@article{87f54dfb245640da8700f32aa682f4d9,
title = "Comparison of NMR and crystal structures of membrane proteins and computational refinement to improve model quality",
abstract = "Membrane proteins are challenging to study and restraints for structure determination are typically sparse or of low resolution because the membrane environment that surrounds them leads to a variety of experimental challenges. When membrane protein structures are determined by different techniques in different environments, a natural question is “which structure is most biologically relevant?” Towards answering this question, we compiled a dataset of membrane proteins with known structures determined by both solution NMR and X-ray crystallography. By investigating differences between the structures, we found that RMSDs between crystal and NMR structures are below 5 {\AA} in the membrane region, NMR ensembles have a higher convergence in the membrane region, crystal structures typically have a straighter transmembrane region, have higher stereo-chemical correctness, and are more tightly packed. After quantifying these differences, we used high-resolution refinement of the NMR structures to mitigate them, which paves the way for identifying and improving the structural quality of membrane proteins.",
keywords = "Rosetta software, membrane proteins, protein modeling, protein structure, structural quality, structure refinement",
author = "{Koehler Leman}, Julia and D'Avino, {Andrew R.} and Yash Bhatnagar and Gray, {Jeffrey J.}",
note = "Funding Information: The authors would like to thank Meera Valliath for work on the database, Dr. Georg K{\"u}nze for the calculation of the Q-factors for DAGK, and RosettaCommons for helpful suggestions. We also thank the reviewers for their constructive comments and sharing detailed observations about specific structures in our database. Funding was provided by RosettaCommons to J.K.L. and NIH R01 GM-078221 to J.J.G. and J.K.L. J.K.L. is funded by the Flatiron Institute at the Simons Foundation. Funding Information: The authors would like to thank Meera Valliath for work on the database, Dr. Georg Ku€nze for the calculation of the Q-factors for DAGK, and RosettaCommons for helpful suggestions. We also thank the reviewers for their constructive comments and sharing detailed observations about specific structures in our database. Funding was provided by RosettaCommons to J.K.L. and NIH R01 GM-078221 to J.J.G. and J.K.L. J.K.L. is funded by the Flatiron Institute at the Simons Foundation. Funding Information: Funding for the study described in this article was provided by Rosetta Commons. Dr. Gray is also an unpaid member of the Executive Board of the RosettaCommons. Under an institutional participation agreement between the University of Washington, acting on behalf of the RosettaCommons, and the Johns Hopkins University (JHU), JHU may be entitled to a portion of revenue received on licensing of software described in this article. This arrangement has been reviewed and approved by the Johns Hopkins University in accordance with its conflict of interest policies. Publisher Copyright: {\textcopyright} 2017 Wiley Periodicals, Inc.",
year = "2018",
month = jan,
doi = "10.1002/prot.25402",
language = "English (US)",
volume = "86",
pages = "57--74",
journal = "Proteins: Structure, Function and Genetics",
issn = "0887-3585",
publisher = "Wiley-Liss Inc.",
number = "1",
}