Theory and practice of using solvent paramagnetic relaxation enhancement to characterize protein conformational dynamics
文献类型：期刊论文
| 作者 | Gong, Zhou1,3; Schwieters, Charles D.2; Tang, Chun1,3 |
| 刊名 | METHODS
 |
| 出版日期 | 2018-09-15 |
| 卷号 | 148页码:48-56 |
| 关键词 | Paramagnetic relaxation enhancement Protein cosolute Structure refinement Molecular dynamics simulation Monte Carlo algorithm Xplor-NIH |
| ISSN号 | 1046-2023 |
| DOI | 10.1016/j.ymeth.2018.04.006 |
| 英文摘要 | Paramagnetic relaxation enhancement (PRE) has been established as a powerful tool in NMR for investigating protein structure and dynamics. The PRE is usually measured with a paramagnetic probe covalently attached at a specific site of an otherwise diamagnetic protein. The present work provides the numerical formulation for probing protein structure and conformational dynamics based on the solvent PRE (sPRE) measurement, using two alternative approaches. An inert paramagnetic cosolute randomly collides with the protein, and the resulting sPRE manifests the relative solvent exposure of protein nuclei. To make the back-calculated sPRE values most consistent with the observed values, the protein structure is either refined against the sPRE, or an ensemble of conformers is selected from a pre-generated library using a Monte Carlo algorithm. The ensemble structure comprises either N conformers of equal occupancy, or two conformers with different relative populations. We demonstrate the sPRE method using GM, a structurally rigid protein, and calmodulin, a protein comprising two domains and existing in open and closed states. The sPRE can be computed with a stand-alone program for rapid evaluation, or with the invocation of a module in the latest release of the structure calculation software Xplor-NIH. As a label-free method, the sPRE measurement can be readily integrated with other biophysical techniques. The current limitations of the sPRE method are also discussed, regarding accurate measurement and theoretical calculation, model selection and suitable timescale. |
| WOS关键词 | CONTRAST AGENTS ; SPIN RELAXATION ; NMR ; COMPLEXES ; TRANSIENT ; DOMAIN ; MACROMOLECULES ; RESOLUTION ; SURFACES ; MOLECULE |
| 资助项目 | National Key R&D Program of China[2016YFA0501200] ; National Natural Science Foundation of China[91753132] ; National Natural Science Foundation of China[31770799] ; National Natural Science Foundation of China[31400735] ; NIH CIT Intramural program |
| WOS研究方向 | Biochemistry & Molecular Biology |
| 语种 | 英语 |
| WOS记录号 | WOS:000445444300007 |
| 出版者 | ACADEMIC PRESS INC ELSEVIER SCIENCE |
| 资助机构 | National Key R&D Program of China ; National Key R&D Program of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; NIH CIT Intramural program ; NIH CIT Intramural program ; National Key R&D Program of China ; National Key R&D Program of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; NIH CIT Intramural program ; NIH CIT Intramural program ; National Key R&D Program of China ; National Key R&D Program of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; NIH CIT Intramural program ; NIH CIT Intramural program ; National Key R&D Program of China ; National Key R&D Program of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; NIH CIT Intramural program ; NIH CIT Intramural program |
| 源URL | [http://ir.wipm.ac.cn/handle/112942/13116]  |
| 专题 | 中国科学院武汉物理与数学研究所 |
| 通讯作者 | Tang, Chun |
| 作者单位 | 1.Chinese Acad Sci, Wuhan Inst Phys & Math, State Key Lab Magnet Resonance & Atom Mol Phys, CAS Key Lab Magnet Resonance Biol Syst, Wuhan 430071, Hubei, Peoples R China 2.NIH, Off Intramural Res, Ctr Informat Technol, Bldg 12A, Bethesda, MD 20892 USA 3.Chinese Acad Sci, Wuhan Inst Phys & Math, Natl Ctr Magnet Resonance Wuhan, Wuhan 430071, Hubei, Peoples R China |
| 推荐引用方式 GB/T 7714 | Gong, Zhou,Schwieters, Charles D.,Tang, Chun. Theory and practice of using solvent paramagnetic relaxation enhancement to characterize protein conformational dynamics[J]. METHODS,2018,148:48-56. |
| APA | Gong, Zhou,Schwieters, Charles D.,&Tang, Chun.(2018).Theory and practice of using solvent paramagnetic relaxation enhancement to characterize protein conformational dynamics.METHODS,148,48-56. |
| MLA | Gong, Zhou,et al."Theory and practice of using solvent paramagnetic relaxation enhancement to characterize protein conformational dynamics".METHODS 148(2018):48-56. |
入库方式： OAI收割
来源：武汉物理与数学研究所
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