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Protein Comparison with Conformation Alignment

With one-dimensional PFSC alphabetic description, the protein conformation structures are able to be compared by protein folding shape alignment (PFSA) approach (Yang, 2011). In PFSA approach, a substitution matrix for 27 PFSC vectors is defined according relationship of vector similarity. Consequencely, a similarity score, as value of PFSA-S, will be applied to evaluate the similarity of proteins. Tthe PFSA approach provides a normalized score between one and zero to evaluate the protein structural similarity.  The PFSA approach can be easily used to compare a pair of proteinseven in lower degree in homology.

Alignment Table. With comparison of one-dimensional alphabetic strings for protein folding conformation, the PFSA alignment table is generated.  There are two types of alignment tables, i.e. sequence-dependence and sequence-independence mode.  For same protein or proteins with mutation, the structural alignment for conformation analysis may prefer the sequence-dependent mode because gap insertion is not necessary.  For proteins with different sequence and size, the structural alignment takes the advantage of the sequence-independent mode, which allows inserting gaps to obtain the best match in local structural similarity.

Example. Protein structure 1M2F (PDB ID) has 25 conformers obtained by NMR spectroscopy and show in Fig. 2(A).   1M2E (PDB ID) in Fig. 2(B) is the average structural models of 25 conformers of 1M2F (Williams et al., 2002).  All of these structures apparently have identical sequence and similar 3D structural conformations. To differentiate the structures with higher similarity requests a tool with higher sensitivity to distinguish each conformer in global and local structure. With PFSA approach, each conformer of protein 1M2F and the structure of 1M2E are converted into one-dimensional PFSC alphabetic description, and then are aligned for comparison. The PFSA alignment table is displayed in Table 2.

Alignment Table.



  1. Yang J. Comprehensive description of protein structures using protein folding shape code. Proteins 2008;71.3:1497-1518
  2. Yang J: Complete Description of Protein Folding Shapes for Structural Comparison. In: Series: Protein Biochemistry, Synthesis, Structure and Cellular Functions: Protein Folding. Edited by Walters EC. New York, Nova Science Publishers, (ISBN: 978-1-61761-259-6), 2011, 421-442
  3. Yang J & Lee WH, Protein Structure Alphabetic Alignment, Protein Structure, Edited by Eshel Faraggi, InTech Publishers, (ISBN 978-953-51-0555-8), 2012, 133-156


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