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NMR characterization of conformational fluctuations and noncovalent interactions of SUMO protein from Drosophila melanogaster (dSmt3)
Author(s) -
Kaur Anupreet,
Kumar Sandeep,
Jaiswal Nancy,
Vashisht Ashutosh,
Kumar Dinesh,
Gahlay Gagandeep K.,
Mithu Venus S.
Publication year - 2019
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.25690
Subject(s) - native state , non covalent interactions , chemistry , biophysics , drosophila melanogaster , population , chemical shift , protein–protein interaction , melanogaster , nuclear magnetic resonance spectroscopy , amino acid , stereochemistry , crystallography , biochemistry , biology , hydrogen bond , molecule , demography , organic chemistry , sociology , gene
Structural heterogeneity in the native‐state ensemble of dSmt3, the only small ubiquitin‐like modifier (SUMO) in Drosophila melanogaster , was investigated and compared with its human homologue SUMO1. Temperature dependence of amide proton's chemical shift was studied to identify amino acids possessing alternative structural conformations in the native state. Effect of small concentration of denaturant (1M urea) on this population was also monitored to assess the ruggedness of near‐native energy landscape. Owing to presence of many such amino acids, especially in the β 2 ‐loop‐α region, the native state of dSmt3 seems more flexible in comparison to SUMO1. Information about backbone dynamics in ns‐ps timescale was quantified from the measurement of 15 N‐relaxation experiments. Furthermore, the noncovalent interaction of dSmt3 and SUMO1 with Daxx12 (Daxx 729 DPEEIIVLSDSD 740 ), a [V/I]‐X‐[V/I]‐[V/I]‐based SUMO interaction motif, was characterized using Bio‐layer Interferometery and NMR spectroscopy. Daxx12 fits itself in the groove formed by β 2 ‐loop‐α structural region in both dSmt3 and SUMO1, but the binding is stronger with the former. Flexibility of β 2 ‐loop‐α region in dSmt3 is suspected to assist its interaction with Daxx12. Our results highlight the role of native‐state flexibility in assisting noncovalent interactions of SUMO proteins especially in organisms where a single SUMO isoform has to tackle multiple substrates single handedly.