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Register a new userThree-dimensional cytoplasmic calcium propagation with boundaries
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Ca$^{2+}$ plays an important role in cell signal transduction. Its intracellular propagation is the most basic process of Ca$^{2+}$ signaling, such as calcium wave and double messenger system. In this work, with both numerical simulation and mean field ansatz, the 3-dimensional probability distribution of Ca$^{2+}$, which is read out by phosphorylation, is studied in two scenarios with boundaries. The coverage of distribution of Ca$^{2+}$ is found at an order of magnitude of $mu$m, which is consistent with experimental observed calcium spike and wave. Our results suggest that the double messenger system may occur in the ER-PM junction to acquire great efficiency. The buffer effect of kinase is also discussed by calculating the average position of phosphorylations and free Ca$^{2+}$. The results are helpful to understand the mechanism of Ca$^{2+}$ signaling.
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Bacteriorhodopsin (bR) is a light-driven proton pump. We use time-resolved crystallography at an X-ray free-electron laser to follow the structural changes in multiphoton-excited bR from 250 femtoseconds to 10 picoseconds. Quantum chemistry and ultrafast spectroscopy allow identifying a sequential two-photon absorption process, leading to excitation of a tryptophan residue flanking the retinal chromophore, as a first manifestation of multi-photon effects. We resolve distinct stages in the structural dynamics of the all-trans retinal in photoexcited bR to a highly twisted 13-cis conformation. Other active site sub-picosecond rearrangements include correlated vibrational motions of the electronically excited retinal chromophore, the surrounding amino acids and water molecules as well as their hydrogen bonding network. These results show that this extended photo-active network forms an electronically and vibrationally coupled system in bR, and most likely in all retinal proteins.
Many cells use calcium signalling to carry information from the extracellular side of the plasma membrane to targets in their interior. Since virtually all cells employ a network of biochemical reactions for Ca2+ signalling, much effort has been devoted to understand the functional role of Ca2+ responses and to decipher how their complex dynamics is regulated by the biochemical network of Ca2+-related signal transduction pathways. Experimental observations show that Ca2+ signals in response to external stimuli encode information via frequency modulation or alternatively via amplitude modulation. Although minimal models can capture separately both types of dynamics, they fail to exhibit different and more advanced encoding modes. By arguments of bifurcation theory, we propose instead that under some biophysical conditions more complex modes of information encoding can also be manifested by minimal models. We consider the minimal model of Li and Rinzel and show that information encoding can occur by amplitude modulation (AM) of Ca2+ oscillations, by frequency modulation (FM) or by both modes (AFM). Our work is motivated by calcium signalling in astrocytes, the predominant type of cortical glial cells that is nowadays recognized to play a crucial role in the regulation of neuronal activity and information processing of the brain. We explain that our results can be crucial for a better understanding of synaptic information transfer. Furthermore, our results might also be important for better insight on other examples of physiological processes regulated by Ca2+ signalling.
The complex dynamics of intracellular calcium regulates cellular responses to information encoded in extracellular signals. Here, we study the encoding of these external signals in the context of the Li-Rinzel model. We show that by control of biophysical parameters the information can be encoded in amplitude modulation, frequency modulation or mixed (AM and FM) modulation. We briefly discuss the possible implications of this new role of information encoding for astrocytes.
The infection pathway of virus in cytoplasm of a living cell is studied from the viewpoint of diffusion theory. The cytoplasm plays a role of a medium for stochastic motion of the virus contained in the endosome as well as the free virus. It is experimentally known that the exponent of anomalous diffusion fluctuates in localized areas of the cytoplasm. Here, generalizing fractional kinetic theory, such fluctuations are described in terms of the exponent locally distributed over the cytoplasm, and a theoretical proposition is presented for its statistical form. The proposed fluctuations may be examined in an experiment of heterogeneous diffusion in the infection pathway.
Biological cells sense external chemical stimuli in their environment using cell-surface receptors. To increase the sensitivity of sensing, receptors often cluster, most noticeably in bacterial chemotaxis, a paradigm for signaling and sensing in general. While amplification of weak stimuli is useful in absence of noise, its usefulness is less clear in presence of extrinsic input noise and intrinsic signaling noise. Here, exemplified on bacterial chemotaxis, we combine the allosteric Monod-Wyman- Changeux model for signal amplification by receptor complexes with calculations of noise to study their interconnectedness. Importantly, we calculate the signal-to-noise ratio, describing the balance of beneficial and detrimental effects of clustering for the cell. Interestingly, we find that there is no advantage for the cell to build receptor complexes for noisy input stimuli in absence of intrinsic signaling noise. However, with intrinsic noise, an optimal complex size arises in line with estimates of the sizes of chemoreceptor complexes in bacteria and protein aggregates in lipid rafts of eukaryotic cells.
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