Elastic properties of ribosomal RNA building blocks: molecular dynamics of the GTPase-associated center rRNA

Explicit solvent molecular dynamics (MD) was used to describe the intrinsic flexibility of the helix 42–44 portion of the 23S rRNA (abbreviated as Kt-42+rGAC; kink-turn 42 and GTPase-associated center rRNA). The bottom part of this molecule consists of alternating rigid and flexible segments. The first flexible segment (Hinge1) is the highly anharmonic kink of Kt-42. The second one (Hinge2) is localized at the junction between helix 42 and helices 43/44. The rigid segments are the two arms of helix 42 flanking the kink. The whole molecule ends up with compact helices 43/44 (Head) which appear to be modestly compressed towards the subunit in the Haloarcula marismortui X-ray structure. Overall, the helix 42–44 rRNA is constructed as a sophisticated intrinsically flexible anisotropic molecular limb. The leading flexibility modes include bending at the hinges and twisting. The Head shows visible internal conformational plasticity, stemming from an intricate set of base pairing patterns including dynamical triads and tetrads. In summary, we demonstrate how rRNA building blocks with contrasting intrinsic flexibilities can form larger architectures with highly specific patterns of preferred low-energy motions and geometries

A Computational Investigation on the Connection between Dynamics Properties of Ribosomal Proteins and Ribosome Assembly

Assembly of the ribosome from its protein and RNA constituents has been studied extensively over the past 50 years, and experimental evidence suggests that prokaryotic ribosomal proteins undergo conformational changes during assembly. However, to date, no studies have attempted to elucidate these conformational changes. The present work utilizes computational methods to analyze protein dynamics and to investigate the linkage between dynamics and binding of these proteins during the assembly of the ribosome. Ribosomal proteins are known to be positively charged and we find the percentage of positive residues in r-proteins to be about twice that of the average protein: Lys+Arg is 18.7% for E. coli and 21.2% for T. thermophilus. Also, positive residues constitute a large proportion of RNA contacting residues: 39% for E. coli and 46% for T. thermophilus. This affirms the known importance of charge-charge interactions in the assembly of the ribosome. We studied the dynamics of three primary proteins from E. coli and T. thermophilus 30S subunits that bind early in the assembly (S15, S17, and S20) with atomic molecular dynamic simulations, followed by a study of all r-proteins using elastic network models. Molecular dynamics simulations show that solvent-exposed proteins (S15 and S17) tend to adopt more stable solution conformations than an RNA-embedded protein (S20). We also find protein residues that contact the 16S rRNA are generally more mobile in comparison with the other residues. This is because there is a larger proportion of contacting residues located in flexible loop regions. By the use of elastic network models, which are computationally more efficient, we show that this trend holds for most of the 30S r-proteins

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Stereotactic Body Radiotherapy of a Solitary Metachronous Sphenoid Metastasis from Renal Cell Cancer: A Case Report

Nasosinus metastases from kidney cancer are an unusual clinical presentation although some cases are reported in the literature. Among these cases, sphenoidal metastases are even rarer. Here we report a case of lone sphenoid metastasis in patients with papillary renal cell cancer. Eight months after radical nephrectomy, the patient presented with progressively worsening diplopia. Magnetic resonance imaging showed a mass in the right sphenoid sinus. Histopathological examination of the biopsy sample confirmed diagnosis of sinonasal metastasis from papillary renal cell carcinoma. The patient was declined for surgical management and received stereotactic body radiation therapy. Reassessment MRI at 4 months showed a complete response of the treated sphenoid lesion. </jats:p

Une pratique funéraire atypique pour l’âge du Bronze final en Lorraine (France)

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