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Faraggi, E1,2; Dunker, AK; Sussman, JL; Kloczkowski, A
Comparing NMR and X-ray protein structure: Lindemann-like parameters and NMR disorder
Source PublicationJOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
Language英语
KeywordBACKBONE TORSION ANGLES MAJOR URINARY PROTEIN INTRINSIC DISORDER STRUCTURE PREDICTION SECONDARY STRUCTURE CRYSTAL-STRUCTURE DYNAMICS DIFFRACTION CRYSTALLOGRAPHY RECOGNITION
AbstractDisordered 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.
2018
ISSN0739-1102
Volume36Issue:9Pages:2331-2341
Subject AreaBiochemistry & Molecular Biology ; Biophysics
MOST Discipline CatalogueBiochemistry & Molecular Biology ; Biophysics
DOI10.1080/07391102.2017.1352539
Indexed BySCIE
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Document Type期刊论文
Identifierhttp://ir.itp.ac.cn/handle/311006/22986
Collection理论物理所科研产出_SCI论文
Affiliation1.Indiana Univ Sch Med, Dept Biochem & Mol Biol, Indianapolis, IN 46202 USA
2.Nationwide Childrens Hosp, Res Inst, Battelle Ctr Math Med, Columbus, OH 43205 USA
3.Res & Informat Syst LLC, Carmel, IN 46032 USA
4.Indiana Univ Sch Med, Ctr Computat Biol & Bioinformat, Indianapolis, IN 46202 USA
5.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
Recommended Citation
GB/T 7714
Faraggi, E,Dunker, AK,Sussman, JL,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 Faraggi, E,Dunker, AK,Sussman, JL,&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 Faraggi, E,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.
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