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PubMed1995

Feed-forward neural networks for secondary structure prediction.

A feed-forward neural network has been employed for protein secondary structure prediction. Attempts were made to improve on previous prediction accuracies using a hierarchical mixture of experts (HME). In this method input data are clustered and used to train a series of different networks. Application of an HME to the prediction of protein secondary structure is shown to provide no advantages over a single network. We have also tried various new input representations, chosen to incorporate the effect of residues a long distance away in the one-dimensional amino acid chain. Prediction accuracy using these methods is comparable to that achieved by other neural networks.

Neural Networks, Computer↗
PubMed1995

Secondary structure in the 3' UTR of EGF and the choice of reverse transcriptases affect the detection of message diversity by RT-PCR.

The secondary structure in mRNA is essential for many processes, but it can present a technical problem in making full-length cDNA with reverse transcriptases. Furthermore, different reverse transcriptases have differing abilities to transcribe through regions with secondary structure, which can alter the products obtained by reverse-transcribing RNA and then PCR-amplifying the product (RT-PCR). We have been interested in studying the posttranscriptional regulation of epidermal growth factor by RT-PCR and have tested the ability of several reverse transcriptases to reverse transcribe the 3'-untranslated region (3'UTR), a region that contains substantial secondary structure. When low levels of either total RNA or poly(A)+ mRNA were used, we found avian myeloblastosis virus reverse transcriptase (AMV-RT) to be the most robust of all the enzymes tested. Furthermore, contrary to reports that AMV-RT is inhibited by tRNA--which should make it less effective than Moloney murine leukemia virus reverse transcriptase (MMLV-RT) at reverse-transcribing total RNA--adding tRNA to poly(A)+ RNA actually increased the amount of specific RT-PCR product obtained with AMV-RT while it decreased the amount of product and enhanced mispriming with MMLV-RT. We found that pre-incubation of the oligo(dT) primer with total RNA at elevated temperature prior to reverse transcription improved the efficiency of both native and modified MMLV-RTs. These findings support the concept that secondary structures in RNA differentially affect the abilities of different reverse transcriptases to detect transcript diversity and raise the possibility that such structures could affect quantitation using RT-PCR with internal mRNA standards.

Avian Myeloblastosis Virus↗
PubMed1995

Prediction and Fourier-transform infrared-spectroscopy estimation of the secondary structure of a recombinant beta-glucosidase from Streptomyces sp. (ATCC 11238).

The secondary structure of a recombinant beta-glucosidase (EC 3.2.1.21) from Streptomyces sp. (ATCC 11238) has been predicted by computer algorithms and also estimated by Fourier-transform IR spectroscopy. From curve fitting of the deconvoluted IR spectra, the most probable distribution of the secondary-structural classes appears to be about 34% alpha-helix, 30% beta-sheet, 25% reverse turns and 11% non-ordered structures. These data showed a good agreement with data from computer prediction (35% alpha-helix, 23% beta-sheet, 31% reverse turns and 11% non-ordered structures).

Algorithms↗
PubMed1997

Secondary structure of the 5'-noncoding region of border disease virus genome RNAs.

The computer predicted secondary structures from the 5'-NC genome region of four border disease virus (BDV) strains collected from sheep in England and Scotland over a period 1976-1986 were prepared. The FOLD program from GCG sequence analysis software package was used for the analysis of a 243 bp RNA fragment. Two typical shapes of secondary structures were observed which contained multiple imperfect stem-loop motifs. The shape of those structures exactly fit with the grouping of BDV strains to two phylogenetic groups. Secondary structures are typical only of BDV strains and they are different from the structures prepared for NADL (BVDV) and Alfort (CSFV) strains.

Animals↗
PubMed1985

Analysis of secondary structures in M13mp8 (+) single-stranded DNA by the pausing of DNA polymerase alpha.

The pausing of DNA replication has been used as a tool for analyzing secondary structures in a single-stranded DNA. M13mp8 (+) single-stranded DNA was replicated in vitro by the DNA polymerase alpha from calf thymus. The positions of pausing were determined from DNA sequencing gels. All experimentally observed pausing sites could be correlated with computer-predicted secondary structures of the M13 single-stranded DNA. In the computer calculations of the secondary structures, long-range base-pairing, G.T mispairs and loop-out of bases were allowed. By using six different primers, the pausing site pattern and the corresponding secondary structure map of a region comprising 1400 nucleotides of the M13 genome has been established. Our experiments indicate that the M13 DNA is highly structured. Most of the stable structures are clustered around the origin of replication. With fragments of the M13 DNA, we show that long-range base-pairing exists in the M13 single-stranded genome and we present evidence for tertiary structure interactions. Furthermore we observe structures that form newly during the course of replication. The Escherichia coli single-stranded DNA-binding protein facilitates replication through the barriers.

Animals↗
PubMed1979

Evolutionary change in 5S RNA secondary structure and a phylogenic tree of 54 5S RNA species.

Secondary structure models of 54 5S RNA species are constructed based on the comparative analyses of their primary structure. All 5S RNAs examined have essentially the same secondary structure. However, there are revealing characteristic differences between eukaryotic and prokaryotic types. The prokaryotic 5S RNAs may be further classified into two types, one having 120 nucleotides (120-N type) and another having 116 (116-N type). A possible mechanism for the conversion of the prokaryotic 116-N type to the 120-N type 5S RNAs (or vice versa) is discussed on the basis of their nucleotide alignments. Finally, by comparing the nucleotide alignments, we propose a phylogenic tree of the 54 5S RNA species.

Animals↗
PubMed2005

Why don't humans get scrapie from eating sheep? A possible explanation based on secondary structure predictions.

In an effort to find a structural explanation for the lack of direct transmission of scrapie from sheep to humans, secondary structure predictions are used to locate the segments of the prion sequence which may be involved in the transformation from the normal form of the prion protein, which has high helix content, to the pathogenic form, which has high beta-sheet content. The Chou-Fasman algorithm, which calculates propensities for both helix and sheet formation, was used to predict the secondary structures of the scrapie-resistant and the scrapie-susceptible variants of the ovine prion protein. The scrapie-susceptible variant, which has a glutamine at residue position 168 (human prion protein numbering), is predicted to have a propensity for sheet formation in that region of the molecule, while the scrapie-resistant variant, which has an arginine at position 168, does not. The valine at position 133, additionally present in the ovine variant which is the most susceptible to scrapie, is predicted to result in even more sheet formation. When the predicted secondary structure of the human prion protein is compared to those of the ovine prion protein variants, the human protein is found to be most similar to the scrapie-resistant variant. This result is proposed to provide a possible explanation for the observation that scrapie is not directly transmitted from sheep to humans.

Amino Acid Sequence↗
PubMed2005

Molecular-level secondary structure, polymorphism, and dynamics of full-length alpha-synuclein fibrils studied by solid-state NMR.

The 140-residue protein alpha-synuclein (AS) is able to form amyloid fibrils and as such is the main component of protein inclusions involved in Parkinson's disease. We have investigated the structure and dynamics of full-length AS fibrils by high-resolution solid-state NMR spectroscopy. Homonuclear and heteronuclear 2D and 3D spectra of fibrils grown from uniformly (13)C/(15)N-labeled AS and AS reverse-labeled for two of the most abundant amino acids, K and V, were analyzed. (13)C and (15)N signals exhibited linewidths of <0.7 ppm. Sequential assignments were obtained for 48 residues in the hydrophobic core region. We identified two different types of fibrils displaying chemical-shift differences of up to 13 ppm in the (15)N dimension and up to 5 ppm for backbone and side-chain (13)C chemical shifts. EM studies suggested that molecular structure is correlated with fibril morphology. Investigation of the secondary structure revealed that most amino acids of the core region belong to beta-strands with similar torsion angles in both conformations. Selection of regions with different mobility indicated the existence of monomers in the sample and allowed the identification of mobile segments of the protein within the fibril in the presence of monomeric protein. At least 35 C-terminal residues were mobile and lacked a defined secondary structure, whereas the N terminus was rigid starting from residue 22. Our findings agree well with the overall picture obtained with other methods and provide insight into the amyloid fibril structure and dynamics with residue-specific resolution.

Carbon Isotopes↗
PubMed1978

Laser Raman evidence for new cloverleaf secondary structures for eukaryotic 5.8S RNA and prokaryotic 5S RNA.

Neither of the two previously proposed secondary structures for eukaryotic 5.8S RNA is consistent with the present laser Raman results. A new, highly stable "cloverleaf" secondary structure not only fits the Raman data but also accounts for previously determined enzymatic partial cleavage patterns, base sequence and pairing homologies, and G-C and A-U base pair numbers and ratios. The new cloverleaf model also conserves several structural features (constant loops, bulges, and stems) consistent with known 5.8S RNA functions. Finally, we propose a similar new cloverleaf secondary structure for Escherichia coli 5S RNA, consonant with many known properties of prokaryotic 5S RNA.

Chemical Phenomena↗
PubMed1995

Stabilization of secondary structure of Alzheimer beta-protein by aluminum(III) ions and D-Asp substitutions.

The CD spectra of the D-Asp substituted analogs of amyloid peptides, beta 6-25 and beta 1-40, showed a distinct blue-shift on Al3+ complexation. The influence of Al3+ coordination was most significant on the triply substituted beta 1-40 (D-Asp 1,7,23). This analog showed a reduction of the minima near 210nm and a simultaneous increase in the maxima near 200nm as compared to the native L-Asp beta 1-40. These observations suggest that Al3+ interaction with D-Asp induces the peptide backbone to increase its antiparallel beta-sheet character. D-Asp substitution and chelation by Al3+ lead to increased stability of higher molecular weight species of beta 1-40, and thereby could increase the toxicity of the Alzheimer amyloid protein.

Amyloid beta-Peptides↗
PubMed2001

Ligand affinity, homodimerization, and ligand-induced secondary structural change of the human vitamin d receptor.

The intrinsic tryptophan fluorescence signal of the full-length nuclear receptor hVDR was used to directly determine the dissociation constants, K(d), of two ligands yielding K(d) = 32 nM for 1alpha,25(OH)(2)D(3) and K(d) = 322 nM for 25(OH)D(3). Ligand binding was accompanied by a conformational change in the alpha-helical part of hVDR as revealed by CD spectroscopy. In addition, the presence of calcitriol was found to be a necessary prerequisite for the homodimerisation of hVDR which was monitored using fluorescence anisotropy. We conclude that the observed ligand-induced structural change of hVDR is conditional for dimerisation of the protein.

Calcifediol↗
PubMed1999

The hydrophobic core sequence modulates the neurotoxic and secondary structure properties of the prion peptide 106-126.

The neurodegeneration seen in spongiform encephalopathies is believed to be mediated by protease-resistant forms of the prion protein (PrP). A peptide encompassing residues 106-126 of human PrP has been shown to be neurotoxic in vitro. The neurotoxicity of PrP106-126 appears to be dependent upon its adoption of an aggregated fibril structure. To examine the role of the hydrophobic core, AGAAAAGA, on PrP106-126 toxicity, we performed structure-activity analyses by substituting two or more hydrophobic residues for the hydrophilic serine residue to decrease its hydrophobicity. A peptide with a deleted alanine was also synthesized. We found all the peptides except the deletion mutant were no longer toxic on mouse cerebellar neuronal cultures. Circular dichroism analysis showed that the nontoxic PrP peptides had a marked decrease in beta-sheet structure. In addition, the mutants had alterations in aggregability as measured by turbidity, Congo red binding, and fibril staining using electron microscopy. These data show that the hydrophobic core sequence is important for PrP106-126 toxicity probably by influencing its assembly into a neurotoxic structure. The hydrophobic sequence may similarly affect aggregation and toxicity observed in prion diseases.

Alanine↗
PubMed1996

Determination of the secondary structure of isomeric forms of human serum albumin by a particular frequency deconvolution procedure applied to Fourier transform IR analysis.

A new deconvolution procedure was applied to the analysis of Fourier transform ir spectra of human serum albumin secondary structure in the native state and in states denatured by heat and acid treatment. The deconvolution method is based on the use of the Conjugate Gradient Minimization Algorithm, with the addition of suitable constraints directly obtained by the application to the measured spectrum of the second derivative operator. This method computes central band frequency, bandwidth, and amplitude of the different spectral components of conformation-sensitive amide bands. In the specific case, it was applied to analysis of the amide I band, and the quantitative determination of the different secondary structures (alpha-helix, beta-sheet, beta-turns, and random) was attempted for all the samples examined. The precision of the quantitative determination depends on the amounts of these structures present in the protein. The coefficient of variation is < 10% for values of amide I component > 15%. The accuracy was tested by comparing, by means of linear regression, the results obtained for human serum albumin, hemoglobin, alpha-chymotrypsin, and cytochrome c, using our method, with those obtained by x-ray crystallography and CD; the results obtained by other vibrational spectroscopic approaches were also compared. The fit standard error between x-ray and ir secondary structure values estimated by our method is 2.5% for alpha-helix, 7.16% for beta structures, and 5.1% for other structures (turns and random coils). Quantitative results are given for the secondary structures (alpha-helix, turns, and beta-strands) present in the native state (turns and beta-strands up to now unknown in aqueous solution), together with the percentages of these structures and additional ones (random coils and beta-sheets) formed during denaturization.

Algorithms↗
PubMed2003

Simple consensus procedures are effective and sufficient in secondary structure prediction.

We have analyzed the performance of majority voting on minimal combination sets of three state-of-the-art secondary structure prediction methods in order to obtain a consensus prediction. Using three large benchmark sets from the EVA server, our results show a significant improvement in the average Q3 prediction accuracy of up to 1.5 percentage points by consensus formation. The application of an additional trivial filtering procedure for predicted secondary structure elements that are too short, does not significantly affect the prediction accuracy. Our analysis also provides valuable insight into the similarity of the results of the prediction methods that we combine as well as the higher confidence in consistently predicted secondary structure.

Computational Biology↗
PubMed2006

A Consensus Data Mining secondary structure prediction by combining GOR V and Fragment Database Mining.

The major aim of tertiary structure prediction is to obtain protein models with the highest possible accuracy. Fold recognition, homology modeling, and de novo prediction methods typically use predicted secondary structures as input, and all of these methods may significantly benefit from more accurate secondary structure predictions. Although there are many different secondary structure prediction methods available in the literature, their cross-validated prediction accuracy is generally <80%. In order to increase the prediction accuracy, we developed a novel hybrid algorithm called Consensus Data Mining (CDM) that combines our two previous successful methods: (1) Fragment Database Mining (FDM), which exploits the Protein Data Bank structures, and (2) GOR V, which is based on information theory, Bayesian statistics, and multiple sequence alignments (MSA). In CDM, the target sequence is dissected into smaller fragments that are compared with fragments obtained from related sequences in the PDB. For fragments with a sequence identity above a certain sequence identity threshold, the FDM method is applied for the prediction. The remainder of the fragments are predicted by GOR V. The results of the CDM are provided as a function of the upper sequence identities of aligned fragments and the sequence identity threshold. We observe that the value 50% is the optimum sequence identity threshold, and that the accuracy of the CDM method measured by Q(3) ranges from 67.5% to 93.2%, depending on the availability of known structural fragments with sufficiently high sequence identity. As the Protein Data Bank grows, it is anticipated that this consensus method will improve because it will rely more upon the structural fragments.

Algorithms↗
PubMed2000

Secondary structure alone is generally not statistically significant for the detection of noncoding RNAs.

MOTIVATION: Several results in the literature suggest that biologically interesting RNAs have secondary structures that are more stable than expected by chance. Based on these observations, we developed a scanning algorithm for detecting noncoding RNA genes in genome sequences, using a fully probabilistic version of the Zuker minimum-energy folding algorithm. RESULTS: Preliminary results were encouraging, but certain anomalies led us to do a carefully controlled investigation of this class of methods. Ultimately, our results argue that for the probabilistic model there is indeed a statistical effect, but it comes mostly from local base-composition bias and not from RNA secondary structure. For the thermodynamic implementation (which evaluates statistical significance by doing Monte Carlo shuffling in fixed-length sequence windows, thus eliminating the base-composition effect) the signals for noncoding RNAs are still usually indistinguishable from noise, especially when certain statistical artifacts resulting from local base-composition inhomogeneity are taken into account. We conclude that although a distinct, stable secondary structure is undoubtedly important in most noncoding RNAs, the stability of most noncoding RNA secondary structures is not sufficiently different from the predicted stability of a random sequence to be useful as a general genefinding approach.

Algorithms↗
PubMed1997

Secondary structure of T4 gene 33 protein. Fourier transform infrared and circular dichroic spectroscopic studies.

The secondary structure of bacteriophage T4 gene 33 protein (gp33) has been quantitatively examined by using Fourier transform infrared (FT-IR) and circular dichroism (CD) spectroscopy. Resolution enhancement techniques, including Fourier deconvolution and derivative spectroscopy were used to quantitate the spectral information from the amide I bands. The relative areas of these component bands indicate 21% alpha-helix, 25% beta-sheet, 34% turn, 12% random coil and 8% other undefined structures in gp33. An analysis of the CD spectrum of gp33 at the same pH and temperature revealed 19% alpha-helix, 25% beta-sheet, 13% turn and 43% random coil structures. The possible reasons for the discrepancies in estimates of the contributions to the secondary structure from turns and random coils are discussed.

Amino Acid Sequence↗
PubMed1988

An approach to the three-dimensional structure of bovine growth hormone based on chemical modification and secondary structure prediction.

Three different methods have been applied to the prediction of secondary structure. The prediction that better fitted the chemical data was chosen. Two regions of the bovine growth hormone molecule (111-117 and 166-174) appear to be exposed to the solvent, according to hydropathic analysis but have several charged residues not reactive towards their specific reagents. Two molecular domains are postulated, each one bearing a region with charged residues on its surface and interacting with the other in the molecule by means of saline bridges. The hydrophobic core of the molecule is formed by the ensemble of the hydrophobic region predicted between residues 81 and 108, and the hydrophobic faces of the amphiphilic helices 109-127 and 9-33.

Amino Acid Sequence↗