Folding of small helical proteins assisted by small-angle X-ray scattering profiles.
This paper reports a computational method for folding small helical proteins. The goal was to determine the overall topology of proteins given secondary structure assignment on sequence. In doing so, a Monte Carlo protocol, which combines coarse-grained normal modes and a Hamiltonian at a different scale, was developed to enhance sampling. In addition to the knowledge-based potential functions, a small-angle X-ray scattering (SAXS) profile was also used as a weak constraint for guiding the folding. The algorithm can deliver structural models with overall correct topology, which makes them similar to those of 5 approximately 6 A cryo-EM density maps. The success could contribute to make the SAXS technique a fast and inexpensive solution-phase experimental method for determining the overall topology of small, soluble, but noncrystallizable, helical proteins.
Wu
Yinghao
Y
Department of Bioengineering, Rice University, Houston, Texas 77005, USA.
Tian
Xia
X
Lu
Mingyang
M
Chen
Mingzhi
M
Wang
Qinghua
Q
Ma
Jianpeng
J
D000818:Animals; D019295:Computational Biology; D008958:Models, Molecular; D009010:Monte Carlo Method; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D012542:Scattering, Radiation; D014961:X-Ray Diffraction; D014965:X-Rays
D011506:Proteins