Determination of the secondary structures of proteins by circular dichroism spectra. Calculation of the protein basic circular dichroism spectra for antiparallel and parallel β‐structures and β‐bends

Abstract

New "reference" circular dichroism spectra of a helix, 0-structure (both parallel and antiparallel), 0-bends, and the unordered form are obtained from circular dichroism spectra and x-ray data for six proteins (myoglobin, lysozyme, lactate dehydrogenase, papain, ribonuclease, and subtilisin BPN'). Circular dichroism spectra for a-helix and antiparallel 0-structure are similar to those for p o l y (~-lysine). The circular dichroism spectrum of the parallel 0-structure is qualitatively similar to that theoretically calculated by Madison and Schellman. The circular dichroism spectrum of @-bends is qualitatively similar to that theoretically calculated by Woody. The spectrum of the unordered form is close to that of the denaturated proteins. These "reference" circular dichroism spectra used for the analysis of the secondary structure of ten globular proteins (besides the six reference proteins D-glyceraldehyde 3-phosphate dehydrogenase, concanavalin A, cytochrome c, and insulin).

Differentiation between transmembrane helices and peripheral helices by the deconvolution of circular dichroism spectra of membrane proteins

“…Even though there are several algorithms available for analyzing CD spectra (Saxena & Wetlaufer, 1971;Chang et al, 1978;Brahms & Brahms, 1980;Bolotina et al, 1981;Hennessey & Johnson, 1981;Provencher & Glockner, 1981;Manavalan & Johnson, 1987), they require the known secondary structures of the proteins in the database (usually determined by X-ray diffraction) and, therefore, compound the errors due to the interpretation of the X-ray data. As yet there is no database whose secondary structures are known for membrane proteins.…”

“…The CD spectrum of each secondary conformation may be obtained on the basis of the CD spectrum either obtained from model polypeptides (Holzwarth & Doty, 1965;Sarkar & Doty, 1966;Greenfield & Fasman, 1969;Woody, 1974;Brahms & Brahms, 1980;Hollosi et al, 1987a,b;Perczel et al, 1991aPerczel et al, , 1992a or extracted from a set of protein CD spectra whose X-ray data are available (Saxena & Wetlaufer, 1971 ;Chen et al, 1974;Chang et al, 1978;Bolotina et al, 1981;Hennessey & Johnson, 1981;Provencher & Glockner, 1981). In one approach (Saxena & Wetlaufer, 1971;Chen et al, 1974;Chang et al, 1978;Bolotina et al, 1981), the references are the pure component spectra extracted from a set of CD spectra of proteins previously determined by X-ray diffraction (fixed reference methods). In the other approach (Hennessey & Johnson, 1981 ;Provencher & Glockner, 1981), a set of the CD spectra of proteins is used as reference (variable reference methods).…”

Dynamic structure of metallothionein

“…Compared to these structural changes the ionic strength-dependent effects on the conformation of MT are less extensive ( fig.2). The saltinduced reduction in ellipticity of MT below 240 nm could indicate a small increase in a-helix content or a decrease in &structure [16,17]. The latter seems particularly plausible since a computer analysis of the far-UV CD spectrum of apo-MT and a structure prediction calculation from sequence data [ 131 indicate a total of about 40% ,& sheet and p-bend conformation.…”

Heme maintains catalytically active structure of cytochrome P‐450

“…The contents of 5 secondary structure forms were calculated from circular dichroism spectra of freshly dissolved proteins by the method of Bolotina et al [16]. Preparations were dissolved in 5 mM potassium phosphate buffer, pH 7.4, in the presence of 5 x 10-4% Emulgen 913.…”