Altered expression of plant lysyl tRNA synthetase promotes tRNA misacylation and translational recoding of lysine

The Arabidopsis thaliana lysyl tRNA synthetase (AtKRS) structurally and functionally resembles the well-characterized prokaryotic class IIb KRS, including the propensity to aminoacylate tRNA(Lys) with suboptimal identity elements, as well as non-cognate tRNAs. Transient expression of AtKRS in carrot cells promotes aminoacylation of such tRNAs in vivo and translational recoding of lysine at nonsense codons. Stable expression of AtKRS in Zea mays causes translational recoding of lysine into zeins, significantly enriching the lysine content of grain.     

Microtubule-binding proteins CLASP1 and CLASP2 interact with actin filaments

Cell morphogenesis requires dynamic communication between actin filaments and microtubules which is mediated, at least in part, by direct structural links between the two cytoskeletal systems. Here, we examined interaction between the CLIP-associated proteins (CLASP) CLASP1 and CLASP2, and actin filaments. We demonstrate that, in addition to a well-established association with the distal ends of microtubules, CLASP2alpha co-localizes with stress fibers, and that both CLASP1alpha and CLASP2alpha co-immunoprecipitate with actin. GFP-CLASP2alpha exhibits retrograde flow in the lamellipodia of Xenopus primary fibroblasts and in the filopodia of Xenopus spinal cord neurons. A deletion mapping analysis reveals that both the microtubule-binding domain of CLASP2 (which is homologous between all CLASPs) and the N-terminal dis1/TOG domain of CLASP2alpha (which is homologous between alpha isoforms) possess actin-binding activity. Fluorescence resonance energy transfer experiments demonstrate significant energy transfer between YFP-CLASP2alpha and CFP-actin. Our results indicate that CLASPs function as actin/microtubule crosslinkers in interphase cells. We propose that CLASPs facilitate recognition of actin filaments by the plus ends of growing microtubules at the initial stages of actin-microtubule interaction. Cell Motil.     

Atomic resolution crystal structures of HIV-1 protease and mutants V82A and I84V with saquinavir

Due to the limited distance data available from the experiments, the structures determined by NMR Spectroscopy may not always be as accurate as desired. Further refinement of the structures is often required and sometimes critical. With the increase of high quality protein structures determined and deposited in PDB Data Bank, commonly shared protein conformational properties can be extracted based on the statistical distributions of the properties in the structural database and used to improve the outcomes of the NMR-determined structures. Here we examine the distributions of protein interatomic distances in known protein structures. We show that based on these distributions, a set of mean-force potentials can be defined for proteins and employed to refine the NMR-determined structures. We report the test results on 70 NMR-determined structures and compare the potential energy, the Ramachandran plot, and the ensemble RMSD of the structures refined with and without using the derived mean-force potentials.     

A recipe for high impact

Our analysis highlights common statistical features of high-impact articles; we also show how information flows among various publication types.     

Fluorescent dyes undergoing intramolecular proton transfer with improved sensitivity to surface charge in lipid bilayers.

4'-(Dialkylamino)-3-hydroxyflavones are characterized by an excited-state proton transfer reaction between two tautomeric excited states, which results in two emission bands well separated on the wavelength scale. Due to the high sensitivity of the relative intensities of the two emission bands to solvent polarity, hydrogen bonding and local electric fields, these dyes found numerous applications in biomembrane studies. In order to further improve their fluorescence characteristics, we have synthesized new dyes where the 2-phenyl group is substituted with a 2-thienyl group. In organic solvents, the new dyes exhibit red shifted absorption and dual fluorescence. Although they show lower sensitivity to solvent polarity and H-bond donor ability (acidicity) than their parent 3-hydroxyflavone dyes, they exhibit a much higher sensitivity to solvent H-bond acceptor ability (basicity). Moreover, when tested in lipid vesicles of different surface charge, the new dyes show much better resolved dual emission and higher sensitivity to the surface charge of lipid bilayers than the parent dyes. The response of the new dyes to surface charge is probably connected with the H-bond basicity of the membrane surface, which is the highest for negatively charged surfaces. As a consequence, the new dyes appear as prospective fluorophores for the development of new fluorescent probes for biomembranes.     

Conserved and species-specific alternative splicing in mammalian genomes

Background  

Alternative splicing has been shown to be one of the major evolutionary mechanisms for protein diversification and proteome expansion, since a considerable fraction of alternative splicing events appears to be species- or lineage-specific. However, most studies were restricted to the analysis of cassette exons in pairs of genomes and did not analyze functionality of the alternative variants.     

Chimeric Agonist of Galanin Receptor GALR2 Reduces Heart Damage in Rats with Streptozotocin-Induced Diabetes

Biochemistry (Moscow) - Neuropeptide galanin and its N-terminal fragments reduce the generation of reactive oxygen species and normalize metabolic and antioxidant states of myocardium in...     

NAR Breakthrough Article: FDF-PAGE: a powerful technique revealing previously undetected small RNAs sequestered by complementary transcripts

Small RNAs, between 18nt and 30nt in length, are a diverse class of non-coding RNAs that mediate a range of cellular processes, from gene regulation to pathogen defense. They guide ribonucleoprotein complexes to their target nucleic acids by Watson–Crick base pairing. We report here that current techniques for small RNA detection and library generation are biased by formation of RNA duplexes. To address this problem, we established FDF-PAGE (fully-denaturing formaldehyde polyacrylamide gel electrophoresis) to prevent annealing of sRNAs to their complement. By applying FDF-PAGE, we provide evidence that both strands of viral small RNA are present in near equimolar ratios, indicating that the predominant precursor is a long double-stranded RNA. Comparing non-denaturing conditions to FDF-PAGE uncovered extensive sequestration of miRNAs in model organisms and allowed us to identify candidate small RNAs under the control of competing endogenous RNAs (ceRNAs). By revealing the full repertoire of small RNAs, we can begin to create a better understanding of small RNA mediated interactions.