TY - JOUR
T1 - Folding of small helical proteins assisted by small-angle X-ray scattering profiles
AU - Wu, Yinghao
AU - Tian, Xia
AU - Lu, Mingyang
AU - Chen, Mingzhi
AU - Wang, Qinghua
AU - Ma, Jianpeng
N1 - Funding Information:
We wish to thank Tom Irving for helpful discussion in the early stage of the project. The authors gratefully acknowledge the support from the National Institutes of Health (R01-GM067801). M.C. and M.L. are partially supported by predoctoral fellowships from the W.M. Keck Foundation of the Gulf Coast Consortia through the Keck Center for Computational and Structural Biology.
PY - 2005/11
Y1 - 2005/11
N2 - 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∼6 Å 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.
AB - 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∼6 Å 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.
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U2 - 10.1016/j.str.2005.07.023
DO - 10.1016/j.str.2005.07.023
M3 - Article
C2 - 16271882
AN - SCOPUS:27644516255
SN - 0969-2126
VL - 13
SP - 1587
EP - 1597
JO - Structure
JF - Structure
IS - 11
ER -