Quantum mechanical calculations of tryptophan and comparison with conformations in native proteins.
We report a detailed analysis of the potential energy surface of N-acetyl-l-tryptophan-N-methylamide, (NATMA) both in the gas phase and in solution. The minima are identified using the density-functional-theory (DFT) with the 6-31g(d) basis set. The full potential energy surface in terms of torsional angles is spanned starting from various initial configurations. We were able to locate 77 distinct L-minima. The calculated energy maps correspond to the intrinsic conformational propensities of the individual NATMA molecule. We show that these conformations are essentially similar to the conformations of tryptophan in native proteins. For this reason, we compare the results of DFT calculations in the gas and solution phases with native state conformations of tryptophan obtained from a protein library. In native proteins, tryptophan conformations have strong preferences for the beta sheet, right-handed helix, tight turn, and bridge structures. The conformations calculated by DFT, the solution-phase results in particular, for the single tryptophan residue are in agreement with native state values obtained from the Protein Data Bank.
Yurtsever
Ersin
E
College of Arts and Sciences and College of Engineering, Koc University, Rumelifeneri Yolu, Sariyer 34450 Istanbul, Turkey.
Yuret
Deniz
D
Erman
Burak
B
D000465:Algorithms; D015394:Molecular Structure; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D011789:Quantum Theory; D014364:Tryptophan / Q000031:analogs & derivatives* / Q000737:chemistry
D011506:Proteins; C071046:N-acetyltryptophan methylamide; D014364:Tryptophan