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PubMed2003

Secondary structure prediction with support vector machines.

MOTIVATION: A new method that uses support vector machines (SVMs) to predict protein secondary structure is described and evaluated. The study is designed to develop a reliable prediction method using an alternative technique and to investigate the applicability of SVMs to this type of bioinformatics problem. METHODS: Binary SVMs are trained to discriminate between two structural classes. The binary classifiers are combined in several ways to predict multi-class secondary structure. RESULTS: The average three-state prediction accuracy per protein (Q(3)) is estimated by cross-validation to be 77.07 +/- 0.26% with a segment overlap (Sov) score of 73.32 +/- 0.39%. The SVM performs similarly to the 'state-of-the-art' PSIPRED prediction method on a non-homologous test set of 121 proteins despite being trained on substantially fewer examples. A simple consensus of the SVM, PSIPRED and PROFsec achieves significantly higher prediction accuracy than the individual methods.

Algorithms↗
PubMed2006

Monitoring single-stranded DNA secondary structure formation by determining the topological state of DNA catenanes.

Single-stranded DNA (ssDNA) has essential biological functions during DNA replication, recombination, repair, and transcription. The structure of ssDNA must be better understood to elucidate its functions. However, the available data are too limited to give a clear picture of ssDNA due to the extremely capricious structural features of ssDNA. In this study, by forming DNA catenanes and determining their topology (the linking number, Lk) through the electrophoretic analysis, we demonstrate that the studies of catenanes formed from two ssDNA molecules can yield valuable new information about the ssDNA secondary structure. We construct catenanes out of two short (60/70 nt) ssDNA molecules by enzymatic cyclization of linear oligodeoxynucleotides. The secondary structure formed between the two DNA circles determines the topology (the Lk value) of the constructed DNA catenane. Thus, formation of the secondary structure is experimentally monitored by observing the changes of linking number with sequences and conditions. We found that the secondary structure of ssDNA is much easier to form than expected: the two strands in an internal loop in the folded ssDNA structure prefer to braid around each other rather than stay separately forming a loop, and a duplex containing only mismatched basepairs can form under physiological conditions.

DNA, Catenated↗
PubMed2006

Protein secondary structure controlled with light and photoresponsive surfactants.

The interaction of a light-responsive azobenzene surfactant with bovine serum albumin (BSA) has been investigated as a means to examine photoreversible changes in protein secondary structure. The cationic azobenzene surfactant undergoes a reversible photoisomeriztion upon exposure to the appropriate wavelength of light, with the visible-light (trans) form being more hydrophobic and, thus, inducing a greater degree of protein unfolding than the UV-light (cis) form. Fourier transform infrared (FT-IR) spectroscopy is used to provide quantitative information on the secondary structure elements in the protein (alpha-helices, beta-strands, beta-turns, and unordered domains). Comparing the secondary structure changes induced by light illumination in the presence of the photoresponsive surfactant with previous measurements of the tertiary structure of BSA obtained from small-angle neutron scattering (SANS) allows the three discrete conformation changes in BSA to be fully characterized. At low surfactant concentrations, an alpha-helix --> beta-structure rearrangement is observed as the tertiary structure of BSA changes from a heart-shaped to a distorted heart-shaped conformation. Intermediate surfactant concentrations lead to a dramatic decrease in the alpha-helix fraction in favor of unordered structures, which is accompanied by an unfolding of the C-terminal portion of the protein as evidenced from SANS. Further increases in photosurfactant concentration lead to a beta --> unordered transition with the protein adopting a highly elongated conformation in solution. Each of these protein conformational changes can be precisely and reversibly controlled with light illumination, as revealed through FT-IR spectra collected during repeated visible-light <--> UV-light cycles.

Animals↗
PubMed1997

A set of constructed type spectra for the practical estimation of peptide secondary structure from circular dichroism.

While reliable methods have been developed for the estimation of globular protein secondary structure content from their far UV circular dichroism spectra, these are not suitable for the analysis of simple peptides. Model peptides have been measured in purely alpha-helical, beta-sheet, and coil form, and are often used for fitting the CD spectra of peptides, but these are mainly derived from homopolymers and exhibit side-chain-dependent characteristics that do not accurately represent the situation in natural sequences. We have attempted to reduce the side-chain bias inherent in these spectra by constructing a series of frequency-weighted "average" spectra from all available data on model peptides. These have proved quite satisfactory in estimating the secondary structure of a number of peptides. A computer program incorporating these spectra has been developed for practical use.

Circular Dichroism↗
PubMed1989

Secondary structure of a core protein from pig skin proteodermatan sulfate: CD and Fourier transform IR spectroscopic studies in solution.

The secondary structure of a 38 kDa core protein from pig skin proteodermatan sulfate (PDS), was investigated in solution using CD and Fourier transform (FT) ir spectroscopy. Both techniques generally have provided complementary data on the secondary structures of proteins. CD spectral analysis has shown that the core protein contains 60% beta-turn and alpha-helical structures, the rest being "unordered" structure. FT ir data do not permit calculation of quantitative contributions of substructures, at the present time, to the overall secondary structure of the core protein. CD spectrum of the intact PDS is similar to the core protein CD spectrum.

Animals↗
PubMed1995

A comparison of the secondary structure of human brain mitochondrial and cytosolic 'malic' enzyme investigated by Fourier-transform infrared spectroscopy.

The secondary structure of human brain cytosolic and mitochondrial 'malic' enzymes purified to homogeneity has been investigated by Fourier-transform IR spectroscopy. The absorbance IR spectra of these two isoenzymes were slightly different, but calculated secondary-structure compositions were essentially similar (38% alpha-helix, 38-39% beta-sheet, 14% beta-turn and 9-10% random structure). These proportions were not affected by succinate, a positive effector of mitochondrial 'malic' enzyme activity. IR spectra indicate that the tertiary structures of human brain cytosolic and mitochondrial 'malic' enzymes are slightly different, and addition of succinate does not cause conformational changes to the tertiary structure of the mitochondrial enzyme. Thermal-denaturation patterns of the cytosolic and mitochondrial enzymes, obtained from spectra recorded at different temperatures in the absence or presence of Mg2+, suggest that the tertiary structure of both isoenzymes is stabilized by bivalent cations and that the cytosolic enzyme possesses a more compact tertiary structure.

Brain↗
PubMed1994

Solution 1H NMR determination of secondary structure for the three-iron form of ferredoxin from the hyperthermophilic archaeon Pyrococcus furiosus.

Two-dimensional 1H NMR data have been used to make sequence-specific assignments and define the secondary structure of the three-iron form of the oxidized ferredoxin, Fd, from the hyperthermophilic archaeon Pyrococcus furiosus, Pf. Signals for at least some protons were located for 65 of the 66 amino acids in the sequence, in spite of the paramagnetic (S = 1/2) ground state, but not all could be assigned. Unassigned and missing signals could be qualitatively correlated with the expected proximity of the protons to the paramagnetic cluster. The secondary structure was deduced from qualitative analysis of the 2D nuclear Overhauser effect, which identified two antiparallel beta-sheets, one triple-stranded including Ala1-Ser5, Val39-Glu41, and Thr62-Ala66, and one double-stranded consisting of Glu26-Asn28 and Lys32-Glu34, as well as an alpha-helix involving Glu43-Glu54. Three tight type I turns are located at residues Asp7-Thr10, Pro22-Phe25, and Asp29-Gly31. Comparison with the crystal structure of Desulfovibrio gigas, Dg, Fd (Kissinger et al., 1991) reveals a very similar folding topology, although several secondary structural elements are extended in Pf relative to Dg Fd. Thus the beta-sheet involving the two termini is expanded to include the two terminal residues and incorporates a third strand from the internal loop that is lengthened by several insertions in Pf relative to Dg Fd. The double-stranded beta-sheet in the interior of Pf Fd is lengthened slightly due to a much tighter type I turn between the two strands. The helix near the C-terminus is three residues longer in Pf than in Dg Fd, as well as being shifted toward the N-terminus. The disulfide link between the two nonligating Cys residues (Cys21 and Cys48) is conserved in Pf Fd, but the link near the C-terminus is in the middle of the long alpha-helix in Pf Fd, instead of at the N-terminus of the helix as in Dg Fd. The extensions of the beta-sheets and alpha-helix increase the number of main-chain hydrogen bonds in Pf Fd by approximately 8 relative to those in Dg Fd and likely contribute to its remarkable thermostability (it is unaffected by anaerobic incubation at 95 degrees C for 24 h).(ABSTRACT TRUNCATED AT 400 WORDS)

Amino Acid Sequence↗
PubMed1997

Complete 1H, 13C, and 15N NMR resonance assignments and secondary structure of human glutaredoxin in the fully reduced form.

Human glutaredoxin is a member of the glutaredoxin family, which is characterized by a glutathione binding site and a redox-active dithiol/disulfide in the active site. Unlike Escherichia coli glutaredoxin-1, this protein has additional cysteine residues that have been suggested to play a regulatory role in its activity. Human glutaredoxin (106 amino acid residues, M(r) = 12,000) has been purified from a pET expression vector with both uniform 15N labeling and 13C/15N double labeling. The combination of three-dimensional 15N-edited TOCSY, 15N-edited NOESY, HNCA, HN(CO)CA, and gradient sensitivity-enhanced HNCACB and HNCO spectra were used to obtain sequential assignments for residues 2-106 of the protein. The gradient-enhanced version of the HCCH-TOCSY pulse sequence and HCCH-COSY were used to obtain side chain 1H and 13C assignments. The secondary structural elements in the reduced protein were identified based on NOE information, amide proton exchange data, and chemical shift index data. Human glutaredoxin contains five helices extending approximately from residues 4-10, 24-36, 53-64, 83-92, and 94-104. The secondary structure also shows four beta-strands comprised of residues 15-19, 43-48, 71-75, 78-80, which form a beta-sheet almost identical to that found in E. coli glutaredoxin-1. Complete 1H, 13C, and 15N assignments and the secondary structure of fully reduced human glutaredoxin are presented. Comparison to the structures of other glutaredoxins is presented and differences in the secondary structure elements are discussed.

Amino Acid Sequence↗
PubMed1989

Improved predictions of secondary structures for RNA.

The accuracy of computer predictions of RNA secondary structure from sequence data and free energy parameters has been increased to roughly 70%. Performance is judged by comparison with structures known from phylogenetic analysis. The algorithm also generates suboptimal structures. On average, the best structure within 10% of the lowest free energy contains roughly 90% of phylogenetically known helixes. The algorithm does not include tertiary interactions or pseudoknots and employs a crude model for single-stranded regions. The only favorable interactions are base pairing and stacking of terminal unpaired nucleotides at the ends of helixes. The excellent performance is consistent with these interactions being the primary interactions determining RNA secondary structure.

Base Composition↗
PubMed1988

An improved algorithm for nucleic acid secondary structure display.

An improved algorithm for the display of nucleic acid secondary structures is presented. It is particularly suitable for large sequence segments and it automatically generates an aesthetically pleasing display of the structure with very limited overlap of strands. Structural similarities in different structures are conserved in the display thus greatly aiding structural homology comparisons. Using the algorithm, we illustrate the effect of ribosome translocation on the secondary structure of a rat neuropeptide messenger RNA.

Algorithms↗
PubMed1989

Detection of common motifs in RNA secondary structures.

We describe a novel computerized system for comparison of RNA secondary structures and demonstrate its use for experimental studies. The system is able to screen a very large number of structures, to cluster similar structures and to detect specific structural motifs. In particular, the system is useful for detecting mutations with specific structural effects among all possible point mutations, and for predicting compensatory mutations that will restore the wild type structure. The algorithms are independent of the folding rules that are used to generate the secondary structures.

Algorithms↗
PubMed1999

Quantitation of secondary structure in ATR infrared spectroscopy.

Polarized attenuated total reflection infrared spectroscopy of aligned membranes provides essential information on the secondary structure content and orientation of the associated membrane proteins. Quantitation of the relative content of different secondary structures, however, requires allowance for geometric relations of the electric field components (E(x), E(y), E(z)) of the evanescent wave, and of the components of the infrared transition moments, in combining absorbances (A and A(perpendicular)) measured with radiation polarized parallel with and perpendicular to, respectively, the plane of incidence. This has hitherto not been done. The appropriate combination for exact evaluation of relative integrated absorbances is A + (2E(z)(2)/E(y)(2) - E(x)(2)/E(y)(2))A(perpendicular), where z is the axis of ordering that is normal to the membrane plane, and the x-axis lies in the membrane plane within the plane of incidence. This combination can take values in the range approximately from A - 0.4A(perpendicular) to A + 2.7A(perpendicular), depending on experimental conditions and the attenuated total reflection crystal used. With unpolarized radiation, this correction is not possible. Similar considerations apply to the dichroic ratios of multicomponent bands, which are also treated.

Animals↗
PubMed1997

Improvement of protein secondary structure prediction using binary word encoding.

We propose a binary word encoding to improve the protein secondary structure prediction. A binary word encoding encodes a local amino acid sequence to a binary word, which consists of 0 or 1. We use an encoding function to map an amino acid to 0 or 1. Using the binary word encoding, we can statistically extract the multiresidue information, which depends on more than one residue. We combine the binary word encoding with the GOR method, its modified version, which shows better accuracy, and the neural network method. The binary word encoding improves the accuracy of GOR by 2.8%. We obtain similar improvement when we combine this with the modified GOR method and the neural network method. When we use multiple sequence alignment data, the binary word encoding similarly improves the accuracy. The accuracy of our best combined method is 68.2%. In this paper, we only show improvement of the GOR and neural network method, we cannot say that the encoding improves the other methods. But the improvement by the encoding suggests that the multiresidue interaction affects the formation of secondary structure. In addition, we find that the optimal encoding function obtained by the simulated annealing method relates to nonpolarity. This means that nonpolarity is important to the multiresidue interaction.

Amino Acid Sequence↗
PubMed2003

3'-Terminal RNA secondary structures are important for accumulation of tomato bushy stunt virus DI RNAs.

The plus-strand RNA genome of tomato bushy stunt virus (TBSV) contains a 351-nucleotide (nt)-long 3'-untranslated region. We investigated the role of the 3'-proximal 130 nt of this sequence in viral RNA accumulation within the context of a TBSV defective interfering (DI) RNA. Sequence comparisons between different tombusviruses revealed that the 3' portion of the 130-nt sequence is highly conserved and deletion analysis confirmed that this segment is required for accumulation of DI RNAs in protoplasts. Computer-aided sequence analysis and in vitro solution structure probing indicated that the conserved sequence consists of three stem-loop (SL) structures (5'-SL3-SL2-SL1-3'). The existence of SLs 1 and 3 was also supported by comparative secondary structure analysis of sequenced tombusvirus genomes. Formation of the stem regions in all three SLs was found to be very important, and modification of the terminal loop sequences of SL1 and SL2, but not SL3, decreased DI RNA accumulation in vivo. For SL3, alterations to an internal loop resulted in significantly reduced DI RNA levels. Collectively, these data indicate that all three SLs are functionally relevant and contribute substantially to DI RNA accumulation. In addition, secondary structure analysis of other tombusvirus replicons and related virus genera revealed that a TBSV satellite RNA and members of the closely related genus Aureusvirus (family Tombusviridae) share fundamental elements of this general structural arrangement. Thus, this secondary structure model appears to extend beyond tombusvirus genomes. These conserved 3'-terminal RNA elements likely function in vivo by promoting and/or regulating minus-strand synthesis.

3' Untranslated Regions↗
PubMed1994

Native disulfide bonds greatly accelerate secondary structure formation in the folding of lysozyme.

To assess the respective roles of local and long-range interactions during protein folding, the influence of the native disulfide bonds on the early formation of secondary structure was investigated using continuous-flow circular dichroism. Within the first 4 ms of folding, lysozyme with intact disulfide bonds already had a far-UV CD spectrum reflecting large amounts of secondary structure. Conversely, reduced lysozyme remained essentially unfolded at this early folding time. Thus, native disulfide bonds not only stabilize the cfinal conformation of lysozyme but also provide, in early folding intermediates, the necessary stabilization that favors the formation of secondary structure.

Circular Dichroism↗
PubMed1995

Ribonuclease A revisited: infrared spectroscopic evidence for lack of native-like secondary structures in the thermally denatured state.

To address a number of conflicting reports in the literature, we undertook an infrared spectroscopic study to test for the presence of native-like secondary structures in thermally denatured ribonuclease A. Ribonuclease A does not aggregate at high temperatures, and the infrared spectrum shows a completely featureless amide I band contour. Using 13C-labeled urea, we were also able to obtain the infrared spectrum of the chemically denatured protein, which is practically identical with that of the heat-denatured protein. To the best of our knowledge, this is the first study that uses 13C-labeled urea as a chemical denaturant which circumvents the problem encountered with the strong absorption of urea in the conformation-sensitive amide I region of proteins; it opens up the possibility of investigating protein folding/unfolding processes in the presence of high concentrations of chemical denaturants. From an analysis of the amide I region of the infrared spectra of thermally and chemically denatured RNase A, it was concluded that heat-denatured ribonuclease A does not contain any significant amount of authentic hydrogen-bonded secondary structures. Furthermore, a comparison of the infrared spectra of ribonuclease A with those of ribonuclease T1 demonstrates that in spite of major differences between their native structures there are practically no differences between their heat-denatured states. This would not be expected if there were residual native-like secondary structures in the thermally denatured state of one or both of these proteins.

Carbon Isotopes↗
PubMed1994

1H-NMR assignments and secondary structure of human plasminogen kringle 1.

The 1H-NMR spectrum of the kringle 1 domain of human plasminogen complexed with 6-aminohexanoic acid, an antifibrinolytic drug, has been assigned. Elements of secondary structure have been identified on the basis of sequential, medium and long-range dipolar interactions, back-bone amide spin-spin couplings (3JHN-H alpha) and 1H-2H exchange rates. The kringle contains scarcely any repetitive secondary structure: eight reverse turns and two short beta-sheets. These comprise 40% and 12% of the domain, respectively. No alpha-helix was found. An aromatic cluster formed by His31, Phe36, Trp62, Phe64, Tyr72 and Tyr74 is indicated by several inter-residue Overhauser connectivities. Contacts between the methyl groups of Leu46 and the side chains of Phe36, Trp62 and Trp25 are observed. A second hydrophobic cluster formed by Tyr9, Ile77 and Leu78 is also indicated. A comparison of secondary structure elements among plasminogen kringles 1 and 4 and tissue-type plasminogen activator kringle 2 suggests that there is variability in the position and number of reverse turns on going from one kringle to another; however, the beta-sheets are conserved among the homologs.

Amino Acid Sequence↗
PubMed2006

Improved performance in protein secondary structure prediction by combining multiple predictions.

In this paper(1) we present a novel framework for protein secondary structure prediction. In this prediction framework, firstly we propose a novel parameterized semi-probability profile, which combines single sequence with evolutionary information effectively. Secondly, different semi-probability profiles are respectively applied as network input to predict protein secondary structure. Then a comparison among these different predictions is discussed in this article. Finally, naïve Bayes approaches are used to combine these predictions in order to obtain a better prediction performance than individual prediction. The experimental results show that our proposed framework can indeed improve the prediction accuracy.

Algorithms↗