Modeling of the structure of ribosomal protein L1 from the archaeon Haloarcula marismortui
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CTURE OF MACROMOLECULAR COMPOUNDS
Modeling of the Structure of Ribosomal Protein L1 from the Archaeon Haloarcula marismortui N. A. Nevskaya*, V. G. Kljashtorny, A. V. Vakhrusheva, M. B. Garber, and S. V. Nikonov Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow oblast, 142290 Russia *e-mail: [email protected] Received November 14, 2016
Abstract—The halophilic archaeon Haloarcula marismortui proliferates in the Dead Sea at extremely high salt concentrations (higher than 3 M). This is the only archaeon, for which the crystal structure of the ribosomal 50S subunit was determined. However, the structure of the functionally important side protuberance containing the abnormally negatively charged protein L1 (HmaL1) was not visualized. Attempts to crystallize HmaL1 in the isolated state or as its complex with RNA using normal salt concentrations (≤500 mM) failed. A theoretical model of HmaL1 was built based on the structural data for homologs of the protein L1 from other organisms, and this model was refined by molecular dynamics methods. Analysis of this model showed that the protein HmaL1 can undergo aggregation due to the presence of a cluster of positive charges unique for proteins L1. This cluster is located at the RNA–protein interface, which interferes with the crystallization of HmaL1 and the binding of the latter to RNA. DOI: 10.1134/S1063774517040137
INTRODUCTION The three-dimensional structure of the ribosomal 50S subunit from the archaeon Haloarcula marismortui was determined at atomic resolution more than 15 years ago [1] and was later refined several times. However, the initial, as well as subsequent, models lack regions belonging to a number of mobile elements, in particular, to L1 and P(L12) protuberances. The latest supplemented model of the structure was obtained in [2] using the atomic coordinates and structure amplitudes from the Protein Data Bank. The structure of the two-domain N-terminal fragment of the protein P0 determined in [3] was inserted into the structure of the 50S subunit from the archaeon H. marismortui, and several refinement cycles alternated with the manual rebuilding of the model were performed. The electron density map calculated from the newly refined model revealed a substantial part of the P(L12) protuberance, a part of the structure of the protein L5, the protein XL, and 12 nucleotide pairs of the helix 76 of the L1 protuberance. However, the electron density corresponding to the protein L1 and nucleotides of the helices 77 and 78 that contact the protein L1 was of a very poor quality and did not allow the determination of the complete structure of the L1 protuberance. The insertion of the known structures of ribosomal proteins L1 in complexes with rRNA fragments into the structure of the large ribosomal subunit of H. marismortui and the subsequent refinement of the resulting model did not lead
to the improvement of the region of the electron density map in question. This suggests that the threedimensional structure of the L1 protuberance portion c
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