Structural and Mutagenesis Studies Evince the Role of the Extended Protuberant Domain of Ribosomal Protein uL10 in Protein Translation

Validation of the solution structure of dimerization domain of PRC1

Cell-cycle dependent proteins are indispensible for the accurate division of cells, a group of proteins called Microtubule-associated proteins (MAPs) are important to cell division as it bind microtubules and participate with other co-factors to form the spindle midbody, which works as the workhorse of cell-division. PRC1 is a distinguishing member of MAPs, as it is a human MAP and works as the key in mediating daughter cell segregation in ana-phase and telo-phase. The physiological significance of PRC1 calls for a high resolution three-dimensional structure. The crystal structure of PRC1 was published but has low resolution (>3 Å) and incomplete sidechains, placing hurdles to understanding the structure-function relationships of PRC1, therefore, we determined the high-resolution solution structure of PRC1’s dimerization domain using NMR spectroscopy. Significant differences between the crystal structure and the solution structure can be observed, the main differences center around the N terminus and the end of the alpha-Helix H2. Furthermore, detailed structure analyses revealed that the hydrophobic core packing of the solution and crystal structures are also different. To validate the solution structure, we used Hydrogen-deuterium exchange experiments that address the structural discrepancies between the crystal and solution structure; we also generated mutants that are key to the differences in the crystal and solution structures, measuring its structural or thermal stability by NMR spectroscopy and Fluorescence Thermal Shift Assays. These results suggest that N terminal residues are key to the integrity of the whole protein, and the solution structure of the dimerization domain better reflects the conformation PRC1 adopted in solution conditions.

The flexible N-terminal motif of uL11 unique to eukaryotic ribosomes interacts with P-complex and facilitates protein translation

Eukaryotic uL11 contains a conserved MPPKFDP motif at the N-terminus that is not found in archaeal and bacterial homologs. Here, we determined the solution structure of human uL11 by NMR spectroscopy and characterized its backbone dynamics by 15N-1H relaxation experiments. We showed that these N-terminal residues are unstructured and flexible. Structural comparison with ribosome-bound uL11 suggests that the linker region between the N-terminal domain and C-terminal domain of human uL11 is intrinsically disordered and only becomes structured when bound to the ribosomes. Mutagenesis studies show that the N-terminal conserved MPPKFDP motif is involved in interacting with the P-complex and its extended protuberant domain of uL10 in vitro. Truncation of the MPPKFDP motif also reduced the poly-phenylalanine synthesis in both hybrid ribosome and yeast mutagenesis studies. In addition, G→A/P substitutions to the conserved GPLG motif of helix-1 reduced poly-phenylalanine synthesis to 9-32% in yeast ribosomes. We propose that the flexible N-terminal residues of uL11, which could extend up to ∼25 Å from the N-terminal domain of uL11, can form transient interactions with the uL10 that help to fetch and fix it into a position ready for recruiting the incoming translation factors and facilitate protein synthesis.

N-Terminus-Mediated Solution Structure of Dimerization Domain of PRC1

Microtubule-associated proteins (MAPs) are essential for the accurate division of a cell into two daughter cells. These proteins target specific microtubules to be incorporated into the spindle midzone, which comprises a special array of microtubules that initiate cytokinesis during anaphase. A representative member of the MAPs is Protein Regulator of Cytokinesis 1 (PRC1), which self-multimerizes to cross-link microtubules, the malfunction of which might result in cancerous cells. The importance of PRC1 multimerization makes it a popular target for structural studies. The available crystal structure of PRC1 has low resolution (>3 Å) and accuracy, limiting a better understanding of the structure-related functions of PRC1. Therefore, we used NMR spectroscopy to better determine the structure of the dimerization domain of PRC1. The NMR structure shows that the PRC1 N terminus is crucial to the overall structure integrity, but the crystal structure bespeaks otherwise. We systematically addressed the role of the N terminus by generating a series of mutants in which N-terminal residues methionine (Met1) and arginine (Arg2) were either deleted, extended or substituted with other rationally selected amino acids. Each mutant was subsequently analyzed by NMR spectroscopy or fluorescence thermal shift assays for its structural or thermal stability; we found that N-terminal perturbations indeed affected the overall protein structure and that the solution structure better reflects the conformation of PRC1 under solution conditions. These results reveal that the structure of PRC1 is governed by its N terminus through hydrophobic interactions with other core residues, such hitherto unidentified N-terminal conformations might shed light on the structure−function relationships of PRC1 or other proteins. Therefore, our study is of major importance in terms of identifying a novel structural feature and can further the progress of protein folding and protein engineering.