3-Dimensional Structures of Proteins-2

Biol/Chem 5310

Lecture: 9

September 19, 2002

3-Dimensional Structures of Proteins

Globular proteins: Compact, nearly spherical, typical example-enzymes.

Tend to be composed of short elements of secondary structure connected by turns. 3-D structure of many globular proteins has been determined by x-ray crystallography or NMR.

The main limitation of x-ray crystallography is the quality of the crystals. But interpretation of the x-ray diffraction patterns is also difficult.

The size of the protein is the main limitation of structure determination by NMR. Current limits are about 250 amino acids.

As of today there are 18691 Coordinate Entries in the Protein Data Bank / 16823 proteins / 1860 nucleic acids & protein-nucleic acid complexes / 18 carbohydrates . The address is <http://www.rcsb.org/pdb>

The first protein structure determined was by John Kendrew (see also) in late 1950's: myoglobin, an oxygen transport and storage protein found in muscle tissue. It consists of 8 segments of alpha-helix wrapped in an irregular fashion. This result indicated that the structure of proteins would not be as simple as that of DNA. Over the years diverse structures have continued to be discovered, although certain patterns have emerged. Several databases of structural hierarchy exist, such as CATH and SCOP.

Also see the JENA Image Library

Motifs of secondary structure:

b-a-b : parallel b-strands with a right-hand-crossover<LINK>
b-hairpin : anti-parallel b-strands with a tight turn.<LINK>
a-a : 2 a-helices packed antiparallel in a bundle, or crosswise.<LINK>
Greek key: 4 anti-parallel b-strands with "Greek key" connections<LINK>
Mouse Control

These motifs are used to form structural domains

All a

4 helix bundle
globin fold

All b

Up and down
Beta sandwich

a/b

a/b barrel
open twisted sheet

See Guided Exploration #8: Secondary structures in proteins

Prosthetic groups: Some proteins also contain components that are not amino acids.

metal ions (stability, catalysis) (See Chime link)
heme (porphyrin + Fe)
cofactors (often derived from vitamins, for catalysis)
lipids (membrane binding)

Proteins have insides and outsides.

Hydrophobic amino acids tend to be found buried inside proteins: Val, Leu, Ile, Phe, Trp.
Charged amino acids tend to be on the surface of proteins, in contact with water: Lys, Arg, Glu, Asp, (His).
Other amino acids, uncharged polar, can be found both on the surface and buried inside. If buried, the side chains with O or N should form H-bonds.

Location of Elements of Secondary structure:

The cores of globular proteins tend to be made from regular secondary structures: a-helices and b-strands.
Turns and longer connections tend to be found on the surfaces.

Large Proteins

Small proteins of 100-200 amino acids usualy form a single domain.
A domain is a largely self-interacting and self-stable region of a protein.
Large proteins tend to be formed from several domains, rather than one large domain.
Domains often have specialized functions.

Thermodynamics of protein stability

Protein stability refers to the DG of folding:
{unfolded state} <==> {folded state}
DGfolding = Gfolded - G unfolded

Proteins are typically only marginal stable.
DG may be the magnitude of only a few H-bonds.
DG is a delicate balance of various energetic contributions involving both enthalpy and entropy: DG = DH - TDS

1) Ionic interactions


Called ion pair or salt bridge
Ion pairs can occur on surface or buried.
Magnitude is much greater if buried because inside a protein D is much less than in water: 3-5 vs. 80
But DG of desolvation of charged groups can almost cancel the favorable interaction of buried ion pairs.
Conclusion: Ion pairs make a small DH contribution to DG of folding.

2) Vander Waals and Dipole interactions

These interactions are significant only at close range.
Dipole interactions are directional.
These interactions tend to be maximized in the highly dense interiors of proteins.
But, significant interactions could also exist in contacts with solvent.
Conclusion: These interactions make a small DH contribution to DG of folding.

3) Hydrogen bonds

It is important to realize that H-bonds in water are readily formed.
Since all possible H-bonds in an unfolded protein can be made with water, it is necessary that a folded protein also makes all possible H-bonds.
In each case the sum of the H-bond contributions may be similar, with the possible exception of a few especially favorable H-bonds in the folded protein.
Conclusion: H bonds make a small DH contribution to DG of folding.

4) Entropy contributions

a) Entropy of the protein: The protein loses considerable entropy as it folds. The interior adopts a largely fixed conformation and only exterior side chains remain mobile.

b) Entropy of the solvent: The solvent gains considerable entropy as a protein folds because of the hydrophobic effect. This is the largest favorable contribution to the stability of folded proteins. Unfolded proteins immobilize large numbers of water molecules in contact with hydrophobic side chains. These water molecules experience a large increase in entropy when the hydrophobic side chains are buried in the interior of the protein.

Summary: The stability of a folded protein is due to the sum of many contributions to DG. No contribution is essential. One can be compensated by others. The typical protein has a hydrophobic interior, which allows a favorable entropy term from the solvent. In general, vander waals and H-bonds do not contribute to stability, but instability will result if they are not maximized in a folded protein. Ion pairs are not necessary in general, but do stabilize some proteins. This is also true of disulfide bonds.

Try a quiz from Ch.6

Last updated Friday, September 13, 2002

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