SEARCH · Search PubMed

Results for “Secondary structure”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

SourceResearch connectionFrom yearThrough year

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 829 records · Page 46Linked to original sources

PubMed2001

Secondary structure prediction and structure-specific sequence analysis of single-stranded DNA.

DNA sequence analysis by oligonucleotide binding is often affected by interference with the secondary structure of the target DNA. Here we describe an approach that improves DNA secondary structure prediction by combining enzymatic probing of DNA by structure-specific 5'-nucleases with an energy minimization algorithm that utilizes the 5'-nuclease cleavage sites as constraints. The method can identify structural differences between two DNA molecules caused by minor sequence variations such as a single nucleotide mutation. It also demonstrates the existence of long-range interactions between DNA regions separated by >300 nt and the formation of multiple alternative structures by a 244 nt DNA molecule. The differences in the secondary structure of DNA molecules revealed by 5'-nuclease probing were used to design structure-specific probes for mutation discrimination that target the regions of structural, rather than sequence, differences. We also demonstrate the performance of structure-specific 'bridge' probes complementary to non-contiguous regions of the target molecule. The structure-specific probes do not require the high stringency binding conditions necessary for methods based on mismatch formation and permit mutation detection at temperatures from 4 to 37 degrees C. Structure-specific sequence analysis is applied for mutation detection in the Mycobacterium tuberculosis katG gene and for genotyping of the hepatitis C virus.

5' Untranslated Regions↗

PubMed1994

Secondary structure of the ETS domain places murine Ets-1 in the superfamily of winged helix-turn-helix DNA-binding proteins.

The members of the ets gene family of transcription factors are characterized by a conserved 85-residue DNA-binding region, termed the ETS domain, that lacks sequence homology to structurally characterized DNA-binding motifs. The secondary structure of the ETS domain of murine Ets-1 was determined on the basis of NMR chemical shifts, NOE and J-coupling constraints, amide hydrogen exchange, circular dichroism, and FT-IR spectroscopy. The ETS domain is composed of three alpha-helices (H) and four beta-strands (S) arranged in the order H1-S1-S2-H2-H3-S3-S4. The four-stranded antiparallel beta-sheet is the scaffold for a putative helix-turn-helix DNA recognition motif formed by helices 2 and 3. The 25 residues extending beyond the ETS domain to the native C-terminus of the truncated Ets-1 also contain a helical segment. On the basis of the similarity of this topology with that of catabolite activator protein (CAP), heat shock factor (HSF), and hepatocyte nuclear factor (HNF-3 gamma), we propose that ets proteins are members of the superfamily of winged helix-turn-helix DNA-binding proteins.

Amino Acid Sequence↗

PubMed2001

Dihedral psi angle dependence of the amide III vibration: a uniquely sensitive UV resonance Raman secondary structural probe.

UV resonance Raman studies of peptide and protein secondary structure demonstrate an extraordinary sensitivity of the amide III (Am III) vibration and the C(alpha)H bending vibration to the amide backbone conformation. We demonstrate that this sensitivity results from a Ramachandran dihedral psi angle dependent coupling of the amide N-H motion to (C)C(alpha)H motion, which results in a psi dependent mixing of the Am III and the (C)C(alpha)H bending motions. The vibrations are intimately mixed at psi approximately 120 degrees, which is associated with both the beta-sheet conformation and random coil conformations. In contrast, these motions are essentially unmixed for the alpha-helix conformation where psi approximately -60 degrees. Theoretical calculations demonstrate a sinusoidal dependence of this mixing on the psi angle and a linear dependence on the distance separating the N-H and (C)C(alpha)H hydrogens. Our results explain the Am III frequency dependence on conformation as well as the resonance Raman enhancement mechanism for the (C)C(alpha)H bending UV Raman band. These results may in the future help us extract amide psi angles from measured UV resonance Raman spectra.

Amides↗

PubMed1997

SS3D-P2: a three dimensional substructure search program for protein motifs based on secondary structure elements.

This paper discusses the implementation of a three-dimensional (3D) structure motif search of proteins. Each protein structure is represented by a set of secondary structure elements (SSEs) which involves alpha-helix segments and beta-strand segments. In describing it, every SSE is further reduced into a two-node graph that consists of the starting amino acid residue, the ending residue and a pseudo-bond between them. The searching algorithm is based on a graph theoretical clique-finding algorithm that has been used for 3D substructure searching in small organic molecules. The program SS3D-P2 was validated using proteins that have well-known 3D motifs, and it correctly found the Greek key motif within an eye lens protein, crystallin, that consists of four anti-parallel beta strands. The program was also successfully applied to searching for the more complex 3D motif, TIM-type beta-barrel motif, with a protein structure database from the Protein Data Bank.

Algorithms↗

PubMed2004

Porter: a new, accurate server for protein secondary structure prediction.

UNLABELLED: Porter is a new system for protein secondary structure prediction in three classes. Porter relies on bidirectional recurrent neural networks with shortcut connections, accurate coding of input profiles obtained from multiple sequence alignments, second stage filtering by recurrent neural networks, incorporation of long range information and large-scale ensembles of predictors. Porter's accuracy, tested by rigorous 5-fold cross-validation on a large set of proteins, exceeds 79%, significantly above a copy of the state-of-the-art SSpro server, better than any system published to date. AVAILABILITY: Porter is available as a public web server at http://distill.ucd.ie/porter/ CONTACT: gianluca.pollastri@ucd.ie.

Algorithms↗

PubMed1995

Comparison of spatial arrangements of secondary structural elements in proteins.

We have developed a new method of protein structure comparison based on spatial arrangements of secondary structural elements (SSEs). Each SSE is represented by a single vector, and common spatial arrangements of vectors in a pair of proteins are detected. The method allows not only insertions and deletions of SSEs, but also topological permutations. It has a flexible target function that can be adjusted depending upon particular levels or definitions of structural similarity, and it is fast enough to allow structural comparisons for many pairs of proteins. The parameters for the target function are determined based on distributions of the geometrical variables for the spatial arrangements of the equivalent SSEs in well-known structural motifs. The obtained parameter set is tuned for detecting relatively strong structural similarity. We report several tests on examples including comparisons of known structural similarity and database searches for a target structure, and examine the results when this parameter set is used for the comparison of distantly related structures.

Alcohol Dehydrogenase↗

PubMed2004

Clustering of amino acids for protein secondary structure prediction.

Simple hidden Markov models are proposed for predicting secondary structure of a protein from its amino acid sequence. Since the length of protein conformation segments varies in a narrow range, we ignore the duration effect of length distribution, and focus on inclusion of short range correlations of residues and of conformation states in the models. Conformation-independent and -dependent amino acid coarse-graining schemes are designed for the models by means of proper mutual information. We compare models of different level of complexity, and establish a practical model with a high prediction accuracy.

Algorithms↗

PubMedDate not supplied

Heat-induced changes in the photochemical centres and the protein secondary structures of photosystem II studied by variable fluorescence and difference FT-IR spectroscopy.

Variable fluorescence (Fv), i.e., Fv = Fm-Fo where Fo is the minimal fluorescence and Fm the maximum fluorescence, and difference Fourier transform infrared (FT-IR) spectroscopy were used to study the effect of heat stress in the 25-55 degrees C range on photosystem II (PSII) structure and function. First, the Fv intensity reflects accurately the changes in the number of open photochemical centers in PSII. Secondly, the use of Fv in combination with FT-IR spectroscopy can disclose structure-function correlations in the heat inactivation of the PSII complex. Analysis of the midpoint temperatures of thermal denaturation, i.e., 50% inactivation, reported so far in investigations of the thylakoid membrane components has revealed that most of the thermal transitions attributed to PSII are in the 39-46 degrees C range. In this work, it is shown specifically that the midpoint temperature of PSII inactivation is at about 40 degrees C. Moreover, it was clearly demonstrated that the heat-induced changes above 40 degrees C are the result of a marked decrease in the number of open photochemical centers in PSII. It was also seen that above this same temperature the loss of photochemical centers has its structural counterpart in overall modifications of the secondary structures of the PSII proteins resulting from the decrease in the alpha-helix content concomitant with the increase in extended chain (beta-strand) conformations. In brief, a novel finding reported here is that the number of open photochemical centers in PSII is dependent on a dynamic equilibrium between the contents of the PSII proteins in alpha-helix and extended chains (beta-strands), but not in beta-sheets and beta-turn structures except for the antiparallel-beta-sheet conformations. This therefore associates the thermal inactivation of the photochemical centers in photosystem II with distinct conformational changes in the proteins of the PSII supramolecular complex. In the particular context of the present study, these findings constitute a significant contribution to the investigation of structure-function correlations in the photosynthetic membrane. In a broader context, this information might be essential for the comprehension of the molecular arrangements or local structure order that are involved directly or indirectly in biological catalysis.

Pisum sativum↗

PubMed1990

Kinetic assembling of the biologically active secondary structure for CAR, the target sequence for the Rev protein of HIV-1.

We predict the metastable secondary structure for the CAR (cis anti-repressor sequence) which is active in the regulation of the interaction with the Rev protein of HIV-1. We prove that the active structure sustained between nts 7364 and 7559 of the env RNA is the most probable metastable structure whose formation is kinetically governed and not thermodynamically determined. The structure is obtained by means of a Monte Carlo simulation which computes refolding events which occur as the CAR portion of the viral RNA is being assembled. Thus, the regulatory role of the secondary structure is determined as soon as the new RNA has been synthesized and it is preserved for further recognition by the Rev protein. In analogy with previous work by the author, it is shown that the destabilization by site-directed mutagenesis of the secondary structure for a non-chain-specific recognition site enhances the Rev response.

Base Sequence↗

PubMed2003

Local secondary structure content predicts folding rates for simple, two-state proteins.

Many single-domain proteins exhibit two-state folding kinetics, with folding rates that span more than six orders of magnitude. A quantity of much recent interest for such proteins is their contact order, the average separation in sequence between contacting residue pairs. Numerous studies have reached the surprising conclusion that contact order is well-correlated with the logarithm of the folding rate for these small, well-characterized molecules. Here, we investigate the physico-chemical basis for this finding by asking whether contact order is actually a composite number that measures the fraction of local secondary structure in the protein; viz. turns, helices, and hairpins. To pursue this question, we calculated the secondary structure content for 24 two-state proteins and obtained coefficients that predict their folding rates. The predicted rates correlate strongly with experimentally determined rates, comparable to the correlation with contact order. Further, these predicted folding rates are correlated strongly with contact order. Our results suggest that the folding rate of two-state proteins is a function of their local secondary structure content, consistent with the hierarchic model of protein folding. Accordingly, it should be possible to utilize secondary structure prediction methods to predict folding rates from sequence alone.

Kinetics↗

PubMed1997

Prediction of protein secondary structure using the 3D-1D compatibility algorithm.

A new method for the prediction of protein secondary structure is proposed, which relies totally on the global aspect of a protein. The prediction scheme is as follows. A structural library is first scanned with a query sequence by the 3D-1D compatibility method developed before. All the structures examined are sorted with the compatibility score and the top 50 in the list are picked out. Then, all the known secondary structures of the 50 proteins are globally aligned against the query sequence, according to the 3D-1D alignments. Prediction of either alpha helix, beta strand or coil is made by taking the majority among the observations at each residue site. Besides 325 proteins in the structural library, 77 proteins were selected from the latest release of the Brookhaven Protein Data Bank, and they were divided into three data sets. Data set 1 was used as a training set for which several adjustable parameters in the method were optimized. Then, the final form of the method was applied to a testing set (data set 2) which contained proteins of chain length < or = 400 residues. The average prediction accuracy was as high as 69% in the three-state assessment of alpha, beta and coil. On the other hand, data set 3 contains only those proteins of length > 400 residues, for which the present method would not work properly because of the size effect inherent in the 3D-1D compatibility method. The proteins in data set 3 were, therefore, subdivided into constituent domains (data set 4) before being fed into the prediction program. The prediction accuracy for data set 4 was 66% on average, a few percent lower than that for data set 2. Possible causes for this discrepancy are discussed.

Algorithms↗

PubMed1999

A holistic approach to protein secondary structure characterization using amide I band Raman spectroscopy.

We have developed a holistic protein structure estimation technique using amide I band Raman spectroscopy. This technique combines the superposition of reference spectra for pure secondary structure elements with simultaneous aromatic, fluorescence, and solvent background subtraction, and is applicable to solution, suspension, and solid protein samples. A key component of this technique was the calculation of the reference spectra for ordered helix, unordered helix, and sheet, turns, and unordered structures from a series of well-characterized reference proteins. We accurately account for the overlap between the amide I and non-amide I regions and allow for different scattering efficiencies for different secondary structures. For hydrated samples, we allowed for the possibility that bound water spectra differ from the bulk water spectra. Our computed reference spectra compare well with previous experimental and theoretical results in the literature. We have demonstrated the use of these reference spectra for the estimation of secondary structures of proteins in solution, suspension, and dry solid forms. The agreement between our structure estimates and the corresponding determinations from X-ray crystallography is good.

Algorithms↗

PubMed1994

Translation through an uncDC mRNA secondary structure governs the level of uncC expression in Escherichia coli.

Escherichia coli expresses the beta and epsilon subunits of F1F0-ATP synthase at relative levels consistent with the 3:1 (beta/epsilon) stoichiometry in the holoenzyme. The mechanism of translational control of expression of the uncC gene (epsilon subunit) relative to the immediately 5' uncD gene (beta subunit) was examined. Previous expression studies and a computer analysis suggested the presence of an RNA secondary structure including the 3' end of uncD, the uncDC intergenic region, and the uncC Shine-Dalgarno sequence (S. D. Dunn and H. G. Dallmann, J. Bacteriol. 172:2782-2784, 1990). Analysis of in vitro-transcribed RNA by cleavage with RNases T1, V1, and CL3 and by chemical modification with dimethyl sulfate and diethyl pyrocarbonate confirmed a predicted structure. Introduction of premature uncD stop codons inserted 5' of the secondary structure strongly reduced epsilon expression, whereas stop codons inserted at positions within the secondary structure showed smaller effects, indicating that translational control of epsilon synthesis involves partial coupling to beta synthesis. Possible mechanisms by which the RNA secondary structure and the unfolding of this structure by translation of uncD may govern the level of uncC expression are discussed.

Base Sequence↗

PubMed2006

Rnall: an efficient algorithm for predicting RNA local secondary structural landscape in genomes.

BACKGROUND: The information of RNA local secondary structures (LSSs) can help retrieve biologically important motifs and study functions of RNA molecules. Most of the current RNA secondary structure prediction tools are not suitable for RNA LSS prediction on the genome scale due to high computational complexity. METHODS: We developed a new computer package Rnall based on a dynamic programming technique, which scans an RNA sequence with a sliding window and extracts all RNA LSSs with sizes no larger than the window size using the nearest neighbor thermodynamic parameters. The worst case running time of Rnall is O(W(3)L), where W is the window size and L is the query sequence length. In practice we observed a running time of O(W(2)L). We further introduced the concept of energy landscape for illustrating RNA LSS, which may facilitate RNA motif mining on the genomic scale. RESULTS: Rnall shows better prediction accuracy than two other prediction tools Lfold and Quickfold. Rnall is also applied to scan for RNA LSSs in three genomes, and the prediction maps well with known RNA motifs. CONCLUSIONS: Rnall is designed for RNA LSS prediction and together with the energy landscape, it has unique features that could be used for RNA structural motif mining. Rnall is freely available for download at http://digbio.missouri.edu/~wanx/Rnall or http://www.sysbio.muohio.edu/Rnall.

Algorithms↗

PubMed1990

Secondary structures of Tetrahymena thermophila rRNA IVS sequence involved in its self-splicing reactions: a new computer analysis.

The secondary structures of Tetrahymena thermophila rRNA IVS sequence involved in the self-splicing reactions, are theoretically investigated with a refined computer method previously proposed, able to select a set of the deepest free energy RNA secondary structures under constraints of model hypotheses and experimental evidences. The secondary structures obtained are characterized by the close proximity of self-reactions sites and account for double mutations experiments, and differential digestion data.

Animals↗

PubMed2002

The hepatitis C virus 5' untranslated region gene amplified by rapid amplification of cDNA ends and its secondary structure.

OBJECTIVES: To obtain very end full-length cDNA of hepatitis C virus (HCV) 5'untranslated region (5'UTR) and analyze its primary and secondary structure. METHODS: A patient infected genotype 2a HCV was identified by reverse transcription-nested polymerase chain reaction (RT-PCR) and restriction fragment length polymorphism (RFLP). Total RNA isolated from the serum was used as template, and the cDNA of the 5'untranslated region was amplified using rapid amplification of cDNA ends (RACE). The fragments were recombinated by A-T clone strategy, and the recombinants were confirmed by RFLP and PCR, and sequenced subsequently. Secondary structures were analysed by RNAdraw. RESULTS: Very end full-length cDNA of genotype 2a HCV 5'UTR was obtained by RACE. In five clones obtained, three contained full-length 5'UTR cDNA; A21G, G170A, T222C, T247C, C339T substitutions were found as compared to HC-J6. Homological results of HCV-1, HC-J6, HC-C2, HC-J8 were 93.6%-94.4%, 92.1%-93%, 98.8%-99.7%, 96.2%-96.5%, respectively; however, the substitutions did not alter secondary structure. Two of 5 clones were deletions of 53bp and 135bp at the 5'terminal of HCV 5'UTR, respectively. CONCLUSIONS: RACE can be used to obtain the full-length cDNA of 2a genotype HCV 5'UTR. Genes deleted at the 5'terminal of HCV circulate in hepatitis C patients.

5' Untranslated Regions↗

PubMed1994

Prediction of protein secondary structure from circular dichroism spectra using artificial neural network techniques.

An approach to predict protein secondary structure is presented using circular dichroism (CD) spectra as input to two types of artificial neural networks (ANNs): (i) a three-layer backpropagation network and (ii) a hybrid self-organisation to backpropagation network. The dataset comprised the CD spectra of 22 proteins in the 178-260 nm wavelength range whose secondary structures were known. A total of 22 networks were trained by each method, using the jackknife technique for testing the prediction on each protein in turn. The performance, measured in terms of root mean square residuals and Pearson product-moment correlation coefficients, compares well with that obtained by other statistical and ANN methods, and is likely to improve with the growth of the dataset.

Circular Dichroism↗

PubMed2002

Protein secondary structure and stability determined by combining exoproteolysis and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.

In the post-genomic era, several projects focused on the massive experimental resolution of the three-dimensional structures of all the proteins of different organisms have been initiated. Simultaneously, significant progress has been made in the ab initio prediction of protein three-dimensional structure. One of the keys to the success of such a prediction is the use of local information (i.e. secondary structure). Here we describe a new limited proteolysis methodology, based on the use of unspecific exoproteases coupled with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), to map quickly secondary structure elements of a protein from both ends, the N- and C-termini. We show that the proteolytic patterns (mass spectra series) obtained can be interpreted in the light of the conformation and local stability of the analyzed proteins, a direct correlation being observed between the predicted and the experimentally derived protein secondary structure. Further, this methodology can be easily applied to check rapidly the folding state of a protein and characterize mutational effects on protein conformation and stability. Moreover, given global stability information, this methodology allows one to locate the protein regions of increased or decreased conformational stability. All of this can be done with a small fraction of the amount of protein required by most of the other methods for conformational analysis. Thus limited exoproteolysis, together with MALDI-TOF MS, can be a useful tool to achieve quickly the elucidation of protein structure and stability.

Carboxypeptidases↗