Design and screening of M13 phage display cDNA libraries

The last decade has seen a steady increase in screening of cDNA expression product libraries displayed on the surface of filamentous bacteriophage. At the same time, the range of applications extended from the identification of novel allergens over disease markers to protein-protein interaction studies. However, the generation and selection of cDNA phage display libraries is subjected to intrinsic biological limitations due to their complex nature and heterogeneity, as well as technical difficulties regarding protein presentation on the phage surface. Here, we review the latest developments in this field, discuss a number of strategies and improvements anticipated to overcome these challenges making cDNA and open reading frame (ORF) libraries more readily accessible for phage display. Furthermore, future trends combining phage display with next generation sequencing (NGS) will be presented.     

Isolation of the cytoplasmatic 5S ribosomal RNA from cotton seeds by preparative electrophoresis

Summary 1. The complete separation of low-molecular-weight 5S rRNA and tRNA from fractions of high-molecular-weight rRNAs (28S + 18S) in a preparation of the total rRNA from cotton seeds has been achieved.2. The optimum conditions have been selected for the preparative electrophoresis and isolation of homogeneous preparations of 5S rRNA and total tRNA.Institute of the Chemistry of Plant Substances, Academy of Sciences of the Uzbek SSR, Tashkent. Translated from Khimiya Prirodnykh Soedinenii, No. 4, pp. 489–494, July–August, 1978.     

Identification of RNA pseudoknot-binding ligand that inhibits the -1 ribosomal frameshifting of SARS-coronavirus by structure-based virtual screening

Programmed -1 ribosomal frameshifting (-1 RF) is an essential regulating mechanism of translation used by SARS-CoV (severe acute respiratory syndrome coronavirus) to synthesize the key replicative proteins encoded by two overlapping open reading frames. The integrity of RNA pseudoknot stability and structure in the -1 RF site is important for efficient -1 RF. Thus, small molecules interacting with high affinity and selectivity with the RNA pseudoknot in the -1 RF site of SARS-CoV (SARS-pseudoknot) would disrupt -1 RF and be fatal to viral infectivity and production. To discover ligands for the SARS-pseudoknot by virtual screening, we constructed a 3D structural model of the SARS-pseudoknot and conducted a computational screening of the chemical database. After virtual screening of about 80,000 compounds against the SARS-pseudoknot structure, high-ranked compounds were selected and their activities were examined by in vitro and cell-based -1 RF assay. We successfully identified a novel ligand 43 that dramatically inhibits the -1 RF of SARS-CoV. This antiframeshift agent is an interesting lead for the design of novel antiviral agents against SARS-CoV.     

The role of 23S ribosomal RNA residue A2451 in peptide bond synthesis revealed by atomic mutagenesis

Peptide bond formation is a fundamental reaction in biology, catalyzed by the ribosomal peptidyl-transferase ribozyme. Although all active-site 23S ribosomal RNA nucleotides are universally conserved, atomic mutagenesis suggests that these nucleobases do not carry functional groups directly involved in peptide bond formation. Instead, a single ribose 2'-hydroxyl group at A2451 was identified to be of pivotal importance. Here, we altered the chemical characteristics by replacing its 2'-hydroxyl with selected functional groups and demonstrate that hydrogen donor capability is essential for transpeptidation. We propose that the A2451-2'-hydroxyl directly hydrogen bonds to the P-site tRNA-A76 ribose. This promotes an effective A76 ribose C2'-endo conformation to support amide synthesis via a proton shuttle mechanism. Simultaneously, the direct interaction of A2451 with A76 renders the intramolecular transesterification of the peptide from the 3'- to 2'-oxygen unfeasible, thus promoting effective peptide bond synthesis.     

Secondary structure of peptides 16th. Characterization of proteins by means of13C NMR CP/MAS spectroscopy

50.3 or 75.4 MHz¹³C NMR cross-polarization/magic angle spinning spectra of human hair, horse hair, horse hoof, parrot feather, sperm whale myoglobin, and horse heart cytochrome C were measured. The spectra of human hair and horse hair indicate nearly equal mole fractions of-sheets and-helices and a low percentage of amorphous regions, whereas horse hoof contains a higher fraction of amorphous proteins. The parrot feathers contain a small-helix fraction (ca. 10±5 %) in additon to a large-sheet fraction whereas cytochrome C contains 70–90%-helices. The spectrum of myoglobin could not interpreted in terms of defined secondary structures. The usefulness of the¹³C NMR CP/MAS spectroscopy for the characterization of proteins is compared with that of IR spectroscopy and X-ray diffraction.     

RNA targeting at any chosen site of interest by the novel RNA-protein hybrid ribozyme and the gene discovery based on the hybrid ribozyme libraries

RNA targeting by the RNA-protein hybrid ribozymes, whose protein part can specifically bind to the RNA helicase, is described.     

Stereochemical Definition of the Natural Product (6R,10R,13R, 14R,16R,17R,19S,20S,21R,24S,25S,28S,30S,32R,33R,34R,36S,37S,39R)‐Azaspiracid‐3 by Total Synthesis and Comparative Analyses

The previously accepted structure of the marine toxin azaspiracid‐3 is revised based upon an original convergent and stereoselective total synthesis of the natural product. The development of a structural revision hypothesis, its testing, and corroboration are reported. Synthetic (6R,10R,13R,14R,16R,17R,19S,20S,21R,24S,25S,28S,30S,32R, 33R,34R,36S,37S,39R)‐azaspiracid‐3 chromatographically and spectroscopically matched naturally occurring azaspiracid‐3, whereas the previously assigned 20R epimer did not.     

Structural organization of the tetranuclear zinc di-iso-propyl phosphorodithioate complex [Zn4O{S2P(O-iso-C3H7))2}6] as probed by single-crystal x-ray diffraction and 13C and 31P CP/MAS NMR

The zinc O,O’-di-iso-propyl phosphorodithioate complex [Zn₄O?ub;S₂P(O-iso-C₃H₇)₂?ub;₆] (I) has been synthesized and characterized by multinuclear MAS NMR (¹³C, ³¹P). The metal core of the tetranuclear structure of I, determined by single-crystal X-ray diffraction, is a tetrahedron centered by an oxygen atom. All Dtph ligands are structurally nonequivalent and act as μ₂ bridges combining pairs of zinc atoms. Bonding of all metal atoms to the μ₄ oxygen atom provides additional stabilization of the structure. For ³¹P NMR signals, the chemical shift anisotropy δ_aniso and the asymmetry parameter η were calculated, which allowed to assign them to the phosphorus positions in the structure of I.