Protein primary sequence

A number of tools have been around for several years that aim to predict likely areas of secondary structure from a primary protein sequence or based on an RNA sequence [50]. These models have varying degrees of accuracy of prediction, with some of the best reaching up to 70% accuracy [57]. 

While the Uterature is rich in scientific information on glucosylases, recent interest has focused on the hypothesis that all these enzymes share a common catal3iic mechanism, despite differences in their product specificity (57). Indeed, it has been proposed that all glycosylases share the same basic chemical mechanism (58). Tlie a-amylases have been the focus of much of this attention, as the primary protein sequence (59), tertiary protein structure (54,55) and catalytic mechanism (57) have been recently delineated. 

Because of the importance of validating the moist-heat treatments and related processes, it is necessary to develop a BI that can efficiently assess the success of the treatment. The use of a fluorescent marker designed for a quick and reliable assay, detectable by microscopy, spectrofluorometry, or a handheld UV lamp, is examined herein. GFPuv provides the basis for its potential utility as a fluorescent BI, to monitor moist-heat treatments (T < 100°C). GFPuv is a compact, globular acidic protein (p/ 4.6-5.4) with one fluorophore consisting of a cyclic tripeptide in the primary protein sequence, a chain of 238 amino acids. It has been shown to be resistant to heat (T > 70°C) and alkaline pH (between 5.5 and 12.0 optimum = 8.0). 

Primary Protein sequencing, TV-term Verifies primary amino acid sequence... 

The generation of protein sequences (or equivalently the DNA sequences which provide the protein sequence) is accelerating at a great pace. In the foreseeable future the complete human genome will be sequenced. The challenge for the protein chemist is to assimilate and utilize this information [1], Given the strong correlation between structure and function, the question is therefore the determination of structure from the primary protein sequence. 

For example, a DNA fragment of 600 nucleotides comprises the informa tion in the amount Idna — loga = 1200 bit, while the information Ip in the primary protein sequence synthesized on this fragment and contain ing 20 amino acids is smaller Ip = log2 20 = 860 bit. 

A path from primary protein sequence to ligand recognition. Proteins 50, 589-599. 

Figure 1 shows the results of phylogenetic analysis of the seven genes that are discussed in this review, based on the primary protein sequences of either the... 

The UniProt Archive (UniParc) provides a stable, comprehensive, nonredundant sequence collection by storing the complete body of publicly available protein sequence data. Although most protein sequence data are derived from the translation of DDBJ/EMBL/GenBank sequences, primary protein sequence data are also submitted directly to UniProt or derived from the PDB entries. The Archive also captures protein sequence data from other sources such as Ensemble, International Protein Index (IPI), NCBI-RefSeq, FlyBase, and WormBase. Each protein sequence is assigned to a unique UniParc identifier (UPI ) and represented only once in the Archive. In UniParc, the... 

We have employed the usual notation for amino acids His - histidine, Asp - aspartate, Ser - serine, etc. The number following the symbol for an amino acid indicates its number in the primary protein sequence. Greek letters denote the position of atoms in the amino acid molecule, starting from a-C associated with the carboxyl group. The imidazole group (a side-chain of His) is denoted by Im. 

Primary structure is determined, as we ve seen, by sequencing the pTotein. Secondary, tertiary, and quaternary structures are determined by X-ray crystallography (Chapter 22 Focus On) because it s not yet possible to predict computationally how a given protein sequence will fold. 

Biological raw data are stored in public databanks (such as Genbank or EMBL for primary DNA sequences). The data can be submitted and accessed via the World Wide Web. Protein sequence databanks like trEMBL provide the most likely translation of all coding sequences in the EMBL databank. Sequence data are prominent, but also other data are stored, e.g.yeast two-hybrid screens, expression arrays, systematic gene-knock-out experiments, and metabolic pathways. 

The primary data of sequencing projects are DNA sequences. These become only really valuable through their annotation. Several layers of analysis with bioinformatics tools are necessary to arrive from a raw DNA sequence at an annotated protein sequences ... 

Starting from the protein sequence (primary structure) several algorithms can be used to analyze the primary structure and to predict secondary structural elements like beta-strands, turns, and helices. The first algorithms from Chou and Fasman occurred already in 1978. The latest algorithms find e.g., that predictions of transmembrane... 

At this time, more then thirty channel DNAs have been cloned and characterized from various sources, predominantly from Drosophila melanogaster, mouse, rat and human cDNA/genomic libraries [6-31]. Inspection of the derived primary K channel protein sequences indicates that voltage-gated channels belong to a... 

Historically the Shaker (Sh) K channel was the first K channel which was cloned and characterized [6-10]. Subsequently many more channel cDNAs and genes have been isolated and studied. Yet Sh channels remained in the forefront of channel research. The study of Sh channel mutants has provided the most thorough insight into structure-function relationships of K channels to date. I will first discuss in this chapter the primary sequences of voltage-gated channels. I will only use a few selected examples for discussion. As of this time, so many related K channel protein sequences have been published that it is not feasible to discuss all of them. Subsequently, I will describe in detail the present knowledge about functional K" " channel domains which are implicated in activation, inactivation and selectivity of the channel. 

When one inspects the multiple channel protein sequences that have been derived, one readily recognizes that they have related primary sequences. This suggests that they have similar three-dimensional structures. The primary sequences can be subdivided into an amino-terminal, a core and a carboxy-terminal domain (see Fig. 5). Each domain seems to contribute separately to the structure and function of a given channel [49]. Following this hypothesis, it has been possible to carry out domain swapping experiments between Sh and RCK proteins [49] as well as between... 

With the advent of protein sequencing, also in the 1950s, attempts were made to study protein variation directly on the primary structure. However, the method was very expensive and time-consuming and could not be applied to population genetics. It remained confined to evolutionary study of differences between species (applied to molecular phylogenetics) and to the demonstration of sequence mutation in important heritable diseases. 

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