Comparison of NMR and crystal structures of membrane proteins and computational refinement to improve model quality.
| Publication Type | Academic Article |
| Authors | Koehler Leman J, D'Avino A, Bhatnagar Y, Gray J |
| Journal | Proteins |
| Volume | 86 |
| Issue | 1 |
| Pagination | 57-74 |
| Date Published | 11/08/2017 |
| ISSN | 1097-0134 |
| Keywords | Computer Simulation, Crystallography, X-Ray, Membrane Proteins, Nuclear Magnetic Resonance, Biomolecular |
| 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 |
| PubMed ID | 29044728 |
| PubMed Central ID | PMC5790426 |