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Secondary structure of alpha (light) and beta (heavy) chains of human haptoglobin was proposed. The Chou-Fasman predictive method was used in conjunction with the hydrophobic character and hydropathy scale value assigned to each amino acid residue in the primary sequence of the protein. Moreover, by means of hydrophilicity values of amino acids, the location of antigenic determinants was predicted.
We report 2D cluster analyses of 1Halpha, 1HN, 13Calpha, and 13C' versus 13Cbeta NMR chemical shifts (CSs) that can be used to predict the redox state and secondary structure of cysteine residues in proteins. A database of cysteine 1Halpha, 1Hbeta2, 1Hbeta3, 1HN, 13Calpha, 13Cbeta, 13C', and 15NH CSs as a function of secondary structure and redox state was constructed from BioMagResBank entries. One-dimensional statistical analysis showed that cysteine 1Halpha, 1HN, 13Calpha, 13C', and 15NH CSs reflected the secondary structure, and that cysteine Cbeta CS is extremely sensitive to the redox state. In contrast, cysteine 1Hbeta CS was not correlated with its redox state or secondary structure. Two-dimensional cluster analysis revealed that 2D Calpha/Cbeta, C'/Cbeta, HNu/Cbeta, and Halpha/Cbeta clusters were helpful in distinguishing both the redox state and secondary structure of cysteine residues. Based on these results, we derived rules using a score matrix to predict the redox state and secondary structure of cysteines using their CSs. The score matrix predicts the redox state and secondary structure of cysteine residues in proteins with approximately 90% accuracy. This suggests that the redox state and secondary structure of cysteine residues in peptides and proteins can be obtained from their CSs without recourse to nuclear Overhauser effect measurements.
Changes in RNA secondary structure have been found to play important roles in translational regulation, protein synthesis, and mRNA splicing. In studies utilizing a 66 nucleotide RNA template with a stable hairpin structure, we have examined the effects of RNA secondary structure on HIV-1 reverse transcriptase activity. We identify several pause sites in the stem of the hairpin and show that these pause sites are correlated with the free energy of melting the next base pair in the stem. We also identify a pause site appearing in the loop of the hairpin and show that this is due to the rapid formation of a new hairpin structure occurring during the progress of DNA polymerization through the hairpin. The rapid change in RNA secondary structure to form the new hairpin selectively destabilizes the major hairpin and thereby accelerates the rate at which reverse transcriptase reads through RNA secondary structure.
A multivariate linear model (Gauss-Markoff model) with noise is used to analyze the estimation of protein secondary structure from spectra of 21 reference proteins whose structures are known from X-ray studies. Fourier transform infrared (FTIR) spectra from 1700 to 1500 cm-1 and circular dichroism (CD) spectra from 178 to 260 nm have been used. The secondary structure categories of interest are alpha-helix, antiparallel beta-sheets, parallel beta-sheets, beta-turns, and "other". The secondary structures are predicted from separate spectra as well as from combined FTIR and CD spectra. The characteristic spectra belonging to the secondary structures and the prediction errors are also estimated. Attention has been paid to the criteria for the choice of rank of matrices of reference spectra, which corresponds to the number of independent pieces of spectral information. Criteria used are: magnitudes of singular values, root mean square error of model fit, relative error of estimable parameters and errors in predicted secondary structure. The ranks of the spectral matrices are found to be between three and six. The model accuracy is determined by removing each protein from the sample and comparing predicted and X-ray values of secondary structure. It is concluded that the linear model is more adequate for the protein FTIR spectra than for the CD spectra. Secondary structure predictions using the FTIR amide I band (1700-1600 cm-1) and the FTIR amide II band (1600-1500 cm-1), or a combination of the two, are of comparable accuracy. In particular, antiparallel beta-sheets and "other" are more reliably estimated from FTIR spectra. However, alpha-helix is more reliably estimated from CD spectra. Combining the spectra yields the best results of both techniques for each class.
We report the sequence and propose a secondary structure for the cytoplasmic large subunit (5.8S and 28S) ribosomal RNA of the mosquito, Aedes albopictus, in an aligned format that incorporates secondary structure comparisons with Homo sapiens, Drosophila melanogaster, and Escherichia coli ribosomal RNAs. This format facilitates comparison of subtle differences between models, allowing nucleotide by nucleotide analysis at each position of discrepancy. Comparison of the A. albopictus large subunit ribosomal RNA gene with those from other species revealed new compensatory base changes. The aligned format focuses attention to the specific contribution of the A. albopictus sequence by facilitating comparison with the sequence of another dipteran, D. melanogaster. This is the second report of a complete large subunit rRNA sequence from an arthropod, and the first 28S rRNA sequence for a member of the lower Diptera (Nematocera).
The secondary structure of microsomal epoxide hydrolase was determined by Raman spectroscopy and the effect of the membrane microenvironment studied. The ratios of the four secondary structure contents, alpha-helix: beta-strand:turn:undefined, were found to be 47:24:17:11 and 58:17:15:10 for the solubilized and the membrane-bound epoxide hydrolase, respectively. Based on the spectral analysis in the 2800-2900 cm-1 range, it was concluded that the protein studied produces the disordering effect on the lipid dimyristoylphosphatidylcholine bilayer at 16 degrees C.
A de novo secondary structure prediction has been prepared for Src homology domain 3, in advance of any crystallographic information concerning any member of this interesting protein family. The prediction can be compared with a crystal structure that will be published in Nature on October 29, 1992. The prediction is based on analysis of a multiple alignment of homologous proteins. The patterns of variation and conservation of amino acids across the alignment allow the determination of surface and internal positions, which then allow the assignment of secondary structure. The prediction is quite different both in method and, in this case, result from predictions based on propensities (e.g. Garnier-Osgurthorpe-Robson) of particular amino acids to appear in particular types of secondary structure.
A simple technique for identifying protein secondary structures through the analysis of backbone 13C chemical shifts is described. It is based on the Chemical-Shift Index [Wishart et al. (1992) Biochemistry, 31, 1647-1651] which was originally developed for the analysis of 1H(alpha) chemical shifts. By extending the Chemical-Shift Index to include 13C(alpha), 13C(beta) and carbonyl 13C chemical shifts, it is now possible to use four independent chemical-shift measurements to identify and locate protein secondary structures. It is shown that by combining both 1H and 13C chemical-shift indices to produce a 'consensus' estimate of secondary structure, it is possible to achieve a predictive accuracy in excess of 92%. This suggests that the secondary structure of peptides and proteins can be accurately obtained from 1H and 13C chemical shifts, without recourse to NOE measurements.
The secondary structure of seven variant surface glycoproteins (VSGs) of trypanosomes has been determined by Raman spectroscopy. They are all predominantly alpha-helical, the alpha-helix content varying between 50 and 60%. The beta-strand content varies between 20 and 25%, and the content of beta-turn and nonregular structures is about 25%. For three VSGs the N-terminal domain obtained by proteolytic cleavage was found to have essentially the same secondary structure as the complete VSGs. For three VSGs a secondary structure prediction has been performed applying the rules of Chou and Fasman. In all cases, two long alpha-helices extending over about 50 residues or 80 A are predicted in agreement with the X-ray diffraction data of Freymann et al. [(1984) Nature 311, 167-169] and Metcalf et al. [(1987) Nature 325, 84-86]. The region between the two alpha-helical segments exhibits a high potential of beta-turns, suggesting that this segment may be exposed on the cell surface and carry major antigenic determinants.
Bovine immunoglobulin G (IgG) solutions were subjected to pulsed electric fields (PEF) or heat treatment to investigate the effect of processing on secondary structure monitored using circular dichroism spectrometry. Under heat treatment, the critical temperature for bovine IgG to change secondary structure at neutral pH in borate buffer is 72 degrees C. A conversion of the secondary structure from beta-sheets into random coils along with the loss of immunoactivity of bovine IgG was observed when heated at 82 degrees C for 120 s. In contrast, PEF treatment at 41.1 kV/cm for 54 mus with bipolar pulses (outlet at 43.8 degrees C) caused no detectable changes in the secondary structure or the thermal stability of secondary structure. A shape factor, S (200nm) over (217nm), ratio of magnitude of the positive CD band at 200 nm to that of the negative CD band at 217 nm, was closely correlated to the immunoactivity of bovine IgG (r(2) = 0.99) and quantifies changes of secondary structure.
In terms of the classification of the protein secondary structures, we propose a 2D representation of protein secondary structure sequences. The representation are used to display, analyze, and compare the secondary structure sequences. Based on this representation, we assign the structural class to the protein, and verify the advantage or disadvantage of the methods of predicted protein second structure.
The secondary structure of human monoamine oxidase A and bovine monoamine oxidase B has been investigated by Fourier Transform Attenuated Total Reflection Spectroscopy (FTIR ATR). The experimental results are compared for both isoenzymes and the data are incorporated in a statistical attribution of secondary structure of the enzyme describing the distinct folding and molecular specificity of the two types of monoamine oxidase.
Secondary structure prediction of the catalytic domain of matrix metalloproteinases is evaluated in the light of recently published experimentally determined structures. The prediction was made by combining conformational propensity, surface probability, and residue conservation calculated for an alignment of 19 sequences. The position of each observed secondary structure element was correctly predicted with a high degree of accuracy, with a single beta-strand falsely predicted. The domain fold was also anticipated from the prediction by analogy with the structural elements found in the distantly related metalloproteinases thermolysin, astacin, and adamalysin.
The secondary structure of urokinase with molecular weight 33 000 dalton was studied by the circular dichroism method. The secondary structure parameters were calculated based on the protein reference CD spectra resulted in the following secondary structure parameters: approximately 30% aminoacid residues constitute the alpha-helical regions, the same amount forms the beta-structure and an essential fractions contributes the beta-turns. Conformational stability of urokinase to alkaline pH (up to 11.6) and high temperature (up to 80 degrees) in 0.1 M phosphate buffer pH 6.6 was found.
Thermodynamic parameters of the cloverleaf secondary structure of tRNAs of several major taxons (archaebacteria, eubacteria, eukaryotes, chloroplasts, and mitochondria) were subjected to computer analysis. The distribution of free-energy values was close to normal in all groups (except for the mitochondrial tRNA). In the organisms existing under extreme environmental conditions, the stability of the tRNA secondary structure was higher. Comparative analysis of teh frequency of ¿quasi-complementary¿ GU pairs in stems of randomly generated and real sequences demonstrated preferential fixation of such pairs in the contexts with the most favorable thermodynamics parameters. Noncanonic pairs in tRNA stems set limits on the presence of highly mutable CG dinucleotides. Moreover, the effect of noncanonic pairs other than GU on the frequency of such dinucleotides is far more pronounced than that of GU pairs.
We present an algorithm that is able to propose compact models of protein 3D structures, only starting from the prediction of the nature and length of regular secondary structures. Helices are modeled by cylinders and sheets by helicoid surfaces, all strands of a sheet being considered as a single block. It means that relative topology of the strands inside one sheet is a prerequisite. Loops are only considered as constraints, given by the maximal distance between their Calpha extremities according to their sequence length. Unconnected regular secondary structures are reduced to a single point, the center of their hydrophobic faces. These centers are then repeatedly moved in order to obtain a compact hydrophobic core. To prevent secondary structures from interpenetrating, a repulsive term is introduced in the function whose minimization leads to the compact structure. This RUSSIA (Rigid Unconnected Secondary Structure Assembly) algorithm has the advantage of relying on a small number of variables and therefore many initial conformations can be tested. Flexibility is produced in the following way: helices or sheets are allowed to rotate around the direction leading to the center of the model; residues in a sheet can slide along the main direction of the strand where they are embedded. RUSSIA is fast and simple and it produces on a test set several neighbor good models with an r.m.s. to the native structures in the range 1.4-3.7 A. These models can be further treated by statistical potentials used in threading approaches in order to detect the best candidate. The limits of the present method are the following: small proteins with few secondary structures are excluded; multi domain proteins must be split into several compact globular domains from their sequences; sheets of more than five strands and completely buried helices are not treated. In this first paper the algorithm is developed and in Part II, which follows, some applications are presented and the program is evaluated.
A few years ago, lattice model studies indicated that compactness could induce polymer chains to develop protein-like secondary structures. Subsequent off-lattice studies have found the amounts of induced structure to be relatively small. Here we use distance geometry to generate random conformations of compact poly-alanine chains of various chain lengths. The poly-alanine chains are subjected only to compactness and excluded volume constraints; no other energies or conformational propensities are included in the chain generation procedure. We find that compactness leads to considerable stabilization of secondary structure, but the absolute amount of secondary structure depends strongly on the criteria used to define helices and sheets. By loose criteria, much secondary structure arises from compactness, but by strict criteria, little does. The stabilization free energy of secondary structure provided by compactness, however, appears to be independent of criteria. Since real helices and sheets in proteins can be identified by strict criteria, we introduced small energy perturbations to compact poly-alanine chains using the AMBER force field. Small refinements produced good alpha-helices. For beta-sheets, however, larger refinements are necessary. Compactness appears to impart stability, but not much structural specificity, to secondary structures in proteins. Compactness acts more like diffusion as a force, a result of ensemble statistics, than like pair interactions such as hydrogen bonding.
Structural genomics meets phylogenetics and vice versa: Knowing rRNA secondary structures is a prerequisite for constructing rRNA alignments for inferring phylogenies, and inferring phylogenies is a precondition to understand the evolution of such rRNA secondary structures. Here, both scientific worlds go together. The rRNA internal transcribed spacer 2 (ITS2) region is a widely used phylogenetic marker. Because of its high variability at the sequence level, correct alignments have to take into account structural information. In this study, we examine the extent of the conservation in structure. We present (1) the homology modeled secondary structure of more than 20,000 ITS2 covering about 14,000 species; (2) a computational approach for homology modeling of rRNA structures, which additionally can be applied to other RNA families; and (3) a database providing about 25,000 ITS2 sequences with their associated secondary structures, a refined ITS2 specific general time reversible (GTR) substitution model, and a scoring matrix, available at http://its2.bioapps.biozentrum.uni-wuerzburg.de.