Protein volumes and hydration effects. The calculations of partial specific volumes, neutron scattering matchpoints and 280-nm absorption coefficients for proteins and glycoproteins from amino acid sequences

Eur J Biochem. 1986 May 15;157(1):169-80. doi: 10.1111/j.1432-1033.1986.tb09653.x.

Abstract

Amino acid sequences, carbohydrate compositions and residue volumes are used to compare critically calculations of partial specific volumes v, neutron scattering matchpoints and 280-nm absorption coefficients with experimental v values for proteins and glycoproteins. The v values that are obtained from amino acid densitometry underestimate experimental v values by 0.01-0.02 ml/g while the v values from crystallographic volumes overestimate the experimental v values by 0.04-0.05 ml/g. An intermediate consensus volume set of amino-acid-residue volumes is proposed in order to predict experimental v values using sequence information. The method is extended to carbohydrates and glycoproteins. Neutron scattering matchpoints can be calculated from crystallographic residue volumes on the basis of the non-exchange of 10% of the main-chain NH protons. Crystallographic results on protein-bound water are used to account for the experimental values of v and matchpoints. Finally, 280-nm absorption coefficients, A1%, 1 cm 280, of 5-27 are found to be well predicted by the Wetlaufer procedure based on the totals of Trp, Tyr and Cys residues. Average errors are +/- 0.7, and the experimental A(1%,1cm)280 values can be larger than the predicted values by 3%.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Carbohydrates / analysis
  • Chemical Phenomena
  • Chemistry, Physical
  • Crystallography
  • Cystine
  • Densitometry
  • Glycoproteins*
  • Hydrogen-Ion Concentration
  • Mathematics
  • Neutrons
  • Proteins*
  • Scattering, Radiation
  • Tryptophan
  • Tyrosine

Substances

  • Carbohydrates
  • Glycoproteins
  • Proteins
  • Tyrosine
  • Cystine
  • Tryptophan