Protein conformation in bacterial spinae

Monitoring of solid phase peptide synthesis by FT-IR spectroscopy

Aggregation phenomena of growing peptides on the resin have seldom been investigated. We report here how conformations are determined by FT-IR spectroscopy. Therefore the sequence 80-99 of HIV 1-protease was synthesized. After every coupling a resin sample was taken out of the reaction column and a FT-IR spectrum recorded. The results were compared with the UV monitoring obtained from another synthesis of the same peptide.

Secondary structural analysis of retrovirus integrase: characterization by circular dichroism and empirical prediction methods

The retrovirus integrase (IN) protein is essential for integration of viral DNA into host DNA. The secondary structure of the purified IN protein from avian myeloblastosis virus was investigated by both circular dichroism (CD) spectroscopy and five empirical prediction methods. The secondary structures determined from the resolving of CD spectra through a least-squares curve fitting procedure were compared with those predicted from four statistical methods, e.g., the Chou-Fasman, Garnier-Osguthorpe-Robson, Nishikawa-Ooi, and a JOINT scheme which combined all three of these methods, plus a pure a priori one, the Ptitsyn-Finkelstein method. Among all of the methods used, the Nishikawa-Ooi prediction gave the closest match in the composition of secondary structure to the CD result, although the other methods each correctly predicted one or more secondary structural group. Most of the alpha-helix and beta-sheet states predicted by the Ptitsyn-Finkelstein method were in accord with the Nishikawa-Ooi method. Secondary structural predictions by the Nishikawa-Ooi method were extended further to include IN proteins from four phylogenetic distinct retroviruses. The structural relationships between the four most conserved amino acid blocks of these IN proteins were compared using sequence homology and secondary structure predictions.

Circular dichroic analysis of protein conformation: inclusion of the beta-turns

The mean residue ellipticity, [theta], at any wavelength, lambda, of a protein in aqueous solution is expressed as [theta]lambda = fH[theta]H infinity(1-k/n) + f beta[theta]beta + ft[theta]t + fR[theta]R with two constraints: 1 > or = fj > or = 0 and sigma fj = 1. The subscripts H, beta, t, and R refer to the helix, beta-form, beta-turn, and unordered form. The fractions, fj's, of 15 proteins are based on X-ray crystallography, ft refers to the net beta-turn after cancelling those residues having dihedral angles of opposite sign. The [theta]H infinity of an infinite helix and its chain-length dependence factor, k, were computed from the myoglobin data (Chen et al., 1974, Biochemistry 13, 3350). The average number of residues per helical segment, n, for 15 proteins was about 10, which can be used for proteins of unknown structure. The reference spectra of other three structural elements are computed by a least-squares method. Once the reference spectra are chosen, the same equation above can be used to estimate the fractions of the secondary structure of a protein from its CD data points between 190 and 240 nm at 1-nm intervals. The computed helical content is usually good to excellent (concanavalin A is a notable exception). Inclusion of the beta-turn in the analysis improves the correlation for the estimates of the beta-form, but the computed beta t values are not significantly correlated with the X-ray results. Matrix formulation proves the equivalence of the least-squares method and the integral curve-fitting.

Physicochemical and immunological homogeneity of spinin, the subunit-protein of bacterial spinae

Bacterial spinae from marine bacterium D71 are multi-subunit structures of a single protein. This protein, called spinin, is homogeneous by immunodiffusion and immunoelectrophoresis, amino acid composition, polyacrylamide gel electrophoresis with a number of buffer systems, sedimentation velocity and diffusion boundary analysis. Sedimentation equilibrium gives Mr = 19,000, while phosphate polyacryl-amide gel electrophoresis in presence of dodecyl sulfate gives Mr = 32,000. The lower Mr estimate for spinin is supported by sedimentation equilibrium in 6 M guanidine . HCl, and covalent cross-linking with dimethyl suberimidate or glutaraldehyde. The higher Mr value probably arises from an anomalous spinin-dodecyl sulfate interaction. Isoelectric focusing in polyacrylamide gel gives pI = 3.45; however, the focusing pattern also contains three distinct bands that may arise from hydrolysis of the spinin protomer during anodic migration. This study presents the first extensive physicochemical characterization of spinin and provides the basis for investigating the subunit assembly of spinae.