to C directionality Use arrows to determine type of sheet Jellyfish and GFP a barrel protein Jellyfish and Useful Proteins Irregular Structure Turns and Loops Some Protein Terminology conformational flexibility Random Coil has no detectable structure and a lot of Coil structure is any structured region that does not fit standard secondary structure definitions Turns and loops are irregular or nonstandard secondary structural units that connect more standard units For example short hairpin turns In all proteins 1 3 helices 1 3 sheets 1 3 irregular structure NOTE Bulk statistics do not hold for individual proteins Irregular Structure Turns and Loops Hairpin Turns generally connect antiparallel strands L L type dihedral L D type dihedral angles angles Glycine and Proline are common in turn regions cis Proline Also Common in Turns Helps to induce change in direction of main chain Ramachandran Dihedral Plot Extra Ramachandran plot depicts allowed or favorable conformations Steric clash of side chain defines large regions The favored green regions also correspond to the main types of secondary structure Ramachandran Plot Secondary Structure Extra Graph and angles for each amino acid in a peptide Repeated similar torsion angles gives rise to secondary structure Common secondary structures to know helix parallel sheet antiparallel sheet Regions correspond to idealized secondary structure Summary Secondary Structure Problems 29 30 Know Torsion angles and Ramachandran plot Know the properties of the secondary structure types Hydrogen bonding patterns amino acid propensity as related to the type of structure Be able to draw and understand both types of sheet in extended structure with hydrogen bonding
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