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Results for “Secondary structure”

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At least 145 records · Page 8Linked to original sources
PubMed1976

Secondary structure of ovalbumin messenger RNA.

The secondary structure of highly purified ovalbumin mRNA was studied by automated thermal denaturation techniques and the data were subjected to computer processing. Comparative studies with 20 natural and synthetic model nucleic acids suggested that the secondary structure of ovalbumin mRNA possesses the following features: the extent of base pairing of ovalbumin mRNA is similar to that found in tRNAs or ribosomal RNAs; the secondary structure of ovalbumin mRNA is more thermolabile than any of the model compounds tested, including the copolymer poly(A-U); ovalbumin mRNA does not have extensive G-C rich stems as found in tRNAs or ribosomal RNAs; the base composition of the double-stranded regions reveals 54% G-C residues which was significantly higher than that noted in the whole molecule (approximately 41.5% G-C). The presence of 46% A-U pairs in short stems of about five base pairs would have a very large destabilizing effect on the secondary structure of ovalbumin mRNA. However, at 0.175 M monovalent cations and 36 degrees C most of the secondary structure of ovalbumin mRNA is preserved. These data suggest that the double-stranded regions in ovalbumin mRNA are of sufficient length to provide the necessary stability for maintaining the open loop regions in an appropriate conformation which may be required for the biological function of ovalbumin mRNA. Furthermore, the lability of the double-stranded regions in ovalbumin mRNA may also be important for the biological function of this mRNA.

Base Sequence↗
PubMed1996

Prediction of the secondary structure of HIV-1 gp120.

The secondary structure of HIV-1 gp120 was predicted using multiple alignment and a combination of two independent methods based on neural network and nearest-neighbor algorithms. The methods agreed on the secondary structure for 80% of the residues in BH10 gp120. Six helices were predicted in HIV strain BH10 gp120, as well as in 27 other HIV-1 strains examined. Two helical segments were predicted in regions displaying profound sequence variation, one in a region suggested to be critical for CD4 binding. The predicted content of helix, beta-strand, and coil was consistent with estimates from Fourier transform infrared spectroscopy. The predicted secondary structure of gp120 compared well with data from NMR analysis of synthetic peptides from the V3 loop and the C4 region. As a first step towards modeling the tertiary structure of gp120, the predicted secondary structure may guide the design of future HIV subunit vaccine candidates.

Algorithms↗
PubMed2006

Organophosphorus hydrolase at the air-water interface: secondary structure and interaction with paraoxon.

The secondary structure of organophosphorus hydrolase (OPH) at the air-water interface was studied using polarization modulation infrared reflection absorption spectroscopy (PM-IRRAS). The shape and position of the amide I and amide II bands were used to estimate the surface conformation and orientation of OPH. The PM-IRRAS results indicated that the enzyme did not unfold for the range of surface pressure used (0-30 mN/m). At low surface pressures, the signal of amide I was very weak and the intensity was almost the same as amide II. Upon further compression, the PM-IRRAS signal and the ratio of the intensity of amide I and amide II both increase, implying an increased interfacial concentration of the enzyme. From the amide I/amide II ratio and the band position, it was deduced that the enzyme adopts a conformation which gives a higher occupied surface at low surface pressure and rotates to a more vertical orientation at high surface pressures. The compression and decompression of the OPH monolayer indicated that the fingerprint of the secondary structure at the air-water interface was reversible. PM-IRRAS was also used to investigate the pH effect of the subphase on the secondary structure of OPH. The secondary structure of OPH at the air-water interface was well defined when the pH of the subphase was near its isoelectric point (IP, pH 7.6). However, it adopted a different orientation when the subphase pH values were higher or lower than the IP with formation of random coil structure. The hydrolysis of organophosphorus compound paraoxon by OPH was also studied at the air-water interface by PM-IRRAS. The pH effect and the interaction with paraoxon both seem to orientate the enzyme more in the plane of the interface and to produce random coil structure.

Air↗
PubMed1999

Human pancreatic thread protein, an exocrine thread protein with possible implications to Alzheimer's disease: secondary structure in solution at acid pH.

The secondary structure of human pancreatic thread protein (HPTP) in solution at acid pH was derived using Fourier transform infrared (FT-IR) and laser Raman spectroscopic studies. The experimentally derived secondary structure of HPTP was compared with the secondary structure obtained by the Chou-Fasman algorithm. Pancreatic thread protein is a major exocrine secretory protein that in vitro forms filamentous bundles reminiscent of the paired helical filaments of Alzheimer's disease (AD). PTP immunoreactivity in brains afflicted with AD has been demonstrated previously and high levels of its mRNA in the developing human brain have also been reported in the literature. The above studies suggest that AD is associated with enhanced expression of PTP-related transcripts with interneuronal accumulation of PTP-like proteins. The experimentally derived secondary structure of HPTP consists of a significant proportion of beta-sheets and beta-turns and lesser amounts of alpha-helical structures. The beta-sheet component presumably plays an important role in the pH-dependent globule-fibril transformation of HPTP leading to antiparallel beta-sheet structure in the aggregated state. The secondary structure of HPTP and its globule-fibril transformation lend credence to the belief that AD may be viewed as a conformational disease.

Algorithms↗
PubMed2000

Effects of fluorescent pseudo-ATP and ATP-metal analogs on secondary structure of Na(+)/K(+)-ATPase.

The secondary structure of Na(+)/K(+)-ATPase after modification of the ATP-binding sites was analyzed. Consistently with recent reports, we found in trypsin-treated Na(+)/K(+)-ATPase additionally to alpha-helix also beta-sheet structures in the transmembrane segments. However, binding of fluorescein 5'-isothiocyanate (FITC), the pseudo-ATP analog, to the ATP-binding site did not affect the secondary structure of undigested Na(+)/K(+)-ATPase. Consequently, fluorescence intensity changes of FITC-labeled Na(+)/K(+)-ATPase commonly used to observe conformational transitions of the enzyme reflect physiological changes of the native structure. The metal complex analogues of ATP, Cr(H(2)O)(4)ATP and Co(NH(3))(4)ATP, on the other hand, affected the secondary structure of Na(+)/K(+)-ATPase. We propose that these changes in the secondary structure are responsible for inhibition of backdoor phosphorylation.

Adenosine Triphosphate↗
PubMedDate not supplied

[Secondary structure of histones in solution].

The secondary structure of histones H2B and H3 from calf thymus has been quantitatively studied in heavy water solutions in a wide range of histone concentrations, pD, and concentrations of sodium chloride by an infrared spectroscopy method. Also, the interactions between molecules of different histones in equimolar mixtures H2A-H2B, H2A-H3, H2A-H4, H2B-H3, H2B-H4, H3-H4, and H2A-H2B-H3-H4 have been investigated using the same method. For H2B and H3 conditions favourable for aggregation have been shown to induce the formation of pleated sheet structure. When the pD and concentration of NaCl are in a physiological range, the secondary structure of H2B and H3 contains about 15% of alpha-helix, 4% of parallel pleated sheet structure, 14% of antipatallel pleated sheet structure in H2B and 18% in H3. For mixtures in all cases, except H2A-H4, there is an interaction between molecules of different histones followed by a reduction of the antiparallel pleated sheet structure content. The data on the secondary structure of histones in different states (under self-association, in mixtures, in nucleosomes, and in chromatin) have been discussed and it is suggested that: 1) the secondary structure of histones in chromatin is essentially similar to that in the state of self-association; 2) in the core nucleosome particle the quantity of DNA (in nucleotide pairs), and the quantities of alpha-helix and antiparallel pleated sheet structure (in peptide groups) satisfy the relation 1 : 1 : 1.

Animals↗
PubMed1988

A study of the structure of human complement component factor H by Fourier transform infrared spectroscopy and secondary structure averaging methods.

Fourier transform infrared spectroscopy was used to investigate the secondary structure of human complement component factor H in H2O and 2H2O buffers. The spectra show a broad amide I band which after second-derivative calculations is shown to be composed of three components at 1645, 1663, and 1685 cm-1 in H2O and at 1638, 1661, and 1680 cm-1 in 2H2O. The frequencies of these components are consistent with the existence of an extensive antiparallel beta-strand secondary structure. The exchange properties of the amide protons of factor H as measured in 2H2O buffers are rapid and lead to an estimate of NH proton nonexchange that is comparable with those for small globular proteins. Human factor H is constructed from a linear sequence of 20 short consensus repeats with a mean of 61 residues in each one. To investigate the secondary structure further, secondary structure predictions were carried out on the basis of an alignment scheme for 101 sequences for these repeats as found in human factor H and 12 other proteins. These predictions were averaged in order to improve the reliability of the calculations. Both the Robson and the Chou-Fasman methods indicate significant beta-structural contents. Residues 21-51 in the 61-residue repeat show a clear prediction of four strands of beta-structure and four beta-turns. A structural model based on antiparallel beta-strands in the secondary structure is proposed and discussed.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗
PubMedDate not supplied

Bayesian segmentation of protein secondary structure.

We present a novel method for predicting the secondary structure of a protein from its amino acid sequence. Most existing methods predict each position in turn based on a local window of residues, sliding this window along the length of the sequence. In contrast, we develop a probabilistic model of protein sequence/structure relationships in terms of structural segments, and formulate secondary structure prediction as a general Bayesian inference problem. A distinctive feature of our approach is the ability to develop explicit probabilistic models for alpha-helices, beta-strands, and other classes of secondary structure, incorporating experimentally and empirically observed aspects of protein structure such as helical capping signals, side chain correlations, and segment length distributions. Our model is Markovian in the segments, permitting efficient exact calculation of the posterior probability distribution over all possible segmentations of the sequence using dynamic programming. The optimal segmentation is computed and compared to a predictor based on marginal posterior modes, and the latter is shown to provide significant improvement in predictive accuracy. The marginalization procedure provides exact secondary structure probabilities at each sequence position, which are shown to be reliable estimates of prediction uncertainty. We apply this model to a database of 452 nonhomologous structures, achieving accuracies as high as the best currently available methods. We conclude by discussing an extension of this framework to model nonlocal interactions in protein structures, providing a possible direction for future improvements in secondary structure prediction accuracy.

Algorithms↗
PubMed1995

Conserved alternative splicing in the 5'-untranslated region of the muscle-specific enolase gene. Primary structure of mRNAs, expression and influence of secondary structure on the translation efficiency.

We report here the isolation and characterization of cDNAs covering the 5'-end region of mouse and rat mRNAs that encode the beta or muscle-specific isoform of the glycolytic enzyme enolase. As previously determined for humans, two classes of beta-enolase transcripts with distinct sequences in their 5'-untranslated regions are present in both mouse and rat muscles. A mechanism of alternative splicing, conserved from mouse to man, generates the two forms of mRNA. Secondary-structure predictions indicated that, in all cases, a more stable secondary structure could exist in the 5' end of the message with the longer leader. In vitro transcripts containing defined human or mouse 5'-untranslated sequences were obtained by fusion of the different cDNA clones and tested for their relative translational efficiencies in rabbit reticulocyte lysates. Transcripts containing the human long and short leader sequences showed differences in the translational rate, suggesting a role for the 5'-untranslated region in the regulation of translation. No detectable difference was found between transcripts with the two distinct mouse leader sequences. In addition, both transcripts are bound to polysomes and are equally distributed along differently sized polysomes in C2C12 myogenic cells. The relative expression of the two spliced forms in developing and adult muscle tissues by means of reverse transcription and polymerase chain reaction did not show a stage-specific or a tissue-type-specific pattern. A putative functional role for the 5'-untranslated sequences of beta-enolase transcripts is discussed.

Alternative Splicing↗
PubMed2002

Thermal folding and mechanical unfolding pathways of protein secondary structures.

Mechanical stretching of secondary structures is studied through molecular dynamics simulations of a Go-like model. Force versus displacement curves are studied as a function of the stiffness and velocity of the pulling device. The succession of stretching events, as measured by the order in which contacts are ruptured, is compared to the sequencing of events during thermal folding and unfolding. Opposite cross-correlations are found for an alpha-helix and a beta-hairpin structure. In a tandem of two alpha-helices, the two constituent helices unravel nearly simultaneously. A simple condition for simultaneous versus sequential unraveling of repeat units is presented.

Computer Simulation↗
PubMed2000

Prediction of protein secondary structure at 80% accuracy.

Secondary structure prediction involving up to 800 neural network predictions has been developed, by use of novel methods such as output expansion and a unique balloting procedure. An overall performance of 77.2%-80.2% (77.9%-80.6% mean per-chain) for three-state (helix, strand, coil) prediction was obtained when evaluated on a commonly used set of 126 protein chains. The method uses profiles made by position-specific scoring matrices as input, while at the output level it predicts on three consecutive residues simultaneously. The predictions arise from tenfold, cross validated training and testing of 1032 protein sequences, using a scheme with primary structure neural networks followed by structure filtering neural networks. With respect to blind prediction, this work is preliminary and awaits evaluation by CASP4.

Neural Networks, Computer↗
PubMed2000

Refinement of modelled structures by knowledge-based energy profiles and secondary structure prediction: application to the human procarboxypeptidase A2.

Knowledge-based energy profiles combined with secondary structure prediction have been applied to molecular modelling refinement. To check the procedure, three different models of human procarboxypeptidase A2 (hPCPA2) have been built using the 3D structures of procarboxypeptidase A1 (pPCPA1) and bovine procarboxypeptidase A (bPCPA) as templates. The results of the refinement can be tested against the X-ray structure of hPCPA2 which has been recently determined. Regions miss-modelled in the activation segment of hPCPA2 were detected by means of pseudo-energies using Prosa II and modified afterwards according to the secondary structure prediction. Moreover, models obtained by automated methods as COMPOSER, MODELLER and distance restraints have also been compared, where it was found possible to find out the best model by means of pseudo-energies. Two general conclusions can be elicited from this work: (1) on a given set of putative models it is possible to distinguish among them the one closest to the crystallographic structure, and (2) within a given structure it is possible to find by means of pseudo-energies those regions that have been defectively modelled.

Amino Acid Sequence↗
PubMed1995

Neural networks for secondary structure and structural class predictions.

A pair of neural network-based algorithms is presented for predicting the tertiary structural class and the secondary structure of proteins. Each algorithm realizes improvements in accuracy based on information provided by the other. Structural class prediction of proteins nonhomologous to any in the training set is improved significantly, from 62.3% to 73.9%, and secondary structure prediction accuracy improves slightly, from 62.26% to 62.64%. A number of aspects of neural network optimization and testing are examined. They include network overtraining and an output filter based on a rolling average. Secondary structure prediction results vary greatly depending on the particular proteins chosen for the training and test sets; consequently, an appropriate measure of accuracy reflects the more unbiased approach of "jackknife" cross-validation (testing each protein in the data-base individually).

Algorithms↗
PubMed1994

Evaluating predictions of secondary structure in proteins.

To learn how secondary structure assignments diverge during divergent evolution, pairs of proteins with solved crystal structures were aligned and their assignments compared as a function of evolutionary distance. Residues assigned in one structure to a helix or a strand are frequently paired with residues assigned in the other to a coil. However, residues assigned to a helix in one structure are almost never paired with residues assigned to a strand in the other. This suggests additional limitations to the "three state residue-by-residue" score commonly used to evaluate secondary structure predictions and suggests recommendations for how secondary structure predictions should be scored to assess accurately their value as starting points for modelling tertiary structure.

Biological Evolution↗
PubMed1989

Evolution of large subunit rRNA structure. The 3' terminal domain contains elements of secondary structure specific to major phylogenetic groups.

Refined secondary structure models supported by phylogenetic evidence have been derived for the 3' terminal domain of large subunit rRNA (the region that exists as a separate 4.5 S molecular entity in chloroplast ribosomes) through a comparative analysis of all the pro- and eukaryotic sequences at present available. While several universally conserved features of secondary structure are found, a few diversified structural elements are also detected which are specific to one of the primary kingdoms, eubacteria, archaebacteria, or eukaryotes. Remarkably, some appear to be selectively preserved during the evolution of the primary kindgom, suggesting they represent functionally important structures. Thus, although the role of this 3' terminal domain in ribosomal function still remains unknown, its mode of sequence variation clearly points to a significant diversification of its function among the primary kindgoms.

Animals↗
PubMed2026

UFold-X: an enhanced Dual & Dynamic U-Mamba model for long-range RNA secondary structure prediction.

RNA secondary structure is essential for understanding the functions of non-coding RNAs, ribosomal RNAs, and viral genomes. However, accurate prediction of long RNA structures remains challenging due to complex long-range interactions and the limited availability of long-RNA training data. We present UFold-X, a dual-branch deep learning framework that combines a convolutional encoder for local structure modeling with a Mamba-based Visual State Space Module for capturing long-range dependencies. A dynamic gating mechanism adaptively integrates the two branches according to sequence length. UFold-X was evaluated on multiple benchmark datasets containing RNAs up to 5000 nucleotides. To rigorously assess generalization, we introduced a cross-clan benchmark for long RNAs. Under this stringent setting, UFold-X achieved performance comparable to state-of-the-art classical approaches while achieving the best performance among deep learning-based methods. Additional cross-family and within-family evaluations further demonstrated robust transferability and competitive predictive performance. UFold-X also maintained excellent computational efficiency, requiring only 0.08 s per sequence on average. To assess biological consistency, we developed a SHAPE-based reactivity prediction variant (UFold-X-R) and an integrated metric, the Hybrid Reactivity-Pairing Score (HRPS). UFold-X-R showed strong agreement with experimental icSHAPE data and achieved the highest HRPS among all evaluated methods. A user-friendly web server is available at https://ufold-x.ai4bread.com.

Nucleic Acid Conformation↗
PubMed2004

Identifying good predictions of RNA secondary structure.

Predicting the secondary structure of RNA molecules from the knowledge of the primary structure (the sequence of bases) is still a challenging task. There are algorithms that provide good results e.g. based on the search for an energetic optimal configuration. However the output of such algorithms does not always give the real folding of the molecule and therefore a feature to judge the reliability of the prediction would be appreciated. In this paper we present results on the expected structural behavior of LSU rRNA derived using a stochastic context-free grammar and generating functions. We show how these results can be used to judge the predictions made for LSU rRNA by any algorithm. In this way it will be possible to identify those predictions which are close to the natural folding of the molecule with a probability of 97% of success.

Algorithms↗
PubMed1997

Availability of a second upstream AUG can completely overcome inhibition of protein synthesis initiation engendered by mRNA secondary structure encompassing the start codon.

Secondary structure analysis of the mRNA from a nonproductive construct carrying the nonstructural gene 3 (NS3) of Japanese Encephalitis Virus revealed the presence of a potential 28 nucleotide long stem and loop beginning with the guanine of the initiation codon AUG that had a calculated stabilization energy of -13 kcal/mol (delta Gfzero). Provision of an additional AUG along with three codons upstream resulted in complete relief of inhibition. N-terminal amino acid sequence of the recombinant protein was consistent with initiation of protein synthesis having occurred from the upstream AUG. Similar levels of NS3 specific RNA in E. coli cells carrying the expressing and nonexpressing constructs and restoration of recombinant protein expression following deletion of segments beginning with the stem and loop confirmed the role of this structure in blocking expression at the level of translation initiation. Our approach exploits the ability of a ribosome in motion to open up downstream secondary structural elements of considerable stability and represents a novel and widely applicable strategy to overcome a block in translation initiation caused by mRNA secondary structure around the translation start site.

Amino Acid Sequence↗