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At least 937 records · Page 52Linked to original sources
PubMed2002

[Fourier transform infrared spectroscopy study on the protein secondary structure of photosystem II reaction center].

A successful study on the secondary structure of the isolated photosystem II (PSII) particles with the Fourier transform infrared spectroscopy is reported in this paper. The beta condensation effect is obviously characterized by infrared absorption spectra. The infrared spectra of both living protein and beta condensed protein samples are measured at room temperature. The amide I band in infrared spectrum is used to perform the quantitative analysis of the sample properties. The recorded spectra show the irreversible effect for the PSII particles after the 400 K heating. A rather strong change of the infrared spectra is observed due to the beta condensation of PSII protein. All the spectra are well fitted by 3-Lorentz-peak. The FTIR spectroscopy shows its effectiveness in studying the heating effect on the PSII particles.

Amides↗
PubMed2006

[FTIR characterization of the secondary structure of a staphylokinase variant (K35R) encapsulated within PLGA microspheres].

The secondary structure of a staphylokinase variant (K35R, DGR) encapsulated in poly (lactic-co-glycolic acid) (PLGA) microspheres was quantitatively examined by Fourier transform infrared (FTIR) spectroscopy. Resolution enhancement technique and Fourier deconvolution were combined with band with curve-fitting procedures to quantitate the spectral information from the amide I bands. Nine component bands were found under the broad, nearly featureless amide I bands and assigned to alpha-helix, beta-sheet, turn and irregular (random) structures. The changes of bands at 1 651 and 1 623 cm(-1) after encapsulation were discussed.

Lactic Acid↗
PubMed1994

Valid and invalid implementations of GOR secondary structure predictions.

GOR algorithms have long been a standard methodology for predicting protein secondary structure from primary sequence. We have developed two short validation sequences for the GOR I and GOR II algorithms. Use of these sequences with seven commercial and non-commercial implementations of these algorithms demonstrated that several were incorrect implementations, including two of the three commercial modules implementing the GOR I algorithm. This may be due to an easy misinterpretation of the GOR I algorithm and related data tables. We present the validation sequences and discuss implications of this widely propagated error on secondary and tertiary structure prediction, using several proteins of known structure in three different structural classes as examples. A valid GOR I implementation predicts secondary structure increases the accuracy of predictions by from 1-13 percentage points over an invalid implementation based on the easy misinterpretation. A valid implementation of the GOR I and GOR II algorithms is available from the authors.

Algorithms↗
PubMed1996

Secondary structure and tertiary fold of the birch pollen allergen Bet v 1 in solution.

Bet v 1 is the major birch pollen allergen and therefore the main cause of type I allergies observed in early spring. It is composed of 159 amino acid residues adding up to a molecular mass of 17 kDa. We determined the secondary structure and tertiary fold of full-length Bet v 1 by NMR spectroscopy. Two- and three-dimensional NMR measurements suggest that Bet v 1 is a globular monomer in solution with a high content of well defined secondary structure. Of the total of 159 residues, 135 could be sequentially assigned, using an improved assignment strategy based mainly on heteronuclear experiments. An improved strategy for structure calculation revealed three helices and two beta-sheets as major elements of secondary structure. The globular tertiary structure is mainly stabilized by two antiparallel beta-sheets. The two helices at the C terminus are in accordance with the results from the solution structure of the chemically synthesized peptide Bet v 1-(125-154). This peptide is composed of two helices connected by a hinge. The structural features of Bet v 1 are highly similar to those found in the Ambrosia allergen Amb t V.

Allergens↗
PubMed1986

Influence of 5' proximal secondary structure on the translational efficiency of eukaryotic mRNAs and on their interaction with initiation factors.

The effects of 5' proximal secondary structure in mRNA molecules on their translation and on their interaction with the eukaryotic initiation factors (eIF)-4F, eIF-4A, and eIF-4B have been examined. Secondary structures were generated in the 5' noncoding region of rabbit globin and reovirus mRNAs by means of hybridization with cDNA molecules. cDNAs hybridized to the first 15 bases downstream from the cap inhibited the translation of the mRNAs in both reticulocyte and wheat germ lysates. The degree of inhibition was directly related to the monovalent ion concentration and inversely related to reaction temperature. These hybrid structures also reduced the competitive ability of the messages. Hybrid structures beginning downstream from the first 15 bases did not inhibit the translation of beta-globin mRNA or reovirus s3 mRNA. None of the hybrid structures were detrimental to the interaction of the mRNAs with the 26-kDa cap binding protein of eIF-4F, as determined by chemical cross-linking assays. However, in the presence of ATP, hybrid structures immediately adjacent to the cap severely inhibited the cross-linking to the p46 subunit of eIF-4F or to additional eIF-4A or eIF-4B. In order to account for these observations, a two-step mechanism is proposed for the interaction of eIF-4F with the 5' end of an mRNA molecule. The first step involves a weak initial interaction of the p26 subunit with the cap. The second step requires the hydrolysis of ATP and results in the formation of a stable initiation factor-mRNA complex, which may involve eIF-4A and eIF-4B. This second step is inhibited by the presence of 5' proximal secondary structure. In any event, our results demonstrate that the effect of mRNA structure on translation rate depends strongly on its position with respect to the 5' end and that this effect is due at least in part to an inhibition of the action of initiation factors normally required for the unwinding of structure.

DNA↗
PubMed2004

A phylogenetically based secondary structure for the yeast telomerase RNA.

BACKGROUND: Telomerase is a ribonucleoprotein complex whose RNA moiety dictates the addition of specific simple sequences onto chromosomes ends. While relevant for certain human genetic diseases, the contribution of the essential telomerase RNA to RNP assembly still remains unclear. Phylogenetic analyses of vertebrate and ciliate telomerase RNAs revealed conserved elements that potentially organize protein subunits for RNP function. In contrast, the yeast telomerase RNA could not be fitted to any known structural model, and the limited number of known sequences from Saccharomyces species did not permit the prediction of a yeast specific conserved structure. RESULTS: We cloned and analyzed the complete telomerase RNA loci (TLC1) from all known Saccharomyces species belonging to the "sensu stricto" group. Complementation analyses in S. cerevisiae and end mappings of mature RNAs ensured the relevance of the cloned sequences. By using phylogenetic comparative analysis coupled with in vitro enzymatic probing, we derived a secondary structure prediction of the Saccharomyces cerevisiae TLC1 RNA. This conserved secondary structure prediction includes a central domain that is likely to orchestrate DNA synthesis and at least two accessory domains important for RNA stability and telomerase recruitment. The structure also reveals a potential tertiary interaction between two loops in the central core. CONCLUSIONS: The predicted secondary structure of the TLC1 RNA of S. cerevisiae reveals a distinct folding pattern featuring well-separated but conserved functional elements. The predicted structure now allows for a detailed and rationally designed study to the structure-function relationships within the telomerase RNP-complex in a genetically tractable system.

Base Sequence↗
PubMed2001

EVA: large-scale analysis of secondary structure prediction.

EVA is a web-based server that evaluates automatic structure prediction servers continuously and objectively. Since June 2000, EVA collected more than 20,000 secondary structure predictions. The EVA sets sufficed to conclude that the field of secondary structure prediction has advanced again. Accuracy increased substantially in the 1990s through using evolutionary information taken from the divergence of proteins in the same structural family. Recently, the evolutionary information resulting from improved searches and larger databases has again boosted prediction accuracy by more than 4% to its current height around 76% of all residues predicted correctly in one of the three states: helix, strand, or other. The best current methods solved most of the problems raised at earlier CASP meetings: All good methods now get segments right and perform well on strands. Is the recent increase in accuracy significant enough to make predictions even more useful? We believe the answer is affirmative. What is the limit of prediction accuracy? We shall see. All data are available through the EVA web site at [cubic.bioc.columbia.edu/eva/]. The raw data for the results presented are available at [eva]/sec/bup_common/2001_02_22/.

Databases, Protein↗
PubMed1986

Evolutionary change in 5S rRNA secondary structure and a phylogenic tree of 352 5S rRNA species.

The secondary structure models of 5S rRNA have been constructed from the primary structure of 352 5S rRNA species available at present. All the 5S rRNAs examined can take essentially the same secondary structure, however they reveal characteristic differences between eukaryotes, metabacteria (= archaebacteria) and eubacteria. These three types of models can be further subgrouped by minor but characteristic differences. A phylogenic tree of organisms has been constructed using these 5S rRNA sequences by the weighted pairing method (WPG method). The tree reveals that there exist several major groups of eubacteria which seem to have diverged into different directions in the early stages of bacterial evolution. After emergence of eubacteria, metabacteria and eukaryotes separated from each other from their common ancestor. In the eukaryotic evolution, red algae (Rhodophyta) emerged first, and thereafter, thraustocytrids-Proctista, Ascomycota, green plants (green algae and land plants), Basidiomycota, Chromophyta (brown algae, diatoms and golden-yellow algae), slime- and water molds, various protozoans, and animals emerged in this order.

Animals↗
PubMed1993

Protein secondary structure prediction with partially recurrent neural networks.

Partially recurrent neural networks with different topologies are applied for secondary structure prediction of proteins. The state of some activations in the network is available after a pattern presentation via feedback connections as additional input during the processing of the next pattern in a sequence. A reference data set containing 91 proteins in the training set and 15 non-homologous proteins in the test set is used for training and testing a network with a modified, hierarchical Elman architecture. The network predicts the secondary structures alpha-helix, beta-sheet, and "coil" for each amino acid. The percentage of correctly classified amino acids is 67.83% on the training set and 63.98% on the test set. The best performance of a three-layer feedforward network is 62.7% on the same test set. A cascaded network, where the outputs of the recurrent network are processed by a second net with 13 x 3 inputs, four hidden and three output units has a predictive performance of 64.49%. The best corresponding feedforward net has a performance of 64.3%.

Amino Acid Sequence↗
PubMed1992

The chemical shift index: a fast and simple method for the assignment of protein secondary structure through NMR spectroscopy.

Previous studies by Wishart et al. [Wishart, D. S., Sykes, B. D., & Richards, F. M. (1991) J. Mol. Biol. (in press)] have demonstrated that 1H NMR chemical shifts are strongly dependent on the character and nature of protein secondary structure. In particular, it has been found that the 1H NMR chemical shift of the alpha-CH proton of all 20 naturally occurring amino acids experiences an upfield shift (with respect to the random coil value) when in a helical configuration and a comparable downfield shift when in a beta-strand extended configuration. On the basis of these observations, a technique is described for rapidly and quantitatively determining the identity, extent, and location of secondary structural elements in proteins based on the simple inspection of the alpha-CH 1H resonance assignments. A number of examples are provided to demonstrate both the simplicity and the accuracy of the technique. This new method is found to be almost as accurate as the more traditional NOE-based methods of determining secondary structure and could prove to be particularly useful in light of the recent development of sequential assignment techniques which are now almost NOE-independent [Ikura, M., Kay, L. E., & Bax, A. (1990) Biochemistry 29, 4659-4667]. We suggest that this new procedure should not necessarily be seen as a substitute to existing rigorous methods for secondary structure determination but, rather, should be viewed as a complement to these approaches.

Amino Acids↗
PubMed1985

Microcomputer programs for prediction and comparative evaluation of protein secondary structure from nucleotide sequence data: application to ribulose-1,5-bisphosphate carboxylase sequences.

Apple II PASCAL computer programs are described for routine evaluation of protein secondary structures predicted from DNA or amino acid sequence data. The programs predict protein secondary structure using the directional information algorithm of Garnier et al. (1978), and calculate hydrophobicity (Kyte and Doolittle, 1982), hydrophilicity (Hopp and Woods, 1981), hydrophobic moment (Eisenberg et al., 1984b), and secondary structure propensity profiles. The novel feature of these programs is the application of numeric and graphic methods, designed to facilitate detection and characterization of structural similarities/divergences using the aforementioned structural parameters. The use of the programs is demonstrated on a set of sequences from the large and small subunits of ribulose-1,5-bisphosphate carboxylase.

Base Sequence↗
PubMed1990

Effect of protease digestion on the secondary structure of sarcoplasmic reticulum Ca2(+)-ATPase as seen by FT-i.r. spectroscopy.

1. Upon controlled protein cleavage the catalytic activity of the Ca2(+)-ATPase from sarcoplasmic reticulum is drastically reduced concomitantly with small but significant changes in secondary structure as seen by Fourier transformed infrared (FT-i.r.) spectroscopy, although no loss of protein bound to the membrane is found. 2. FT-i.r. band fitting procedures show a reduction in the beta-sheet and turns content of the protein which is accompanied by an increase in alpha-helix and/or random structure. 3. These changes in the secondary structure of the protein appear to be well correlated to the tryptic digestion pattern and also to changes in the ATP hydrolysis rate of the Ca2(+)-ATPase. 4. It is concluded that these small changes reflect the disruption of key domains of the protein, which lie outside of the membrane matrix, leading to loss of enzymatic activity. 5. FT-i.r. spectroscopy appears to be a very useful technique to study changes in secondary structure of proteins.

Animals↗
PubMedDate not supplied

Flexible secondary structure based protein structure comparison applied to the detection of circular permutation.

We present a novel method for structural comparison of protein structures. The approach consists of two main phases: 1) an initial search phase where, starting from aligned pairs of secondary structure elements, the space of 3D transformations is searched for similarities and 2) a subsequent refinement phase where interim solutions are subjected to parallel, local, iterative dynamic programming in the areas of possible improvement. The proposed method combines dynamic programming for finding alignments but does not restrict solutions to be sequential. In addition, to deal with the problem of nonuniqueness of optimal similarities, we introduce a consensus scoring method in selecting the preferred similarity and provide a list of top-ranked solutions. The method, called FASE (flexible alignment of secondary structure elements), was tested on well-known data and various standard problems from the literature. The results show that FASE is able to find remote and weak similarities consistently using a reasonable run time. The method was tested (using the SCOP database) on its ability to discriminate interfold pairs from intrafold pairs at the level of the best existing methods. The method was then applied to the problem of finding circular permutations in proteins.

Animals↗
PubMed2000

Conserved features of Y RNAs: a comparison of experimentally derived secondary structures.

In this study, phylogenetically conserved structural features of the Ro RNP associated Y RNAs were investigated. The human, iguana, and frog Y3 and Y4 RNA sequences have been determined previously and the respective RNAs were subjected to enzymatic and chemical probing to obtain structural information. For all of the analyzed RNAs, the probing data were used to compose secondary structures, which partly deviate from previously predicted structures. Our results confirm the existence of two stem structures, which are also found at similar positions in hY1 and hY5 RNA. For the remaining parts of hY3 and hY4 RNA the secondary structures differ from those previously proposed based upon computer predictions. What might be more important is that certain parts of the RNAs appear to be flexible, i.e., to adopt several conformations. Another striking feature is that a characteristic pyrimidine-rich region, present in every Y RNA known, is single-stranded in all secondary structures. This may suggest that this region is readily available for base pairing inter-actions with other cellular nucleic acids, which might be important for the as yet unknown function of the RNAs.

Animals↗
PubMed1994

Two-dimensional 1H-NMR studies of maize lipid-transfer protein. Sequence-specific assignment and secondary structure.

Correlation spectroscopy (COSY), total correlation spectroscopy (TOCSY) and NOE spectroscopy (NOESY) experiments have been used to assign sequentially the 1H 500-MHz NMR spectra of a non-specific (ns) lipid-transfer protein extracted from maize seeds. The spin-system identification and sequential assignment were combined with secondary-structure determination to identify most of the proton resonances of this 93-residue protein. From the sequential connectivities it was established that the secondary structure mainly involved four helical fragments: H1, H2, H3 and H4. This secondary structure was compared with that of wheat ns-lipid-transfer protein recently determined. The four helices are located in nearly the same regions, but helix H4 is appreciably longer in the maize protein than in the wheat protein. Comparison of the transfer activities reveals that the maize protein is more efficient than the wheat ns-lipid-transfer protein and that this difference is probably due to the affinity of the lipid for the binding site and not to the interfacial activation, i.e. adsorption of the ns-lipid-transfer protein to the membrane. From these results, it is suggested that helix H4 is a part of the lipid-binding site or contributes to the folding of this site. The present data define the basis for a further modelling of the three-dimensional structure of the maize ns-lipid-transfer protein which will be compared with that of the wheat ns-lipid-transfer protein in order to establish structure/activity relationships for this class of carriers by using natural ns-lipid-transfer protein mutants.

Amino Acid Sequence↗
PubMed2002

Combining the GOR V algorithm with evolutionary information for protein secondary structure prediction from amino acid sequence.

We have modified and improved the GOR algorithm for the protein secondary structure prediction by using the evolutionary information provided by multiple sequence alignments, adding triplet statistics, and optimizing various parameters. We have expanded the database used to include the 513 non-redundant domains collected recently by Cuff and Barton (Proteins 1999;34:508-519; Proteins 2000;40:502-511). We have introduced a variable size window that allowed us to include sequences as short as 20-30 residues. A significant improvement over the previous versions of GOR algorithm was obtained by combining the PSI-BLAST multiple sequence alignments with the GOR method. The new algorithm will form the basis for the future GOR V release on an online prediction server. The average accuracy of the prediction of secondary structure with multiple sequence alignment and full jack-knife procedure was 73.5%. The accuracy of the prediction increases to 74.2% by limiting the prediction to 375 (of 513) sequences having at least 50 PSI-BLAST alignments. The average accuracy of the prediction of the new improved program without using multiple sequence alignments was 67.5%. This is approximately a 3% improvement over the preceding GOR IV algorithm (Garnier J, Gibrat JF, Robson B. Methods Enzymol 1996;266:540-553; Kloczkowski A, Ting K-L, Jernigan RL, Garnier J. Polymer 2002;43:441-449). We have discussed alternatives to the segment overlap (Sov) coefficient proposed by Zemla et al. (Proteins 1999;34:220-223).

Algorithms↗
PubMed1990

Improvements in protein secondary structure prediction by an enhanced neural network.

Computational neural networks have recently been used to predict the mapping between protein sequence and secondary structure. They have proven adequate for determining the first-order dependence between these two sets, but have, until now, been unable to garner higher-order information that helps determine secondary structure. By adding neural network units that detect periodicities in the input sequence, we have modestly increased the secondary structure prediction accuracy. The use of tertiary structural class causes a marked increase in accuracy. The best case prediction was 79% for the class of all-alpha proteins. A scheme for employing neural networks to validate and refine structural hypotheses is proposed. The operational difficulties of applying a learning algorithm to a dataset where sequence heterogeneity is under-represented and where local and global effects are inadequately partitioned are discussed.

Artificial Intelligence↗
PubMed1993

Secondary structure of globular proteins at the early and the final stages in protein folding.

The ellipticities for an early transient intermediate in refolding observed by kinetic circular dichroism measurements at 220-225 nm for 14 different proteins are summarized, and the ellipticity values are compared with those for the final native proteins and also with the ellipticities expected from a physical theory of protein and polypeptide secondary structure. The results show that a substantial part of the protein secondary structure is in general formed in the earliest detectable intermediate in refolding and that the ellipticities in both the native and the intermediate states are consistent with the physical theory of protein secondary structure.

Animals↗