Non-Shine-Dalgarno initiators of translation selected from combinatorial DNA libraries

In a search for non-Shine-Dalgarno (non-SD) translational initiators, two combinatorial expression libraries (denoted R(1) and R(2)) were constructed containing randomized decanucleotide regions placed at either 6 (R(1)) or 11 (R(2)) nucleotides upstream of a modified chloramphenicol acetyltransferase (CAT) gene. To prevent sporadic formation of SD-like sequences the content of G in the randomized region was restricted to 3% only. The two libraries were transformed in Escherichia coli cells and screened for chloramphenicol (Cm) resistance. More than 50 clones capable of tolerating Cm concentrations from 50 micro g/ml to more than 800 micro g/ml were selected. With few exceptions only, the non-SD sequences found in the Cm-resistant clones did not show any significant homology with other known non-SD initiators or enhancers of translation. Statistical (chi(2)) analysis of the distribution of nucleotides in the new non-SD translational initiators showed a different pattern from that of the conventional SD sequences. In few of the clones the yield of CAT exceeded that of the referent (SD-containing) construct. The most productive clones carried the decanucleotides ATTTACCTCC, CCAATCTAC, TTCAATATTT, and TATTCCCCCA, and the corresponding yield of CAT obtained with them was 2.70, 2.06, 2.12 and 1.32 times, respectively, higher than that of the SD-bearing construct.     

Au(III)-complexes of the alanyl-containing peptides glycylalanine and glycylalanylalanine - Synthesis, spectroscopic and structural characterization

As part of an investigation on the coordination ability of peptides, the dipeptide glycylalanine (H-Gly-Ala-OH), tripeptide glycylalanylalanine (H-Gly-Ala-Ala-OH) and their Au(III)-complexes have been characterized structurally. The quantum chemical calculations and linear-dichroic infrared (IR-LD) spectroscopy predict structures of the compound studied, which are compared with a single crystal X-ray diffraction of H-Gly-Ala-OH. The coordination processes with Au(III) are supported by data for ¹H NMR, ESI-MS, HPLC-MS-MS, TGV and DSC methods. The [Au(Gly-Ala)H₋₁Cl] and [Au(Gly-Ala-Ala)H₋₂] · 2H₂O complexes are formed via -NH₂, N⁻amide/s and groups of the peptides. One Cl⁻ ion is attached to the metal center as terminal ligand in the first complex. In both cases a near to square-planar geometry of the chromophors AuN₂OCl and AuN₃O is yielded.     

Crystal structure of the Nogo-receptor-2

The inhibition of axon regeneration upon mechanical injury is dependent on interactions between Nogo receptors (NgRs) and their myelin-derived ligands. NgRs are composed of a leucine-rich repeat (LRR) region, thought to be structurally similar among the different isoforms of the receptor, and a divergent "stalk" region. It has been shown by others that the LRR and stalk regions of NgR1 and NgR2 have distinct roles in conferring binding affinity to the myelin associated glycoprotein (MAG) in vivo. Here, we show that purified recombinant full length NgR1 and NgR2 maintain significantly higher binding affinity for purified MAG as compared to the isolated LRR region of either NgR1 or NgR2. We also present the crystal structure of the LRR and part of the stalk regions of NgR2 and compare it to the previously reported NgR1 structure with respect to the distinct signaling properties of the two receptor isoforms.     

Structural basis of the cofactor function of denatured albumin in plasminogen activation by tissue-type plasminogen activator

Certain denatured proteins function as cofactors in the activation of plasminogen by tissue-type plasminogen activator. The present study approached the structural requirements for the cofactor activity of a model protein (human serum albumin). Heat denaturation of 100-230 microM albumin (80 degrees C and 60-90 min) reproducibly yielded aggregates with radius in the range of 10-150 nm. The major determinant of the cofactor potency was the size of the aggregates. The increase of particle size correlated with the cofactor activity, and there was a minimal requirement for the size of the cofactor (about 10 nm radius). Similar to other proteins, the molecular aggregates with cofactor function contained a significant amount of antiparallel intermolecular beta-sheets. Plasmin pre-digestion increased the cofactor efficiency (related to C-terminal lysine exposure) and did not affect profoundly the structure of the aggregates, suggesting a long-lasting and even a self-augmenting cofactor function of the denatured protein.     

Solid-state IR-LD spectroscopic and theoretical analysis of glycine-containing peptides and their hydrochlorides

As part of an investigation on the coordination ability of peptides, structural analyses of the solid di-, tri, and tetrapeptides glycyl-glycine (GG), glycyl-glycyl-glycine (GGG), glycyl-glycyl-glycyl-glycine (GGGG), and their protonated hydrochlorides glycyl-glycine.HCl (GGH), glycyl-glycyl-glycine.HCl (GGGH), and glycyl-glycyl-glycyl-glycine.HCl (GGGGH) have been carried out. The quantum chemical calculations (Hartree-Fock/6-31++G**) and linear-dichroic infrared (IR-LD) spectroscopy predict a near to linear structure of the pure ligands, but the experimental IR-LD data are in accordance with a cross-linked disposition of amide fragments in the protonated forms.     

Crystal structures of the Tie2 receptor ectodomain and the angiopoietin-2-Tie2 complex

The Tie receptor tyrosine kinases and their angiopoietin (Ang) ligands play central roles in developmental and tumor-induced angiogenesis. Here we present the crystal structures of the Tie2 ligand-binding region alone and in complex with Ang2. In contrast to prediction, Tie2 contains not two but three immunoglobulin (Ig) domains, which fold together with the three epidermal growth factor domains into a compact, arrowhead-shaped structure. Ang2 binds at the tip of the arrowhead utilizing a lock-and-key mode of ligand recognition-unique for a receptor kinase-where two complementary surfaces interact with each other with no domain rearrangements and little conformational change in either molecule. Ang2-Tie2 recognition is similar to antibody-protein antigen recognition, including the location of the ligand-binding site within the Ig fold. Analysis of the structures and structure-based mutagenesis provide insight into the mechanism of receptor activation and support the hypothesis that all angiopoietins interact with Tie2 in a structurally similar manner.