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PubMed1982

Protein secondary structure. Studies on the limits of prediction accuracy.

A secondary structure prediction technique is proposed which includes nucleation site determination through multiplication of conformational preference parameters as well as weighting factors to represent structurally stabilizing short range interactions. The prediction accuracy of the method is calculated using data bases categorized according to the four protein structural classes and with differing assignments of secondary structural regions. The results indicate that nearest neighbor prediction techniques (a) are insensitive to various assignment criteria for the secondary structural spans, (b) have nearly achieved their upper limit of prediction accuracy, and (c) can be somewhat improved through the use of stereochemical weighting factors and conformational parameters derived from the four structural groups.

Chemical Phenomena↗
PubMed1981

The secondary structure of ovomucoid and its domains as studied by circular dichroism.

The secondary structure of chicken egg white ovomucoid and its domains was studied by means of circular dichroism (CD). The various domains (domain I, domains II . III, domains I . II, and domain III with and without carbohydrate) were prepared from the ovomucoid by cyanogen bromide cleavage and Staphylococcus aureus protease V-8 digestions. The carbohydrate moiety in the ovomucoid was isolated after its extensive pronase and endo-beta-N-acetyl-glucosaminidase H digestions. On the net CD spectra of polypeptide chain in the ovomucoid and domain preparations, which were obtained by subtracting the spectrum of the carbohydrate moiety from their spectra, the fractions of secondary structure were calculated by the method of Chang et al. (Chang, C.T., Wu, C.S.C. and Yang, J.T. (1978) Anal. Biochem. 91, 13-31). The estimated composition of the secondary structure in the ovomucoid was as follows: alpha-helix, 26%; beta-structure, 46%; beta-turn, 10%; and random coil, 18%. The secondary structure compositions estimated for the three domains suggested that domains I and II were homologous to one another but not to domain III in regard to the proportion of secondary structure content.

Animals↗
PubMed1991

Nucleolin promotes secondary structure in ribosomal RNA.

The effect of nucleolin on the secondary structure of RNA was studied using circular dichroism (CD). Nucleolin caused decreases in the main positive bands and shifts to higher wavelengths in the CD spectra of synthetic polynucleotides such as poly(G) and poly(A) indicating helix destabilizing activity. In contrast, nucleolin effected increases in signal and shifts to lower wavelengths of the peaks of CD spectra of ribosomal RNA, suggesting enhancement of secondary structure. Another major nucleolar RNA binding protein, B23, had helix destabilizing activity but did not enhance RNA secondary structure. It is proposed that nucleolin promotes formation of secondary structure in preribosomal RNA during the early stages of ribosome biogenesis.

Animals↗
PubMed2004

A comparative method for finding and folding RNA secondary structures within protein-coding regions.

Existing computational methods for RNA secondary-structure prediction tacitly assume RNA to only encode functional RNA structures. However, experimental studies have revealed that some RNA sequences, e.g. compact viral genomes, can simultaneously encode functional RNA structures as well as proteins, and evidence is accumulating that this phenomenon may also be found in Eukaryotes. We here present the first comparative method, called RNA-DECODER, which explicitly takes the known protein-coding context of an RNA-sequence alignment into account in order to predict evolutionarily conserved secondary-structure elements, which may span both coding and non-coding regions. RNA-DECODER employs a stochastic context-free grammar together with a set of carefully devised phylogenetic substitution-models, which can disentangle and evaluate the different kinds of overlapping evolutionary constraints which arise. We show that RNA-DECODER's parameters can be automatically trained to successfully fold known secondary structures within the HCV genome. We scan the genomes of HCV and polio virus for conserved secondary-structure elements, and analyze performance as a function of available evolutionary information. On known secondary structures, RNA-DECODER shows a sensitivity similar to the programs MFOLD, PFOLD and RNAALIFOLD. When scanning the entire genomes of HCV and polio virus for structure elements, RNA-DECODER's results indicate a markedly higher specificity than MFOLD, PFOLD and RNAALIFOLD.

Codon↗
PubMed1999

Analyzing protein circular dichroism spectra for accurate secondary structures.

We have developed an algorithm to analyze the circular dichroism of proteins for secondary structure. Its hallmark is tremendous flexibility in creating the basis set, and it also combines the ideas of many previous workers. We also present a new basis set containing the CD spectra of 22 proteins with secondary structures from high quality X-ray diffraction data. High flexibility is obtained by doing the analysis with a variable selection basis set of only eight proteins. Many variable selection basis sets fail to give a good analysis, but good analyses can be selected without any a priori knowledge by using the following criteria: (1) the sum of secondary structures should be close to 1.0, (2) no fraction of secondary structure should be less than -0.03, (3) the reconstructed CD spectrum should fit the original CD spectrum with only a small error, and (4) the fraction of alpha-helix should be similar to that obtained using all the proteins in the basis set. This algorithm gives a root mean square error for the predicted secondary structure for the proteins in the basis set of 3.3% for alpha-helix, 2.6% for 3(10)-helix, 4.2% for beta-strand, 4.2% for beta-turn, 2.7% for poly(L-proline) II type 3(1)-helix, and 5.1% for other structures when compared with the X-ray structure.

Algorithms↗
PubMed1980

Chemical modification studies and the secondary structure of HeLa cell 5.8S rRNA.

Various secondary structure models have been proposed for 5.8 S rRNA. In this paper HeLa cell 5.8 S rRNA is shown to possess several sites that are reactive to carbodiimide at 25 degrees, and other regions that are unreactive. Previous work has established the distribution of reactive and unreactive cytidine residues along the primary structure (11). The secondary structure model of Nazar et al. (7) is fully compatible with the chemical reactivity data whereas other models are partly incompatible. We conclude that the model of Nazar et al. provides the best approximation so far available to the conformation of isolated 5.8 S rRNA. Findings on the effect temperature on the chemical reactivity of different parts of the structure are summarized. The findings described in this paper should provide a basis for examining the specific interaction of 5.8 S rRNA with 28 s rRNA.

Base Sequence↗
PubMed1997

Linkers of secondary structures in proteins.

Linkers that connect repeating secondary structures fall into conformational classes based on distance and main-chain torsion clustering. A data set of 300 unique protein chains with low pairwise sequence identity was clustered into only a few groups representing the preferred motifs. The linkers of two to eight residues for the nonredundant data set are designated H-Ln-H, H-Ln-E, E-Ln-H, E-Ln-E, where n is the length, H stands for alpha-helices, and E for beta-strands. Most of the clusters identified here corroborate earlier findings. However, 19 new clusters are identified in this paper, with many of them having seven and eight residue linkers. In our first analysis, the secondary structures flanking the linkers are both interacting and noninteracting and there is no precise angle of orientation between them. A second analysis was performed on a set of proteins with restricted orientations for the flanking elements, namely, mainly alpha class of proteins with orthogonal architecture. Two definite clusters are identified, one corresponding to linkers of orthogonal helices and the other to linkers of antiparallel helices. Loops forming binding sites or involved in catalytic activity are important determinants of the function of proteins. Although the structural conservation of the residues around the catalytic triad of serine proteases has been studied widely, there has not been a systematic analysis of the conformation of the loops that contain them. Residues of the catalytic triad reside in the linkers of beta-strands, with varying lengths of more than eight residues. Here, we analyze the structural conservation of such linkers by superposition, and observe a conserved structural feature of the linkers incorporating each of the three residues of the catalytic triad.

Amino Acid Sequence↗
PubMed1993

Multiple coding and the evolutionary properties of RNA secondary structure.

This article evaluates evolutionary properties of the transition from RNA primary sequence to RNA secondary structure. It focuses on the restrictions that the conservation of a protein code in an RNA sequence puts on its potential to evolve towards a specific secondary structure. Restricting the mutations to those that do not affect the coding for a protein restricts both the accessibility and the connectivity of the sequence space. The accessibility is restricted because only certain point mutations are allowed. The connectivity is restricted because no insertions and deletions are allowed. Simulating an evolutionary search process for a specific secondary structure shows that (i) the reduction of allowable point mutations allows for adaptation to some large-scale topology, but strongly reduces the possibility of small-scale adaptations, (ii) the abolition of insertions and deletions has very little effect on the results of the search process. During the evolutionary search process for a secondary structure with a specific topology and a high frequency of base-pairing the quasispecies moves into a subspace in which the similarity between secondary structures of neighboring sequences is relatively high. Increased similarity between second structures of neighboring sequences is also found in the Rev responsive element (RRE) in the lentiviruses Caprine arthritis-encephalitis virus and Visna virus. In these viruses a biased nucleotide frequency in the RRE region suggests that selection for the RRE RNA secondary structure affects the amino acid sequence of the env gene. Our results show a variation in the ruggedness of fitness landscapes which are based on a high degree of epistatic interactions. Fitness landscapes play an essential role, not only in biotic evolution, but also in all kinds of optimization processes (Hill Climbing, Simulated Annealing, Genetic Algorithms, etc). Variation in their ruggedness should therefore be taken into account in the analysis of these processes.

Amino Acid Sequence↗
PubMed1999

A new method to predict the consensus secondary structure of a set of unaligned RNA sequences.

MOTIVATION: To predict the consensus secondary structure, possibly including pseudoknots, of a set of RNA unaligned sequences. RESULTS: We have designed a method based on a new representation of any RNA secondary structure as a set of structural relationships between the helices of the structure. We refer to this representation as a structural pattern. In a first step, we use thermodynamic parameters to select, for each sequence, the best secondary structures according to energy minimization and we represent each of them using its corresponding structural pattern. In a second step, we search for the repeated structural patterns, i.e. the largest structural patterns that occur in at least one sequence, i.e. included in at least one of the structural patterns associated to each sequence. Thanks to an efficient encoding of structural patterns, this search comes down to identifying the largest repeated word suffixes in a dictionary. In a third step, we compute the plausibility of each repeated structural pattern by checking if it occurs more frequently in the studied sequences than in random RNA sequences. We then suppose that the consensus secondary structure corresponds to the repeated structural pattern that displays the highest plausibility. We present several experiments concerning tRNA, fragments of 16S rRNA and 10Sa RNA (including pseudoknots); in each of them, we found the putative consensus secondary structure.

Algorithms↗
PubMed1983

Transcription termination in vitro at the tryptophan operon attenuator is controlled by secondary structures in the leader transcript.

The role of alternative RNA secondary structures in regulating transcription termination at the attenuator of the tryptophan (trp) operon of Serratia marcescens was examined in vitro by transcribing mutant DNA templates having deletions of different segments of the trp leader region. Deletions that removed sequences corresponding to successive segments of postulated RNA secondary structures either increased or decreased transcription termination at the attenuator. The results obtained are consistent with the hypothesis that transcription termination results from RNA polymerase recognition of a particular RNA secondary structure, the terminator. This structure forms only in the absence of an alternative, preceding, RNA secondary structure, the antiterminator.

Chromosome Deletion↗
PubMed1993

The secondary structure of milk proteins and their biological function.

A brief overview is given of the methods of determining and predicting secondary structure in proteins. The secondary structures of the milk serum proteins, lactoferrin, alpha-lactalbumin, lysozyme, and beta-lactoglobulin, as determined by x-ray crystallography, are compared with the results of a joint prediction method. This comparison evaluates critically the degree of success achieved and helps define what can reasonably be expected from a prediction in the absence of a known structure. The value of supplementary information from spectroscopic methods and the use of templates and sequence information from related proteins in improving the confidence of predictions are illustrated. One point that emerges is the general overprediction of helix content by the joint prediction method such that, for an all-beta protein such as beta-lactoglobulin, the method of Garnier, Osguthorpe, and Robson, applied with the correctly selected decision constants, provides a somewhat better approach. Secondary structure of the caseins can be predicted with less confidence than for globular proteins, and the results should be interpreted as evidence of a propensity to form transient secondary structures of the indicated type in view of the generally open and flexible conformation of caseins in solution.

Amino Acid Sequence↗
PubMed1982

An algorithm for the display of nucleic acid secondary structure.

A simple algorithm is presented for the graphic display of nucleic acid secondary structure. Examples of secondary structure displays are given for tRNA, 5S RNA and part of the 16S RNA. Due to its speed, this algorithm could easily be used in conjunction with secondary structure programs which calculate various alternate structures.

Base Sequence↗
PubMed1998

In unison: regularization of protein secondary structure predictions that makes use of multiple sequence alignments.

We present a method whose purpose is to post-process the fuzzy results of secondary structure prediction methods that use multiple sequence alignments, in order to obtain 'realistic' secondary structures, i.e., secondary structure elements whose length is greater than or equal to some predefined minimum length. This regularization helps with interpretation of the secondary structure prediction.

Algorithms↗
PubMed1992

Improvement of protein secondary structure prediction by combination of statistical algorithms and circular dichroism.

Three different approaches (propensity curve shifting, hydropathy index evaluation, and iterative attribution/cancellation of secondary structure) to the use of secondary structure percentages derived from circular dichroism measurements to improve the success rate of a protein secondary structure prediction method, without using decision constants, are described and compared. Propensity-curve shifting appears to be the best-performing approach, bearing an increase of 5.3% in the success rate of single-residue structural prediction when exact information on the secondary structure, obtained by X-ray crystallography, is employed; with information of an accuracy comparable to that obtainable by circular dichroism, the improvement stays between 3.5 and 4.9%, for a three-state prediction. Although developed with circular dichroism in mind, the method can use percentages of secondary structure obtained by any other experimental methodology from which they can be inferred, for instance Raman spectroscopy and infrared spectroscopy.

Algorithms↗
PubMed1996

Nuclear magnetic resonance chemical shift: comparison of estimated secondary structures in peptides by nuclear magnetic resonance and circular dichroism.

Traditionally, CD has been used extensively for peptides in secondary structure analysis. In recent years, NMR chemical shifts and nuclear Overhauser enhancements have been widely used in conjunction with CD to assess the secondary structures of peptides and proteins; however, there are many instances where the estimation of secondary structure contents differs significantly between the two methods. In order to elucidate the perceived differences between the two methods, secondary structure estimations by CD and 1H NMR chemical shifts were compared for over 50 peptides. The linear peptides investigated were largely unstructured, approximately 15-50 residues in size, and lacked stable tertiary conformation. These peptides were studied in different solvent systems including water, alcohol-water, micelles and urea. A strong correlation exists for secondary structure assessment by CD and NMR chemical shifts; however, an interesting trend of higher estimation of helical contents by NMR was observed for peptide fragments from globular proteins studied in water. This may be a result of associative properties of these peptides in water. Additionally, a new method of quantitating secondary structure contents based on 1H NMR chemical shifts is reported.

Alcohols↗
PubMed2003

Protein structure comparison by probability-based matching of secondary structure elements.

MOTIVATION: Protein structure comparison (PSC) has been used widely in studies of structural and functional genomics. However, PSC is computationally expensive and as a result almost all of the PSC methods currently in use look only for the optimal alignment and ignore many alternative alignments that are statistically significant and that may provide insight into protein evolution or folding. RESULTS: We have developed a new PSC method with efficiency to detect potentially viable alternative alignments in all-against-all database comparisons. The efficiency of the new PSC method derives from the ability to directly home in on a limited number of viable and ranked alignment solutions based on intuitively derived SSE (secondary structure element)-matching probabilities.

Algorithms↗
PubMed2003

Protein secondary structure prediction based on an improved support vector machines approach.

The prediction of protein secondary structure is an important step in the prediction of protein tertiary structure. A new protein secondary structure prediction method, SVMpsi, was developed to improve the current level of prediction by incorporating new tertiary classifiers and their jury decision system, and the PSI-BLAST PSSM profiles. Additionally, efficient methods to handle unbalanced data and a new optimization strategy for maximizing the Q(3) measure were developed. The SVMpsi produces the highest published Q(3) and SOV94 scores on both the RS126 and CB513 data sets to date. For a new KP480 set, the prediction accuracy of SVMpsi was Q(3) = 78.5% and SOV94 = 82.8%. Moreover, the blind test results for 136 non-redundant protein sequences which do not contain homologues of training data sets were Q(3) = 77.2% and SOV94 = 81.8%. The SVMpsi results in CASP5 illustrate that it is another competitive method to predict protein secondary structure.

Artificial Intelligence↗
PubMed1994

NMR structure determination of the Escherichia coli DnaJ molecular chaperone: secondary structure and backbone fold of the N-terminal region (residues 2-108) containing the highly conserved J domain.

DnaJ from Escherichia coli is a 376-amino acid protein that functions in conjunction with DnaK and GrpE as a chaperone machine. The N-terminal fragment of residues 2-108, DnaJ-(2-108), retains many of the activities of the full-length protein and contains a structural motif, the J domain of residues 2-72, which is highly conserved in a superfamily of proteins. In this paper, NMR spectroscopy was used to determine the secondary structure and the three-dimensional polypeptide backbone fold of DnaJ-(2-108). By using 13C/15N doubly labeled DnaJ-(2-108), nearly complete sequence-specific assignments were obtained for 1H, 15N, 13C alpha, and 13C beta, and about 40% of the peripheral aliphatic carbon resonances were also assigned. Four alpha-helices in polypeptide segments of residues 6-11, 18-31, 41-55, and 61-68 in the J domain were identified by sequential and medium-range nuclear Overhauser effects. For the J domain, the three-dimensional structure was calculated with the program DIANA from an input of 536 nuclear Overhauser effect upper-distance constraints and 52 spin-spin coupling constants. The polypeptide backbone fold is characterized by the formation of an antiparallel bundle of two long helices, residues 18-31 and 41-55, which is stabilized by a hydrophobic core of side chains that are highly conserved in homologous J domain sequences. The Gly/Phe-rich region from residues 77 to 108 is flexibly disordered in solution.

Amino Acid Sequence↗