Vitamin D Association with Renal Health and Filtration in Healthy Individuals Free of Cardiometabolic Diseases: A Pilot Study

The effect of vitamin D (VITD) on bone, muscle, and over health is well know in renal failure and chronic kidney disease (CKD). However, the influence of VITD on renal health and filtration (RHF) in healthy individuals is unclear. Currently, only serum creatinine concentration (sCr) methods are used to assess renal status in health individuals. However, newer biomarkers like serum Cystatin C (CyC) and urine epidermal growth factor (uEGF) show promise in evaluating baseline RHF. The impact of Vitamin D on filtration in healthy individuals of various ages is still unknown. PURPOSE: To determine the impact of VITD on RHF in healthy individuals of middle-aged status. METHODS: Thirty-six participants (n = 22 men; n = 14 women; age 37.6 + 12.4 yr; BF% 19.2 + 7.1%) agreed to participate in the research study. Blood and urine samples were obtained under standardized conditions for all individuals. VITD, CyC, uEGF, urine creatinine (uCr), uCr/uEGF ratio, sCR, and multiple estimates of glomerular filtration rate (eGFR) - modification of diet in renal disease (MDRD), CKD-EPI, CyC equations (CyC only and CyC combined with sCr) were assessed as a whole cohort and grouped (young = 20-39 yrs. (n = 22), older = 40-60 yrs. (n = 14)). Analysis was done using a paired sample t-tests, Pearson Correlation to compare VITD concentrations and markers of RHF. Linear regression analyses was performed to examine the relationship between VITD ability to predict RHF. All analyses were performed using SPSS (v. 28.0.1.1). RESULTS: There was no significant correlations found between VITD and markers of RHF in the entire cohort. Therefore, no predictive model was performed. The younger group showed strong negative correlation between VITD and MDRD (r = -0.575, p = 0.008), and that VITD was able to predict MDRD (R2 = 0.331, p = 0.008). No significant correlation observed in older group. CONCLUSIONS: VITD was correlated and able to predict a marker of RHF in healthy younger individuals, but not in older individuals. Based on the sample size and overall outcomes, continued research is needed to more accurately determine VITD effects on RHF in healthy populations

Conformational effects on the Circular Dichroism of Human Carbonic Anhydrase II: a multilevel computational study

Circular Dichroism (CD) spectroscopy is a powerful method for investigating conformational changes in proteins and therefore has numerous applications in structural and molecular biology. Here a computational investigation of the CD spectrum of the Human Carbonic Anhydrase II (HCAII), with main focus on the near-UV CD spectra of the wild-type enzyme and it seven tryptophan mutant forms, is presented and compared to experimental studies. Multilevel computational methods (Molecular Dynamics, Semiempirical Quantum Mechanics, Time-Dependent Density Functional Theory) were applied in order to gain insight into the mechanisms of interaction between the aromatic chromophores within the protein environment and understand how the conformational flexibility of the protein influences these mechanisms. The analysis suggests that combining CD semi empirical calculations, crystal structures and molecular dynamics (MD) could help in achieving a better agreement between the computed and experimental protein spectra and provide some unique insight into the dynamic nature of the mechanisms of chromophore interactions

Mechanochemical modeling of dynamic microtubule growth involving sheet-to-tube transition

Microtubule dynamics is largely influenced by nucleotide hydrolysis and the resultant tubulin configuration changes. The GTP cap model has been proposed to interpret the stabilizing mechanism of microtubule growth from the view of hydrolysis effects. Besides, the microtubule growth involves the closure of a curved sheet at its growing end. The curvature conversion also helps to stabilize the successive growth, and the curved sheet is referred to as the conformational cap. However, there still lacks theoretical investigation on the mechanical-chemical coupling growth process of microtubules. In this paper, we study the growth mechanisms of microtubules by using a coarse-grained molecular method. Firstly, the closure process involving a sheet-to-tube transition is simulated. The results verify the stabilizing effect of the sheet structure, and the minimum conformational cap length that can stabilize the growth is demonstrated to be two dimers. Then, we show that the conformational cap can function independently of the GTP cap, signifying the pivotal role of mechanical factors. Furthermore, based on our theoretical results, we describe a Tetris-like growth style of microtubules: the stochastic tubulin assembly is regulated by energy and harmonized with the seam zipping such that the sheet keeps a practically constant length during growth.Comment: 23 pages, 7 figures. 2 supporting movies have not been uploaded due to the file type restriction

Outer membrane protein G: engineering a quiet pore for biosensing

Bacterial outer membrane porins have a robust ?-barrel structure and therefore show potential for use as stochastic sensors based on single-molecule detection. The monomeric porin OmpG is especially attractive compared with multisubunit proteins because appropriate modifications of the pore can be easily achieved by mutagenesis. However, the gating of OmpG causes transient current blockades in single-channel recordings that would interfere with analyte detection. To eliminate this spontaneous gating activity, we used molecular dynamics simulations to identify regions of OmpG implicated in the gating. Based on our findings, two approaches were used to enhance the stability of the open conformation by site-directed mutagenesis. First, the mobility of loop 6 was reduced by introducing a disulfide bond between the extracellular ends of strands ?12 and ?13. Second, the interstrand hydrogen bonding between strands ?11 and ?12 was optimized by deletion of residue D215. The OmpG porin with both stabilizing mutations exhibited a 95% reduction in gating activity. We used this mutant for the detection of adenosine diphosphate at the single-molecule level, after equipping the porin with a cyclodextrin molecular adapter, thereby demonstrating its potential for use in stochastic sensing applications

Designing biomimetic pores based on carbon nanotubes

Biomimetic nanopores based on membrane-spanning single-walled carbon nanotubes have been designed to include selectivity filters based on combinations of anionic and cationic groups mimicking those present in bacterial porins and in voltage-gated sodium and calcium channels. The ion permeation and selectivity properties of these nanopores when embedded in a phospholipid bilayer have been explored by molecular dynamics simulations and free energy profile calculations. The interactions of the nanopores with sodium, potassium, calcium, and chloride ions have been explored as a function of the number of anionic and cationic groups within the selectivity filter. Unbiased molecular dynamics simulations show that the overall selectivity is largely determined by the net charge of the filter. Analysis of distribution functions reveals considerable structuring of the distribution of ions and water within the nanopores. The distributions of ions along the pore axis reveal local selectivity for cations around filter, even in those nanopores (C0) where the net filter charge is zero. Single ion free energy profiles also reveal clear evidence for cation selectivity, even in the C0 nanopores. Detailed analysis of the interactions of the C0 nanopore with Ca2+ ions reveals that local interactions with the anionic (carboxylate) groups of the selectivity filter lead to (partial) replacement of solvating water as the ion passes through the pore. These studies suggest that a computational biomimetic approach can be used to evaluate our understanding of the design principles of nanopores and channels