SUMMARY Eukaryotic cells contain large RNA-protein assemblies referred to as RNP granules, whose assembly is promoted by both traditional protein interactions and intrinsically disordered protein domains. Using RNP granules as an example, we provide evidence for an assembly mechanism of large cellular structures wherein specific protein-protein or protein-RNA interactions act together with promiscuous interactions of intrinsically disordered regions (IDRs). This synergistic assembly mechanism illuminates RNP granule assembly and explains why many components of RNP granules, and other large dynamic assemblies, contain IDRs linked to specific protein-protein or protein-RNA interaction modules. We suggest assemblies based on combinations of specific interactions and promiscuous IDRs are common features of eukaryotic cells.

We describe a large number of binding studies in aqueous media designed to provide new insights into noncovalent binding interactions, especially the cation-a interaction. The studies include 7 different hosts, over 70 guests, and over 150 new binding constants. In addition to the now standard NMR methods, circular dichroism has proven to be an especially useful tool for determining aqueous binding constants. We have found that, in addition to the alkyliminium and tetraalkylammonium guests we have studied previously, sulfonium and guanidinium guests also show substantial cation-r effects. Bromination of the host greatly enhances its binding ability in a general fashion, primarily as a result of hydrophobic interactions. Addition of methoxy groups did not enhance binding, apparently as a result of a collapse of the host into a conformation that is not suitable for binding. Replacement of two benzene rings of the host by furans or thiophenes also did not enhance binding. Ab initio calculations provide a rationalization for this effect and suggest a clearer model for the cation-a interaction.

The CC chemokine, MCP-1, has been identified as a major chemoattractant for T cells and monocytes, and plays a significant role in the pathology of inflammatory diseases. To identify the regions of MCP-1 that contact its receptor, CCR2, we substituted all surface-exposed residues with alanine. Some residues were also mutated to other amino acids to identify the importance of charge, hydrophobicity, or aromaticity at specific positions. The binding affinity of each mutant for CCR2 was assayed with THP-1 and CCR2-transfected CHL cells. The majority of point mutations had no effect. Residues at the N-terminus of the protein, known to be crucial for signaling, contribute less than a factor of 10 to the binding affinity. However, two clusters of primarily basic residues (R24, K35, K38, K49, and Y13), separated by a 35 A hydrophobic groove, reduced the level of binding by 15-100-fold. A peptide fragment encompassing residues 13-35 recapitulated some of the mutational data derived from the intact protein. It exhibited modest binding as a linear peptide and dramatically improved affinity when the region which adopts a single turn of a 3(10)-helix in the protein, which includes R24, was constrained by a disulfide bond. Additional constraints at the ends of the peptide, corresponding to the disulfide between the first and third cysteines in MCP-1, yielded further improvements in affinity. Together, these data suggest a model in which a large surface area of MCP-1 contacts the receptor, and the accumulation of a number of weak interactions results in the 35 pM affinity observed for the wild-type (WT) protein. The receptor binding site of MCP-1 also is significantly different from the binding sites of RANTES and IL-8, providing insight into the issue of receptor specificity. It was previously shown that the N-terminus of CCR2 is critical for binding MCP-1 [Monteclaro, F. S., and Charo, I. F. (1996) J. Biol. Chem. 271, 19084-92; Monteclaro, F. S., and Charo, I. F. (1997) J. Biol. Chem. 272, 23186-90]. Point mutations of six acidic residues in this region of the receptor were made to test their role in ligand binding. This identified D25 and D27 of the DYDY motif as being important. On the basis of our data, we propose a model in which the receptor N-terminus lies along the hydrophobic groove in an extended fashion, placing the DYDY motif near the basic cluster involving R24 and K49 of MCP-1. This in turn orients the signaling residues (Y13 and the N-terminus) for productive interaction with the receptor.

RNAs besides tRNA and rRNA contain chemical modifications, including the recently described 5′ nicotinamide-adenine dinucleotide (NAD + ) RNA in bacteria. Whether 5′ NAD-RNA exists in eukaryotes remains unknown. We demonstrate that 5′ NAD-RNA is found on subsets of nuclear and mitochondrial encoded mRNAs in Saccharomyces cerevisiae. NAD-mRNA appears to be produced cotranscriptionally because NAD-RNA is also found on pre-mRNAs, and only on mitochondrial transcripts that are not 5′ end processed. These results define an additional 5′ RNA cap structure in eukaryotes and raise the possibility that this 5′ NAD + cap could modulate RNA stability and translation on specific subclasses of mRNAs.T he number and prevalence of known chemical modifications on mRNAs have dramatically increased in the past several years (1). Quantification of these modification events suggests they occur in many RNAs (2, 3). Importantly, several of these modifications have functional consequences (4-6). For example, the presence of a single N 6 -methyladenosine within the 5′ UTR of an mRNA increases translation initiation (4). In addition, the methylation status of cytosine residues within the 3′ UTR of the p16(INK4) human mRNA affects mRNA stability (6). Due to the increasing sensitivity of RNA sequencing (RNA-Seq) and small-molecule mass spectrometry, it is reasonable to hypothesize that many novel chemical modifications within mRNAs remain to be discovered.One modification recently identified in bacteria is 5′ nicotinamide-adenine dinucleotide (NAD + )-linked RNA (7, 8). Because canonical bacterial RNAs contain a 5′ triphosphate terminus, addition of NAD + to the 5′ end of RNAs represents a rudimentary "capping" mechanism, perhaps designed to impart specific properties for these RNAs by granting them a more structurally complex 5′ end. Consistent with this idea, NAD + addition to RNAs appears to occur during transcription initiation (9), as opposed to the more complex eukaryote 5′ capping, which occurs after transcription has commenced (10). Because the NAD + modification defines the 5′ end of NAD-RNAs, this modification can affect RNA stability in Escherichia coli (7, 9).For decades, 5′ end classification and study of eukaryotic mRNAs have been restricted to canonical 7-methylguanosine (m 7 G) "caps" and their methylated variants (11). The m 7 G cap modulates numerous facets of mRNA metabolism, including stability (12, 13), translation (14, 15), and export (16). The importance of this modification is underscored by the substantial cellular machinery dedicated to its addition and removal (17,18). Thus, mRNAs containing noncanonical 5′ termini may have distinct properties and be subject to alternative metabolic events.Described herein is the identification of NAD-RNAs in the eukaryote Saccharomyces cerevisiae. Examples of NAD-RNAs in S. cerevisiae include nuclear encoded mRNAs for ribosomal proteins, as well as some mitochondrial encoded transcripts. Our data suggest that the NAD + moiety is added during initiation in both nuclear and mitoc...