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At least 865 records · Page 48Linked to original sources
PubMed1999

Conserved features of Y RNAs revealed by automated phylogenetic secondary structure analysis.

Y RNAs are small 'cytoplasmic' RNAs which are components of the Ro ribonucleoprotein (RNP) complex. The core of this complex, which is found in the cell nuclei of higher eukaryotes as well as the cytoplasm, is composed of a complex between the 60 kDa Ro protein and Y RNAs. Human cells contain four distinct Y RNAs (Y1, Y3, Y4 and Y5), while other eukaryotes contain a variable number of Y RNA homologues. When detected in a particular species, the Ro RNP has been present in every cell type within that particular organism. This characteristic, along with its high conservation among vertebrates, suggests an important function for Ro RNP in cellular metabolism; however, this function has not yet been definitively elucidated. In order to identify conserved features of Y RNA sequences and structures which may be directly involved in Ro RNP function, a phylogenetic comparative analysis of Y RNAs has been performed. Sequences of Y RNA homologues from five vertebrate species have been obtained and, together with previously published Y RNA sequences, used to predict Y RNA secondary structures. A novel RNA secondary structure comparison algorithm, the suboptimal RNA analysis program, has been developed and used in conjunction with available algorithms to find phylogenetically conserved secondary structure models for YI, Y3 and Y4 RNAs. Short, conserved sequences within the Y RNAs have been identified and are invariant among vertebrates, consistent with a direct role for Y RNAs in Ro function. A subset of these are located wholly or partially in looped regions in the Y3 and Y4 RNA predicted model structures, in accord with the possibility that these Y RNAs base pair with other cellular nucleic acids or are sites of interaction between the Ro RNP and other macromolecules.

Animals↗
PubMed1997

Differentiation of the maturity of cataractous human lens capsules according to changes in protein secondary structures determined by Fourier-transformed infrared spectroscopy.

PURPOSE: Cataract-induced alterations in the protein secondary structure of human lens capsules in different maturity of cataractous patients was investigated. METHODS: Fourier-transformed infrared (FT-IR) spectroscopy with Fourier self-deconvolution and curve-fitting algorithms was used. Twenty-seven immature and four mature cataractous patients (previously classified through observations of the depth of the shadow cast by the iris on oblique illumination) were investigated in the present study. RESULTS: Two groups with progressive cataract formation could be effectively redifferentiated and re-arranged. In the first group, all the peak positions were the same and the peak at 1651 cm-1 assigned to the alpha-helix structure was predominant, but the structural compositions of the beta-sheet and beta-turn changed with progressive cataractogenesis. In the second group, in which cataract formation was more advanced, the peak at 1651 cm-1 assigned to the alpha-helix structure shifted to 1658 cm-1 and a new peak appeared at 1647 cm-1, due to random coil structure; the structural compositions of triple helix significantly decreased but the compositions of the beta-sheet and beta-turn slightly increased. Amides II and III of the IR spectra seemed to be less changed in secondary structures. CONCLUSIONS: These results suggest that FT-IR spectroscopy with Fourier self-deconvolution and curve-fitting programs can be used as a diagnostic tool for the determination of the cataractous maturity of human lens capsules.

Aged↗
PubMed2000

Estimation of protein secondary structure from circular dichroism spectra: inclusion of denatured proteins with native proteins in the analysis.

We have expanded our reference set of proteins used in the estimation of protein secondary structure by CD spectroscopy from 29 to 37 proteins by including 3 additional globular proteins with known X-ray structure and 5 denatured proteins. We have also modified the self-consistent method for analyzing protein CD spectra, SELCON3, by including a new selection criterion developed by W. C. Johnson, Jr. (Proteins Struct. Funct. Genet. 35, 307-312, 1999). The secondary structure corresponding to the denatured proteins was approximated to be 90% unordered, owing to the spectral similarity of the denatured proteins and unordered structures. We examined the thermal denaturation of ribonuclease T1 by CD using both the original and expanded sets of reference proteins and obtained more consistent results with the expanded set. The expanded set of reference proteins will be helpful for the determination of protein secondary structure from protein CD spectra with higher reliability, especially of proteins with significant unordered structure content and/or in the course of denaturation.

Circular Dichroism↗
PubMed2004

HYPROSP: a hybrid protein secondary structure prediction algorithm--a knowledge-based approach.

We develop a knowledge-based approach (called PROSP) for protein secondary structure prediction. The knowledge base contains small peptide fragments together with their secondary structural information. A quantitative measure M, called match rate, is defined to measure the amount of structural information that a target protein can extract from the knowledge base. Our experimental results show that proteins with a higher match rate will likely be predicted more accurately based on PROSP. That is, there is roughly a monotone correlation between the prediction accuracy and the amount of structure matching with the knowledge base. To fully utilize the strength of our knowledge base, a hybrid prediction method is proposed as follows: if the match rate of a target protein is at least 80%, we use the extracted information to make the prediction; otherwise, we adopt a popular machine-learning approach. This comprises our hybrid protein structure prediction (HYPROSP) approach. We use the DSSP and EVA data as our datasets and PSIPRED as our underlying machine-learning algorithm. For target proteins with match rate at least 80%, the average Q3 of PROSP is 3.96 and 7.2 better than that of PSIPRED on DSSP and EVA data, respectively.

Algorithms↗
PubMed1996

Secondary structure and location of a magainin analogue in synthetic phospholipid bilayers.

Magainins are cationic, membrane-active peptides which show broad-spectrum antimicrobial activity. We have investigated the secondary structure and location of an analogue of magainin 2 in synthetic phospholipid bilayers using a combination of Fourier transform infrared (FTIR) spectroscopy and solid-state nuclear magnetic resonance (NMR) spectroscopy. Ala19-magainin 2 amide exhibits both alpha-helix and beta-sheet secondary structures in lipid bilayers containing either dipalmitoylphosphatidylglycerol (DPPG) or a 1:1 molar mixture of DPPG and dipalmitoylphosphatidylcholine (DPPC). The combination of FTIR and solid-state NMR results suggests that there are two populations of peptide. The secondary structure of one population is alpha-helix while that of the other population is beta-sheet. We demonstrate that the solid-state NMR technique, rotational-echo double resonance (REDOR), can be used to measure both intra- and intermolecular dipole-dipole interactions in membrane-bound peptides. Our REDOR experiments indicate that alpha-helical Ala19-magainin 2 amide is bound near the phospholipid head groups.

Amino Acid Sequence↗
PubMed2002

Secondary structure of antisauvagine analogues is important for CRF receptor antagonism: development of antagonists with increased potency and receptor selectivity.

Antisauvagine-30 (aSVG) is the only high-affinity antagonist for the corticotropin-releasing factor (CRF) type 2 (CRF(2)) receptor. A structure-activity relationship study was performed to pinpoint residues conferring aSVG's selectivity. The aSVG-analogues being N-terminally extended by one or two residues or containing the Ala(22)Arg(23)Ala(24) (ARA-motif) of CRF, were synthesized. Additionally, a lactam bridge between positions 29 and 32 was introduced. The modified peptides were analyzed for alpha-helicity properties, binding affinities and antagonistic potencies at the rat CRF(1) and mouse CRF(2B) receptors. While N-terminal prolongation and replacement of D-Phe(11) by Tyr(11) increased the affinity for the CRF(2) receptor, the introduction of the ARA motif resulted in a loss of CRF(2) receptor selectivity. These data show that aSVG(10-40) analogues are more potent CRF(2) receptor antagonists than aSVG(11-40) peptides, while introduction of the ARA-motif or a cyclic constraint between residues 29 and 32 favors binding to the CRF(1) receptor.

Amino Acid Motifs↗
PubMed1987

Variable selection method improves the prediction of protein secondary structure from circular dichroism spectra.

A new procedure based on the statistical method of "variable selection" is used to predict the secondary structure of proteins from circular dichroism spectra. Variable selection adds the flexibility found in the Provencher and Glöckner method (S. W. Provencher and J. Glöckner, 1981, Biochemistry 20, 33-37) to the method of Hennessey and Johnson (J. P. Hennessey and W. C. Johnson, 1981, Biochemistry 20, 1085-1094). Two analytical methods are presented for choosing a solution from the series generated by the Provencher and Glöckner method, and this improves the technique. All three methods are compared and it is shown that both the variable selection method and the improved Provencher and Glöckner methods have equivalent reliability superior to the original Hennessey and Johnson method. For the new variable selection method, correlation coefficients calculated between X-ray structure and predicted secondary structures for data measured to 178 nm are: 0.97 for alpha-helix, 0.75 for beta-sheet, 0.50 for beta-turn, and 0.89 for other structures. Although the variable selection method improves the analysis of circular dichroism data truncated at 190 nm, data measured to 178 nm gives superior results. It is shown that improving the fit to the measured CD beyond the accuracy of the data can result in poorer analyses.

Circular Dichroism↗
PubMed1989

Secondary structure in properdin of the complement cascade and related proteins: a study by Fourier transform infrared spectroscopy.

Six structural repeat motifs of 58 amino acids are found in the sequence of both mouse and human properdins. Twelve more examples of the motif are available from the sequences of thrombospondin, the terminal complement components, and the thrombospondin-related anonymous protein. The averaged Robson and Chou-Fasman secondary structure predictions show that there are 57-66% turn and 19-38% beta-sheet structures in the typical repeat motif. The high amount of turn structure is consistent with Gly, Pro, Cys, and Ser being the four most abundant amino acid residues in properdin. Comparisons with sequences found in the circumsporozoite protein from several species of malaria parasites show that their sequences and secondary structures strongly coincide only in a 18-residue segment. Further secondary structure analysis utilized Fourier transform infrared spectroscopy of human properdin in 2H2O buffers. These show a broad amide I band that, after second-derivative and deconvolution calculations, is shown to be composed of several components. Two at 1633 and 1683 cm-1 are strong evidence for beta-sheet structure, although overlap from beta-turns can also contribute. The presence of beta-turn structure is indicated by absorptions at 1662-1675 and 1645 cm-1. The properdin structure contains substantial quantities of beta-sheet and beta-turn structures, which is consistent with the secondary structure predictions and amino acid compositions. The length of the repeat motif is estimated as 3.3-4.3 nm, and an estimated 14-22% of nonexchanged amide protons reside in properdin. This is suggestive of a high degree of solvent accessibility in the structure.

Amino Acid Sequence↗
PubMed1994

Backbone 1H, 13C, and 15N assignments and secondary structure of bovine low molecular weight phosphotyrosyl protein phosphatase.

Phosphotyrosyl protein phosphatases play an important role in mediating cellular signal transduction; yet three-dimensional structures of this important class of proteins have not been reported. We present the sequence-specific 1H, 13C, and 15N backbone assignments for the low molecular weight bovine heart phosphotyrosyl protein phosphatase (BHPTPase) (157 residues, 17,900). The assignments were obtained from a combination of double- and triple-resonance multidimensional NMR experiments. From these assignments, the secondary structure of BHPTPase was determined from an analysis of NOE patterns, 3JHNH alpha coupling constants, 13C alpha and 13CO chemical shifts, and amide 1H exchange rates. BHPTPase was found to consist of a four-stranded parallel beta-sheet (residues K6-C12, W39-A45, Y87-M91, and K112-L116), four alpha-helices (residues I21-D32, R58-G67, S94-N104, and D135-R157), and one stretch of beta 10-helix (residues K79-F85). The secondary structure is characteristic of the beta alpha beta structural motif. The secondary structure elements identified in this study are consistent with previous chemical and mutagenesis studies of BHPTPase structure.

Amino Acid Sequence↗
PubMed1999

Complete suboptimal folding of RNA and the stability of secondary structures.

An algorithm is presented for generating rigorously all suboptimal secondary structures between the minimum free energy and an arbitrary upper limit. The algorithm is particularly fast in the vicinity of the minimum free energy. This enables the efficient approximation of statistical quantities, such as the partition function or measures for structural diversity. The density of states at low energies and its associated structures are crucial in assessing from a thermodynamic point of view how well-defined the ground state is. We demonstrate this by exploring the role of base modification in tRNA secondary structures, both at the level of individual sequences from Escherichia coli and by comparing artificially generated ensembles of modified and unmodified sequences with the same tRNA structure. The two major conclusions are that (1) base modification considerably sharpens the definition of the ground state structure by constraining energetically adjacent structures to be similar to the ground state, and (2) sequences whose ground state structure is thermodynamically well defined show a significant tendency to buffer single point mutations. This can have evolutionary implications, since selection pressure to improve the definition of ground states with biological function may result in increased neutrality.

Base Sequence↗
PubMed1995

Molecular evolution and secondary structural conservation in the B-cell lymphoma leukemia 2 (bcl-2) family of proto-oncogene products.

The nature of the bcl-2 family of proto-oncogenes was analyzed by sequence alignment, secondary structure prediction, and phylogenetic techniques. Phylogenies were inferred from both the nucleic acid and amino acid sequences of the human, murine, rat, and chicken sequences for BCL-2 and BCL-X, human MCL1, murine A1, the nematode Caenorhabditis elegans and Caenorhabditis briggsiae ced-9 proteins, and the sequences BHRF1 from Epstein-Barr and LMW5-HL from African swine fever viruses. Both sequence alignment and secondary structure prediction techniques supported the conservation of both the overall secondary structure and the carboxy-terminal transmembrane domain in all members of the family. All the treeing methods employed (distance matrix, maximum likelihood, and parsimony) supported a tree in which the proapoptotic proteins BCL-2 and BCL-X represent the most recent additions to the group. All the trees also indicated that the viral proteins BHRF1 and LMW-HL arose from a common ancestor, an ancestor they shared in common with the pro-apoptotic control protein BAX, indicating that this function of BAX evolved only recently. The most ancient branches are represented by the nematode ced-9 protein and by the control genes MCL1 and A1, which in the treeing methods employed represent separate lineages within the most ancient grouping. These results demonstrate the evolution of a highly conserved family of developmental control genes from nematode to man--genes that encode proteins essential for normal development but which are highly conserved in terms of predicted structure and possible cellular localization. The evolutionary analysis also indicates that the family may be even larger than originally predicted and that other members are waiting to be discovered.

Amino Acid Sequence↗
PubMed1988

The secondary structure of human plasma fibronectin: conformational changes induced by acidic pH and elevated temperatures; a circular dichroic study.

The secondary structure of native human plasma fibronectin, based on circular dichroic spectra, has been estimated to contain 79% beta sheet and 21% beta turn structures (Osterlund, E., Eronen, I., Osterlund, K. and Vuento, M. (1985) Biochemistry 24, 2661-2667). In this work changes in the secondary structure of the protein molecule are followed as a function of different temperatures and pH values by using circular dichroic spectroscopy in far- and near-ultraviolet regions. Conformational changes are reversible when raising the temperature quickly to 55 degrees C, and then cooling slowly to 20 degrees C. A few percent of alpha-helix is apparent, when the temperature is raised to 58.5 degrees C, but only about 9% random coil is formed, when the temperature is raised up to 70 degrees C. The largest conformational change is taking place, when fibronectin samples are heated from 57 to 58.5 degrees C. According to this study more than 90% of the secondary structure of the fibronectin molecule is preserved throughout the whole temperature range studied from 20 to 70 degrees C, and this is a fact even at pH as low as 3.0, when samples are fresh and not denatured by preparative procedures.

Circular Dichroism↗
PubMed1995

Secondary structure of holo- and apo-aminoacylase from prediction, circular dichroism, and FT-Raman spectroscopy.

The secondary structures of native (Holo-) and Zn(2+)-free (Apo-) aminoacylase were examined by circular dichroism (CD) and Fourier transform Raman (FT-Raman) spectroscopic techniques and prediction methods. Quantitative analysis of the conformationally sensitive amide I band indicates that Holo- and Apo-enzyme contain 19.3 and 17.2% helical structure, respectively. Far-UV CD spectra of Holo- and Apo-enzyme show that they contain 20.1 and 17.6% alpha-helix, respectively. Secondary structure prediction of aminoacylase indicates that it contains approximately 20.9% alpha-helical structure including 10 alpha-helix segments. The results show that after removal of Zn2+ in aminoacylase, the extent of ordered structure was decreased markedly. The conformation at or near the active site of aminoacylase may contain more ordered structure and the presence of Zn2+ may help to maintain the catalytically active conformation at the active site.

Amidohydrolases↗
PubMed1995

A secondary-structure model for the self-cleaving region of Neurospora VS RNA.

Neurospora VS RNA performs an RNA-mediated self-cleavage reaction whose products contain 2',3'-cyclic phosphate and 5'-hydroxyl termini. This reaction is similar to those of hammerhead, hairpin, and hepatitis delta virus ribozymes; however, VS RNA is not similar in sequence to these other self-cleaving motifs. Here we propose a model for the secondary structure of the self-cleaving region of VS RNA, supported by site-directed mutagenesis and chemical modification structure probing data. The secondary structure of VS RNA is distinct from those of the other naturally occurring RNA self-cleaving domains. In addition to a unique secondary structure, several Mg-dependent interactions occur during the folding of VS RNA into its active tertiary conformation.

Cloning, Molecular↗
PubMed2000

Dynamics of beta and proliferating cell nuclear antigen sliding clamps in traversing DNA secondary structure.

Chromosomal replicases of cellular organisms utilize a ring shaped protein that encircles DNA as a mobile tether for high processivity in DNA synthesis. These "sliding clamps" have sufficiently large linear diameters to encircle duplex DNA and are perhaps even large enough to slide over certain DNA secondary structural elements. This report examines the Escherichia coli beta and human proliferating cell nuclear antigen clamps for their ability to slide over various DNA secondary structures. The results show that these clamps are capable of traversing a 13-nucleotide ssDNA loop, a 4-base pair stem-loop, a 4-nucleotide 5' tail, and a 15-mer bubble within the duplex. However, upon increasing the size of these structures (20-nucleotide loop, 12-base pair stem-loop, 28-nucleotide 5' tail, and 20-nucleotide bubble) the sliding motion of the beta and proliferating cell nuclear antigen over these elements is halted. Studies of the E. coli replicase, DNA polymerase III holoenzyme, in chain elongation with the beta clamp demonstrate that upon encounter with an oligonucleotide annealed in its path, it traverses the duplex and resumes synthesis on the 3' terminus of the oligonucleotide. This sliding and resumption of synthesis occurs even when the oligonucleotide contains a secondary structure element, provided the beta clamp can traverse the structure. However, upon encounter with a downstream oligonucleotide containing a large internal secondary structure, the holoenzyme clears the obstacle by strand displacing the oligonucleotide from the template. Implications of these protein dynamics to DNA transactions are discussed.

Base Pairing↗
PubMed1991

RNA secondary structure analysis of the packaging signal for Moloney murine leukemia virus.

We have examined the cis-acting RNA packaging signal (psi) from Moloney murine leukemia virus using a combination of chemical and primary sequence analysis techniques. For our chemical analyses, we used dimethyl sulfate, kethoxal, and 1-cyclohexyl-3-(2-morpholinoethyl)-carbodiimide metho-p-toluene sulfonate as probes for RNA secondary structure. The structural information obtained from these studies was used to constrain computer algorithms for prediction of RNA secondary structure. In addition, we generated and analyzed a phylogenetic comparison of homologous sequences from related retroviruses. From these data, we have developed two models for the RNA secondary structure of the packaging signal psi. Both of these models suggest the presence of secondary structure elements in a region of the psi RNA known to be required for function.

Aldehydes↗
PubMed2005

A hybrid genetic-neural system for predicting protein secondary structure.

BACKGROUND: Due to the strict relation between protein function and structure, the prediction of protein 3D-structure has become one of the most important tasks in bioinformatics and proteomics. In fact, notwithstanding the increase of experimental data on protein structures available in public databases, the gap between known sequences and known tertiary structures is constantly increasing. The need for automatic methods has brought the development of several prediction and modelling tools, but a general methodology able to solve the problem has not yet been devised, and most methodologies concentrate on the simplified task of predicting secondary structure. RESULTS: In this paper we concentrate on the problem of predicting secondary structures by adopting a technology based on multiple experts. The system performs an overall processing based on two main steps: first, a "sequence-to-structure" prediction is enforced by resorting to a population of hybrid (genetic-neural) experts, and then a "structure-to-structure" prediction is performed by resorting to an artificial neural network. Experiments, performed on sequences taken from well-known protein databases, allowed to reach an accuracy of about 76%, which is comparable to those obtained by state-of-the-art predictors. CONCLUSION: The adoption of a hybrid technique, which encompasses genetic and neural technologies, has demonstrated to be a promising approach in the task of protein secondary structure prediction.

Algorithms↗
PubMed1987

The secondary structure of a messenger RNA precursor probed with psoralen is melted in an in vitro splicing reaction.

The secondary structure of the SP6/mouse insulin precursor RNA was determined by psoralen cross-linking experiments. A series of long-range contacts occur within the left half of the pre-mRNA that contains the intervening sequence. Multiple secondary structures for the pre-mRNA exist since some of the interactions share common sites. In splicing buffer but without the splicing extract added, many of these interactions are stable up to at least 50 degrees C. These interactions, however, are dissociated during the in vitro splicing reaction. This dissociation requires ATP and it occurs during the first 30 min. of the splicing reaction. Pre-mRNAs containing psoralen cross-links in different locations within the RNA molecule were purified and used as substrates for in vitro splicing. Psoralen cross-links at any of the double-stranded regions resulted in complete inhibition of the splicing reaction. This indicates that destabilization of the secondary structure of the SP6/mouse insulin pre-mRNA is necessary for in vitro splicing.

Animals↗