The Solution Structure of Ribosomal Protein L18 from Bacillus stearothermophilus

A creature with a hundred waggly tails: intrinsically disordered proteins in the ribosome

Intrinsic disorder (i.e., lack of a unique 3-D structure) is a common phenomenon, and many biologically active proteins are disordered as a whole, or contain long disordered regions. These intrinsically disordered proteins/regions constitute a significant part of all proteomes, and their functional repertoire is complementary to functions of ordered proteins. In fact, intrinsic disorder represents an important driving force for many specific functions. An illustrative example of such disorder-centric functional class is RNA-binding proteins. In this study, we present the results of comprehensive bioinformatics analyses of the abundance and roles of intrinsic disorder in 3,411 ribosomal proteins from 32 species. We show that many ribosomal proteins are intrinsically disordered or hybrid proteins that contain ordered and disordered domains. Predicted globular domains of many ribosomal proteins contain noticeable regions of intrinsic disorder. We also show that disorder in ribosomal proteins has different characteristics compared to other proteins that interact with RNA and DNA including overall abundance, evolutionary conservation, and involvement in protein-protein interactions. Furthermore, intrinsic disorder is not only abundant in the ribosomal proteins, but we demonstrate that it is absolutely necessary for their various functions.

A creature with a hundred waggly tails: intrinsically disordered proteins in the ribosome

Intrinsic disorder (i.e., lack of a unique 3-D structure) is a common phenomenon, and many biologically active proteins are disordered as a whole, or contain long disordered regions. These intrinsically disordered proteins/regions constitute a significant part of all proteomes, and their functional repertoire is complementary to functions of ordered proteins. In fact, intrinsic disorder represents an important driving force for many specific functions. An illustrative example of such disorder-centric functional class is RNA-binding proteins. In this study, we present the results of comprehensive bioinformatics analyses of the abundance and roles of intrinsic disorder in 3,411 ribosomal proteins from 32 species. We show that many ribosomal proteins are intrinsically disordered or hybrid proteins that contain ordered and disordered domains. Predicted globular domains of many ribosomal proteins contain noticeable regions of intrinsic disorder. We also show that disorder in ribosomal proteins has different characteristics compared to other proteins that interact with RNA and DNA including overall abundance, evolutionary conservation, and involvement in protein–protein interactions. Furthermore, intrinsic disorder is not only abundant in the ribosomal proteins, but we demonstrate that it is absolutely necessary for their various functions.

Association of a novel preribosomal complex in Trypanosoma brucei determined by fluorescence resonance energy transfer

We have previously reported that the trypanosome-specific proteins P34 and P37 form a unique preribosomal complex with ribosomal protein L5 and 5S rRNA in the nucleoplasm. We hypothesize that this novel trimolecular complex is necessary for stabilizing 5S rRNA in Trypanosoma brucei and is essential for the survival of the parasite. In vitro quantitative analysis of the association between the proteins L5 and P34 is fundamental to our understanding of this novel complex and thus our ability to exploit its unique characteristics. Here we used in vitro fluorescence resonance energy transfer (FRET) to analyze the association between L5 and P34. First, we demonstrated that FRET can be used to confirm the association between L5 and P34. We then determined that the binding constant for L5 and P34 is 0.60 ± 0.03 μM, which is in the range of protein-protein binding constants for RNA binding proteins. In addition, we used FRET to identify the critical regions of L5 and P34 involved in the protein-protein association. We found that the N-terminal APK-rich domain and RNA recognition motif (RRM) of P34 and the L18 domain of L5 are important for the association of the two proteins with each other. These results provide us with the framework for the discovery of ways to disrupt this essential complex.

The RCI server: rapid and accurate calculation of protein flexibility using chemical shifts

Protein motions play important roles in numerous biological processes such as enzyme catalysis, muscle contractions, antigen–antibody interactions, gene regulation and virus assembly. Knowledge of protein flexibility is also important in rational drug design, protein docking and protein engineering. However, the experimental measurement of protein motions is often difficult, requiring sophisticated experiments, complex data analysis and detailed information about the protein's tertiary structure. As a result, there is a considerable interest in developing simpler, more effective ways of quantifying protein flexibility. Recently, we described a method, called the random coil index (RCI), which is able to quantitatively estimate backbone root mean square fluctuations (RMSFs) of structural ensembles and order parameters using only chemical shifts. The RCI method is very fast (<5 s) and exceedingly robust. It also offers an excellent alternative to traditional methods of measuring protein flexibility. We have recently extended the RCI concept and implemented it as a web server. This server allows facile, accurate and fully automated predictions of MD RMSF values, NMR RMSF values and model-free order parameters (S²) directly from chemical shift assignments. It also performs automatic chemical shift re-referencing to ensure consistency and reproducibility. On average, the correlation between RCI predictions and experimentally obtained motional amplitudes is within the range from 0.77 to 0.82. The server is available at http://wishart.biology.ualberta.ca/rci.

NMR for structural proteomics of Thermotoga maritima: screening and structure determination

This paper describes the NMR screening of 141 small (<15 kDa) recombinant Thermotoga maritima proteins for globular folding. The experimental data shows that approximately 25% of the screened proteins are folded under our screening conditions, which makes this procedure an important step for selecting those proteins that are suitable for structure determination. A comparison of screening based either on 1D 1H NMR with unlabeled proteins or on 2D [1H,15N]-COSY with uniformly 15N-labeled proteins is presented, and a comprehensive analysis of the 1D 1H NMR screening data is described. As an illustration of the utility of these methods to structural proteomics, the NMR structure determination of TM1492 (ribosomal protein L29) is presented. This 66-residue protein consists of a N-terminal 3(10)-helix and two long alpha-helices connected by a tight turn centered about glycine 35, where conserved leucine and isoleucine residues in the two alpha-helices form a small hydrophobic core.