Title | Comparison of NMR and crystal structures of membrane proteins and computational refinement to improve model quality. |
Publication Type | Journal Article |
Year of Publication | 2018 |
Authors | Leman JKoehler, D'Avino AR, Bhatnagar Y, Gray JJ |
Journal | Proteins |
Volume | 86 |
Issue | 1 |
Pagination | 57-74 |
Date Published | 2018 Jan |
ISSN | 1097-0134 |
Keywords | Algorithms, Computer Simulation, Crystallography, X-Ray, Databases, Protein, Membrane Proteins, Models, Molecular, Molecular Structure, Nuclear Magnetic Resonance, Biomolecular, Protein Conformation |
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. |
DOI | 10.1002/prot.25402 |
Alternate Journal | Proteins |
PubMed ID | 29044728 |
PubMed Central ID | PMC5790426 |
Grant List | R01 GM078221 / GM / NIGMS NIH HHS / United States |
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