|
|||||
|
|
Integration of small-angle X-ray scattering data into structural modeling of proteins and their assemblies |
|
| Authors: | Förster Friedrich Webb Benjamin Krukenberg Kristin A Tsuruta Hiro Agard David A Sali Andrej |
| Affiliation: | 1 Department of Bioengineering and Therapeutic Sciences, University of California at San Francisco, San Francisco, CA, USA 2 Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA, USA 3 California Institute for Quantitative Biosciences (QB3), University of California at San Francisco, San Francisco, CA, USA 4 Graduate Program in Chemistry and Chemical Biology, University of California at San Francisco, San Francisco, CA, USA 5 Stanford Synchrotron Radiation Laboratory, Stanford Linear Accelerator Center, 2575 Sand Hill Road, MS 69, Menlo Park, CA 94025-7015, USA 6 Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, CA, USA 7 Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA, USA |
| Abstract: | A major challenge in structural biology is to determine the configuration of domains and proteins in multidomain proteins and assemblies, respectively. All available data should be considered to maximize the accuracy and precision of these models. Small-angle X-ray scattering (SAXS) efficiently provides low-resolution experimental data about the shapes of proteins and their assemblies. Thus, we integrated SAXS profiles into our software for modeling proteins and their assemblies by satisfaction of spatial restraints. Specifically, we modeled the quaternary structures of multidomain proteins with structurally defined rigid domains as well as quaternary structures of binary complexes of structurally defined rigid proteins. In addition to SAXS profiles and the component structures, we used stereochemical restraints and an atomic distance-dependent statistical potential. The scoring function is optimized by a biased Monte Carlo protocol, including quasi-Newton and simulated annealing schemes. The final prediction corresponds to the best scoring solution in the largest cluster of many independently calculated solutions. To quantify how well the quaternary structures are determined based on their SAXS profiles, we used a benchmark of 12 simulated examples as well as an experimental SAXS profile of the homotetramer d-xylose isomerase. Optimization of the SAXS-dependent scoring function generally results in accurate models if sufficiently precise approximations for the constituent rigid bodies are available; otherwise, the best scoring models can have significant errors. Thus, SAXS profiles can play a useful role in the structural characterization of proteins and assemblies if they are combined with additional data and used judiciously. Our integration of a SAXS profile into modeling by satisfaction of spatial restraints will facilitate further integration of different kinds of data for structure determination of proteins and their assemblies. |
| Keywords: | SAXS, small-angle X-ray scattering EM, electron microscopy IMP, Integrative Modeling Platform DOPE, discrete optimized protein energy XI, xylose isomerase RBNC, rigid body in the native configuration |
| 本文献已被 ScienceDirect PubMed 等数据库收录！ | |