Identification and temporal expression of putative circadian clock
... All data files for time-course RNAseq can be found on the NCBI SRA data base, bioproject Accession No. 297565. ...
... All data files for time-course RNAseq can be found on the NCBI SRA data base, bioproject Accession No. 297565. ...
AmpliScribe™ T7 High Yield Transcription Kit
... to obtain the maximum possible yields of RNA from an in vitro transcription reaction. The standard 2-hour, 20-µl AmpliScribe reaction will incorporate up to 90% of input NTPs and produce up to 150 µg of RNA from 1 µg of the control template. These yields are made possible by the high-performance pro ...
... to obtain the maximum possible yields of RNA from an in vitro transcription reaction. The standard 2-hour, 20-µl AmpliScribe reaction will incorporate up to 90% of input NTPs and produce up to 150 µg of RNA from 1 µg of the control template. These yields are made possible by the high-performance pro ...
Structural Influences: Cholesterol, Drug, and Proton Binding to Full
... has been observed, and it was suggested that it could have been induced by heterogeneity in helix packing (44). In other words, it is not expected that a single set of rotameric states represents the native structure at even the low temperatures used here. Although no significant pH dependence in th ...
... has been observed, and it was suggested that it could have been induced by heterogeneity in helix packing (44). In other words, it is not expected that a single set of rotameric states represents the native structure at even the low temperatures used here. Although no significant pH dependence in th ...
Pharmacophore screening of the Protein Data Bank for specific
... pockets possessing a specific binding site chemistry and geometry. The method employs two commonly used 3D screening technologies, namely identification of cavities in protein structures and pharmacophore screening of chemical libraries. For each protein structure, a pocket finding algorithm is used ...
... pockets possessing a specific binding site chemistry and geometry. The method employs two commonly used 3D screening technologies, namely identification of cavities in protein structures and pharmacophore screening of chemical libraries. For each protein structure, a pocket finding algorithm is used ...
Functional Conservation of Calreticulin in Euglena gracilis
... Converting one signal/stimulus into another Influences how cell can react and respond to environment. ...
... Converting one signal/stimulus into another Influences how cell can react and respond to environment. ...
bioinformatics - Noble Research Lab
... whether two pairs of sequences are interacting or not. The standard sequence kernels (A kernel is a measure of similarity that satisfies the additional condition of being a dot product in some feature space; see Schölkopf and Smola, 2002 for details.) described in the literature measure similarity b ...
... whether two pairs of sequences are interacting or not. The standard sequence kernels (A kernel is a measure of similarity that satisfies the additional condition of being a dot product in some feature space; see Schölkopf and Smola, 2002 for details.) described in the literature measure similarity b ...
Molecular Cloning and Expression of a 2-Arylpropionyl
... amplification, with primers incorporating the desired sequences, which included a BamHI site in front of the starting methionine codon and a SacI site 39 behind the termination codon. The PCR product was ligated directly into the pCRII vector (TA Cloning Kit; Invitrogen, Leek, The Netherlands) and t ...
... amplification, with primers incorporating the desired sequences, which included a BamHI site in front of the starting methionine codon and a SacI site 39 behind the termination codon. The PCR product was ligated directly into the pCRII vector (TA Cloning Kit; Invitrogen, Leek, The Netherlands) and t ...
Table S4: Domains present in a network region characterized by
... Swiss:P18196 a component of this system, is an inhibitor of FtsZ assembly that is positioned within the cell by interaction with MinDE. MinC is an oligomer, probably a dimer. The C terminal half of MinC is the most conserved and interacts with MinD. The N terminal half is thought interact with FtsZ. ...
... Swiss:P18196 a component of this system, is an inhibitor of FtsZ assembly that is positioned within the cell by interaction with MinDE. MinC is an oligomer, probably a dimer. The C terminal half of MinC is the most conserved and interacts with MinD. The N terminal half is thought interact with FtsZ. ...
Holliday.EPO.Claim.Types.Antibodies
... Why do you need to demonstrate a UTE? Acceptable to provide an alternative solution to a known problem (T92/92, T495/91) For an inventive step to be present, it is not necessary to show improvement – substantial or gradual – over the prior art (T583/93) c/f chemical inventions: “providing the public ...
... Why do you need to demonstrate a UTE? Acceptable to provide an alternative solution to a known problem (T92/92, T495/91) For an inventive step to be present, it is not necessary to show improvement – substantial or gradual – over the prior art (T583/93) c/f chemical inventions: “providing the public ...
nutrient composition of dandelions and its potential as human food
... die every year due to hunger. Expansion of present agriculture practices into marginal land is not expected to solve the problem of increasing the food supply. New methods of feeding the ever increasing world population must be developed. The aim of the study was to evaluate the usefulness of the da ...
... die every year due to hunger. Expansion of present agriculture practices into marginal land is not expected to solve the problem of increasing the food supply. New methods of feeding the ever increasing world population must be developed. The aim of the study was to evaluate the usefulness of the da ...
mbe.oxfordjournals.org - Oxford Academic
... Tagging of S6 Fragments Lacking the 3 Authentic NLSs with the Heterologous SV40 NLS To produce the SV40 NLS–tagged S6 constructs, the oligonucleotides T-Ag1 and T-Ag2 (table 2) were hybridized giving rise to a double-stranded DNA fragment with a NotI site at the 5# end and an EcoRI site at the 3# en ...
... Tagging of S6 Fragments Lacking the 3 Authentic NLSs with the Heterologous SV40 NLS To produce the SV40 NLS–tagged S6 constructs, the oligonucleotides T-Ag1 and T-Ag2 (table 2) were hybridized giving rise to a double-stranded DNA fragment with a NotI site at the 5# end and an EcoRI site at the 3# en ...
Recognizing metal and acid radical ion
... approaches. The sequence-based methods mostly rely on residue conservation analyses under the assumption that ligand-binding residues are functionally important and therefore should be conserved in the evolution. Although the sequence-based approaches have the advantage in generating binding-site pr ...
... approaches. The sequence-based methods mostly rely on residue conservation analyses under the assumption that ligand-binding residues are functionally important and therefore should be conserved in the evolution. Although the sequence-based approaches have the advantage in generating binding-site pr ...
Characterizing the complexity of enzymes on the basis of their
... complexity and determine the total number of reactions in vivo, and thus the potential size of the MACiE database, we estimated the number of protein families per EC node on the basis of sequence data (for an upper limit) and structures (for a lower limit). Although this approach does not take into ...
... complexity and determine the total number of reactions in vivo, and thus the potential size of the MACiE database, we estimated the number of protein families per EC node on the basis of sequence data (for an upper limit) and structures (for a lower limit). Although this approach does not take into ...
PowerPoint-presentation
... • 1) Structural: Find out where the regions of interest (usually genes) are in the genome and ...
... • 1) Structural: Find out where the regions of interest (usually genes) are in the genome and ...
Article A Model of Substitution Trajectories in
... Such studies are often statistical in nature and usually cannot identify specific interactions, yet they provide a broader outlook on the nature of the fitness landscape across different areas of the sequence space. Many of these studies claimed that different aspects of molecular evolution are not ...
... Such studies are often statistical in nature and usually cannot identify specific interactions, yet they provide a broader outlook on the nature of the fitness landscape across different areas of the sequence space. Many of these studies claimed that different aspects of molecular evolution are not ...
Protein conformational changes induced by adsorption onto material
... electrostatic interactions. As a result, proteins and materials interact by multiple short-range (Å) interactions (H-bonding, electrostatic, van der Waals or dispersive forces, hydrophobic effect), which are individually rather weak (a few kB T or less) but sum up and give important adsorption ener ...
... electrostatic interactions. As a result, proteins and materials interact by multiple short-range (Å) interactions (H-bonding, electrostatic, van der Waals or dispersive forces, hydrophobic effect), which are individually rather weak (a few kB T or less) but sum up and give important adsorption ener ...
Эволюция генетического кода
... synthesis of catalytically active protein. Proline, glycine, alanine, and arginine – no combination of these amino acids can yield a wide diversity of structures and properties. Moreover, I assume that there was no start signal or translation stop signal. One can only suppose that synthesis could st ...
... synthesis of catalytically active protein. Proline, glycine, alanine, and arginine – no combination of these amino acids can yield a wide diversity of structures and properties. Moreover, I assume that there was no start signal or translation stop signal. One can only suppose that synthesis could st ...
Identification of a putative flexible loop in Arabidopsis glutathione
... acid Arabidopsis GSH synthetase sequence between Phe$'% and Gly$(% contains three similar and four identical amino acids. While this similarity is not exceptional and might not normally warrant consideration, the similarity overlaps two important regions in the E. coli enzyme. Lys$'( in the Arabidop ...
... acid Arabidopsis GSH synthetase sequence between Phe$'% and Gly$(% contains three similar and four identical amino acids. While this similarity is not exceptional and might not normally warrant consideration, the similarity overlaps two important regions in the E. coli enzyme. Lys$'( in the Arabidop ...
Cyanuric acid hydrolase: evolutionary innovation by structural
... by AtzD is likely to be magnesium (Dudev et al., 1999; Fig. 3D). Anomalous scattering data show that the native metal ion is either magnesium or sodium (Supplemental Fig. S1). Unfortunately, it is not possible to distinguish between Na+ and Mg2+ by anomalous scattering as both cations have an identi ...
... by AtzD is likely to be magnesium (Dudev et al., 1999; Fig. 3D). Anomalous scattering data show that the native metal ion is either magnesium or sodium (Supplemental Fig. S1). Unfortunately, it is not possible to distinguish between Na+ and Mg2+ by anomalous scattering as both cations have an identi ...
Journal of Bacteriology
... Nitrogen fixation of Azospirillum spp., as free-living organisms and in association with the roots of a variety of nonleguminous plants, has been studied intensively since rediscovery of Azospirillum spp. as N2 fixers (for reviews, see references 1, 7, 22, 32). The organisms can grow and fix N2 unde ...
... Nitrogen fixation of Azospirillum spp., as free-living organisms and in association with the roots of a variety of nonleguminous plants, has been studied intensively since rediscovery of Azospirillum spp. as N2 fixers (for reviews, see references 1, 7, 22, 32). The organisms can grow and fix N2 unde ...
Molecular Docking
... Flexibility Through Soft Docking Methods The simple approach to tackle the protein flexibility problem is the 'soft docking' method It allows for slight penetrations between the receptor and the ligand molecules; this is a mathematical trick where the receptor and the ligand are held rigid and a ...
... Flexibility Through Soft Docking Methods The simple approach to tackle the protein flexibility problem is the 'soft docking' method It allows for slight penetrations between the receptor and the ligand molecules; this is a mathematical trick where the receptor and the ligand are held rigid and a ...
Homology modeling
Homology modeling, also known as comparative modeling of protein, refers to constructing an atomic-resolution model of the ""target"" protein from its amino acid sequence and an experimental three-dimensional structure of a related homologous protein (the ""template""). Homology modeling relies on the identification of one or more known protein structures likely to resemble the structure of the query sequence, and on the production of an alignment that maps residues in the query sequence to residues in the template sequence. It has been shown that protein structures are more conserved than protein sequences amongst homologues, but sequences falling below a 20% sequence identity can have very different structure.Evolutionarily related proteins have similar sequences and naturally occurring homologous proteins have similar protein structure.It has been shown that three-dimensional protein structure is evolutionarily more conserved than would be expected on the basis of sequence conservation alone.The sequence alignment and template structure are then used to produce a structural model of the target. Because protein structures are more conserved than DNA sequences, detectable levels of sequence similarity usually imply significant structural similarity.The quality of the homology model is dependent on the quality of the sequence alignment and template structure. The approach can be complicated by the presence of alignment gaps (commonly called indels) that indicate a structural region present in the target but not in the template, and by structure gaps in the template that arise from poor resolution in the experimental procedure (usually X-ray crystallography) used to solve the structure. Model quality declines with decreasing sequence identity; a typical model has ~1–2 Å root mean square deviation between the matched Cα atoms at 70% sequence identity but only 2–4 Å agreement at 25% sequence identity. However, the errors are significantly higher in the loop regions, where the amino acid sequences of the target and template proteins may be completely different.Regions of the model that were constructed without a template, usually by loop modeling, are generally much less accurate than the rest of the model. Errors in side chain packing and position also increase with decreasing identity, and variations in these packing configurations have been suggested as a major reason for poor model quality at low identity. Taken together, these various atomic-position errors are significant and impede the use of homology models for purposes that require atomic-resolution data, such as drug design and protein–protein interaction predictions; even the quaternary structure of a protein may be difficult to predict from homology models of its subunit(s). Nevertheless, homology models can be useful in reaching qualitative conclusions about the biochemistry of the query sequence, especially in formulating hypotheses about why certain residues are conserved, which may in turn lead to experiments to test those hypotheses. For example, the spatial arrangement of conserved residues may suggest whether a particular residue is conserved to stabilize the folding, to participate in binding some small molecule, or to foster association with another protein or nucleic acid. Homology modeling can produce high-quality structural models when the target and template are closely related, which has inspired the formation of a structural genomics consortium dedicated to the production of representative experimental structures for all classes of protein folds. The chief inaccuracies in homology modeling, which worsen with lower sequence identity, derive from errors in the initial sequence alignment and from improper template selection. Like other methods of structure prediction, current practice in homology modeling is assessed in a biennial large-scale experiment known as the Critical Assessment of Techniques for Protein Structure Prediction, or CASP.