Sep 18, 2008 ... Steric restrictions on allowed φ and ψ. 6. Garrett & Grisham, 'Biochemistry' Fig.
6.3. Relatively few combinations are allowed. A: 0, 0. B: flip top.
Microreview ΔG= ΔG°’ + RT ln Q,
Q=Π[products]/Π[reactants]
Essence of life: unfavourable processes are executed by coupling them to favourable ones. ATP + H2O → ADP + Pi
ΔG°’ = -30.5 kJ/mol
Energy brokers, and high-energy bonds 64.5 kG ATP used /day. 50 g present. Amino acids: how many ? Chiral ? Charged ? Polar ? Bulky ? A.-F. Miller, 2008, pg
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Note that the concentrations in products and reagents imply 1 M, except for [H+] for which 10-7 M is implied: How to deal with that.
Amino acid prevalence Also: cofactors
G&G Fig. 5.24 for 100k proteins from swissProt
A.-F. Miller, 2008, pg
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Deviations for membranes, globulars, fibrilar ,. . . Composition dets chemical and structural funcionality
Amino acid sequence determination Reduce S-S bridges. Separate different chains. ID N- and C-terminal amino acids. Cleave into define fragments (by multiple distinct means). ID N- and C- termini of these, determine sequences for Small fragments, composition. Reconstruct overall sequence from overlapping fragments. Locate positions of S-S bridges. A.-F. Miller, 2008, pg
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Commonalities related to function, across phyla
Cytochrome c, ≥104 amino acids, Fig 5.26 A.-F. Miller, 2008, pg
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Aa sequences are better conserved than nucleotide sequences Synonymous codons Silent mutations Structure is better conserved still: can retain the same fold with only 10% aa seq identity.
The peptide bond restricts possible configurations
-.28 +.28
A.-F. Miller, 2008, pg
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Garrett & Grisham, ‘Biochemistry Fig. 5.4, 6.2
polar, 40% pi character keeps it flat, consider two resonance structures. Due to steric clash between carbonyl O and side chain, only certain φ and ψ values are favourable. Backbone is restricted to certain conformations. Also, driven to satisfy H-bonding 6 atoms in a plane. Rotation only allowed about bonds to Cα. Names of angles, (also χ).
Steric restrictions on allowed φ and ψ B: flip top
D: Flip bottom
C: Allowed
Relatively few combinations are allowed. A.-F. Miller, 2008, pg
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Garrett & Grisham, ‘Biochemistry’ Fig. 6.3
entire path of the backbone can be known from the φ and ψ angles
A: 0, 0
Ramachandran plot Backbone restricted to certain conformations wrt φ and ψ. Also, driven to satisfy H-bonding.
A.-F. Miller, 2008, pg
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Figure 1.11 from Fersht (“Structure and mechanism in protein science”)
Angles associated with Diff Struct; Statistics by Ramachandran for diff AA Definition of 0° for each angle is rel to bisector of Ha and side chain **source
α helix
Correct ⇓ φ = −60 and ψ = -45 to –50. 3.6 residues per turn. A.-F. Miller, 2008, pg
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Garrett & Grisham, ‘Biochemistry’ Fig. 6.6
3.6 aa per turn, right-handed. 1.5 Å per aa, 5.4 Å per turn (the pitch) 13 atoms per turn: 3.613 helix. (310 helices, 27 ribbon and π helix: 4.416 ) NON-Integral number of residues per turn: why ?? 6 Å diameter without the side chains.
α helix H-bonding between i and i+4. Molecular dipole: stabilizes oxy anions or phosphates at the N end. Worth 2 kCal / mol. Discourages isolated short helices Typical helices: 10-12 residues For 12 res: 8 H-bonds, plus helix caps. A.-F. Miller, 2008, pg
H bonds along helix axis, in the same sense.
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Garrett and Grisham, Fig. 6.8
Exposure of side chains (and peculiar φ, ψ preferences) result in aa biases in favour or against α helices.
Cooperative ‘zipping up’ s= [cchhhhhcc]/[ccchhhhcc] σs is Keq = [ccchccc]/[ccccccc]
σs G A S L
1x10-5 8x10-4 7.5x10-5 33x10-4
s
0.62 bad at initiating 1.06 0.79 1.14 high α helix propensity
Cantor and Schimmel A.-F. Miller, 2008, pg
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s equilibrium constant for adding a residue to a chain of helices [cchhhhhcc]/[ccchhhhcc] σs is Keq for making the first helical residue [ccchccc]/[ccccccc]. Like hazing, if membership in the frat is good (large s) it is worth going through hazing (sigmaS).
Secondary structures are preferred by different amino acids ↑↑: less stabilized by Hbonds. 3.25 Å between strands ↑↓: better H-bonds. 3.47 Å between strands
A.-F. Miller, 2008, pg
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Fig. 5.11 of Garrett & Grisham
Two-fold helices Cα is still tetrahedral -> pleating Inter strand (not intra-strand) more strands (>5) needed to stabilize a sheet of parallel. **avg length Each edge presents C=O and NH like velcro ready to bind the next incoming strand
|| is less extended backbone, H bonds are at angles, smaller range of φ ψ. SC point up then down, perp to plane, places ↑↑ Hphobics on both sides of the sheet
Secondary structures are preferred by different amino acids ↑↓: steric restrictions on side chain identities.
Linker and side chain requirements recurring motifs. A.-F. Miller, 2008, pg
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Fig. 5.10 of Garrett & Grisham
Td Cα centres at peaks and troughs. SIde chains presented below and above, but also tilted to one or other side. In antiparallel, they point at one another, steric clash limits the identities two side chains can have. Hydorphobes on ONE side of sheet usually, so residues alternate in polarity in 1er seq.
READ Chapters 4 and 5 regarding analytical methods, etc. Finish Chapter 6 this weekend and begin Chapter 7 !! DO all the problems at the back of each chapter (answers are at the back of the book). Spend at least 5 hours studying for each class-room hour.
A.-F. Miller, 2008, pg
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α helices and β sheets represent possibilities that remain after taking into account the sterics of the protein backbone: the volumes of atoms severely limits the possibilities. Proline and Gly have distinct folding preferences because they have distinct sterics. α helices and β sheets represent ways to satisfy the H-bonding needs of the backbone. The backbone is regular, and so are they. α helix involves a single strand and contracts it. β sheet brings together multiple strands without shortening them as much. H-bonding at the ends are often dealt with by side-chains : “helix capping” (serine in trypsin inhibitor Fig 6.25, Asn often) Asn can satisfy two orphan interactions from a β strand.
A.-F. Miller, 2008, pg
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