RNA-protein binding

In most four-helix bundle structures, including those shown in Figure 3.7, the a helices are packed against each other according to the "ridges in grooves" model discussed later in this chapter. However, there are also examples where coiled-coil dimers packed by the "knobs in holes" model participate in four-helix bundle structures. A particularly simple illustrative example is the Rop protein, a small RNA-binding protein that is encoded by certain plasmids and is involved in plasmid replication. The monomeric sub unit of Rop is a polypeptide chain of 63 amino acids built up from two... 

The coiled-coil structure of the leucine zipper motif is not the only way that homodimers and heterodimers of transcription factors are formed. As we saw in Chapter 3 when discussing the RNA-binding protein ROP, the formation of a four-helix bundle structure is also a way to achieve dimerization, and the helix-loop-helix (HLH) family of transcription factors dimerize in this manner. In these proteins, the helix-loop-helix region is preceded by a sequence of basic amino acids that provide the DNA-binding site (Figure 10.23), and... 

As it is the case in polypeptide folding, nonspecific or promiscuous RNA-binding proteins can prevent RNA mis-folding and resolve mis-foldedRNAs, thereby ensuring that RNA is accessible for its biological function [ 1 ]. Certain DEAD-box proteins as well as some proteins that are involved in the assembly of ribonuleoparticles were shown to act as RNA chaperones. 

Bennasser Y, Yeung ML, Jeang KT (2006) HIV-1 TAR RNA subverts RNA interference in transfected cells through sequestration of TAR RNA-binding protein, TRBP. J Biol Chem 281(38) 27674-27678... 

Nakagawa J, Meyer-Monard S, Hof-steenge J, Jeno P, Moroni C. AUH, a gene encoding an AU-specific RNA binding protein with intrinsic enoyl-CoA hy-dratase activity. Proc Natl Acad Sci USA 1995 92 2051-2055. 

Naranda, T., MacMillan, S. E., and Hershey, J. W. B. (1994). Purified yeast translational initiation factor eIF-3 is an RNA-binding protein complex that contains the PRT1 protein. J. Biol. Chem. 269, 32286—32292. 

Hofmann, I., Casella, M., Schnolzer, M., Schlechter, T., Spring, H., and Franke, W. W. (2006). Identification of the junctional plaque protein plakophilin 3 in cytoplasmic particles containing RNA-binding proteins and the recruitment of plakophilins 1 and 3 to stress granules. Mol. Biol. Cell 17, 1388—1398. 

Hunt, S. L., Hsuan, J. J., Totty, N., and Jackson, R. J. (1999). Unr, a cellular cytoplasmic RNA-binding protein with five cold-shock domains, is required for internal initiation of translation of human rhinovirus RNA. Genes Dev. 13, 437—448. 

Paraneoplastic neuropathies often occur in patients with carcinoma. Subacute sensory or sensorimotor axonal polyneuropathy, often with associated limbic encephalitis and cerebellar degeneration, is a common complication of small-cell lung cancer and other carcinomas, occasionally presenting even prior to diagnosis of the underlying neoplasm. Some patients with paraneoplastic neuropathy express anti-Hu antibodies, which recognize epitopes associated with the HuD neuronal RNA binding protein [37,38]. 

Yang C, Maiguel DA, Carrier F (2002) Identification of nucleolin and nucleophosmin as genotoxic stress-responsive RNA-binding proteins. Nucleic Acids Res 30 2251-2260 Yang TH, Tsai WH, Lee YM, Lei HY, Lai MY, Chen DS, Yeh NH, Lee SC (1994) Purification and characterization of nucleolin and its identification as a transcription repressor. Mol Cell Biol 14 6068-6074... 

Fig. 12. Cross-linking of proteins within the E. coli (a) 30 S and (b) 50 S subunits (Traut et at., 1980). Asterisks denote proteins cross-linked to initiation factors, (c) Protein neig h-borhoods at the subunit interface (Lambert and Traut, 1981). Scheme 1 shows the crosslinks found in highest amount Scheme 2 those among 50 S proteins LI and L2 and several 30 S proteins and Scheme 3 those between 5 S RNA binding proteins and 30 S proteins. Reproduced with permission from Wittmann (1983).

Messenger RNAs (mRNAs) transfer genetic information from the cell nucleus to the cytoplasm. The primary transcripts are substantially modified while still in the nucleus (mRNA maturation see p.246). Since mRNAs have to be read codon by codon in the ribosome, they must not form a stable tertiary structure. This is ensured in part by the attachment of RNA-binding proteins, which prevent base pairing. Due to the varying amounts of information that they carry, the lengths of mRNAs also vary widely. Their lifespan is usually short, as they are quickly broken down after translation. 

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