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Protein Structures

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Protein Structures Protein interactome for plants (Science 333:596, 601 29 July 2011) shows multiple physical interactions among proteins: 6200 interactions ... – PowerPoint PPT presentation

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Title: Protein Structures


1
Protein Structures
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Ramachandran plot
Shows grouping of f? combinations and relates
them to structures in real proteins Repetitive
structures (?- helices, ?-sheets) are common.
5
?-helix
3.6 amino acids per turn 0.54 nm per turn
side chains pointed out H-bonds parallel to
axis n-4 H-bonds dipole moment (neg. at C
end) no pro, less gly, ser limited similar
side chain charges
6
?-helices have a dipole moment some side
chains are preferred
7
ß-sheets are parallel or anti-parallel
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And ß-sheets are pleated
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ß-sheets can form a ß-barrel A recent paper
elucidates the ß-barrel structure of a toxic
amyloid protein
Laganowsky et al., Atomic view of a toxic
amyloid small oligomer, Science 9 March 2012,
3351228
10
A reverse turn (ß-bend) R2 (CO side) is
often G,A R3 (N-H side) is often D
Proline is often R2 or R3
11
Tertiary structure involves bonds between and
among side chains
  • Hydrogen (-O-HO-)
  • Ionic (generally repulsion -CH2-NH3H3N-
    CH2-)
  • Van der Waals (short distance attraction)
  • Disulfide (covalent -CH2-S-S-CH2-)
  • Hydrophobic

12
The types of side chains, and the tertiary bonds
they form, influence the positions of secondary
structures.
13
And the position of a secondary structure in a
protein will influence the types of side chains
(tertiary structure).
An ?-helix on the surface of a protein will have
hydrophilic side chains on one side of the helix
axis and hydrophobic side chains on the other.
14
An ?-helix in the interior of a protein will have
primarily hydrophobic side chains.
15
An ?-helix exposed to the solution on all sides
(unusual) will have hydrophilic side chains on
all sides of the helix axis (mostly).
16
Quaternary structures Involve separate
polypeptides held together with weak bonds in
various symmetries
Symmetries Homomultimer heteromultimer Isolog
ous heterologous Closedopen
E.g. tubulin, actin, TMV coat E.g.
hemoglobin
17
Secondary-tertiary structure of UVR8 subunits
involves multiple ß-sheets. Quaternary structure
involves electrostatic interactions between
positively charged arginines and negatively
charged aspartates.
18
The folding of a protein reduces the free energy
(?G) of the system.
Folding states
19
The folding of a protein involves both protein
and solvent.
  • ?G GF- GU
  • ?H - T?S
  • ?H(protein)
  • ?H(solvent)
  • - T?S(protein)
  • - T?S(solvent)
  • ??????G for folding is small (-20 to -60
    kJ/mol) and primarily from hydrophobic
    interactions
  • Why so low?

20
Changes in shape are an important part of protein
function and control. For example a change in
shape allows DNA methyltransferase to choose
hemi-methylated meCG/GC for bimethylation to
meCG/GmeC
Science 25 Feb 2011 Song, et al., 3311036
21
Summary Primary structure involves bonds
between amino and carboxylic groups, stabilizing
the amino acid sequence Secondary structure
involves hydrogen bonds between back- bone
atoms, forming ?-helices, ß-sheets, and
ß-bends. Tertiary structure involves bonds
between side chains. Quaternary structure
involves bonds connecting separate poly- peptide
chains. ?G for folding is small and primarily
from hydrophobic interactions.
Stigler et al., The complex folding network of
single calmodulin molecules. Science 334512, 28
October 2011 Lindorff-Larsen et al., How
fast-folding proteins fold. Science 334517, 28
October 2011 Dill and MacCallum, The
protein-folding problem, 50 years on.
Science 3381042, 23 November 2012 Saibil,
Machinery to reverse irreversible aggregates.
Science 3391040, 1080 March 2013
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