Screening of N-alkyl-cyanoacetamido oximes as substitutes for N-hydroxysuccinimide.

Peptide-bond formation is a pivotal process in the synthesis of peptide oligomers. Among the various coupling methodologies described, carbodiimides combine strong acylation potency and smooth reaction conditions, and they are commonly used in the presence of N-hydroxylamine additives. In recent years, acidic oxime templates, mainly ethyl 2-cyano-2-(hydroxyimino) acetate (Oxyma), have emerged as highly reactive alternatives to the classic and explosive-prone benzotriazolic additives, 1-hydroxybenzotriazole (HOBt) and 1-hydroxy-7-azabenzotriazole (HOAt).

The role of structural disorder in the rewiring of protein interactions through evolution.

Structurally disordered regions play a key role in protein-protein interaction networks and the evolution of highly connected proteins, enabling the molecular mechanisms for multiple binding. However, the role of protein disorder in the evolution of interaction networks has only been investigated through the analysis of individual proteins, making it impossible to distinguish its specific impact in the (re)shaping of their interaction environments. Now, the availability of large interactomes for several model organisms permits exploration of the role of disorder in protein interaction networks not only at the level of the interacting proteins but of the interactions themselves.

Small molecule fluorescent probes for the detection of amyloid self-assembly in vitro and in vivo.

The misfolding and aggregation of amyloidogenic polypeptides are characteristics of many neurodegenerative syndromes including Alzheimer's and Parkinson's disease. There is a major interest in the availability of amyloid-specific probes that exhibit fluorescence properties, for its use as reporters of protein aggregation in spectroscopy and microscopy methodologies. In this review, we intend to provide an overview of novel fluorescence-based probes and procedures applied for addressing fundamental aspects of amyloid self-assembly in vitro and in vivo.

The MRE11 complex: starting from the ends.

The maintenance of genome stability depends on the DNA damage response (DDR), which is a functional network comprising signal transduction, cell cycle regulation and DNA repair. The metabolism of DNA double-strand breaks governed by the DDR is important for preventing genomic alterations and sporadic cancers, and hereditary defects in this response cause debilitating human pathologies, including developmental defects and cancer. The MRE11 complex, composed of the meiotic recombination 11 (MRE11), RAD50 and Nijmegen breakage syndrome 1 (NBS1; also known as nibrin) proteins is central to the DDR, and recent insights into its structure and function have been gained from in vitro structural analysis and studies of animal models in which the DDR response is deficient.

Characterization of Trex1 induction by IFN-γ in murine macrophages.

3' Repair exonuclease (Trex1) is the most abundant mammalian 3' → 5' DNA exonuclease with specificity for ssDNA. Trex1 deficiency has been linked to the development of autoimmune disease in mice and humans, causing Aicardi-Goutières syndrome in the latter. In addition, polymorphisms in Trex1 are associated with systemic lupus erythematosus.

Acetylation of GAGA factor modulates its interaction with DNA.

GAGA is a Drosophila transcription factor that shows a high degree of post-translational modification. Here, we show that GAGA factor is acetylated in vivo. Lysine residues K325 and K373 on basic regions BR1 and BR3 of the DNA binding domain, respectively, are shown to be acetylated by PCAF.

Approaching Elastic Network Models to Molecular Dynamics Flexibility.

Elastic network models (ENMs) are coarse-grained descriptions of proteins as networks of coupled harmonic oscillators. However, despite their widespread application to study collective movements, there is still no consensus parametrization for the ENMs. When compared to molecular dynamics (MD) flexibility in solution, the ENMs tend to disperse the important motions into multiple modes.

Solid-phase synthesis of oligodeoxynucleotides containing N4-[2-(t-butyldisulfanyl)ethyl]-5-methylcytosine moieties.

An efficient route for the synthesis of the phosphoramidite derivative of 5-methylcytosine bearing a tert-butylsulfanyl group protected thiol is described. This building block is used for the preparation of oligonucleotides carrying a thiol group at the nucleobase at the internal position of a DNA sequence. The resulting thiolated oligonucleotides are useful intermediates to generate oligonucleotide conjugates carrying molecules of interest at internal positions of a DNA sequence.

The interphase microtubule aster is a determinant of asymmetric division orientation in Drosophila neuroblasts.

The mechanisms that maintain the orientation of cortical polarity and asymmetric division unchanged in consecutive mitoses in Drosophila melanogaster neuroblasts (NBs) are unknown. By studying the effect of transient microtubule depolymerization and centrosome mutant conditions, we have found that such orientation memory requires both the centrosome-organized interphase aster and centrosome-independent functions. We have also found that the span of such memory is limited to the last mitosis.

N-methyl phenylalanine-rich peptides as highly versatile blood-brain barrier shuttles.

Here we studied the capacity of N-MePhe-(N-MePhe)(3)-CONH(2), Cha-(N-MePhe)(3)-CONH(2), and 2Nal-(N-MePhe)(3)-CONH(2) to carry various drugs (cargos) in in vitro blood-brain barrier (BBB) models in order to determine the versatility of these peptides as BBB-shuttles for drug delivery to the brain. Using SPPS, the peptides were coupled to GABA, Nip, and ALA to examine their passive BBB permeation by means of PAMPA and their lipophilicity by IAMC. Unaided, these nonpermeating drugs alone did not cross the PAMPA barrier and the BBB passively; however, the peptides tested as potential BBB shuttles transferred them by passive transfer through the PAMPA phospholipid.

Preparative enantioseparation of (+/-)-N-(3,4-cis-3-decyl-1,2,3,4-tetrahydrophenanthren-4-yl)-3,5-dinitrobenzamide by centrifugal partition chromatography.

The racemic compound (+/-)-N-(3,4-cis-3-decyl-1,2,3,4-tetrahydrophenanthren-4-yl)-3,5-dinitrobenzamide ((+/-)-1), an analogue of increased lipophilicity of the chiral selector (CS) contained in the Whelk-O HPLC chiral stationary phase (CSP) has been resolved into its enantiomers by applying centrifugal partition chromatography (CPC). Considering the known enantioselectivity of the Whelk-O CS for naproxen, and the reciprocity concept in enantioseparation, (S)-naproxen related compounds were tested as CSs. In the search for an adequate solvent system, the partition behaviour of the two solutes, CS and racemate, has been studied using several biphasic solvent mixtures.

Exploiting gene deletion fitness effects in yeast to understand the modular architecture of protein complexes under different growth conditions.

Background: Understanding how individual genes contribute towards the fitness of an organism is a fundamental problem in biology. Although recent genome-wide screens have generated abundant data on quantitative fitness for single gene knockouts, very few studies have systematically integrated other types of biological information to understand how and why deletion of specific genes give rise to a particular fitness effect. In this study, we combine quantitative fitness data for single gene knock-outs in yeast with large-scale interaction discovery experiments to understand the effect of gene deletion on the modular architecture of protein complexes, under different growth conditions.

p21(waf1/CIP1), a CDK inhibitor and a negative feedback system that controls macrophage activation.

p21(WAF1/CIP1) (p21) is a crucial CDK inhibitor that controls the cell cycle. This molecule is also involved in the regulation of apoptosis and gene expression. However, like many other cell regulators, the functional activity of p21 depends on its cellular context and is controlled through phosphorylation and protein-protein interactions.

Stepwise synthesis of RNA conjugates carrying peptide sequences for RNA interference studies.

Oligoribonucleotide conjugates carrying nuclear localization peptide sequences at the 3'-end were prepared stepwise on a single support. The siRNA duplex carrying the nuclear localization peptide sequence at the 3'-end of the passenger strand has similar inhibitory properties as those of unmodified or cholesterol-modified RNA duplexes.

Regulation of neural migration by the CREB/CREM transcription factors and altered Dab1 levels in CREB/CREM mutants.

The family of CREB transcription factors is involved in a variety of biological processes including the development and plasticity of the nervous system. To gain further insight into the roles of CREB family members in the development of the embryonic brain, we examined the migratory phenotype of CREB1(Nescre)CREM(-/-) mutants. We found that the lack of CREB/CREM genes is accompanied by anatomical defects in specific layers of the olfactory bulb, hippocampus and cerebral cortex.