Tertiary protein structure identification

Primary protein structure is the sequence of the amino acids in that protein and this has been discussed in the section on Protein identification. Secondary protein structure is the arrangement of the amino acid sequence that makes up the polypeptide backbone of the protein. Tertiary protein structure is the overall... 

A description of the protein-structure hierarchy is incomplete without a discussion of structural motifs, which are critical to an understanding of protein structure [17]. Identification of recurring motifs in protein structures has refined our knowledge of the protein-structure hierarchy these motifs occur at all levels from primary to tertiary. The Phe-Asp-Thr-Gly-Ser sequence found in the active site of all aspartic acid proteinases, and the Gly-Gly-X-Leu sequence (where X represents any amino acid residue) that predicts a 3-strand for the last two residues [17], are examples of sequence motifs a-helices, P-strands, and turns are examples of secondary-structural motifs PaP and PxP units, P-hairpins, and Greek keys are examples of supersecondary-structural motifs and four-a-helix bundles and TIM barrels are examples of tertiary-structural motifs. The tertiary fold of a protein is characterized by its tertiary-structural motif. 

These predictive methods are very useful in many contexts for example, in the design of novel polypeptides for the identification of possible antigenic epitopes, in the analysis of common motifs in sequences that direct proteins into specific organelles (for instance, mitochondria), and to provide starting models for tertiary structure predictions. 

Altogether, the identification of the coordinating residues in the endogenous hDAT Zn2+ binding site followed by the engineering artificial sites have defined an important series of structural constraints in this transporter. This includes not only a series of proximity relationships in the tertiary structure, but also secondary structure relationships. The data also provided information about the orientation of TM7 relative to TM8. A model of the TM7/8 microdomain that incorporates all these structural constraints is shown in Fig. 4 (36). The model is an important example of how structural inferences derived from a series of Zn2+ binding sites can provide sufficient information for at least an initial structural mapping of a selected protein domain. 

ExPASy Proteomics tools (http //expasy.org/tools/), tools and online programs for protein identification and characterization, similarity searches, pattern and profile searches, posttranslational modification prediction, topology prediction, primary structure analysis, or secondary and tertiary structure prediction. 

The delicate structure of proteins makes it difficult to achieve all goals of a separation procedure simultaneously. At the moment, the best approach is to find the main goal of a separation and to set the chromatographic conditions according to it. Protein mapping for identification and analytical information, or the isolation of proteins for subsequent chemical analysis of the ratio and sequence of the amino acids can be conducted under conditions that violate the tertiary structure. Separations for this purpose can be performed in reversed-phase mode using organic solvents. 

Figure 11,4. ExPASy Proteomic tools. ExPASy server provides various tools for proteomic analysis which can be accessed from ExPASy Proteomic tools. These tools (locals or hyperlinks) include Protein identification and characterization, Translation from DNA sequences to protein sequences. Similarity searches, Pattern and profile searches, Post-translational modification prediction, Primary structure analysis, Secondary structure prediction, Tertiary structure inference, Transmembrane region detection, and Sequence alignment.

Other applications of the MCSS method include the work of Brown et al. [84] for the construction of hyperstructures from a set of 2-D structures for improving the speed of atom-by-atom searches, the MCSS-based 2-D [85,86] and 3-D [87] similarity searching, as well as identification of tertiary structure resemblance in proteins [88]. 

Grindley HM, Artymiuk PJ, Rice DW, Willett P. Identification of tertiary structure resemblance in proteins using a maximal common subgraph isomorphism algorithm. J Mol Biol 1993 229 707-721. 

H. M. Grindley, P. J. Artymiuk, D. W. Rice, and P. Willett, J. Mol. Biol., 229, 707 (1993). Identification of Tertiary Structure Resemblance in Proteins Using a Maximal Common Subgraph Isomorphism Algorithm. 

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