scholarly journals Salt-Dependent RNA Pseudoknot Stability: Effect of Spatial Confinement

2021 ◽  
Vol 8 ◽  
Author(s):  
Chenjie Feng ◽  
Ya-Lan Tan ◽  
Yu-Xuan Cheng ◽  
Ya-Zhou Shi ◽  
Zhi-Jie Tan
Keyword(s):  
Rna Structure ◽  
Coarse Grained ◽  
Spatial Confinement ◽  
Functional Roles ◽  
Coarse Grained Model ◽  
Mouse Mammary Tumor ◽  
Wide Range ◽  
Tumor Virus ◽  
Folded Structures ◽  
Rna Pseudoknot

Macromolecules, such as RNAs, reside in crowded cell environments, which could strongly affect the folded structures and stability of RNAs. The emergence of RNA-driven phase separation in biology further stresses the potential functional roles of molecular crowding. In this work, we employed the coarse-grained model that was previously developed by us to predict 3D structures and stability of the mouse mammary tumor virus (MMTV) pseudoknot under different spatial confinements over a wide range of salt concentrations. The results show that spatial confinements can not only enhance the compactness and stability of MMTV pseudoknot structures but also weaken the dependence of the RNA structure compactness and stability on salt concentration. Based on our microscopic analyses, we found that the effect of spatial confinement on the salt-dependent RNA pseudoknot stability mainly comes through the spatial suppression of extended conformations, which are prevalent in the partially/fully unfolded states, especially at low ion concentrations. Furthermore, our comprehensive analyses revealed that the thermally unfolding pathway of the pseudoknot can be significantly modulated by spatial confinements, since the intermediate states with more extended conformations would loss favor when spatial confinements are introduced.

scholarly journals Quantitative insights into the cyanobacterial cell economy

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Tomáš Zavřel ◽  
Marjan Faizi ◽  
Cristina Loureiro ◽  
Gereon Poschmann ◽  
Kai Stühler ◽  
...  
Keyword(s):  
Growth Rate ◽  
Coarse Grained ◽  
Translational Machinery ◽  
Coarse Grained Model ◽  
Green Biotechnology ◽  
Photosynthetic Productivity ◽  
Heterotrophic Microorganisms ◽  
Wide Range ◽  
Growth Laws ◽  
Phototrophic Growth

Phototrophic microorganisms are promising resources for green biotechnology. Compared to heterotrophic microorganisms, however, the cellular economy of phototrophic growth is still insufficiently understood. We provide a quantitative analysis of light-limited, light-saturated, and light-inhibited growth of the cyanobacterium Synechocystis sp. PCC 6803 using a reproducible cultivation setup. We report key physiological parameters, including growth rate, cell size, and photosynthetic activity over a wide range of light intensities. Intracellular proteins were quantified to monitor proteome allocation as a function of growth rate. Among other physiological acclimations, we identify an upregulation of the translational machinery and downregulation of light harvesting components with increasing light intensity and growth rate. The resulting growth laws are discussed in the context of a coarse-grained model of phototrophic growth and available data obtained by a comprehensive literature search. Our insights into quantitative aspects of cyanobacterial acclimations to different growth rates have implications to understand and optimize photosynthetic productivity.

Parameterization of a coarse-grained model with short-ranged interactions for modeling fuel cell membranes with controlled water uptake

2017 ◽  
Vol 19 (27) ◽  
pp. 17698-17707 ◽  
Author(s):  
Jibao Lu ◽  
Chance Miller ◽  
Valeria Molinero
Keyword(s):  
Fuel Cell ◽  
Activity Coefficient ◽  
Water Uptake ◽  
Coarse Grained ◽  
Fuel Cell Membranes ◽  
Coarse Grained Model ◽  
Experimental Activity ◽  
Tetramethylammonium Chloride ◽  
Atomistic Models ◽  
Wide Range

The coarse-grained model FFpvap reproduces the experimental activity coefficient of water in tetramethylammonium chloride solutions over a wide range of concentrations, with a hundred-fold gain in computing efficiency with respect to atomistic models.

scholarly journals Quantitative insights into the cyanobacterial cell economy

2018 ◽  
Author(s):  
Tomáš Zavřel ◽  
Marjan Faizi ◽  
Cristina Loureiro ◽  
Gereon Poschmann ◽  
Kai Stühler ◽  
...  
Keyword(s):  
Growth Rate ◽  
Coarse Grained ◽  
Translational Machinery ◽  
Coarse Grained Model ◽  
Green Biotechnology ◽  
Photosynthetic Productivity ◽  
Heterotrophic Microorganisms ◽  
Wide Range ◽  
Growth Laws ◽  
Phototrophic Growth

AbstractPhototrophic microorganisms are promising resources for green biotechnology. Compared to heterotrophic microorganisms, however, the cellular economy of phototrophic growth is still insufficiently understood. We provide a quantitative analysis of light-limited, light-saturated, and light-inhibited growth of the cyanobacteriumSynechocystissp. PCC 6803 using a reproducible cultivation setup. We report key physiological parameters, including growth rate, cell size, and photosynthetic activity over a wide range of light intensities. Intracellular proteins were quantified to monitor proteome allocation as a function of growth rate. Among other physiological adaptations, we identify an upregulation of the translational machinery and downregulation of light harvesting components with increasing light intensity and growth rate. The resulting growth laws are discussed in the context of a coarse-grained model of phototrophic growth and available data obtained by a comprehensive literature search. Our insights into quantitative aspects of cyanobacterial adaptations to different growth rates have implications to understand and optimize photosynthetic productivity.

scholarly journals Analyzing the electrogenicity of cytochrome c oxidase

2016 ◽  
Vol 113 (28) ◽  
pp. 7810-7815 ◽  
Author(s):  
Ilsoo Kim ◽  
Arieh Warshel
Keyword(s):  
Molecular Mechanisms ◽  
Molecular Level ◽  
Theoretical Models ◽  
Proton Pumping ◽  
Coarse Grained ◽  
Transfer Reactions ◽  
Coarse Grained Model ◽  
Fundamental Information ◽  
Wide Range ◽  
Charge Transfer Reactions

Measurements of voltage changes in response to charge separation within membrane proteins can offer fundamental information on spectroscopically “invisible” steps. For example, results from studies of voltage changes associated with electron and proton transfer in cytochrome c oxidase could, in principle, be used to discriminate between different theoretical models describing the molecular mechanism of proton pumping. Earlier analyses of data from these measurements have been based on macroscopic considerations that may not allow for exploring the actual molecular mechanisms. Here, we have used a coarse-grained model describing the relation between observed voltage changes and specific charge-transfer reactions, which includes an explicit description of the membrane, the electrolytes, and the electrodes. The results from these calculations offer mechanistic insights at the molecular level. Our main conclusion is that previously assumed mechanistic evidence that was based on electrogenic measurements is not unique. However, the ability of our calculations to obtain reliable voltage changes means that we have a tool that can be used to describe a wide range of electrogenic charge transfers in channels and transporters, by combining voltage measurements with other experiments and simulations to analyze new mechanistic proposals.

scholarly journals SNARE machinery is optimized for ultrafast fusion

2019 ◽  
Vol 116 (7) ◽  
pp. 2435-2442 ◽  
Author(s):  
Fabio Manca ◽  
Frederic Pincet ◽  
Lev Truskinovsky ◽  
James E. Rothman ◽  
Lionel Foret ◽  
...  
Keyword(s):  
Synaptic Vesicles ◽  
Snare Proteins ◽  
Coarse Grained ◽  
Optimum Number ◽  
Biological Processes ◽  
Cooperative Action ◽  
Fusion Barrier ◽  
Coarse Grained Model ◽  
Wide Range

SNARE proteins zipper to form complexes (SNAREpins) that power vesicle fusion with target membranes in a variety of biological processes. A single SNAREpin takes about 1 s to fuse two bilayers, yet a handful can ensure release of neurotransmitters from synaptic vesicles much faster: in a 10th of a millisecond. We propose that, similar to the case of muscle myosins, the ultrafast fusion results from cooperative action of many SNAREpins. The coupling originates from mechanical interactions induced by confining scaffolds. Each SNAREpin is known to have enough energy to overcome the fusion barrier of 25–35 kBT; however, the fusion barrier only becomes relevant when the SNAREpins are nearly completely zippered, and from this state, each SNAREpin can deliver only a small fraction of this energy as mechanical work. Therefore, they have to act cooperatively, and we show that at least three of them are needed to ensure fusion in less than a millisecond. However, to reach the prefusion state collectively, starting from the experimentally observed half-zippered metastable state, the SNAREpins have to mechanically synchronize, which takes more time as the number of SNAREpins increases. Incorporating this somewhat counterintuitive idea in a simple coarse-grained model results in the prediction that there should be an optimum number of SNAREpins for submillisecond fusion: three to six over a wide range of parameters. Interestingly, in situ cryoelectron microscope tomography has very recently shown that exactly six SNAREpins participate in the fusion of each synaptic vesicle. This number is in the range predicted by our theory.

scholarly journals Modeling structure, stability and flexibility of double-stranded RNAs in salt solutions

2018 ◽  
Author(s):  
L. Jin ◽  
Y.Z. Shi ◽  
C.J. Feng ◽  
Y.L. Tan ◽  
Z.J. Tan
Keyword(s):  
Electrostatic Potential ◽  
Cell Metabolism ◽  
3D Structure ◽  
Three Dimensional ◽  
Coarse Grained ◽  
Structure Stability ◽  
Salt Solutions ◽  
3D Structures ◽  
Coarse Grained Model ◽  
Wide Range

AbstractDouble-stranded (ds) RNAs play essential roles in many processes of cell metabolism. The knowledge of three-dimensional (3D) structure, stability and flexibility of dsRNAs in salt solutions is important for understanding their biological functions. In this work, we further developed our previously proposed coarse-grained model to predict 3D structure, stability and flexibility for dsRNAs in monovalent and divalent ion solutions through involving an implicit structure-based electrostatic potential. The model can make reliable predictions for 3D structures of extensive dsRNAs with/without bulge/internal loops from their sequences, and the involvement of the structure-based electrostatic potential and corresponding ion condition can improve the predictions on 3D structures of dsRNAs in ion solutions. Furthermore, the model can make good predictions on thermal stability for extensive dsRNAs over the wide range of monovalent/divalent ion concentrations, and our analyses show that thermally unfolding pathway of a dsRNA is generally dependent on its length as well as its sequence. In addition, the model was employed to examine the salt-dependent flexibility of a dsRNA helix and the calculated salt-dependent persistence lengths are in good accordance with experiments.

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