Protein Structure Alphabetic Alignment

Yang, Jiaan; Lee, Wei-Hua

doi:10.5772/38063

Cited by 1 publication

(5 citation statements)

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“… Note : Top section: the sequence 21–44,50–89 of SUMO1_HUMAN protein with numeric ruler. Middle section: the 17 PSCF strings for conformations of seven known 3D structures of SUMO1_HUMAN.…”

Section: Resultsmentioning

confidence: 99%

“…Thus, these seven SUMO1 protein structures contain total of 17 folding conformations, and they are, respectively, converted into 17 of PFSC strings according their coordinates of alpha C‐atoms. The PFSC strings for fragment 21–44,50–89 for 17 folding conformations of SUMO1_HUMAN are aligned and listed in the top section of Table 5.…”

Section: Resultsmentioning

confidence: 99%

“…Thus, the PFSC letters with yellow color on each column will reveal what different types of folding shapes exist for each of five successive amino acid residues. For the 17 known conformations, the fragment 21–44,50–89 in SUMO1 has 64 columns, that is, 64 sets of five successive amino acid residues in structure. There are nine columns which have the identical local folding shapes as 1A5R‐01, and the remainder 55 columns have at least one different local folding shape from 1A5R‐01.…”

Section: Resultsmentioning

confidence: 99%

“…Finally, the PFVM produces the ensemble of conformations to probe the structure for any protein as well as the structural information for biological drug design and disease research. [22][23][24] Thus, the protein structure fingerprint provided a signification foundation for the solution of protein folding and applications.…”

Section: Introductionmentioning

confidence: 99%

“…Third, all possible conformations with an astronomical number for a protein can be assembled with various combinations of local folding variations, and the most possible conformation and 3D structure can be easily determined. Finally, the PFVM produces the ensemble of conformations to probe the structure for any protein as well as the structural information for biological drug design and disease research 22–24 . Thus, the protein structure fingerprint provided a signification foundation for the solution of protein folding and applications.…”

Section: Introductionmentioning

confidence: 99%

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Comprehensive folding variations for protein folding

et al. 2022

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The revelation of protein folding is a challenging subject in both discovery and description. Except for acquirement of accurate 3D structure in protein stable state, another big hurdle is how to discover structural flexibility for protein innate character. Even if a huge number of flexible conformations are known, difficulty is how to represent these conformations. A novel approach, protein structure fingerprint, has been developed to expose the comprehensive local folding variations, and then construct folding conformations for entire protein. The backbone of five amino acid residues was identified as a universal folden, and then a set of Protein Folding Shape Code (PFSC) was derived for completely covering folding space in alphabetic description. Sequentially, a database was created to collect all possible folding shapes of local folding variations for all permutation of five amino acids. Successively, Protein Folding Variation Matrix (PFVM) assembled all possible local folding variations along sequence for a protein, which possesses several prominent features. First, it showed the fluctuation with certain folding patterns along sequence which revealed how the protein folding was related the order of amino acids in sequence. Second, all folding variations for an entire protein can be simultaneously apprehended at a glance within PFVM. Third, all conformations can be determined by local folding variations from PFVM, so total number of conformations is no longer ambiguous for any protein.Finally, the most possible folding conformation and its 3D structure can be acquired according PFVM for protein structure prediction. Therefore, the protein structure fingerprint approach provides a significant means for investigation of protein folding problem.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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