Chapter 6 - Chapter 6 ability of a protein to carry out its...

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Chapter 6 ability of a protein to carry out its function is determined by its conformation (overall 3D shape), which is determined by o interactions w solvent molecules (usu. water) o pH and ionic composition of solvent o protein sequence: facilitates short-range interactions (adjacent parts of sequence) and long-range interactions (distant parts of sequence) o interacting proteins/DNA/RNA/small molecule effectors o temperature Secondary Structure o noncovalent interactions hydrogen bonds – form whenever possible (both between residues and between hydrophilic side chains and water; most specific interaction) hydrophobic bonds drive protein folding (the major contribution to it) form b/c nonpolar side chains/solutes prefer to cluster in nonpolar environment than intercalate in polar solvents entropically driven AA interior almost completely non polar AA exterior can be polar/nonpolar electrostatic interactions (by charged residue and N- and C- terminal residues) usually occur on protein surface energetically unfavorable for ionized residue to be located on the hydrophobic core of the protein these can be interfered w/ by salts (↑ [salt] dampens interactions on surface) van der Waals interactions (include attractive/repulsive forces) can be major contributor to stability b/c they are so common o protein recognition and interpretation of AA sequence not understood assumed that certain loci along chain act as nucleation points, which initiate folding processes local-energy minimum state ≠ native state o elements of secondary structure all protein structure is based on the amide plane (resonance structures by peptide bond – O, C, N, Hs of peptide group; adjacent α-C)
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resonance stabilization energy for planar structure: 88 kJ/mol o twist of θ degrees = 88 sin 2 θ kJ/mol rotation about α-C o α-C – N : φ; α-C – Carbonyl C : ψ o 0 o = orientation w/ amide plane bisecting side chain plane and a cis conformation of the main chain around the rotating bond in question o entire path of backbone is known if all φ and ψ angles are known o forbidden φ and ψ values φ = 180 o and ψ = 0 o (overlap btwn N-H Hs) φ = 0 o and ψ = 180 o (overlap btwn carb. Os) Ramachandran plot plots φ against ψ – shows most common α-Helix carbonyl O and amide H can H-bond 1 turn = ~3.6 AA residues = 13 atoms = 3.6 13 helix = 0.54 nm (called pitch of the turn; 0.15 nm/residue) = diameter (w/ side chain) = 0.6 nm in diameter φ = -60 o and ψ = -45 – -50 o all H bonds parallel to axis all carbonyl point in one direction of axis and all amide the other (creates dipole moments) o – charged ligands bind to N-terminus and + charged ligans bind to C-terminus each peptide carbonyl H-bonds to peptide N-H 4 residues further up chain (3 residues away) avg of 10 residues / helix helix capping – provides H-bond partners of first 4 N-H and last 4 C=O groups
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Chapter 6 - Chapter 6 ability of a protein to carry out its...

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