CDS feature

What does the Pn-helix fraction really mean, and what is the nature of the unordered high-temperature ensemble The positive CD feature... 

Bibliographic reference titles Full CDS feature text... 

The CD features of bacteriochlorophyll a in light-harvesting bacteriochlorophy 11-protein complexes from native bacteria is more interesting and is not compatible with Boxer s experiments. Bacteriochlorophyll(Bchl)-protein complexes exhibit various CD spectral profiles, depending on the species of bacteria and their culture conditions 201 206). Thus, CD of Bchl arises from the asymmetric environment in which the Bchl is situated, and from the specialized arrangement which affords a specific interaction between Bchl molecules, as well as from the asymmetry of Bchl... 

The CD feature produced by an electronic transition within a chromophore is a simple Gaussian peak centred on the Amax seen in the UV spectrum for the chromophore and the UV spectrum for such a transition within a chromophore is a simple smooth curve conversely, the fine structure seen in the UV spectrum (e.g. for aromatic chromophores) is also superimposed on the smooth CD curve when more complex absorption features arise (numerous electronic transitions of similar energy, therefore generating absorption peaks appearing at similar wavelengths Figure 3.2). 

The amine, amide and carboxy chromophores that are common to the general family of amino acids, peptides and proteins show absorption features in the short-wavelength part of the ultraviolet range to establish their associated CD features requires more sophisticated spectrometers. Much of the detailed conformational information gained from CD studies depends on data from this wavelength region. 

CD spectra carry much more information than do UV spectra the intensity of the CD absorption is dependent upon the spatial relationship between the chromo-phore and groupings at the chiral centre and therefore there is no chromo-phore-intensity-of-absorption relationship such as that which exists for UV spectra (i.e. the Bouguer-Bccr Lambert law does not apply to CD spectra). Also, the sign of the CD feature can be positive or negative, unlike the isotropic absorption (i.e. the UV spectrum), which has no sign. 

The CD spectrum can be interpreted in terms of absolute configuration the sign of a particular CD feature corresponds to a particular absolute configuration of the solute, for the chiral centre nearest the chromophore responsible for that CD feature. Information on conformation (based on the sign and specific details of an overall CD spectrum for a compound of known absolute configuration) can be obtained for amino acids and peptides. An example given in Chapter 2 (Section 2.7) illustrates a simple example of this type of result. 

Table 3.3. CD features for a-helix, -sheet and random (i.e. conformations unordered)...

Protein databases used to be from direct protein sequencing, but now they are made almost exclusively from the translation of ORFs (Open Reading Frames on DNA sequences). Both the European Bioinformatics Institute (EBI) and National Center for Biotechnology Information (NCBI) provide databases, TREMBL [15] and GENPEPT [19] respectively, which are automatic translations from the CDS features of the DNA in their nucleotide databases. This includes some automated annotation of the role which the protein plays. 

Following development, the patterned wafer is inspected for defects, and specific CD features are measured to check if they meet preset process control targets. This step is necessary to identify and remove defective wafers before they continue... 

CD and absorption spectra of four duplexes with different mixtures of complementary DNA and RNA strands, each duplex containing alternating A T and G C base pairs (except that T in the DNA strands is replaced by U in the analogous RNA strands). The RNA duplex r(AG)i2 r(CU),2 had a negative band at 210 nm and a larger positive band above 250 nm than did the DNA duplex d(AG),2-d(CT) 2. These CD features are characteristics that generally distinguish the A-RNA conformation from the B-DNA conformation. ... 

The Nuc-prot set, containing a nucleotide and one or more protein products, is the type of set most frequently produced by a Sequin data submission. The component Bioseqs are coimected by coding sequence region (CDS) features that describe how translation from nucleotide to protein sequence is to proceed. In a traditional nucleotide or protein sequence database, these records might have cross-references to each... 

Proteins. A Protein feature names (or at least describes) a protein or proteolytic product of a protein. A single protein Bioseq may have many Protein features on it. It may have one over its full length describing a pro-peptide, the primary product of translation. (The name in this feature is used for the /product qualifier in the CDS feature that produces the protein.) It may have a shorter protein feature describing the mature peptide or, in the case of viral polyproteins, several mature peptide features. Signal peptides that guide a protein through a membrane may also be indicated. 

Implicit in the BioSource and the organism that is assigned to it is the genetic code used by the DNA/RNA, which will be used to translate the nucleic acid to represent the protein sequence (if one is present in the record). This information is shown on the CDS feature. 

If this information is not present in the sequence definition line. Sequin will prompt the user for it before proceeding. Annotations on the definition line can be very convenient, since the information stays with the sequence and caimot be forgotten or mixed-up later. In addition to building the proper CDS feature. Sequin will automatically make gene and protein features with this information. 

Figure 4.1. Viewing a sequence record with Sequin. The sequence record viewer uses GenBank format, by default. In this example, a CDS feature has been clicked, as indicated by the bar next to its paragraph. Double-clicking on a paragraph will launch an editor for the feature, descriptor, or sequence that was selected. The viewer can be duplicated, and multiple viewers can show the same record in different formats.

If the change in CD features at a particular wavelength that occurs with change in pH is due solely to one chromophore, and no major conformational transition is associated with the change, then the relative variation of ellipticity is expected to follow an empirical equation ... 

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