Simulations of Functional Motions of Super Large Biomolecules with a Mixed-Resolution Model.

Many large protein machines function through an interplay between large-scale movements and intricate conformational changes. Understanding functional motions of these proteins through simulations becomes challenging for both all-atom and coarse-grained (CG) modeling techniques because neither approach alone can readily capture the full details of these motions. In this study, we develop a multiscale model by employing the popular MARTINI CG model to represent a heterogeneous environment and structurally stable proteins and using the united-atom (UA) model PACE to describe proteins undergoing subtle conformational changes. PACE was previously developed to be compatible with the MARTINI solvent and membrane. Here, we couple the protein descriptions of the two models by directly mixing UA and CG interaction parameters to greatly simplify parameter determination. Through extensive validations with diverse protein systems in solution or membrane, we demonstrate that only additional parameter rescaling is needed to enable the resulting model to recover the stability of native structures of proteins under mixed representation. Moreover, we identify the optimal scaling factors that can be applied to various protein systems, rendering the model potentially transferable. To further demonstrate its applicability for realistic systems, we apply the model to a mechanosensitive ion channel Piezo1 that has peripheral arms for sensing membrane tension and a central pore for ion conductance. The model can reproduce the coupling between Piezo1's large-scale arm movement and subtle pore opening in response to membrane stress while consuming much less computational costs than all-atom models. Therefore, our model shows promise for studying functional motions of large protein machines.

On the linkage of thermodynamics and pathogenicity.

This review outlines the effect of disease-causing mutations on proteins' thermodynamics. Two major thermodynamics quantities, which are essential for structural integrity, the folding and binding free energy changes caused by missense mutations, are considered. It is emphasized that disease effects in case of complex diseases may originate from several mutations over several genes, while monogenic diseases are caused by mutation is a single gene. Nevertheless, in both cases it is shown that pathogenic mutations cause larger perturbations of the above-mentioned thermodynamics quantities as compared with the benign mutations. Recent works demonstrating the effect of pathogenic mutations on the above-mentioned thermodynamics quantities, as well as on structural dynamics and allosteric pathways, are reviewed.

Opioid Addiction and Opioid Receptor Dimerization: Structural Modeling of the OPRD1 and OPRM1 Heterodimer and Its Signaling Pathways.

Opioid addiction is a complex phenomenon with genetic, social, and other components. Due to such complexity, it is difficult to interpret the outcome of clinical studies, and thus, mutations found in individuals with these addictions are still not indisputably classified as opioid addiction-causing variants. Here, we computationally investigated two such mutations, A6V and N40D, found in the mu opioid receptor gene OPRM1. The mutations are located in the extracellular domain of the corresponding protein, which is important to the hetero-dimerization of OPRM1 with the delta opioid receptor protein (OPRD1). The hetero-dimerization of OPRD1-OPRM1 affects the signaling pathways activated by opioids and natural peptides and, thus, could be considered a factor contributing to addiction. In this study, we built four 3D structures of molecular pathways, including the G-protein signaling pathway and the ß-arrestin signaling pathway of the heterodimer of OPRD1-OPRM1. We also analyzed the effect of mutations of A6V and N40D on the stability of individual OPRM1/OPRD1 molecules and the OPRD1-OPRM1 heterodimer with the goal of inferring their plausible linkage with opioid addiction. It was found that both mutations slightly destabilize OPRM1/OPRD1 monomers and weaken their association. Since hetero-dimerization is a key step for signaling processes, it is anticipated that both mutations may be causing increased addiction risk.

Computational Investigation of the pH Dependence of Stability of Melanosome Proteins: Implication for Melanosome formation and Disease.

Intravesicular pH plays a crucial role in melanosome maturation and function. Melanosomal pH changes during maturation from very acidic in the early stages to neutral in late stages. Neutral pH is critical for providing optimal conditions for the rate-limiting, pH-sensitive melanin-synthesizing enzyme tyrosinase (TYR). This dramatic change in pH is thought to result from the activity of several proteins that control melanosomal pH. Here, we computationally investigated the pH-dependent stability of several melanosomal membrane proteins and compared them to the pH dependence of the stability of TYR. We confirmed that the pH optimum of TYR is neutral, and we also found that proteins that are negative regulators of melanosomal pH are predicted to function optimally at neutral pH. In contrast, positive pH regulators were predicted to have an acidic pH optimum. We propose a competitive mechanism among positive and negative regulators that results in pH equilibrium. Our findings are consistent with previous work that demonstrated a correlation between the pH optima of stability and activity, and they are consistent with the expected activity of positive and negative regulators of melanosomal pH. Furthermore, our data suggest that disease-causing variants impact the pH dependence of melanosomal proteins; this is particularly prominent for the OCA2 protein. In conclusion, melanosomal pH appears to affect the activity of multiple melanosomal proteins.

Novel Genetic Markers for Early Detection of Elevated Breast Cancer Risk in Women.

This study suggests that two newly discovered variants in the MSH2 gene, which codes for a DNA mismatch repair (MMR) protein, can be associated with a high risk of breast cancer. While variants in the MSH2 gene are known to be linked with an elevated cancer risk, the MSH2 gene is not a part of the standard kit for testing patients for elevated breast cancer risk. Here we used the results of genetic testing of women diagnosed with breast cancer, but who did not have variants in BRCA1 and BRCA2 genes. Instead, the test identified four variants with unknown significance (VUS) in the MSH2 gene. Here, we carried in silico analysis to develop a classifier that can distinguish pathogenic from benign mutations in MSH2 genes taken from ClinVar. The classifier was then used to classify VUS in MSH2 genes, and two of them, p.Ala272Val and p.Met592Val, were predicted to be pathogenic mutations. These two mutations were found in women with breast cancer who did not have mutations in BRCA1 and BRCA2 genes, and thus they are suggested to be considered as new bio-markers for the early detection of elevated breast cancer risk. However, before this is done, an in vitro validation of mutation pathogenicity is needed and, moreover, the presence of these mutations should be demonstrated in a higher number of patients or in families with breast cancer history.

Parametrization of MARTINI for Modeling Hinging Motions in Membrane Proteins.

Helical hinges are common in transmembrane (TM) proteins. Hinging motions of TM helices are associated with the functional dynamics of many important membrane proteins such as various G-protein-coupled receptors and potassium channels. Although coarse-grained (CG) simulations are useful for studying membrane proteins, they are limited in describing accurately the hinge-related protein dynamics. In this study, we have overcome this limitation through a further development of the MARTINI CG model. The key improvement lies in implementation of additional local structural types and parameterization of the model against a structural library of TM helices obtained from the Protein Data Bank. Through simulations of 12 membrane proteins, we have demonstrated that the improved model not only accurately describes the local hinge structures of these proteins but also reproduces the overall structures of TM domains better than the original MARTINI is able to do. Furthermore, we show that the improved model, when combined with an elastic network, can now be used to explore the deactivation of the human ß2 adrenergic receptor and the gating motions of the KcsA potassium channel. The important details of these hinge-associated transitions captured in our simulations agree well with previous experiments and all-atom simulations, and it was concluded that the improved model shows promise as a useful tool for the study of functional dynamics of membrane proteins.

Effects of Tempeh Fermentation with Lactobacillus plantarum and Rhizopus oligosporus on Streptozotocin-Induced Type II Diabetes Mellitus in Rats.

The increased consumption of high fat-containing foods has been linked to the prevalence of obesity and abnormal metabolic syndromes. Rhizopus oligosporus, a fungus in the family Mucoraceae, is widely used as a starter for homemade tempeh. Although R. oligosporus can prevent the growth of other microorganisms, it grows well with lactic acid bacteria (LAB). Lactobacillus plantarum can produce ß-glucosidase, which catalyzes the hydrolysis of glucoside isoflavones into aglycones (with greater bioavailability). Therefore, the development of a soybean-based functional food by the co-inoculation of R. oligosporus and L. plantarum is a promising approach to increase the bioactivity of tempeh. In this study, the ameliorative effect of L. plantarum in soy tempeh on abnormal carbohydrate metabolism in high-fat diet (HFD)-induced hyperglycemic rats was evaluated. The co-incubation of L. plantarum with R. oligosporus during soy tempeh fermentation reduced the homeostatic model assessment of insulin resistance, HbA1c, serum glucose, total cholesterol, triglyceride, free fatty acid, insulin, and low-density lipoprotein contents, and significantly increased the high-density lipoprotein content in HFD rats. It also increased the LAB counts, as well as the bile acid, cholesterol, triglyceride, and short-chain fatty acid contents in the feces of HFD rats. Our results suggested that the modulation of serum glucose and lipid levels by LAB occurs via alterations in the internal microbiota, leading to the inhibition of cholesterol synthesis and promotion of lipolysis. Tempeh, which was produced with both L. plantarum and R. oligosporus, might be a beneficial dietary supplement for individuals with abnormal carbohydrate metabolism.

A computational study on the N-heterocyclic carbene-catalyzed Csp(2)-Csp(3) bond activation/[4+2] cycloaddition cascade reaction of cyclobutenones with imines: a new application of the conservation principle of molecular orbital symmetry.

A comprehensive density functional theory (DFT) investigation has been performed to interrogate the mechanisms and stereoselectivities of the Csp(2)-Csp(3) single bond activation of cyclobutenones and their [4+2] cycloaddition reaction with imines via N-heterocyclic carbene (NHC) organocatalysis. According to our calculated results, the fundamental reaction pathway contains four steps: nucleophilic addition of NHC to cyclobutenone, C-C bond cleavage for the formation of an enolate intermediate, [4+2] cycloaddition of the enolate intermediate with isatin imine, and the elimination of the NHC catalyst. In addition, the calculated results also reveal that the second reaction step is the rate-determining step, whereas the third step is the regio- and stereo-selectivity determining step. For the regio- and stereo-selectivity determining step, all four possible attack modes were considered. The addition of the C[double bond, length as m-dash]N bond in isatin imine to the dienolate intermediate is more energy favorable than the addition of the C[double bond, length as m-dash]O bond to a dienolate intermediate. Moreover, the Re face addition of the C[double bond, length as m-dash]N bond in isatin imine to the Re face of the dienolate intermediate leading to the SS configuration N-containing product was demonstrated to be most energy favorable, which is mainly due to the stronger second-order perturbation energy value in the corresponding transition state. Furthermore, by tracking the frontier molecular orbital (FMO) changes in the rate-determining C-C bond cleavage step, we found that the reaction obeys the conservation principle of molecular orbital symmetry. We believe that the present work would provide valuable insights into this kind of reaction.

Chronic Beryllium Disease: revealing the role of beryllium ion and small peptides binding to HLA-DP2.

Chronic Beryllium (Be) Disease (CBD) is a granulomatous disorder that predominantly affects the lung. The CBD is caused by Be exposure of individuals carrying the HLA-DP2 protein of the major histocompatibility complex class II (MHCII). While the involvement of Be in the development of CBD is obvious and the binding site and the sequence of Be and peptide binding were recently experimentally revealed [1], the interplay between induced conformational changes and the changes of the peptide binding affinity in presence of Be were not investigated. Here we carry out in silico modeling and predict the Be binding to be within the acidic pocket (Glu26, Glu68 and Glu69) present on the HLA-DP2 protein in accordance with the experimental work [1]. In addition, the modeling indicates that the Be ion binds to the HLA-DP2 before the corresponding peptide is able to bind to it. Further analysis of the MD generated trajectories reveals that in the presence of the Be ion in the binding pocket of HLA-DP2, all the different types of peptides induce very similar conformational changes, but their binding affinities are quite different. Since these conformational changes are distinctly different from the changes caused by peptides normally found in the cell in the absence of Be, it can be speculated that CBD can be caused by any peptide in presence of Be ion. However, the affinities of peptides for Be loaded HLA-DP2 were found to depend of their amino acid composition and the peptides carrying acidic group at positions 4 and 7 are among the strongest binders. Thus, it is proposed that CBD is caused by the exposure of Be of an individual carrying the HLA-DP2*0201 allele and that the binding of Be to HLA-DP2 protein alters the conformational and ionization properties of HLA-DP2 such that the binding of a peptide triggers a wrong signaling cascade.

Remote ischemic postconditioning protects against gastric mucosal lesions in rats.

AIM: To investigate the protective effects of remote ischemic postconditioning (RIP) against limb ischemia-reperfusion (IR)-induced gastric mucosal injury. METHODS: Gastric IR was established in male Wistar rats by placing an elastic rubber band under a pressure of 290-310 mmHg on the proximal part of both lower limbs for 3 h followed by reperfusion for 0, 1, 3, 6, 12 or 24 h. RIP was performed using three cycles of 30 s of reperfusion and 30 s of reocclusion of the femoral aortic immediately after IR and before reperfusion for up to 24 h. Rats were randomly assigned to receive IR (n = 36), IR followed by RIP (n = 36), or sham treatment (n = 36). Gastric tissue samples were collected from six animals in each group at each timepoint and processed to determine levels of malondialdehyde (MDA), superoxide dismutase (SOD), xanthine oxidase (XOD) and myeloperoxidase (MPO). Additional samples were processed for histologic analysis by hematoxylin and eosin staining. Blood samples were similarly collected to determine serum levels of lactate dehydrogenase (LDH), creatine kinase (CK), tumor necrosis factor (TNF)-α and interleukin (IL)-10. RESULTS: The pathologic changes in gastric tissue induced by IR were observed by light microscopy. Administration of RIP dramatically reduced the gastric damage score after 6 h of reperfusion (5.85 ± 0.22 vs 7.72 ± 0.43; P < 0.01). In addition, RIP treatment decreased the serum activities of LDH (3.31 ± 0.32 vs 6.46 ± 0.03; P < 0.01), CK (1.94 ± 0.20 vs 4.54 ± 0.19; P < 0.01) and the concentration of TNF-α (53.82 ± 0.85 vs 88.50 ± 3.08; P < 0.01), and elevated the concentration of IL-10 (101.46 ± 5.08 vs 99.77 ± 4.32; P < 0.01) induced by IR at 6 h. Furthermore, RIP treatment prevented the marked elevation in MDA (3.79 ± 0.29 vs 6.39 ± 0.81) content, XOD (7.81 ± 0.75 vs 10.37 ± 2.47) and MPO (0.47 ± 0.05 vs 0.82 ± 0.03) activities, and decrease in SOD (4.95 ± 0.32 vs 3.41 ± 0.38; P < 0.01) activity in the gastric tissue as measured at 6 h. CONCLUSION: RIP provides effective functional protection and prevents cell injury to gastric tissue induced by limb IR via anti-inflammatory and antioxidant actions.

The impact of genomics on oncology nursing.

Since 2003, genetics and genomics information has led to exciting new diagnostics, prognostics, and treatment options in oncology practice. Profiling of cancers offers providers insight into treatment and prognostic factors. Germline testing provides an individual with information for surveillance or therapy that may help them prevent cancer in their lifetime and options for family members as yet untouched by malignancy. This offers a challenge for oncology nurses and other oncology health care providers to become comfortable with incorporating education about genetics/genomics into their clinical practice and patient education.

Asymptomatic hepatobiliary cystadenoma of the hepatic caudate lobe: a case report.

Human hepatobiliary cystadenoma is a rare benign cystic tumor of the liver, and is extremely rare in the caudate lobe. We herein present a case of a 70-year-old male with a hepatobiliary cystadenoma originating from the caudate lobe.

Chitosan-functionalized carbon nanotubes as support for the high dispersion of PtRu nanoparticles and their electrocatalytic oxidation of methanol.

Carbon nanotubes (CNTs) were non-covalently functionalized with chitosan (Chit) and then employed as the support for PtRu nanoparticles. The functionalization was carried out at room temperature without the use of corrosive acids, thereby preserving the integrity and the electronic conductivity of the CNTs. Transmission electron microscopy reveals that PtRu nanoparticles were highly dispersed on the surface of Chit-functionalized CNTs (CNT-Chit) with small particle-size. Cyclic voltammetry studies indicated that the PtRu nanoparticle/CNT-Chit nanohybrids have a higher electrochemical surface area, electrocatalytic performance, and stability towards methanol oxidation compared to PtRu nanoparticles supported on the pristine CNTs.

High dispersion of platinum-ruthenium nanoparticles on the 3,4,9,10-perylene tetracarboxylic acid-functionalized carbon nanotubes for methanol electro-oxidation.

Due to lots of carboxyl groups introduced uniformly on the carbon nanotube (CNT) surface, platinum-ruthenium nanoparticles were highly dispersed on the 3,4,9,10-perylene tetracarboxylic acid-functionalized CNT surface and showed improved electrochemical properties for methanol electrooxidation.

Stabilization of platinum nanoparticles dispersed on carbon nanotubes by ionic liquid polymer.

Due to the protection of ionic liquid polymer thin film, the long-term operation stability of carbon nanotube-supported platinum nanoparticles for methanol electrooxidation has been improved.

Polymerized ionic liquid-wrapped carbon nanotubes: the promising composites for direct electrochemistry and biosensing of redox protein.

Polymerized ionic liquid-wrapped carbon nanotubes (PIL-CNTs) were firstly designed for direct electrochemistry and biosensing of redox proteins. The CNTs were coated successfully with polymerized ionic liquid (PIL) layer, as verified by transmission electron microscopy (TEM), thermogravimetric analysis (TGA) and Fourier transform infrared (FT-IR) spectroscopy. The PIL-CNTs were dispersed better in water and showed superior electrocatalysis toward O(2) and H(2)O(2) comparing to pristine CNTs and the mixture of IL monomer and CNTs. With glucose oxidase (GOD) as a protein model, the direct electrochemistry of the redox protein was investigated on the PIL-CNTs modified glassy carbon (GC) electrode and excellent direct electrochemical performance of GOD molecules was observed. The proposed biosensor (GOD/PIL-CNTs/GC electrode) displayed good analytical performance for glucose with linear response up to 6mM, response sensitivity of 0.853 microA mM(-1), good stability and selectivity.

Functionalization of carbon nanotubes by an ionic-liquid polymer: dispersion of Pt and PtRu nanoparticles on carbon nanotubes and their electrocatalytic oxidation of methanol.

Small beginnings: Metal nanoparticle/CNT nanohybrids are synthesized from carbon nanotubes (CNTs) functionalized with an ionic-liquid polymer. The Pt and PtRu nanoparticles with narrow size distribution (average diameter: (1.3+/-0.4) nm for PtRu, (1.9+/-0.5) nm for Pt) are dispersed uniformly on the CNTs (see images) and show good performance in methanol electrooxidation.