A sequence-compatible amount of native burial information is sufficient for determining the structure of small globular proteins.
Protein tertiary structures are known to be encoded in amino acid sequences, but the problem of structure prediction from sequence continues to be a challenge. With this question in mind, recent simulations have shown that atomic burials, as expressed by atom distances to the molecular geometrical center, are sufficiently informative for determining native conformations of small globular proteins. Here we use a simple computational experiment to estimate the amount of this required burial information and find it to be surprisingly small, actually comparable with the stringent limit imposed by sequence statistics. Atomic burials appear to satisfy, therefore, minimal requirements for a putative dominating property in the folding code because they provide an amount of information sufficiently large for structural determination but, at the same time, sufficiently small to be encodable in sequences. In a simple analogy with human communication, atomic burials could correspond to the actual "language" encoded in the amino acid "script" from which the complexity of native conformations is recovered during the folding process.
Pereira de Araujo
Antonio F
AF
Laboratório de Biologia Teórica, Departamento de Biologia Celular, Universidade de Brasília, DF 70910-900 Brasília, Brazil.
Onuchic
José N
JN
D000596:Amino Acids / Q000737:chemistry*; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D008956:Models, Chemical; D008958:Models, Molecular; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*
D000596:Amino Acids; D011506:Proteins