Functional characterization of ECP-heparin interaction: a novel molecular model

Estimation of non-constant variance in isothermal titration calorimetry using an ITC measurement model

Isothermal titration calorimetry (ITC) is the gold standard for accurate measurement of thermodynamic parameters in solution reactions. In the data processing of ITC, the non-constant variance of the heat requires special consideration. The variance function approach has been successfully applied in previous studies, but is found to fail under certain conditions in this work. Here, an explicit ITC measurement model consisting of main thermal effects and error components has been proposed to quantitatively evaluate and predict the non-constant variance of the heat data under various conditions. Monte Carlo simulation shows that the ITC measurement model provides higher accuracy and flexibility than variance function in high c-value reactions or with additional error components, for example, originated from the fluctuation of the concentrations or other properties of the solutions. The experimental design of basic error evaluation is optimized accordingly and verified by both Monte Carlo simulation and experiments. An easy-to-run Python source code is provided to illustrate the establishment of the ITC measurement model and the estimation of heat variances. The accurate and reliable non-constant variance of heat is helpful to the application of weighted least squares regression, the proper evaluation or selection of the reaction model.

Characterization of structural motifs for interactions between glycosaminoglycans and proteins

Glycosaminoglycans (GAGs) are a family of linear and anionic polysaccharides that play essential roles in many biological and physiological processes. Interactions between GAGs and proteins regulate function in many proteins and are related to many human diseases and disorders. The structural motifs and mechanisms for interactions between GAGs and proteins are not fully understood. Specific bindings, including minor but unique sequences sporadically distributed along the GAG chains or variably sulfated domains interspersed by undersulfated regions, may be specifically recognized by defined domains of a variety of proteins. Understanding the molecular basis of these interactions will provide a template for developing novel glycotherapeutic agents. The present article reviews recent methodologies and progress on the characterization of structural motifs in both GAGs and proteins involved in GAG-protein interactions. The analytical approaches are categorized into three groups: affinity-based methods; molecular docking, nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography; and mass spectrometry (MS) techniques. The advantages and limitations of each category of methods are discussed and are based on examples of using these techniques to investigate binding between GAGs and proteins.

Cell Penetrating Peptide Derived from Human Eosinophil Cationic Protein Decreases Airway Allergic Inflammation

Cell penetrating peptide derived from human eosinophil cationic protein (CPPecp) is a 10-amino-acid peptide containing a core heparan sulfate (HS)-binding motif of human eosinophil cationic protein (ECP). It binds and penetrates bronchial epithelial cells without cytotoxic effects. Here we investigated airway-protective effects of CPPecp in BEAS-2B cell line and mite-induced airway allergic inflammation in BALB/c mice. In BEAS-2B cell, CPPecp decreases ECP-induced eotaxin mRNA expression. CPPecp also decreases eotaxin secretion and p-STAT6 activation induced by ECP, as well as by IL-4. In vivo studies showed CPPecp decreased mite-induced airway inflammation in terms of eosinophil and neutrophil count in broncho-alveolar lavage fluid, peri-bronchiolar and alveolar pathology scores, cytokine production in lung protein extract including interleukin (IL)-5, IL-13, IL-17A/F, eotaxin; and pause enhancement from methacholine stimulation. CPPecp treated groups also showed lower serum mite-specific IgE level. In this study, we have demonstrated the in vitro and in vivo anti-asthma effects of CPPecp.

Docking server for the identification of heparin binding sites on proteins

Many proteins of widely differing functionality and structure are capable of binding heparin and heparan sulfate. Since crystallizing protein-heparin complexes for structure determination is generally difficult, computational docking can be a useful approach for understanding specific interactions. Previous studies used programs originally developed for docking small molecules to well-defined pockets, rather than for docking polysaccharides to highly charged shallow crevices that usually bind heparin. We have extended the program PIPER and the automated protein-protein docking server ClusPro to heparin docking. Using a molecular mechanics energy function for scoring and the fast Fourier transform correlation approach, the method generates and evaluates close to a billion poses of a heparin tetrasaccharide probe. The docked structures are clustered using pairwise root-mean-square deviations as the distance measure. It was shown that clustering of heparin molecules close to each other but having different orientations and selecting the clusters with the highest protein-ligand contacts reliably predicts the heparin binding site. In addition, the centers of the five most populated clusters include structures close to the native orientation of the heparin. These structures can provide starting points for further refinement by methods that account for flexibility such as molecular dynamics. The heparin docking method is available as an advanced option of the ClusPro server at http://cluspro.bu.edu/ .