Abstract
The revelation of protein folding is a challenging subject in both
discovery and description. Except acquirement of accurate 3D structure
for 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
describe 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 5 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 5 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.