The "random-coil" state of proteins: comparison of database statistics and molecular simulations.
This study presents a comparison of two models of the random-coil state, one based on statistical distributions from the structural database and the other based on molecular dynamics simulations. The database model relies on the assumption that the random- or statistical-coil state of a particular residue can be described by its conformational distribution in a sufficiently diverse subset of protein structures. The molecular dynamics model is based on distributions from molecular simulations carried out on "dipeptide" models (single residues with N-terminal acetyl and C-terminal N'-methyl amide blocking groups). A comparison of the two models for the residues Ala, Asn, Asp, Gly, and Val indicates that the database distributions are greatly influenced by long-range interactions and dominated by specific recognizable elements of protein structure. In contrast, the limited structural scope of the dipeptide models presents the extreme case of a peptide under the influence of only short-range interactions. The models were evaluated by a comparison of scalar coupling constants calculated from the conformational distributions and compared with experimentally values determined for unstructured peptides. Although the models gave different distributions, there was similar agreement with experiment. This comparison emphasizes the differences and limitations in each model and highlights the difficulty in presenting an accurate picture of the random-coil state. Proteins 1999;36:407- 418.
O'Connell
T M
TM
Division of Medicinal Chemistry, School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599-7260, USA.
Wang
L
L
Tropsha
A
A
Hermans
J
J
D003198:Computer Simulation; D016208:Databases, Factual; D004151:Dipeptides / Q000737:chemistry; D016013:Likelihood Functions; D008958:Models, Molecular; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D016008:Statistical Distributions; D013816:Thermodynamics
D004151:Dipeptides; D011506:Proteins