Protein Structures

Protein structures • Primary structure (linear polymer of amino acids)

(backbone held together with peptide bonds) • Secondary structure (standard 3-D patterns)

( -helix, ß-sheet, held together with H-bonds between backbone atoms)

• Tertiary structure (detailed 3-D conformation) (bonds between side-chain atoms)

• Quaternary structure (combined polymer chains) (bonds between monomer side-chain atoms)

Peptide bonds influence secondary structure Recall that the planar amide bond constrains chain’s bends

planes: no rotation around CO-N bonds, but planes rotate around -C-N ( ) and -C-C=O bonds ( )

Ramachandran plot

Shows grouping of φψ combinations and relates them to structures in real proteins

Repetitive structures (α-helices, β-sheets) arecommon.

α-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

α-helices have a dipole moment

some side chains are preferred

ß-sheets areparallelor anti-parallel

And ß-sheets are “pleated”

ß-sheets can form a “ß-barrel”A recent paper elucidates the ß-barrel structure of atoxic amyloid protein

Laganowsky et al., “Atomic view of a toxic amyloid small oligomer”, Science 9 March 2012, 335:1228

A reverse turn (ß-bend): R2 (C=O side) is often G,A R3 (N-H side) is often D Proline is often R2 or R3

Tertiary structure involves bonds between and among side chains:

•Hydrogen (-O-H…O-)

•Ionic (generally repulsion: -CH2-NH4+:::::::+H4N-CH2-)

•Van der Waal’s (short distance attraction)

•Disulfide (covalent: -CH2-S-S-CH2-)

•Hydrophobic

The types of side chains, and the tertiary bonds they form, influence the positions of secondary structures.

And the position of a secondary structure in a protein will influence the types of side chains (tertiary structure).

An α-helix on the surface of a protein will have hydrophilic side chainson one side of the helix axis and hydrophobic side chains on the other.

An α-helix in the interior of a protein will have primarily hydrophobic side chains.

An α-helix exposed to the solution on all sides (unusual) will have hydrophilic side chains on all sides of the helix axis (mostly).

Quaternary structures Involveseparate polypeptides held togetherwith weak bonds in various symmetries

Symmetries

Homomultimer:: heteromultimerIsologous:: heterologousClosed::open

E.g.: tubulin, actin, TMV coat E.g.: hemoglobin

Secondary-tertiary structure of UVR8 subunits involves multiple ß-sheets.Quaternary structure involves electrostatic interactions between positivelycharged arginines and negatively charged aspartates.

The folding of a protein reduces the free energy (ΔG) of the system.

Folding states

ΔG = GF- GU

= ΔH - TΔS

=+ ΔH(protein)+ ΔH(solvent)-- TΔS(protein)-- TΔS(solvent)

ΔG for foldingis small (-20 to-60 kJ/mol) andprimarily fromhydrophobicinteractions

Why so low?

The folding of a protein involves both protein and solvent.

Changes in shape are an important part of protein function and control.

For example: a change in shape allows DNA methyltransferaseto choose hemi-methylated meCG/GC for bimethylation to meCG/GmeC

Science 25 Feb 2011: Song, et al., 331:1036

Summary:

Primary structure involves bonds between amino and carboxylicgroups, stabilizing the amino acid sequence

Secondary structure involves hydrogen bonds between back-bone atoms, forming α-helices, ß-sheets, and ß-bends.

Tertiary structure involves bonds between side chains.Quaternary structure involves bonds connecting separate poly-

peptide chains.ΔG for folding is small and primarily from hydrophobic interactions.

Stigler et al., The complex folding network of single calmodulin molecules.Science 334:512, 28 October 2011Lindorff-Larsen et al., How fast-folding proteins fold. Science 334:517,28 October 2011Dill and MacCallum, The protein-folding problem, 50 years on. Science338:1042, 23 November 2012Saibil, Machinery to reverse irreversible aggregates. Science 339:1040, 1080 March 2013