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Transcript
Protein Structure BL4010 09.26.06 The relationship of structure and function Desirable conformations will be at energy minima 1° structure: amino acid sequence 2° structure: structures localized to certain short stretches of the polypeptide chain - form wherever possible stabilized by large numbers of H-bonds 3° structure: overall folding of the entire polypeptide 4° structure: overall structure for multimeric proteins (several polypeptides) The peptide bond The Peptide Bond • 0.133 nm (1.33 Å) - shorter than a typical single bond but longer than a double bond • 40% double bond character • the six atoms of the peptide bond group are planar (C,C=O,N-H, C) • Rotation in the polymer occurs at C • Inherent dipole (N partially positive; O partially negative) Limited Rotation about Peptide Bond • Two degrees of freedom per residue for the peptide chain • Backbone and side groups limited free rotation Further conformational restriction Backbone Torsion Angles • ω angle tends to be planar (0º - cis, or 180 º trans) due to delocalization of carbonyl pi electrons and nitrogen lone pair • φ and ψ are flexible, therefore rotation occurs here • However, φ and ψ of a given amino acid residue are limited due to steric hindrance • Only 10% of the {φ, ψ} combinations are generally observed for proteins • First noticed by G.N. Ramachandran Computed Ramachandran Plot Plot of φ vs. ψ The computed angles which are sterically allowed fall on certain regions of plot White = sterically disallowed conformations (atoms come closer than sum of van der Waals radii) Blue = sterically allowed conformations Experimental Ramachandran Plot X-ray crystallography Secondary Structure • Repeating values of φ and ψ along the chain result in regular structure • The ability to do this is dependent on steric considerations...i.e. secondary structure is dependent to some degree on primary structure (sequence) Secondary Structure - alpha helix •For example, repeating values of φ ~ -57° and ψ ~ -47° give a right-handed helical fold (the alphahelix) e.g. cytochrome c, an alpha helical protein Secondary Structure - beta sheet Similarly, repetitive values in the region of φ = -110 to –140 and ψ = +110 to +135 give beta sheets. Plastocyanin is composed mostly of beta Note more allowed regions due to less steric hindrance - Turns Note less allowed regions due to structure rigidity Name φ ψ Structure ------------------- ------- ------- --------------------------------alpha-L 57 47 left-handed alpha helix 3-10 Helix -49 -26 right-handed. π helix -57 -80 right-handed. Type II helices -79 150 left-handed helices formed by polyglycine and polyproline. Collagen -51 153 right-handed coil formed of three left handed helicies. Hydrogen Bonding And Secondary Structure alpha-helix beta-sheet Alpha helix Alpha helix •Residues per turn: 3.6 •Rise per residue: 1.5 Angstroms •Rise per turn (pitch): 3.6 x 1.5A = 5.4 Angstroms •The backbone loop that is closed by any H-bond in an alpha helix contains 13 atoms •phi = -60 degrees, psi = -45 degrees •The non-integral number of residues per turn was a surprise to crystallographers Beta sheet Beta sheet •Postulated by Pauling and Corey (1951) •Strands may be parallel or antiparallel •Rise per residue: • –3.47 Angstroms for antiparallel strands –3.25 Angstroms for parallel strands –Each strand of a beta sheet may be pictured as a helix with two residues per turn Beta turn •allows the peptide chain to reverse direction •carbonyl C of one residue is H-bonded to the amide proton of a residue three residues away •proline and glycine are prevalent in beta turns Turns & Random Coils • Loops & Turns ( turns) – 1/3 globular protein – Mostly at surface of protein – allows the peptide chain to reverse direction – C=O H-bonded to the NH three residues away – proline and glycine • Random coil – can't assign 2° structure, adopts multiple conformations depending on conditions but not random energy minima – flexible linkers, hinges Structure Stabilizing Interactions • Noncovalent – Van der Waals forces (transient, weak electrical attraction of one atom for another) – Hydrophobic (clustering of nonpolar groups) – Hydrogen bonding • Covalent – Disulfide bonds Disulfide Bonds • Side chain of cysteine contains highly reactive thiol group • Two thiol groups form a disulfide bond • Contribute to the stability of the folded state by linking distant parts of the polypeptide chain Other factors that affect 2° structure • Prosthetic groups – Coenzymes – Cations • Intramolecular/Intermolecular bonds – disulfides – dityrosine – aldol cross-linking Tertiary Structure • The backbone links between elements of secondary structure are usually short and direct • Proteins fold to make the most stable structures (make H-bonds and minimize solvent contact Protein classification • Structural motif • Biochemical function Protein evolution • Divergent evolution – Similar sequence – Different function •Convergent evolution –Different sequence –Similar function