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At least 1,711 records · Page 95Linked to original sources
PubMed2002

DNA-phospholipid recognition: modulation by metal ion and lipid nature. Complexes structure and stability calculated by molecular mechanics.

The structures and formation energies of nucleic acid-phospholipid complexes both in the absence and in the presence of Mg(2+) ions were calculated taking double-stranded trinucleoside diphosphates NpNpN or heptanucleotides ApAp(NpNpN)pApA, composed of 64 possible combinations of genetic code, and phosphatidylcholine (PC) and sphingomyelin (SM) as model compounds. The dependence of intramolecular interactions on the primary structure of nucleic acid molecules and on the presence of a cationic bridge was revealed. The formation energies and structure of oligonucleotides were found by molecular mechanics calculations with the AMBER force field. The structures of phospholipid and MgCl(2) molecules were calculated by the semiempirical PM3 method, while the energies of phospholipid-oligonucleotide complexes were calculated by the molecular mechanics method. Calculations of complexes were carried out with consideration of solvation effects. Considerable gain in the formation energy of triple complexes is achieved due to the presence of the electroneutral metal bridge. A tendency toward increasing the stability of "triple" PC complexes (but not SM ones), containing guanosine- and cytidine-enriched triplets was revealed. Depending on the structure of NpNpN trinucleotides, the formation energy values of NpNpN-MgCl(2)-PC and ApAp(NpNpN)pApA-MgCl(2)-PC complexes differ by 1.7-2.6 kcal mol(-1), which can be considered as the atomic-scale manifestation of the recognition phenomenon. Presence of metal (II) ion bridge results in a greater stabilization of the phospholipid-nucleic acid complexes for SM in comparison to PC (the total energy difference equals to 4-16 kcal mol(-1)). Depending on the structure of NpNpN trinucleotides, the formation energies of NpNpN-MgCl(2)-SM and ApAp(NpNpN)pApA-MgCl(2)-SM complexes differ by 1.7-2.1 kcal.mol(-1), which is essential at physiological conditions and can also be considered as the recognition effect.

Base Sequence↗
PubMed1990

The accuracy of aminoacylation--ensuring the fidelity of the genetic code.

The fidelity of protein biosynthesis rests not only on the proper interaction of the messenger RNA codon with the anticodon of the tRNA, but also on the correct attachment of amino acids to their corresponding (cognate) transfer RNA (tRNA) species. This process is catalyzed by the aminoacyl-tRNA synthetases which discriminate with remarkable selectivity amongst many structurally similar tRNAs. The basis for this highly specific recognition of tRNA by these enzymes (also referred to as 'tRNA identity') is currently being elucidated by genetic, biochemical and biophysical techniques. At least two factors are important in determining the accuracy of aminoacylation: a) 'identity elements' in tRNA denote nucleotides in certain positions crucial for protein interactions determining specificity, and b) the occurrence in vivo of competition between synthetases for a particular tRNA which may have ambiguous identity.

Amino Acyl-tRNA Synthetases↗
PubMed2004

Discreet mutations from c-Rel to v-Rel alter kappaB DNA recognition, IkappaBalpha binding, and dimerization: implications for v-Rel oncogenicity.

The avian Rev-T retrovirus encodes the oncoprotein v-Rel, a member of the Rel/nuclear factor (NF)-kappaB transcription factor family. The aggressive oncogenic potential of v-Rel has arisen from multiple mutations within the coding sequence of the avian cellular protein c-Rel. In this study, using quantitative biochemical experiments, we have tested the role of a limited set of alterations between v-Rel and c-Rel located within the Rel homology region (RHR) of the family that might confer functional differences. Our results show that only a set of six mutations within the RHR of v-Rel are responsible for its ability to bind to a broad spectrum of kappaB-DNA that are normally regulated by distinct NF-kappaB dimers. We also observe that both v-Rel homodimer and p50/v-Rel heterodimer bind IkappaBalpha weakly compared to other cellular Rel/NF-kappaB dimers with transcription activation potential. We suggest that the ability of v-Rel homodimer to deregulate subunit-specific gene expression and its ability to evade IkappaB inhibition are crucial to its strong oncogenic potential.

Animals↗
PubMed1999

Improved performance in protein secondary structure prediction by inhomogeneous score combination.

MOTIVATION: In many fields of pattern recognition, combination has proved efficient to increase the generalization performance of individual prediction methods. Numerous systems have been developed for protein secondary structure prediction, based on different principles. Finding better ensemble methods for this task may thus become crucial. Furthermore, efforts need to be made to help the biologist in the post-processing of the outputs. RESULTS: An ensemble method has been designed to post-process the outputs of discriminant models, in order to obtain an improvement in prediction accuracy while generating class posterior probability estimates. Experimental results establish that it can increase the recognition rate of protein secondary structure prediction methods that provide inhomogeneous scores, even though their individual prediction successes are largely different. This combination thus constitutes a help for the biologist, who can use it confidently on top of any set of prediction methods. Moreover, the resulting estimates can be used in various ways, for instance to determine which areas in the sequence are predicted with a given level of reliability. AVAILABILITY: The prediction is freely available over the Internet on the Network Protein Sequence Analysis (NPS@) WWW server at http://pbil.ibcp.fr/NPSA/npsa_server.ht ml. The source code of the combiner can be obtained on request for academic use.

Amino Acid Sequence↗
PubMed2005

Recognition complex between the HMG domain of LEF-1 and its cognate DNA studied by molecular dynamics simulations with explicit solvation.

Molecular dynamics simulations of the complex formed between the HMG box of the lymphoid enhancer-binding factor (LEF-1) and its cognate DNA duplex were carried out with explicit inclusion of water. The simulation started with an NMR-based model (pdb code 2LEF) and the dynamics was pursued for 10 nanoseconds without constraints. It revealed that water intervenes in many ionic/polar interactions, establishing in particular local equilibria between direct and water-mediated hydrogen bonds, and thus increasing the entropy of the complex. Quite unexpectedly, the simulation indicated that a binding pocket for a specific water molecule may be reversibly formed at the apex of the bend induced in the DNA helix by LEF-1 binding, where a methionine side chain intercalates between two destacked adenines. We observed that the specific water molecule can temporarily replace the intercalated S-CH(3) group, acting as a sort of "extension" of the side chain. The residence time of this water molecule was about 3.5 ns. Simulations of the cognate DNA alone showed that this sequence has no intrinsic tendency to bend; therefore, the bending occurs solely as a consequence of the recognition, following the "induced-fit" mechanism.

Adenine↗
PubMedDate not supplied

Temporal contiguity and contingency judgments: a Pavlovian analogue.

The two experiments reported examine the role of temporal contiguity on judgments of contingency in a human analogue of the Pavlovian task. The data show that the effect of the actual delay on contingency judgment depends on the observer's expectation regarding the delay. For a fixed contingency between the cue and the outcome, ratings of the contingency are higher when the actual delay is congruent with the observer's expectation than when it is incongruent. We argue that our data can be understood within the context of the temporal coding hypothesis.

Association Learning↗
PubMed2002

Dynamic modification of cortical orientation tuning mediated by recurrent connections.

Receptive field properties of visual cortical neurons depend on the spatiotemporal context within which the stimuli are presented. We have examined the temporal context dependence of cortical orientation tuning using dynamic visual stimuli with rapidly changing orientations. We found that tuning to the orientation of the test stimulus depended on a briefly presented preceding stimulus, with the preferred orientation shifting away from the preceding orientation. Analyses of the spatial-phase dependence of the shift showed that the effect cannot be explained by purely feedforward mechanisms, but can be accounted for by activity-dependent changes in the recurrent interactions between different orientation columns. Thus, short-term plasticity of the intracortical circuit can mediate dynamic modification of orientation tuning, which may be important for efficient visual coding.

Animals↗
PubMed1982

Signs as pictures and signs as words: effect of language knowledge on memory for new vocabulary.

The role of sensory attributes in a vocabulary learning task was investigated for a non-oral language. Deaf and hearing individuals, more or less skilled in the use of sign language, were asked to learn the English meanings of 22 invented signs which followed the rules of formation for signs in American Sign Language. Each sign stimulus was highly similar in formation to another sign in the set. It was expected that skilled signers would be less affected by this formational similarity because of their greater familiarity with the linguistic structure of sign language. Furthermore, it was suggested that skilled signers would form a visual-linguistic code for the signs while unskilled signers would produce a code from general visual-pictorial processes. These representation differences were expected to lead to qualitatively different error patterns in response to sign similarity. All expectations were confirmed. Skilled signers encoded invented signs in terms of linguistic structure, while unskilled individuals approached the signs as visual-pictorial events. Although both codes are sensory, one reflects linguistic abstraction, and the other does not.

Deafness↗
PubMed2006

A specialized learner for inferring structured cis-regulatory modules.

BACKGROUND: The process of transcription is controlled by systems of transcription factors, which bind to specific patterns of binding sites in the transcriptional control regions of genes, called cis-regulatory modules (CRMs). We present an expressive and easily comprehensible CRM representation which is capable of capturing several aspects of a CRM's structure and distinguishing between DNA sequences which do or do not contain it. We also present a learning algorithm tailored for this domain, and a novel method to avoid overfitting by controlling the expressivity of the model. RESULTS: We are able to find statistically significant CRMs more often then a current state-of-the-art approach on the same data sets. We also show experimentally that each aspect of our expressive CRM model space makes a positive contribution to the learned models on yeast and fly data. CONCLUSION: Structural aspects are an important part of CRMs, both in terms of interpreting them biologically and learning them accurately. Source code for our algorithm is available at: http://www.cs.wisc.edu/~noto/crm.

Algorithms↗
PubMed1998

Influenza C virus CM2 integral membrane glycoprotein is produced from a polypeptide precursor by cleavage of an internal signal sequence.

The influenza C virus CM2 protein is a small glycosylated integral membrane protein (115 residues) that spans the membrane once and contains a cleavable signal sequence at its N terminus. The coding region for CM2 (CM2 ORF) is located at the C terminus of the 342-amino acid (aa) ORF of a colinear mRNA transcript derived from influenza C virus RNA segment 6. Splicing of the colinear transcript introduces a translational stop codon into the ORF and the spliced mRNA encodes the viral matrix protein (CM1) (242 aa). The mechanism of CM2 translation was investigated by using in vitro and in vivo translation of RNA transcripts. It was found that the colinear mRNA derived from influenza C virus RNA segment 6 serves as the mRNA for CM2. Furthermore, CM2 translation does not depend on any of the three in-frame methionine residues located at the beginning of CM2 ORF. Rather, CM2 is a proteolytic cleavage product of the p42 protein product encoded by the colinear mRNA: a cleavage event that involves the recognition and cleavage of an internal signal peptide presumably by signal peptidase resident in the endoplasmic reticulum. Alteration of the predicted signal peptidase cleavage site by mutagenesis blocked generation of CM2. The other polypeptide species resulting from the cleavage of p42, designated p31, contains the CM1 coding region and an additional C-terminal 17 aa (formerly the CM2 signal peptide). Protein p31, in comparison to CM1, displays characteristics of an integral membrane protein.

Amino Acid Sequence↗
PubMed1993

Recognition by HLA-A2-restricted cytotoxic T lymphocytes of endogenously generated and exogenously provided synthetic peptide analogues of the influenza A virus matrix protein.

Experiments were carried out to determine whether complexes between MHC class I molecules and synthetic peptides are representative of those formed under more physiologically relevant conditions, with peptides derived intracellularly from processed antigens. Lysis of cells sensitized with exogenously provided and endogenously generated peptide analogues of the optimal nonameric peptide 58-66 (GILGFVFTL; derived from the influenza virus matrix protein) was compared. Endogenous loading was accomplished by expressing minigene DNA coding for alanine-substituted analogues of peptide 58-66 in HLA-A2-positive cells. Susceptibility to lysis by HLA-A2-restricted, peptide-specific cytotoxic lymphocytes was compared with lysis of cells sensitized with the same synthetic peptides. Although results were quite comparable, differences were observed. The endogenously presented analogues 58-66L60A, G61A, T65A, and L66A were recognized more efficiently than the corresponding exogenously presented analogues. This difference in recognition was most striking for peptide 58-66G61A. These results indicate the need for caution in using synthetic peptides in defining peptide binding motifs. Additional experiments with endogenously expressed analogues of 58-66 with substitutions other than alanine were carried out to define the interaction between this peptide and HLA-A2. Results are compatible with the interpretation that residues 58, 59, and 60 interact with pockets A, B, and D, respectively, in the HLA-A2 binding groove and that these interactions contribute to peptide binding.

Amino Acid Sequence↗
PubMed1995

Characterization and transcriptional activity of the mouse biliary glycoprotein 1 gene, a carcinoembryonic antigen-related gene.

The mouse biliary glycoprotein 1 gene (bgp1) encodes several multifunctional glycoprotein isoforms. These glycoproteins represent members of the carcinoembryonic antigen (CEA) family which belongs to the immunoglobulin superfamily. The Bgp1 glycoproteins function as cell adhesion molecules and receptors for the mouse hepatitis viruses. In contrast to CEA, whose overexpression has been correlated with cancer progression, the human and mouse Bgp proteins are generally down-regulated upon tumor formation. In this study, we report on the mouse bgp1 gene organization and transcriptional activation. We have isolated phage and cosmid clones encompassing the entire bgp1 coding region. This gene consists of nine exons, some of which are subjected to alternative splicing producing a minimum of four splice variants. A comparison of the murine bgp1 proximal promoter with the human BGP and mouse cea10/bgp3 genes revealed sequence conservation of 66% and 95%, respectively. RNase protection assays and primer extension analyses indicated that the mouse bgp1 transcriptional start site is positioned 240 nucleotides upstream of the ATG translational initiation codon, which is 140 nucleotides further upstream than in any other CEA family member. The bgp1 promoter is transcriptionally active in reporter gene activation in vitro transfection studies and in vivo using a bgp1-containing cosmid clone. We identified three putative AP-2 or AP-2-like sites and an upstream stimulatory factor (USF) recognition sequence within the proximal mouse bgp1 promoter region at positions similar to those used by the human BGP promoter region. These data suggest that the regulation of the mouse and human BGP genes may follow some common spatial and temporal expression. Interestingly, the bgp1 proximal promoter and coding region are also well conserved throughout evolution.

Animals↗
PubMed1990

Position-numeral equivalences and delayed position recognition span.

The role of equivalence class formation in delayed position recognition span performance was examined. Initially, the 3 subjects, adults with mental retardation, could not name the nine positions on the span test board. Thus, mnemonic facilitation of span performance based on position naming was not possible. Each subject, however, could name printed numerals and match these stimuli to their dictated names. Matching-to-sample training then established nine equivalence classes, each consisting of a position, a printed numeral, and the numeral name. In subsequent span tests, subject-produced numeral names led to dramatic increases in span scores. The equivalences provided precursors of a kind of verbal code that facilitated performance outside the training context.

Aged↗
PubMed1992

A glycine250--> aspartate substitution in the alpha-subunit of hexosaminidase A causes juvenile-onset Tay-Sachs disease in a Lebanese-Canadian family.

The mutation causing juvenile Tay-Sachs disease (TSD) in two sibs of Lebanese-Maronite origin is described. An mRNA-containing extract of cultured fibroblasts obtained from one of the probands was used as a template to amplify the coding sequence of the hexosaminidase A (Hex A) alpha-subunit. Sequencing of amplified cDNA fragments revealed a single alteration, guanine to adenine at nt 749 creating a G250D mutation. The mutation introduces a new recognition site for the restriction enzyme Eco RV, permitting identification of heterozygotes for this allele following PCR amplification and Eco RV digestion of exon 7 sequences from genomic DNA templates. In order to test the effect of this substitution, an in vitro mutagenized cDNA construct was introduced into a mammalian expression vector and transfected into monkey Cos-1 cells separately or along with a beta-cDNA expression vector. When the mutant alpha-cDNA was the only gene introduced into COS cells no enzymatic activity above endogenous COS cell activity was detected. Cotransfection of normal alpha-cDNA and beta-cDNA followed by immunoprecipitation of human Hex A resulted in 20-fold increase in the ratio between positive and negative (mock transfection) control values. This allowed the detection of some residual activity (12% of the positive control) when the mutant alpha-cDNA replaced its wild-type counterpart. The predicted protein environment in which the mutation occurs is compared to that of the adult-onset Tay-Sachs disease mutation caused by a Gly269-->Ser substitution in exon 7.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗
PubMed2002

Identification of transcription factor binding sites in the human genome sequence.

The identification of transcription factor binding sites (TFBS) is an important initial step in determining the DNA signals that regulate transcription of the genome. We tested the performance of three distinct computational methods for the identification of TFBS applied to the human genome sequence, as judged by their ability to recover the location of experimentally determined, and uniquely mapped, TFBS taken from the TRANSFAC database. These identification methods all attempt to filter the quantity of TFBS identified by aligning positional weight matrices that describe the binding site and employ either (i) a P-value threshold for accepting a site, (ii) an over-representation measure of neighboring sites, or (iii) conservation with the mouse genome and application of P-value thresholds. The results show that the best recognition of TFBS is achieved by combining the identification of TFBS in regions of human-mouse conservation and also by applying a high stringency P-value to the TFBS identified in non-coding regions that are not conserved. Additionally, we find that only half of the 481 experimentally mapped sites can be found in sequence regions conserved with mouse, but the predictive power of the binding site identification method is up to threefold higher in the conserved regions.

Animals↗
PubMed1988

Total chemical synthesis of a gene for hepatitis B virus core protein and its functional characterization.

We have chemically synthesized a DNA duplex of 560 nucleotides that codes for the hepatitis B virus (HBV) core protein. The synthetic gene contains 27 unique internal restriction sites. Thereby, it can easily be mutagenized by replacement of rather short restriction fragments. A number of restriction recognition sequences are in common between the synthetic and the authentic gene, thus allowing for the transfer of synthetic segments into the cloned viral genome. Several unexpected mutations in the synthetic gene were readily corrected utilizing the multiple unique restriction sites. In Escherichia coli, the expression level of the synthetic gene product amounts to about 4% of the total soluble protein. It forms particles closely resembling native HBV cores. After transfer of the synthetic gene into the viral genome, transient expression in a hepatoma cell line yields proteins indistinguishable from the native gene products. The synthetic gene thus provides a useful tool for studies on the structure and function of the isolated HBV core protein as well as the gene and its various products in the viral life-cycle.

Base Sequence↗