PREDICTION OF PROTEIN SECONDARY STRUCTURE FROM CIRCULAR-DICHROISM SPECTRA - AN ATTEMPT TO SOLVE THE PROBLEM OF THE BEST-FITTING REFERENCE PROTEIN SUBSETS
B. Dalmas et Wh. Bannister, PREDICTION OF PROTEIN SECONDARY STRUCTURE FROM CIRCULAR-DICHROISM SPECTRA - AN ATTEMPT TO SOLVE THE PROBLEM OF THE BEST-FITTING REFERENCE PROTEIN SUBSETS, Analytical biochemistry, 225(1), 1995, pp. 39-48
In least-squares fitting of protein circular dichroism (CD) spectra us
ing basis CD spectra for the respective secondary structure components
, as given by reference proteins of known structural composition, good
fits of the CD spectrum do not necessarily correspond to appropriate
fits of the underlying structural composition of a test protein, In an
attempt to overcome this problem, CD similarity measures were used to
construct a subset of five reference CD spectra which permitted three
-component fitting of the CD and prediction of the relative magnitude
of total beta-sheet (antiparallel + parallel) and total other structur
e (beta-turn + remainder), relative to helix, in the test protein. A b
ackpropagation neural network (BPN) was also trained to make this pred
iction, In subsequent five-component fitting of the CD spectrum, using
a Monte Carlo method to generate subsets of reference proteins from t
he working data set, only those secondary structure fits which conform
ed to the consensus prediction of the CD similarity measures and the B
PN were accepted, The method enhanced the fitting of antiparallel beta
-sheet and beta-turn for 16 proteins, compared to the variable selecti
on method of P, Manavalan and W. C, Johnson (1987, Anal, Biochem, 167,
76-85), Some other proteins were less well fitted. Improvement in res
ults is expected with a larger representation of feasible basis CD spe
ctra in the working reference proteins, (C) 1995 Academic Press,Inc.