Jul 22, 1998

Side-chains in native and random coil protein conformations. Analysis of NMR coupling constants and chi1 torsion angle preferences

Journal of Molecular Biology
N J West, L J Smith

Abstract

The behaviour of amino acid side-chains in proteins in solution has been characterised by analysing NMR 3JHalphaH beta coupling constants and crystallographic chi1 torsion angles. Side-chains both in the core of native folded proteins and in situations where there is an absence of close packing including the random coil state have been considered. An analysis of experimental 3JHalphaH beta coupling constant data for ten proteins shows that in the core of native proteins a very close similarity is observed between the chi1 conformations adopted in solution and in crystals. There is clear evidence, however, for significant motional averaging about the chi1 torsion angles in solution. Using a model of a Gaussian distribution about the average torsion angles the extent of these fluctuations has been quantified; the standard deviation for the motion is 26 degrees, the fluctuations about chi1 in the protein core being similar in size to those found for main-chain phi torsion angles in solution. From the distribution of chi1 torsion angles in a data base of protein crystal structures, torsion angle populations and coupling constants have been predicted for a random coil polypeptide. Significant variations in the chi1 distributions for...Continue Reading

Mentioned in this Paper

Anethum graveolens
Cerebellar Decompression Injury
Fluctuation
In Vivo NMR Spectroscopy
Crystal - Body Material
Torsion (Malposition)
Amides
Ligand Binding
Aspartate
Amino Acids, I.V. solution additive

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