Oligomeric states of bacteriophage T7 gene 4 primase/helicase

Electron microscopic and crystallographic data have shown that the gene 4 primase/helicase encoded by bacteriophage T7 can form both hexamers and heptamers. After cross-linking with glutaraldehyde to stabilize the oligomeric protein, hexamers and heptamers can be distinguished either by negative stain electron microscopy or electrophoretic analysis using polyacrylamide gels. We find that hexamers predominate in the presence of either dTTP or beta,gamma-methylene dTTP whereas the ratio between hexamers and heptamers is nearly the converse in the presence of dTDP. When formed, heptamers are unable to efficiently bind either single-stranded DNA or double-stranded DNA. We postulate that a switch between heptamer to hexamer may provide a ring-opening mechanism for the single-stranded DNA binding pathway. Accordingly, we observe that in the presence of both nucleoside di- and triphosphates the gene 4 protein exists as a hexamer when bound to single-stranded DNA and as a mixture of heptamer and hexamer when not bound to single-stranded DNA. Furthermore, altering regions of the gene 4 protein postulated to be conformational switches for dTTP-dependent helicase activity leads to modulation of the heptamer to hexamer ratio.     

Structural Modelling of the Sm-like Protein Hfq from Escherichia coli

The Hfq polypeptide of Escherichia coli is a nucleic acid-binding protein involved in the expression of many proteins. Derivation of its three-dimensional structure is important for our understanding of its role in gene regulation at the molecular level. In this study, we combined computational and biophysical analysis to derive a possible structure for Hfq. As a first step towards determining the structure, we searched for possible sequence-structure compatibility, using secondary structure prediction and protein domain and fold-recognition methods available on the WEB. One fold, essentially beta sheet in character, the Sm motif of small nuclear ribonucleoproteins, even though it initially fell well below the confidence thresholds, was proposed and further validated by a series of biophysical and biochemical studies. The Hfq hexamer structure was modelled on the human Sm D3B structure using optimised sequence alignments and molecular mechanics methods. This structure accounts for the physico-chemical properties of Hfq and highlights amino acid residues that could interact with RNA.     

α-Enolase binds to RNA

To detect proteins binding to CUG triplet repeats, we performed magnetic bead affinity assays and North-Western analysis using a (CUG)₁₀ ssRNA probe and either nuclear or total extracts from rat L6 myoblasts. We report the isolation and identification by mass spectrometry and immunodetection of α-enolase, as a novel (CUG)n triplet repeat binding protein. To confirm our findings, rat recombinant α-enolase was cloned, expressed and purified; the RNA binding activity was verified by electrophoretic mobility shift assays using radiolabeled RNA probes. Enolase may play other roles in addition to its well described function in glycolysis.     

人GRY-RBP基因的表达及其RNA结合活性的初步鉴定

ＲＲＭ ＲＮＡ 结合蛋白在基因的转录后调控中起着重要作用．人ＧＲＹ－ＲＢＰ 是我们实验室最近克隆的一个新的全长ｃＤＮＡ,编码一个ＲＲＭ ＲＮＡ 结合蛋白．ＧＲＹ－ＲＢＰ 的全编码区用ＰＣＲ扩增后,克隆到ｐＥＴ３０ａ＋ 表达载体中,在Ｅ．ｃｏｌｉ中获得了高效表达,表达的ＧＲＹ－ＲＢＰ重组蛋白占细菌总蛋白的２１％ ．利用融合在ＧＲＹ－ＲＢＰＮ 端的Ｈｉｓ．Ｔａｇ,采取亲和层析的方法纯化了表达的重组蛋白．为了检测ＧＲＹ－ＲＢＰ的ＲＮＡ 结合活性及其所结合的ＲＮＡ 性质,将表达的蛋白与ｐｏｌｙ（Ａ）－Ｓｅｐｈａｒｏｓｅ ４Ｂ结合,发现ＧＲＹ－ＲＢＰ能与ｐｏｌｙＡ （Ａ）结合,结合活性能被可溶性的ｐｏｌｙ（Ａ）、ｐｏｌｙ（Ｃ）减弱．改变ＮａＣｌ浓度和加入不同浓度的酵母ｔＲＮＡ竞争物后,ｐｏｌｙ（Ａ）结合活性不变．     

RNA剪接因子结构与功能研究进展

RNA剪接是一个多步骤、形成多种中间状态复合物的复杂过程.尽管在已经发现的一百多种pre-mRNA剪接相关因子中,仅研究了约8%相关蛋白质的空间结构,已充分显示对剪接相关因子三维晶体结构以及溶液结构的测定与研究,在理解RNA剪接的复杂机理以及生物学特性中具有不可替代的重要意义.     

Archaeal Sm proteins form heptameric and hexameric complexes: crystal structures of the Sm1 and Sm2 proteins from the hyperthermophile Archaeoglobus fulgidus

Proteins of largely unknown function related to the Sm proteins present in the core domain of eukaryotic small nuclear ribonucleoprotein particles have recently been detected in Archaea. In contrast to eukaryotes, Archaea contain maximally two distinct Sm-related proteins belonging to different subfamilies, we refer to as Sm1 and Sm2. Here we report the crystal structures of the Sm1- and Sm2-type proteins from the hyperthermophilic euryarchaeon Archaeoglobus fulgidus (AF-Sm1 and AF-Sm2) at a resolution of 2.5 and 1.95 A, respectively. While the AF-Sm1 protein forms a heptameric ring structure similar to that found in other archaeal Sm1-type proteins, the AF-Sm2 protein unexpectedly forms a homo-hexamer in the crystals, and, as is evident from the mass spectrometric analysis, also in solution. Both proteins have essentially the same monomer fold and inter-subunit beta-sheet hydrogen bonding giving rise to a similar overall architecture of the doughnut-shaped six and seven-membered rings. In addition, a conserved uracil-binding pocket identified previously in an AF-Sm1/RNA complex, suggests a common RNA-binding mode for the AF-Sm1 and AF-Sm2 proteins, in line with solution studies showing preferential binding to U-rich oligonucleotides for both proteins. Clear differences are however seen in the charge distribution within the two structures. The rough faces of the rings, i.e. the faces not containing the base binding pockets, have opposite charges in the two structures, being predominantly positive in AF-Sm1 and negative in AF-Sm2. Differences in the ionic interactions between subunits provide an explanation for the distinctly different oligomerisation behaviour of the AF-Sm1 and AF-Sm2 proteins and of Sm1- and Sm2-type proteins in general, as well as the stability of their complexes. Implications for the functions of archaeal Sm proteins are being discussed.