Comparing NMR and X-ray protein structure: Lindemann-like parameters and NMR disorder
文献类型：期刊论文
| 作者 | Sussman, JL; Faraggi, E4,5; Dunker, AK; Kloczkowski, A |
| 刊名 | JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
 |
| 出版日期 | 2018 |
| 卷号 | 36期号:9页码:2331-2341 |
| 关键词 | BACKBONE TORSION ANGLES MAJOR URINARY PROTEIN INTRINSIC DISORDER STRUCTURE PREDICTION SECONDARY STRUCTURE CRYSTAL-STRUCTURE DYNAMICS DIFFRACTION CRYSTALLOGRAPHY RECOGNITION |
| ISSN号 | 0739-1102 |
| DOI | 10.1080/07391102.2017.1352539 |
| 英文摘要 | Disordered protein chains and segments are fast becoming a major pathway for our understanding of biological function, especially in more evolved species. However, the standard definition of disordered residues: the inability to constrain them in X-ray derived structures, is not easily applied to NMR derived structures. We carry out a statistical comparison between proteins whose structure was resolved using NMR and using X-ray protocols. We start by establishing a connection between these two protocols for obtaining protein structure. We find a close statistical correspondence between NMR and X-ray structures if fluctuations inherent to the NMR protocol are taken into account. Intuitively this tends to lend support to the validity of both NMR and X-ray protocols in deriving biomolecular models that correspond to in vivo conditions. We then establish Lindemann-like parameters for NMR derived structures and examine what order/disorder cutoffs for these parameters are most consistent with X-ray data and how consistent are they. Finally, we find critical value of L = 4 for the best correspondence between X-ray and NMR derived order/disorder assignment, judged by maximizing the Matthews correlation, and a critical value L = 1.5 if a balance between false positive and false negative prediction is sought. We examine a few non-conforming cases, and examine the origin of the structure derived in X-ray. This study could help in assigning meaningful disorder from NMR experiments. |
| 学科主题 | Biochemistry & Molecular Biology ; Biophysics |
| 语种 | 英语 |
| 源URL | [http://ir.itp.ac.cn/handle/311006/22986]  |
| 专题 | 理论物理研究所_理论物理所1978-2010年知识产出 |
| 作者单位 | 1.Sussman, Joel L.] Weizmann Inst Sci, Dept Struct Biol, IL-76100 Rehovot, Israel; Nationwide Childrens Hosp, Battelle Ctr Math Med, Columbus, OH 43215 USA; Ohio State Univ, Dept Pediat, Columbus, OH 43215 USA; Chinese Acad Sci, Kavli Inst Theoret Phys China, Beijing 100190, Peoples R China 2.Indiana Univ Sch Med, Ctr Computat Biol & Bioinformat, Indianapolis, IN 46202 USA 3.Res & Informat Syst LLC, Carmel, IN 46032 USA 4.Nationwide Childrens Hosp, Res Inst, Battelle Ctr Math Med, Columbus, OH 43205 USA 5.Indiana Univ Sch Med, Dept Biochem & Mol Biol, Indianapolis, IN 46202 USA |
| 推荐引用方式 GB/T 7714 | Sussman, JL,Faraggi, E,Dunker, AK,et al. Comparing NMR and X-ray protein structure: Lindemann-like parameters and NMR disorder[J]. JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS,2018,36(9):2331-2341. |
| APA | Sussman, JL,Faraggi, E,Dunker, AK,&Kloczkowski, A.(2018).Comparing NMR and X-ray protein structure: Lindemann-like parameters and NMR disorder.JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS,36(9),2331-2341. |
| MLA | Sussman, JL,et al."Comparing NMR and X-ray protein structure: Lindemann-like parameters and NMR disorder".JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS 36.9(2018):2331-2341. |
入库方式： OAI收割
来源：理论物理研究所
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