Geometric and statistical properties of the mean-field hydrophobic-polar model, the large-small model, and real protein sequences.
Lattice models, for their coarse-grained nature, are best suited for the study of the "designability problem," the phenomenon in which most of the about 16 000 proteins of known structure have their native conformations concentrated in a relatively small number of about 500 topological classes of conformations. Here it is shown that on a lattice the most highly designable simulated protein structures are those that have the largest number of surface-core switchbacks. A combination of physical, mathematical, and biological reasons that causes the phenomenon is given. By comparing the most foldable model peptides with protein sequences in the Protein Data Bank, it is shown that whereas different models may yield similar designabilities, predicted foldable peptides will simulate natural proteins only when the model incorporates the correct physics and biology, in this case if the main folding force arises from the differing hydrophobicity of the residues, but does not originate, say, from the steric hindrance effect caused by the differing sizes of the residues.
Shih
C T
CT
National Center for High-Performance Computing, Hsinchu, Taiwan, Republic of China.
Su
Z Y
ZY
Gwan
J F
JF
Hao
B L
BL
Hsieh
C H
CH
Lo
J L
JL
Lee
H C
HC
D000595:Amino Acid Sequence; D019295:Computational Biology / Q000379:methods / Q000706:statistics & numerical data; D030562:Databases, Protein; D057927:Hydrophobic and Hydrophilic Interactions; D008954:Models, Biological; D008956:Models, Chemical; D015233:Models, Statistical; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*
D011506:Proteins