title: Reduced alphabet for protein folding prediction.
abstract: What are the key building blocks that would have been needed to construct complex protein folds? This is an important issue for understanding protein folding mechanism and guiding de novo protein design. Twenty naturally occurring amino acids and eight secondary structures consist of a 28-letter alphabet to determine folding kinetics and mechanism. Here we predict folding kinetic rates of proteins from many reduced alphabets. We find that a reduced alphabet of 10 letters achieves good correlation with folding rates, close to the one achieved by full 28-letter alphabet. Many other reduced alphabets are not significantly correlated to folding rates. The finding suggests that not all amino acids and secondary structures are equally important for protein folding. The foldable sequence of a protein could be designed using at least 10 folding units, which can either promote or inhibit protein folding. Reducing alphabet cardinality without losing key folding kinetic information opens the door to potentially faster machine learning and data mining applications in protein structure prediction, sequence alignment and protein design.
authors: Department of Chemistry and National Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin, 300071, People's Republic of China.
authors: Jitao T
authors: JT
authors: Huang
authors: Titi
authors: T
authors: Wang
authors: Shanran R
authors: SR
authors: Huang
authors: Xin
authors: X
authors: Li
mesh_terms: D000465:Algorithms; D000596:Amino Acids / Q000737:chemistry / Q000378:metabolism; D019295:Computational Biology / Q000379:methods*; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D020539:Sequence Analysis, Protein
chemical_list: D000596:Amino Acids; D011506:Proteins
keywords: folding unit; prediction; protein folding; reduced alphabet