BC351 Lecture 3 Protein Structure Terms Peptide bond N terminus and C terminus Peptide Backbone Primary Structure Ramachandran plot Secondary structure helix sheet Hydrophobic core Protein folding Tertiary structure Quaternary structure Denatured state Native state Conformation Amphipathic helix Long range interactions Subunit Cooperative folding unfolding Principles 1 Form follows function 2 Overview of some basic forms found in proteins a Myoglobin ribonuclease and hemoglobin as examples 3 Protein folding a This is a directed process b This is a HIGHLY specific process i Determined by thermodynamic properties such as enthalpy and entropy I Introduction pg 113 a Function follows form i Hand tools 1 Cutters a What are things that need to be cut and what cutter tool is used to do this b Loss of form loss of function ii What functions sustain life 1 What molecular tools are used for these functions II Amino Acid polymers AKA Proteins peptides pgs 82 83 92 93 a Formation of the Peptide bond LN03 1 i Definition of a Peptide bond 1 ii The reaction 1 Favors free amino acids at standard conditions 2 Notice that the carboxyl and the amino can no longer accept or lose protons iii Formation of the N and C terminus 1 Definition of N and C terminus a b LN03 2 c Implications i There are only 2 amino acids in the protein that could have as many as 2 ionizable groups 1 N and C terminus 2 Only if they are Asp Glu Lys His Arg Tyr and Cys ii All other amino acids in a protein have at the most 1 ionizable group 1 Only if they are Asp Glu Lys His Arg Tyr and Cys 2 Definition of the Peptide Backbone a LN03 3 b Levels of Protein Structure i Primary Secondary Tertiary and quaternary III Primary structure pgs 115 117 a Definition of Primary Structure i b The peptide bond i Bond characteristics 1 Partial double bond character O C C N C H LN03 4 2 Planar bond 3 The two carbons are trans O C C C N H 4 The electric dipole O C C N C H a Carbonyl oxygen partial negative b Amino nitrogen partial positive c Implications i The peptide backbone is laced with hydrogen bond donors and acceptors LN03 5 c The phi and psi angles i Rotation about the carbon 1 N C and C C free to rotate 2 The angle as described by a convention the N C bond adopts is the phi angle 3 The angle as described by a convention the C C bond adopts is the psi angle LN03 6 4 Conformation a Definition of Conformation i ii We will see next how phi and psi angles affect the secondary structure of the protein 5 Restrictions of these angles a Ramachandran plot i Definition of Ramachandran plot 1 ii How is this plot generated 180 degrees 0 180 180 IV 0 degress 180 Secondary structure pgs 117 122 a Definition of Secondary structure i LN03 7 b The helix 1st recurring pattern i Definition of an helix 1 ii of all amino acids in polypeptides are found in an helix iii Features 1 Right or left handed helix a Right handed helices are by far the most common found in protein structure 2 5 4 0 1nm pitch a What does this mean i Amount helix rises per turn 3 3 6 residues turn 4 R groups point away from the helical axis LN03 8 5 Backbone hydrogen bonding network a The nth carbonyl points in the direction of the n 4 amino hydrogen Electrostatic interaction hydrogen bond i 4 H bonds for every turn iv What affects the stability of an helix 1 Side chain identity a Ala Arg Leu Lys Met have a greater propensity to be found in a helix b Asn Ser Thr and Cys have a lesser propensity to be found in a helix c Gly and Pro are very rarely found in a helix 2 Side chain interactions a Which side chains will interact b The amphipathic helix i Definition LN03 9 v Ramachandran plot and the helices c The sheet 2nd recurring pattern i Definition of a sheet 1 ii strand 1 Fully extended polypeptide chain a Pleated LN03 10 iii Sheet 1 Strands interacting with one another a Parallel vs antiparallel sheets 2 Side chains point perpendicular to the plane a Up and down pattern LN03 11 iv Ramachandran plot d Everything else i Turns 1 These can be well defined structural patterns found in a number of different proteins a turn ii Loops undefined random coils 1 These three terms are equivalent and are used to describe any section of a protein structure that does not exhibit the structural patterns discussed above 2 Random coil is misleading in that structural patterns found in proteins are RARELY if ever random These sections of protein structure are typically very specific to that proteins structure and function LN03 12 V Tertiary Structure pgs 123 129 131 a Definition of tertiary structure i b Myoglobin i Function 1 O2 storage tank in the muscle 2 Heme an oxygen binder a Prosthetic group i Definition ii Primary structure 1 153 amino acids iii Secondary structure 1 8 helices a 70 of all residues are found in a helix 2 The rest are found in loops iv Tertiary structure Interactive 3 D software 1 What I hope to illustrate in this portion of the lecture a The structural features of a helix b A demonstration of loops c Long range interactions i Definition of long range interaction 1 Covalent only disulfide bonds or non covalent interaction in a protein LN03 13 between two amino acids far apart in primary structure but close in tertiary structure 2 Salt bridges d Hydrophobic core i Definition of the hydrophobic core 1 Describes the interior of the protein that consists primarily of hydrophobic residues c Ribonuclease i Function 1 Cleaves nucleic acids ii Primary structure 1 124 amino acids iii Secondary structure 1 26 of residues in an helix 2 35 in strands 3 The rest are in loops iv Tertiary structure 1 What I hope to illustrate in this portion of the lecture a The structural features of a sheet b Long range interactions i Disulfide bond LN03 14 VI Quaternary structure pgs 138 140 a Definition of quaternary 4 structure i ii Definition of a subunit 1 iii Proteins that have multiple subunits are also often called multimers or oligomers 1 There can be specific nomenclature for multimers depending on the number of subunits a 1 subunit monomer exhibits no 4 structure b 2 subunits dimer c 3 subunits trimer d 4 subunits tetramer e Etc b Hemoglobin i Function 1 Oxygen carrier in the blood 2 Prosthetic groups Hemes ii Structure 1 Quaternary structure a Tetramer b 2 copies of a subunit and 2 copies of a subunit LN03 15 2 Primary structure for human hemoglobin a subunit 141 amino acids with no disulfide bonds b subunit 146 amino acids with no disulfide bonds 3 Secondary structure for human hemoglobin a subunit