Molecular dynamics (MD) in homocysteine nanosystems - computer simulation

Excessive of homocysteine in the human body is recently considered as a factor increasing the risk of the cardiovascular system diseases. The nanosystem composed of finite number of homocysteine molecules (n=20, 50 and 80) have been studied by MD technique. Several physical quantities of homocysteine nanosystem have been calculated as a function of temperature and a number of molecules in homocysteine cluster. The total dipole moment autocorrelation function and dielectric loss of the cluster have been also obtained.     

Dynamical effects of diffusive cell coupling on cardiac excitation and propagation: a simulation study

Cell coupling is considered to be important for cardiac action potential propagation and arrhythmogenesis. We carried out computer simulations to investigate the effects of stimulation strength and cell-to-cell coupling on action potential duration (APD) restitution, APD alternans, and stability of reentry in models of isolated cell, one-dimensional cable, and two-dimensional tissue. Phase I formulation of the Luo and Rudy action potential model was used. We found that stronger stimulation resulted in a shallower APD restitution curve and onset of APD alternans at a faster pacing rate. Reducing diffusive coupling between cells prolonged APD. Weaker diffusive currents along the direction of propagation steepened APD restitution and caused APD alternans to occur at a slower pacing rate in tissue. Diffusive current due to curvature changed APD but had little effect on APD restitution slope and onset of instability. Heterogeneous cell coupling caused APD inhomogeneities in space. Reduction in coupling strength either uniformly or randomly had little effect on the rotation period and stability of a reentry, but random cell decoupling slowed the rotation period and, thus, stabilized the reentry, preventing it from breaking up into multiple waves. Therefore, in addition to its effects on action potential conduction velocity, diffusive cell coupling also affects APD in a rate-dependent manner, causes electrophysiological heterogeneities, and thus modulates the dynamics of cardiac excitation. These effects are brought about by the modulation of ionic current activation and inactivation.     

Initiation and propagation of a neuronal intracellular calcium wave

The ability to image calcium movement within individual neurons inspires questions of functionality including whether calcium entry into the nucleus is related to genetic regulation for phenomena such as long term potentiation. Calcium waves have been initiated in hippocampal pyramidal cells with glutmatergic signals both in the presence and absence of back propagating action potentials (BPAPs). The dendritic sites of initiation of these calcium waves within about 100 μm of the soma are thought to be localized near oblique junctions. Stimulation of synapses on oblique dendrites leads to production of inositol 1,4,5-trisphosphate (IP₃) which diffuses to the apical dendrite igniting awaiting IP₃ receptors (IP₃Rs) and initiating and propagating catalytic calcium release from the endoplasmic reticulum. We construct a reduced mathematical system which accounts for calcium wave initiation and propagation due to elevated IP₃. Inhomogeneity in IP₃ distribution is responsible for calcium wave initiation versus subthreshold or spatially uniform suprathreshold activation. However, the likelihood that a calcium wave is initiated does not necessarily increase with more calcium entering from BPAPs. For low transient synaptic stimuli, timing between IP₃ generation and BPAPs is critical for calcium wave initiation. We also show that inhomogeneity in IP₃R density can account for calcium wave directionality. Simulating somatic muscarinic receptor production of IP₃, we can account for the critical difference between calcium wave entry into the soma and failure to do so.     

Criticality in intracellular calcium signaling in cardiac myocytes

Calcium (Ca) is a ubiquitous second messenger that regulates many biological functions. The elementary events of local Ca signaling are Ca sparks, which occur randomly in time and space, and integrate to produce global signaling events such as intra- and intercellular Ca waves and whole-cell Ca oscillations. Despite extensive experimental characterization in many systems, the transition from local random to global synchronous events is still poorly understood. Here we show that criticality, a ubiquitous dynamical phenomenon in nature, is responsible for the transition from local to global Ca signaling. We demonstrate this first in a computational model of Ca signaling in a cardiac myocyte and then experimentally in mouse ventricular myocytes, complemented by a theoretical agent-based model to delineate the underlying dynamics. We show that the interaction between the Ca release units via Ca-induced Ca release causes self-organization of Ca spark clusters. When the coupling between Ca release units is weak, the cluster-size distribution is exponential. As the interactions become strong, the cluster-size distribution changes to a power-law distribution, which is characteristic of criticality in thermodynamic and complex nonlinear systems, and facilitates the formation and propagation of Ca waves and whole-cell Ca oscillations. Our findings illustrate how criticality is harnessed by a biological cell to regulate Ca signaling via self-organization of random subcellular events into cellular-scale oscillations, and provide a general theoretical framework for the transition from local Ca signaling to global Ca signaling in biological cells.     

Local positive feedback by calcium in the propagation of intracellular calcium waves.

In many types of eukaryotic cells, the activation of surface receptors leads to the production of inositol 1,4,5-trisphosphate and calcium release from intracellular stores. Calcium release can occur in complex spatial patterns, including waves of release that traverse the cytoplasm. Fluorescence video microscopy was used to view calcium waves in single mouse neuroblastoma cells. The propagation of calcium waves was slowed by buffers that bind calcium quickly, such as BAPTA, but not by a buffer with slower on-rate, EGTA. This shows that a key feedback event in wave propagation is rapid diffusion of calcium occurring locally on a scale of < 1 micron. The length-speed product of wavefronts was used to determine that calcium acting in feedback diffuses at nearly the rate expected for free diffusion in aqueous solution. In cytoplasm, which contains immobile Ca2+ buffers, this rate of diffusion occurs only in the first 0.2 ms after release, within 0.4 micron of a Ca2+ release channel mouth. Calcium diffusion from an open channel to neighboring release sites is, therefore, a rate-determining regenerative step in calcium wave propagation. The theoretical limitations of the wave front analysis are discussed.     

Mechanisms by which cytoplasmic calcium wave propagation and alternans are generated in cardiac atrial myocytes lacking T-tubules-insights from a simulation study

This study investigated the mechanisms underlying the propagation of cytoplasmic calcium waves and the genesis of systolic Ca²⁺ alternans in cardiac myocytes lacking transverse tubules (t-tubules). These correspond to atrial cells of either small mammals or large mammals that have lost their t-tubules due to disease-induced structural remodeling (e.g., atrial fibrillation). A mathematical model was developed for a cluster of ryanodine receptors distributed on the cross section of a cell that was divided into 13 elements with a spatial resolution of 2 μm. Due to the absence of t-tubules, L-type Ca²⁺ channels were only located in the peripheral elements close to the cell-membrane surface and produced Ca²⁺ signals that propagated toward central elements by triggering successive Ca²⁺-induced Ca²⁺ release (CICR) via Ca²⁺ diffusion between adjacent elements. Under control conditions, the Ca²⁺ signals did not fully propagate to the central region of the cell. However, with modulation of several factors responsible for Ca²⁺ handling, such as the L-type Ca²⁺ channels (Ca²⁺ influx), SERCA pumps (sarcoplasmic reticulum (SR) Ca²⁺ uptake), and ryanodine receptors (SR Ca²⁺ release), Ca²⁺ wave propagation to the center of the cell could occur. These simulation results are consistent with previous experimental data from atrial cells of small mammals. The model further reveals that spatially functional heterogeneity in Ca²⁺ diffusion within the cell produced a steep relationship between the SR Ca²⁺ content and the cytoplasmic Ca²⁺ concentration. This played an important role in the genesis of Ca²⁺ alternans that were more obvious in central than in peripheral elements. Possible association between the occurrence of Ca²⁺ alternans and the model parameters of Ca²⁺ handling was comprehensively explored in a wide range of one- and two-parameter spaces. In addition, the model revealed a spontaneous second Ca²⁺ release in response to a single voltage stimulus pulse with SR Ca²⁺ overloading and augmented Ca²⁺ influx. This study provides what to our knowledge are new insights into the genesis of Ca²⁺ alternans and spontaneous second Ca²⁺ release in cardiac myocytes that lack t-tubules.     

Cooperativity can reduce stochasticity in intracellular calcium dynamics

The opening of inositol (1,4,5)-triphosphate (IP(3)) receptors, clustered at discrete sites on the endoplasmic reticulum, can lead to large-scale intracellular calcium waves. Recent experiments in Xenopus oocytes have shown that the inter-wave intervals for these waves have a standard deviation that is much smaller than their mean and that the background calcium concentration exhibits a slow rise during the interwave interval. Using a simple mathematical model, we examine the possibility that this slow rise increases the cooperativity between the openings of the clusters. We find that our model, coupled to the usual assumption that the pumps on the endoplasmic reticulum are activated instantaneously, is unable to explain the observed data: the clusters are found to fire independently and the inter-wave interval distribution is a Poisson distribution with a standard deviation that is approximately equal to its mean. On the other hand, we find that incorporating pumps that slowly activate leads to a slow increase in the background calcium concentration which makes global events progressively more likely to occur. We show that this cooperativity results in much smaller standard deviations and inter-wave interval distributions that are clearly not Poisson distributions.     

A simulation study of cellular hypertrophy and connexin lateralization in cardiac tissue

Many cardiac diseases coincide with changes in cell size and shape. One example of such a disease is cardiac hypertrophy. It is established that cardiac impulse propagation depends on the cell size, as well as other factors, but interrelations between conduction velocity (CV), cell size, and gap junction (GJ) conductance (g_GJ) are complex. Furthermore, cardiac diseases are often accompanied by connexin (Cx) lateralization. To analyze the effects of cell size and Cx lateralization in cardiac disease, a two-dimensional computer simulation of ventricular myocytes based on the Luo-Rudy model was used. Control cells (80 μm/20 μm (length/diameter)), long cells (160 μm/20 μm), and wide cells (80 μm/40 μm) were simulated as was a redistribution of lateral GJs (constant lateral g_GJ and increased lateral g_GJ). CV in long cells showed high stability, i.e., it declined very slowly when g_GJ was gradually reduced. Wide cells, however, were more affected by reduced g_GJ, resulting in early transition to discontinuous propagation and low CV. Conduction block occurred earlier in enlarged cells than in control cells due to increased cell capacitance. Increased lateral g_GJ stabilized longitudinal CV, which was a result of two-dimensional effects during planar wave propagation. Therefore, Cx lateralization may compensate for cardiac inhomogeneities. High lateral g_GJ and enhanced cell diameter increased the susceptibility to conduction block at tissue expansion, providing a substrate for arrhythmia.     

Relationships between mitochondrial DNA subhaplogroups and intracellular calcium dynamics

Although an association between mitochondrial DNA (mtDNA) subhaplogroups and complex traits has been suggested, few functional analyses have been reported. To identify the mtDNA subhaplogroups that alter intracellular calcium dynamics, we analysed data on intracellular calcium dynamics in 35 transmitochondrial hybrid cells (cybrids). One cybrid showing decreased calcium levels had mtDNA subhaplogroup G3 or G4, characterised by 1413T>C, 2109A>T, 3434A>G, 5460G>A, 7521G>A, 9011C>T, 9670A>G and 15940T>C. The cybrid having higher calcium levels was subhaplogroup D4a, characterised by a non-synonymous polymorphism, 13651A>G. These mtDNA subhaplogroups might have functional effects.     

Diabetes alters intracellular calcium transients in cardiac endothelial cells

Diabetic cardiomyopathy (DCM) is a diabetic complication, which results in myocardial dysfunction independent of other etiological factors. Abnormal intracellular calcium ([Ca(2+)](i)) homeostasis has been implicated in DCM and may precede clinical manifestation. Studies in cardiomyocytes have shown that diabetes results in impaired [Ca(2+)](i) homeostasis due to altered sarcoplasmic reticulum Ca(2+) ATPase (SERCA) and sodium-calcium exchanger (NCX) activity. Importantly, altered calcium homeostasis may also be involved in diabetes-associated endothelial dysfunction, including impaired endothelium-dependent relaxation and a diminished capacity to generate nitric oxide (NO), elevated cell adhesion molecules, and decreased angiogenic growth factors. However, the effect of diabetes on Ca(2+) regulatory mechanisms in cardiac endothelial cells (CECs) remains unknown. The objective of this study was to determine the effect of diabetes on [Ca(2+)](i) homeostasis in CECs in the rat model (streptozotocin-induced) of DCM. DCM-associated cardiac fibrosis was confirmed using picrosirius red staining of the myocardium. CECs isolated from the myocardium of diabetic and wild-type rats were loaded with Fura-2, and UTP-evoked [Ca(2+)](i) transients were compared under various combinations of SERCA, sarcoplasmic reticulum Ca(2+) ATPase (PMCA) and NCX inhibitors. Diabetes resulted in significant alterations in SERCA and NCX activities in CECs during [Ca(2+)](i) sequestration and efflux, respectively, while no difference in PMCA activity between diabetic and wild-type cells was observed. These results improve our understanding of how diabetes affects calcium regulation in CECs, and may contribute to the development of new therapies for DCM treatment.     

Model for computer simulation of bone tissue

The paper deals with the dependence of the torsional moment on the angle of the compact bone torsion in laboratory animals and humans. Based on the data for laboratory animals obtained by measurements, the data on dependence of the torsional moment and the angle of torsion were predicted for humans. The measurements were carried out in four groups of laboratory animals. One was the control group, and the other three groups were treated by various vitamin D3 metabolites. The same measurements were performed also in only one group of humans, due to the impossibility to treat humans with vitamin D3 metabolites. The functional relationship between the angle of torsion and the torsional moment for all the groups of animal bone tissue were determined by measurements, and results were used to predict the reaction of the human compact bone tissue if treated by vitamin D3 metabolites.     

Tacticity effects on conformational structure and hydration of poly-(methacrylic acid) in aqueous solutions-a molecular dynamics simulation study

The influence of tacticity on chain dimensions, backbone and side-group conformational states and relaxation dynamics, intermolecular hydrogen bonding and its relaxation dynamics was investigated for 30 repeat unit poly(methacrylic acid) (PMA) as a function of the degree-of-neutralisation, f (i.e. charge density) [0 < f < 1 range] in explicit water with Na⁺ neutralising counter-ions, using molecular dynamics simulations. Chain expansion with increase in charge density is observed. Simulation results, where applicable, compare well with experimental results in the literature. Isotactic (i-PMA) chain exhibits the largest expansion (89% change in R_g), and syndiotactic (s-PMA-RR-0.7) chain shows 31%. For fully neutralised chain (high charge density), the probability for trans conformation at backbone bonds follows the trend i-PMA > a-PMA > s-PMA. At high charge density, a higher probability of trans state is obtained at meso dyads as compared to racemic dyads and the side group in i-PMA relative to other tacticity is conformationally more extended. RR triads impart better hydrogen bonding with water. In the COOH side group, greater rotational mobility is observed for i-PMA as compared to s-PMA. Water coordination to PMA is invariant with tacticity at low f. For f = 1, s-PMA exhibits the best level of H-bonding, due to its 3D chemical structural configuration. Binding distance between water and PMA atoms and their coordination number remain unchanged with respect to ionisation of COOH groups. Isotactic (i-PMA) exhibits the fastest relaxation of polymer-water H-bonds. While counter-ion coordination on to PMA is unaffected by tacticity, the intensity of ion condensation as well as hydrogen bond relaxation time at f = 1 varies in the order i-PMA > a-PMA > s-PMA.     

心肌细胞发育过程中胞浆内钙稳态的调控

Ca^2＋信号是细胞和各器官生长发育、行使其生理功能的基础,维持心肌细胞的钙稳态是保持正常心脏功能的先决条件。作为在胚胎发育过程中最早出现并行使功能的器官,胚胎期心脏的形态结构发生了明显的变化,泵血功能不断增强,以适应不断增强的机体的生理需求。从胚胎到成年,心肌细胞的功能有非常大的改变,各钙离子通道的表达也发生明显变化。因此,发育早期心肌细胞的钙稳态调控与成熟心肌细胞有明显的不同,在发育过程中引起细胞收缩的Ca^2＋来源也有明显的变化。随着分子和细胞生物学研究的发展,以及胚胎干细胞体外分化模型的应用,人们对心肌细胞发育过程中钙稳态的调控有了进一步的认识。本文综述了早期心肌细胞发育过程中胞浆内钙稳态的变化,总结了早期心肌细胞钙稳态调控机制的最新研究进展。