A nexus of intrinsic dynamics underlies translocase priming

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Motifier: An IgOme Profiler Based on Peptide Motifs Using Machine Learning

Antibodies provide a comprehensive record of the encounters with threats and insults to the immune system. The ability to examine the repertoire of antibodies in serum and discover those that best represent “discriminating features” characteristic of various clinical situations, is potentially very useful. Recently, phage display technologies combined with Next-Generation Sequencing (NGS) produced a powerful experimental methodology, coined “Deep-Panning”, in which the spectrum of serum antibodies is probed. In order to extract meaningful biological insights from the tens of millions of affinity-selected peptides generated by Deep-Panning, advanced bioinformatics algorithms are a must. In this study, we describe Motifier, a computational pipeline comprised of a set of algorithms that systematically generates discriminatory peptide motifs based on the affinity-selected peptides identified by Deep-Panning. These motifs are shown to effectively characterize antibody binding activities and through the implementation of machine-learning protocols are shown to accurately classify complex antibody mixtures representing various biological conditions.     

Amino Acid Sequence and Antimicrobial Activity of Chitin-Binding Peptides,Pp-AMP 1 and Pp-AMP 2, from Japanese Bamboo Shoots (Phyllostachys pubescens)

Two novel chitin-binding peptides, designated Pp-AMP 1 and Pp-AMP 2, which had antimicrobial activity against pathogenic bacteria and fungi, were purified from Japanese bamboo shoots (Phyllostachys pubescens) by a simple procedure based on chitin affinity chromatography. They had the common structural features of the plant defensin family, but they could not be grouped in any type of that family. They showed a high degree of homology to mistletoe toxins.     

A common binding motif in the ET domain of BRD3 forms polymorphic structural interfaces with host and viral proteins

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Structural insights into the interplay of protein biogenesis factors with the 70S ribosome

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Effect of Ionic Strength in the Gel Filtration of Charged Polysaccharides

ABSTRACT

Collagen-derived dipeptide prolyl hydroxyproline (Pro-Hyp) is involved in the proliferation and differentiation of various types of cultured cells. To elucidate the mechanism underlying Pro-Hyp actions during osteoblast differentiation, we hypothesized that proteins binding to Pro-Hyp serve to mediate cellular signaling, affecting Runx2 expression. Recently, we performed the characterization of Foxg1, that it enhances Runx2 expression in the presence of Pro-Hyp. Our findings indicate that Pro-Hyp directly binds to the Foxg1 recombinant protein, which leads to the structural alteration of the Foxg1 protein. In addition, Foxg1 appears to interact with Runx2 in the absence of Pro-Hyp, with Pro-Hyp disrupting the interaction between Foxg1 and Runx2. Collectively, our results indicate that the Pro-Hyp bound Foxg1 alters the structured conformation of Foxg1, resulting in conformational changes that lead to dissociation from Runx2. These novel findings suggest that during osteoblast differentiation, Pro-Hyp mediates Runx2 activity though directly binding to Foxg1 and increases Runx2 expression.

Abbreviations: CPT: collagen peptide; GST: Glutathione S-transferase; PAGE: Polyacrylamide gel electrophoresis; PCR: Polymerase chain reaction; prolyl hydroxyproline: Pro-Hyp     

Epitope Analysis of Soybean Major Allergen Gly m Bd 30K Recognized by the Mouse Monoclonal Antibody Using Overlapping Peptides

The epitopes of the major soybean allergen, Gly m Bd 30K, recognized by mouse monoclonal antibodies H6 and F5 were investigated by using synthetic peptides bound to pins. The epitopes are shown to be localized in peptide ³¹QGGCGRGWAFSATGAI-EA⁴⁸ for H6, and in ¹¹⁵ DKVTIDGYETLIMSDEST¹³² for F5.     

Cloning and Nucleotide Sequence of the Gene Encoding a Serine Proteinase Inhibitor Named Marinostatin from a Marine Bacterium,Alteromonas sp. Strain B-10-31

The gene (mstI) encoding a serine proteinase inhibitor named marinostatin from marine Alteromonas sp. strain B-10-31 was cloned and its nucleotide sequence was analyzed. A short open reading frame of 192 bp encoded 63 amino acids with a molecular weight of 6,985. Furthermore, the initial product of marinostatin (marinostatin L) was purified and its amino acid sequence was analyzed. These results indicate that marinostatin is produced as a unique precursor consisting of the mature peptide and the leader peptide for an ATP-binding cassette (ABC) transporter, and furthermore the initial product of marinostatin is dehydrated and processed by proteolysis to give homologous forms of marinostatin.     

Peptides as Active Ingredients: A Challenge for Cosmeceutical Industry

Cosmeceutical field, which merges cosmetics and pharmaceuticals, is nowadays a highly investigated research area, because a scientific demonstration of the claimed bioactivity of new cosmeceutical ingredients is increasingly requested. In fact, an aspect differentiating traditional cosmetics from cosmeceuticals is the identification and characterization of the active ingredients and demonstrating its efficacy in the claimed activity. An interesting group of bioactive cosmeceutical ingredients are peptides, which due to their particular properties, meets most of the requirements presented by the cosmeceutical industry when composing new formulas. In this context, beside bioactivity, two additional aspects have been recently considered, when dealing with peptides as cosmeceutical ingredients: bioavailability and stability. We describe herein novel methods applied in order to enhance peptides skin-penetration and stability, reviewing both scientific articles and patents, issued in the cosmeceutical arena.     

Atrial fibrillation after thoracic surgery for lung cancer: use of a single cut-off value of N-terminal pro-B type natriuretic peptide to identify patients at risk

Postoperative atrial fibrillation (AF) is a well-known complication occurring after thoracic surgery. B-type natriuretic peptide has recently been investigated as a predictive marker of postoperative AF after cardiac surgery. The aim of this study was to evaluate a definite cut-off for N-terminal pro-B type natriuretic peptide (NT-proBNP) in predicting postoperative AF in lung cancer patients. NT-proBNP was determined before and after surgery in 400 patients. Cardiac function was monitored by continuous postoperative ECG and clinical cardiological evaluation. AF occurred in 18% of the patients. Receiver operating characteristic curve analyses identified a cut-off of 182.3?ng l^?1 as the one with the highest sensitivity and specificity. Perioperative increased levels of NT-proBNP seem to predict postoperative AF in patients undergoing thoracic surgery, and a single cut-off of 182.3?ng l^?1 can be used to select high-risk patients who could receive preventive therapy, leading to a considerable decrease in the total costs associated with the management of this complication.