Computational models for the helix tilt angle.
The concept of hydrophobic imbalance and that of hydrophobic and hydrophilic centers are used along with side chain models in the computation of helix orientation and tilt angle in or near a membrane. Rotamer statistics are used to infer typical side chain positions and chain length for each amino acid, and the results are used in fast computation of helix orientation. Sliding windows are used to compute local tilt angles on long alpha-helices that defy idealized modeling and generate tilt angle profiles. Seven different procedures based on different formulas and hydrophobicity scales are used for comparison. These procedures generated very similar tilt angle profiles. These profiles provide insights into helix deformation, membrane destabilization, and similarity and differences between membrane proteins.
Cheng
Yizong
Y
Department of ECECS, University of Cincinnati, Cincinnati, Ohio 45221-0030, USA. yizong.cheng@uc.edu
Liu
Anping
A
Guo
Yuping
Y
Qi
Xiaoyang
X
D000465:Algorithms; D003198:Computer Simulation; D057927:Hydrophobic and Hydrophilic Interactions; D008565:Membrane Proteins / Q000737:chemistry; D008962:Models, Theoretical; D011487:Protein Conformation
D008565:Membrane Proteins