Atomistic Modeling of Peptide Aggregation and ß-Sheet Structuring in Corn Zein for Viscoelasticity.

The structure-function relationships of plant-based proteins that give rise to desirable texture attributes in order to mimic meat products are generally unknown. In particular, it is not clear how to engineer viscoelasticity to impart cohesiveness and proper mouthfeel; however, it is known that intermolecular ß-sheet structures have the potential to enhance the viscoelastic property. Here, we investigated the propensity of selected peptide segments within common corn α-zein variants to maintain stable aggregates and ß-sheet structures. Simulations on dimer systems showed that stability was influenced by the initial orientation and the presence of contiguous small hydrophobic residues. Simulations using eight-peptide ß-sheet oligomers revealed that peptide sequences without proline had higher levels of ß-sheet structuring. Additionally, we identified that sequences with a dimer hydrogen-bonding density of >22% tended to have a larger percent ß-sheet conformation. These results contribute to understanding how the viscoelasticity of zein can be increased for use in plant-based meat analogues.

Association of MIR-499a expression and seed region variant (rs3746444) with cardiovascular disease in Egyptian patients.

BACKGROUND: Circulating microRNAs could be powerful markers of acute myocardial infarction (MI) and its functional genetic variants could increase susceptibility to cardiovascular disease (CVD). The current study aimed to quantify the microRNA (miR)-499a levels in serum of MI patients compared to hypertensive and healthy subjects and to investigate the association of its A/G variant rs3746444 with CVD in a sample of an Egyptian population. METHODS: Serum miR-499a relative expressions were measured in 110 acute MI patients, 76 hypertensive patients, and 121 healthy controls by Real-time quantitative polymerase chain reaction. MIR-499a genotyping was performed for an additional 107 coronary artery disease patients by Real-time allele discrimination assay. RESULTS: Acute MI patients showed high relative expression of miR-499a (> 105-fold, p < .001), and it was nearly undetectable in healthy controls and hypertensive patients. It showed an area under the curve of 0.953, with a sensitivity of 97.2% and a specificity of 75.0%. ST-elevation MI (STEMI) patients had higher miR-499a serum levels than patients with Non-STEMI. There was a significant association of MIR-499a variant with acute MI but not with hypertension under all genetic models tested. As a new finding, in overall and stratified analysis, the miR-499a variant was not correlated with its expression profile. CONCLUSIONS: Circulating miR-499a levels could be a useful biomarker, discriminating acute MI within 12 hours from healthy subjects. Its variant rs3746444 A/G is associated with increased susceptibility to acute MI and CAD in Egyptian population.

Stemness-related transcriptional factors and homing gene expression profiles in hepatic differentiation and cancer.

Stem cell transcriptional signature activation is an essential event in the development of cancer. This study aimed to investigate the differential expression profile of three pluripotency-associated genes (OCT4, NANOG, and SOX2), G-protein-coupled chemokine receptor 4 (CXCR4) and the ligand (CXCL2), and alpha feto-protein (AFP) in hepatogenic differentiated stem cells and in sera of hepatitis C virus (HCV) and HCV-induced hepatocellular carcinoma (HCC) patients. Mesenchymal stem cells derived from umbilical cord blood were differentiated using hepatogenic differentiation media. Serum specimens were collected from 96 patients (32 cirrhotic HCV, 32 early HCC, and 32 late HCC) and 96 controls. Real-time quantitative reverse transcription polymerase chain reaction was performed for relative quantification of the 6 target genes using LIVAC method. In silico network analysis was also executed to explore the pluripotency and tumorigenic regulatory circuits in liver cancer. The expression levels of all genes declined gradually during the stages of stem cell differentiation. On univariate and multivariate analyses, NANOG, CXCR4 and AFP were significantly up-regulated in HCC patients with late clinical stage. In contrast, SOX2 and CXCL2 were markedly over-expressed in cirrhotic patients and could be used for clear demarcation between cirrhotic and HCC patients in our cases. In conclusion, our data highlight the potential role of SOX2 stem cell marker and CXCL2 chemokine in liver cell degeneration and fibrogenesis in HCV-induced hepatic cirrhosis in our sample of the Egyptian population. In addition, the significant association of NANOG and CXCR4 high-expression with late HCC, could contribute to the acquisition of stem cell-like properties in hepatic cancer and dissemination in late stages, respectively. Taken together, our results could have a potential application in HCC prognosis and treatment.

Modelling of bone fracture and strength at different length scales: a review.

In this paper, we review analytical and computational models of bone fracture and strength. Bone fracture is a complex phenomenon due to the composite, inhomogeneous and hierarchical structure of bone. First, we briefly summarize the hierarchical structure of bone, spanning from the nanoscale, sub-microscale, microscale, mesoscale to the macroscale, and discuss experimental observations on failure mechanisms in bone at these scales. Then, we highlight representative analytical and computational models of bone fracture and strength at different length scales and discuss the main findings in the context of experiments. We conclude by summarizing the challenges in modelling of bone fracture and strength and list open topics for scientific exploration. Modelling of bone, accounting for different scales, provides new and needed insights into the fracture and strength of bone, which, in turn, can lead to improved diagnostic tools and treatments of bone diseases such as osteoporosis.

Mechanical Reinforcement of Proteins with Polymer Conjugation.

Conjugating poly(ethylene glycol) (PEG) to peptides, also known as PEGylation, is proven to increase the thermodynamical stability of peptides, and has been successfully applied to prolong the lifetime of peptide-based vaccines and therapeutic agents. While it is known that protein structure and function can be altered by mechanical stress, whether PEGylation can reinforce proteins against mechanical unfolding remains to be ascertained. Here, we illustrate that PEGylation prolongs the lifetime of α-helices subject to constant stress. PEGylation is found to increase the unfolding time through two mechanisms. We see that (1) the unfolding rate of a helical segment is decreased through prolonged plateau regimes where the peptide helical content remains constant, and (2) the proportion of refolding to unfolding is increased, primarily by shielding water molecules from replacing forcibly exposed backbone hydrogen bonds near the conjugation site. Our findings demonstrate the feasibility of improving peptide mechanical stability with polymer conjugation. This provides a basis for future studies on optimizing conjugation location and chemistry to build custom biomolecules with unforeseen mechanical functions and stability.

Experimentally-based multiscale model of the elastic moduli of bovine trabecular bone and its constituents.

The elastic moduli of trabecular bone were modeled using an analytical multiscale approach. Trabecular bone was represented as a porous nanocomposite material with a hierarchical structure spanning from the collagen-mineral level to the trabecular architecture level. In parallel, compression testing was done on bovine femoral trabecular bone samples in two anatomical directions, parallel to the femoral neck axis and perpendicular to it, and the measured elastic moduli were compared with the corresponding theoretical results. To gain insights on the interaction of collagen and minerals at the nanoscale, bone samples were deproteinized or demineralized. After such processing, the treated samples remained as self-standing structures and were tested in compression. Micro-computed tomography was used to characterize the hierarchical structure of these three bone types and to quantify the amount of bone porosity. The obtained experimental data served as inputs to the multiscale model and guided us to represent bone as an interpenetrating composite material. Good agreement was found between the theory and experiments for the elastic moduli of the untreated, deproteinized, and demineralized trabecular bone.

Hierarchical cascades of instability govern the mechanics of coiled coils: helix unfolding precedes coil unzipping.

Coiled coils are a fundamental emergent motif in proteins found in structural biomaterials, consisting of α-helical secondary structures wrapped in a supercoil. A fundamental question regarding the thermal and mechanical stability of coiled coils in extreme environments is the sequence of events leading to the disassembly of individual oligomers from the universal coiled-coil motifs. To shed light on this phenomenon, here we report atomistic simulations of a trimeric coiled coil in an explicit water solvent and investigate the mechanisms underlying helix unfolding and coil unzipping in the assembly. We employ advanced sampling techniques involving steered molecular dynamics and metadynamics simulations to obtain the free-energy landscapes of single-strand unfolding and unzipping in a three-stranded assembly. Our comparative analysis of the free-energy landscapes of instability pathways shows that coil unzipping is a sequential process involving multiple intermediates. At each intermediate state, one heptad repeat of the coiled coil first unfolds and then unzips due to the loss of contacts with the hydrophobic core. This observation suggests that helix unfolding facilitates the initiation of coiled-coil disassembly, which is confirmed by our 2D metadynamics simulations showing that unzipping of one strand requires less energy in the unfolded state compared with the folded state. Our results explain recent experimental findings and lay the groundwork for studying the hierarchical molecular mechanisms that underpin the thermomechanical stability/instability of coiled coils and similar protein assemblies.

Poly(ethylene glycol) conjugation stabilizes the secondary structure of α-helices by reducing peptide solvent accessible surface area.

We investigate the effect of poly(ethylene glycol) (PEG) side-chain conjugation on the conformational behavior of an α-helix using molecular dynamics simulations in explicit solvents of varying hydrophobicity. Our simulations illustrate an increase in peptide helicity with increasing PEG molecular weight in the range ~400 to 1800 Da. The data with varying PEG contour lengths as well as constant force pulling simulations that allow control over the end-to-end length of PEG indicate a strong inverse correlation between peptide helicity and solvent accessible surface area (SASA). A residue-based mapping analysis reveals that the formation of a protecting PEG shell around peptide helix in water is facilitated by two distinct mechanisms that depend on the solvent environment. First, cationic residues such as lysine interact favorably with PEG due to strong polar interactions with PEG oxygen atoms. Additionally, we find that hydrophobic residues interact strongly with PEG to reduce their SASA in polar solvents by polymer shielding. Our simulations illustrate that these two mechanisms that involve side-chain chemistry and solvent polarity govern the preferred conformation of PEG on the helix surface and thus the stability of peptide secondary structure. These findings elucidate the molecular mechanisms underpinning recent experimental findings on the stability and conformational dynamics of protein-PEG conjugates.

Multiscale damage and strength of lamellar bone modeled by cohesive finite elements.

A computational multiscale model of damage mechanisms and strength of lamellar bone is presented. The analysis incorporates the hierarchical structure of bone spanning the nanoscale (mineralized collagen fibril), the sub-microscale (single lamella) and the microscale (lamellar structure) levels. Due to the presence of several constituents (collagen, hydroxyapatite minerals, and non-collagenous proteins) and the different microstructural features at each scale, various deformation and failure mechanisms occur in bone at its several levels of hierarchy. The model takes into account the dominant damage mechanisms at the above mentioned three scales and predicts the strength of bone by using a cohesive finite element method. Elastic moduli of bone at these three different scales are also obtained as part of these calculations. The obtained modeling results compare well with other theoretical and experimental data available in the literature.

Significance of HE4 estimation in comparison with CA125 in diagnosis of ovarian cancer and assessment of treatment response.

BACKGROUND: Human epididymis protein 4 (HE4) is a novel and specific biomarker for ovarian cancer. The aim of this study is to evaluate a new tumor marker, HE4, in comparison with CA125 in diagnosis of epithelial ovarian cancer (EOC) and benign gynecological diseases. METHODS: CA125 and HE4 serum levels were determined in 30 patients with epithelial ovarian cancer (21 serous, 6 endometrioid and 3 mucinous tumors), 20 patients with benign gynecological diseases (8 patients with ovarian cyst, 5 patients with endometriosis, 4 patients with fibroid and 3 patients with pelvic inflammatory disease) and 20 healthy women. CA125 and HE4 cut-offs were 35 U/ml and 150 pmol/l, respectively. RESULTS: Serum HE4 and CA125 concentrations were significantly higher in the ovarian cancer patients compared with those seen in patients with benign disease or in the healthy controls (p = 0.001 and p < 0.001 respectively). In the receiver operating characteristic analysis (ROC), the area under the curve (AUC) values for HE4 was 0.96 (95% confidence interval, 0.9-1.0) and CA125 was 0.82 (95% confidence interval, 0.7-0.94). Compared to CA125, HE4 had higher sensitivity (90% vs. 83.3%), specificity (95% vs. 85%), PPV (93.1% vs. 80.7%) and NPV (92.7% vs. 87.2%), the combination of HE4 + CA125 the sensitivity and PPV reached 96.7% and 97% respectively. CONCLUSION: Measuring serum HE4 concentrations along with CA125 concentrations may provide higher accuracy for detecting epithelial ovarian cancer. VIRTUAL SLIDES: The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/1060413168685759.

Vitamin D level and Fok-I vitamin D receptor gene polymorphism in Egyptian patients with type-1 diabetes.

Many cellular, preclinical and observational studies support a role of vitamin D in pathogenesis of type-1 diabetes mellitus (DM). The vitamin D receptor (VDR) locus has been studied in different populations for association with susceptibility to immune-mediated diseases, but with inconsistent findings in type-1 DM. This study aimed to investigate vitamin D status in patients with type-1 DM. We examined the frequency of VDR Fokl (rs10735810) gene polymorphism, and its association with serum 25-hydroxyvitamin D (25(OH) D) level in Egyptian patients with type-1 DM. 132 children with type-1 DM and 40 age and sex matched healthy control subjects were studied. VDR Fokl polymorphism was assessed using polymerase chain reaction and restriction fragment length polymorphism (RFLP) analysis. Diabetic children demonstrated lower circulating levels of 25(OH) D than the controls (13.4 +/- 7.6 vs 32.1 +/- 3.8ng/ml) (P < 0.01). Patients with deficient 25(OH) D showed lower calcium levels and higher HbA1c% than those with sufficient levels (8.1 +/- 2.1 versus 9.1 +/- 1.6 mg/dl & 9.9 +/- 2.5 versus 8.1 +/- 1.4%, respectively (P < 0.05). There was no significant difference in the genotype distribution or the allele frequencies of VDR Fokl between patients and controls. The odds ratio (OR) was 1.08 (P = 0.76), and the 95% confidence interval (CI) ranged from 0.64-1.85. The diabetic carriers of the ff genotype showed low serum levels of 25(OH) D and calcium when compared with the carriers of the F allele (9.1 +/- 4.4 vs 13.1 +/- 7 and 13.9 +/- 6.09 ng/ml & 8.1 +/- 2.1 vs 9.1 +/- 1.1 and 9.3 +/- 1.2 mg/dl, respectively) (P < 0.05). In conclusion, 84.8% of children with type-1 DM have low circulating levels of 25(OH) D. These patients have poor glycemic control (56.06%) than those with sufficient levels of 25(OH) D. Fokl polymorphism of VDR gene is associated with vitamin D deficiency but has no significant role in susceptibility to type-1 diabetes.

Multi-scale modelling of elastic moduli of trabecular bone.

We model trabecular bone as a nanocomposite material with hierarchical structure and predict its elastic properties at different structural scales. The analysis involves a bottom-up multi-scale approach, starting with nanoscale (mineralized collagen fibril) and moving up the scales to sub-microscale (single lamella), microscale (single trabecula) and mesoscale (trabecular bone) levels. Continuum micromechanics methods, composite materials laminate theory and finite-element methods are used in the analysis. Good agreement is found between theoretical and experimental results.