A Continuum Poisson-Boltzmann Model for Membrane Channel Proteins

Membrane proteins constitute a large portion of the human proteome and perform a variety of important functions as membrane receptors, transport proteins, enzymes, signaling proteins, and more. The computational studies of membrane proteins are usually much more complicated than those of globular proteins. Here we propose a new continuum model for Poisson-Boltzmann calculations of membrane channel proteins. Major improvements over the existing continuum slab model are as follows: 1) The location and thickness of the slab model are fine-tuned based on explicit-solvent MD simulations. 2) The highly different accessibility in the membrane and water regions are addressed with a two-step, two-probe grid labeling procedure, and 3) The water pores/channels are automatically identified. The new continuum membrane model is optimized (by adjusting the membrane probe, as well as the slab thickness and center) to best reproduce the distributions of buried water molecules in the membrane region as sampled in explicit water simulations. Our optimization also shows that the widely adopted water probe of 1.4 {\AA} for globular proteins is a very reasonable default value for membrane protein simulations. It gives an overall minimum number of inconsistencies between the continuum and explicit representations of water distributions in membrane channel proteins, at least in the water accessible pore/channel regions that we focus on. Finally, we validate the new membrane model by carrying out binding affinity calculations for a potassium channel, and we observe a good agreement with experiment results.Comment: 40 pages, 6 figures, 5 table

Carboxylesterase from Spodoptera Litura: Immobilization and use for the Degradation of Pesticides

AbstractThe immobilization of carboxylesterase from Spodoptera Litura in mesoporus molecular sieves was studied in this paper. Two different types of mesoporous sieves (MCM-41, SBA-15) were initially used as enzyme support to compare the efficiency of immobilization. The outcome showed the maximum enzyme loadings, twice as many in MCM-41, are 0.0267 L/g in SBA-15 support. The most efficient pH value for immobilization was at 6.5 for both types of the support and the optimal immobilizing time was 2h for SBA-15 and 4h for MCM-41. Hence, the SBA-15 mesoporous support was determined as the enzyme immobilization matrix to continue the investigation because of its superior properties for enzyme immobilization. Then a series of characters of the free and immobilized Carboxylesterase were compared. As a result, the immobilized enzyme was substantiated to be obviously more stable than the free enzyme under the variant conditions. The experiments of pesticides degradation show that, relative to degradation in natural environment, immobilization enzyme had a higher ability to reduce the organic compounds with ester bonds

Protein Surface Structural Recognition in Inactive Areas: A New Immobilization Strategy for Acetylcholinesterase

This work reported a new method of design for the immobilization of acetylcholinesterase (AChE) based on its molecular structure to improve its sensitivity and stability. The immobilization binding site on the surface of AChE was determined using MOLCAD’s multi-channel functionality. Then, 11 molecules ((+)-catechin, (−)-epicatechin, (−)-gallocatechin, hesperetin, naringenin, quercetin, taxifolin, (−)-epicatechin gallate, flupirtine, atropine, and hyoscyamine) were selected from the ZINC database (about 50 000 molecules) as candidate affinity ligands for AChE. The fluorescence results showed that the binding constant <i>K</i>_b between AChE and the ligands ranged from 0.01344 × 10⁴ to 4.689 × 10⁴ M^–1 and there was one independent class of binding site for the ligands on AChE. The AChE-ligand binding free energy ranged from −12.14 to −26.65 kJ mol^–1. Naringenin, hesperetin, and quercetin were the three most potent immobilized affinity ligands. In addition, it was confirmed that the binding between the immobilized ligands only occurred at a single site, located in an inactive area on the surface of AChE, and did not affect the enzymatic activity as shown through a competition experiment and enzyme assay. This method based on protein surface structural recognition with high sensitivity and stability can be used as a generic approach for design of the enzyme immobilization and biosensor development

Association of Abnormal Iron Status with the Occurrence and Prognosis of Peritoneal Dialysis-Related Peritonitis: A Longitudinal Data-Based 10-Year Retrospective Study

This retrospective study investigated the effect of iron status on peritonitis by analyzing longitudinal iron parameters in peritoneal dialysis (PD) patients. Patients who received PD at our center from 1 January 2006 to 31 December 2015 were included and followed up until 31 December 2017. According to the joint quartiles of baseline transferrin saturation and ferritin, iron status was categorized as reference iron status (RIS), absolute iron deficiency (AID), functional iron deficiency (FID), and high iron status (HIS). Generalized estimating equations and Cox regression models with time-dependent covariates were used. A total of 1258 PD patients were included; 752 (59.8%) were male, with a mean (&plusmn;standard deviation) age of 47.4 (&plusmn;14.9) years. During a median follow-up period of 35.5 (interquartile range, 18.4&ndash;60.0) months, 450 (34.3%) patients had 650 episodes of peritonitis. By analyzing longitudinal data, patients with AID were independently positively associated with the occurrence (adjusted odds ratio (AOR) = 1.45) and treatment failure of peritonitis (adjusted hazard ratio (AHR) = 1.85). Patients with HIS were positively associated with the treatment failure of peritonitis (AHR = 2.70). Longitudinal AID and HIS were associated with the episodes and poor prognosis of peritonitis. Active clinical monitoring and correction of iron imbalance in patients with PD are needed