Comparison of NMR and crystal structures of membrane proteins and computational refinement to improve model quality |
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| Authors: | Julia Koehler Leman Andrew R. D'Avino Yash Bhatnagar Jeffrey J. Gray |
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| Affiliation: | 1. Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland;2. Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, New York;3. Department of Biology, Johns Hopkins University, Baltimore, Maryland |
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| 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 Å 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. |
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| Keywords: | membrane proteins protein structure protein modeling structure refinement structural quality Rosetta software |
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