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Test of circular dichroism (CD) methods for crambin and CD‐assisted secondary structure prediction of its homologous toxins
Author(s) -
Teeter M. M.,
Whitlow Marc
Publication year - 1988
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.340040405
Subject(s) - circular dichroism , protein secondary structure , chemistry , homologous chromosome , test (biology) , crystallography , computational biology , biochemistry , biology , botany , gene
Methods that analyze protein circular dichroism (CD) spectra for fractions of secondary structure are evaluated for the plant protein crambin, which has a known high‐resolution crystal structure. In addition, a two‐step secondary structure prediction scheme is presented and used for the toxins homologous to crambin, shown by others to have secondary structures similar to crambin. The test of CD spectral analysis methods with the protein crambin employed two computer programs and several CD basis sets. Crambin's crystal structure, known to 0.945 Å resolution (Hendrickson, W.A., Teeter, M.M. Nature 290:107–113, 1981), allows accurate evaluation of results. Analysis with the protein spectra basis sets (Provencher, S. W., Glöckner, J. Biochemistry 20:33–37, 1981) as modified (Manavalan, P., Johnson, W. C., Jr. Anal. Biochem. 167:76–85, 1987) agreed most closely with crambin's crystal structure. This method was then applied to the CD spectra of the membrane‐active toxins homologous to crambin (α 1 ‐ and β‐purothionin, phoratoxin A and B, an viscotoxin A3 and B). The new program SEQ (pronounced “seek”) was developed to assign the secondary structure along the protein chain in a hierarchical fashion and applied to the plant toxins. The method constrained the secondary structure fractions to those from CD analysis and combined standard statistical methods with amphipathic helix location. Both CD‐arrived secondary structure percentages and sequence assignment indicate that the viscotoxins are structurally most similar to crambin. Purothionin's secondary structure was predicted to be fundamentally similar to crambin's with a difference at the start of the first helix. This assignment agreed with Raman and NMR analyses of Purothionin and lends validity to the method presented here. Differences from the NMR in the CD secondary structure fraction analysis for phoratoxin suggest interference in the CD from tryptophan residues.