scholarly journals Beyond Stability Constraints: A Biophysical Model of Enzyme Evolution with Selection on Stability and Activity

2018 ◽  
Vol 36 (3) ◽  
pp. 613-620 ◽  
Author(s):  
Julian Echave
Keyword(s):  
Enzyme Evolution ◽  
Biophysical Model

scholarly journals Beyond stability constraints: a biophysical model of enzyme evolution with selection for stability and activity

2018 ◽  
Author(s):  
Julian Echave
Keyword(s):  
Amino Acids ◽  
Packing Density ◽  
Solvent Accessibility ◽  
Enzyme Evolution ◽  
Biophysical Model ◽  
Solvent Exposure ◽  
Local Environments ◽  
Distance Dependence ◽  
Selection For ◽  
Functionally Diverse

AbstractProteins trace trajectories in sequence space as their amino acids become substituted by other amino acids. The number of substitutions per unit time, the rate of evolution, varies among sites because of biophysical constraints. Several properties that characterize sites’ local environments have been proposed as biophysical determinants of site-specific evolutionary rates. Thus, rate increases with increasing solvent exposure, increasing flexibility, and decreasing local packing density. For enzymes, rate increases also with increasing distance from the protein’s active residues, presumably due to functional constraints. The dependence of rates on solvent accessibility, packing density, and flexibility has been mechanistically explained in terms of selection for stability. However, as I show here, a stability-based model fails to reproduce the observed rate-distance dependence, overestimating rates close to the active residues and underestimating rates of distant sites. Here, I pose a new biophysical model of enzyme evolution with selection for stability and activity (MSA) and compare it with a stability-based counterpart (MS). Testing these models on a structurally and functionally diverse dataset of monomeric enzymes, I found that MSA fits observed rates better than MS for most proteins. While both models reproduce the observed dependence of rates on solvent accessibility, packing, and flexibility, MSA fits these dependencies somewhat better. Importantly, while MS fails to reproduce the dependence of rates on distance from the active residues, MSA accounts for the rate-distance dependence quantitatively. Thus, the variation of evolutionary rate among enzyme sites is mechanistically underpinned by natural selection for both stability and activity.

scholarly journals Impacts of yeast metabolic network structure on enzyme evolution

2007 ◽  
Vol 8 (8) ◽  
pp. 407 ◽  
Author(s):  
Chenqi Lu ◽  
Ze Zhang ◽  
Lindsey Leach ◽  
MJ Kearsey ◽  
ZW Luo
Keyword(s):  
Metabolic Network ◽  
Network Structure ◽  
Enzyme Evolution

scholarly journals Biofilm Lithography enables high-resolution cell patterning via optogenetic adhesin expression

2018 ◽  
Vol 115 (14) ◽  
pp. 3698-3703 ◽  
Author(s):  
Xiaofan Jin ◽  
Ingmar H. Riedel-Kruse
Keyword(s):  
Escherichia Coli ◽  
Cell Patterning ◽  
Biophysical Model ◽  
Microbial Consortia ◽  
Bacterial Biofilms ◽  
Surface Pretreatment ◽  
Resolution Cell ◽  
Stimulation Of

Bacterial biofilms represent a promising opportunity for engineering of microbial communities. However, our ability to control spatial structure in biofilms remains limited. Here we engineerEscherichia coliwith a light-activated transcriptional promoter (pDawn) to optically regulate expression of an adhesin gene (Ag43). When illuminated with patterned blue light, long-term viable biofilms with spatial resolution down to 25 μm can be formed on a variety of substrates and inside enclosed culture chambers without the need for surface pretreatment. A biophysical model suggests that the patterning mechanism involves stimulation of transiently surface-adsorbed cells, lending evidence to a previously proposed role of adhesin expression during natural biofilm maturation. Overall, this tool—termed “Biofilm Lithography”—has distinct advantages over existing cell-depositing/patterning methods and provides the ability to grow structured biofilms, with applications toward an improved understanding of natural biofilm communities, as well as the engineering of living biomaterials and bottom–up approaches to microbial consortia design.

scholarly journals Global earthworm distribution and activity windows based on soil hydromechanical constraints

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Siul A. Ruiz ◽  
Samuel Bickel ◽  
Dani Or
Keyword(s):  
Soil Structure ◽  
Mechanistic Model ◽  
Biophysical Model ◽  
Ecosystem Functions ◽  
Soil Conditions ◽  
Agricultural Systems ◽  
Occurrence Patterns ◽  
Additional Constraints ◽  
Earthworm Activity ◽  
Good Agreement

AbstractEarthworm activity modifies soil structure and promotes important hydrological ecosystem functions for agricultural systems. Earthworms use their flexible hydroskeleton to burrow and expand biopores. Hence, their activity is constrained by soil hydromechanical conditions that permit deformation at earthworm’s maximal hydroskeletal pressure (≈200kPa). A mechanistic biophysical model is developed here to link the biomechanical limits of earthworm burrowing with soil moisture and texture to predict soil conditions that permit bioturbation across biomes. We include additional constraints that exclude earthworm activity such as freezing temperatures, low soil pH, and high sand content to develop the first predictive global map of earthworm habitats in good agreement with observed earthworm occurrence patterns. Earthworm activity is strongly constrained by seasonal dynamics that vary across latitudes largely due to soil hydromechanical status. The mechanistic model delineates the potential for earthworm migration via connectivity of hospitable sites and highlights regions sensitive to climate.

scholarly journals A model of on/off transitions in neurons of the deep cerebellar nuclei: deciphering the underlying ionic mechanisms

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hugues Berry ◽  
Stéphane Genet
Keyword(s):  
Cerebellar Nuclei ◽  
Biophysical Model ◽  
High Threshold ◽  
Deep Cerebellar Nuclei ◽  
Functional Link ◽  
Electrophysiological Properties ◽  
Voltage Dependent ◽  
Ionic Mechanisms ◽  
The Central Nervous System ◽  
Overall Functioning

AbstractThe neurons of the deep cerebellar nuclei (DCNn) represent the main functional link between the cerebellar cortex and the rest of the central nervous system. Therefore, understanding the electrophysiological properties of DCNn is of fundamental importance to understand the overall functioning of the cerebellum. Experimental data suggest that DCNn can reversibly switch between two states: the firing of spikes (F state) and a stable depolarized state (SD state). We introduce a new biophysical model of the DCNn membrane electro-responsiveness to investigate how the interplay between the documented conductances identified in DCNn give rise to these states. In the model, the F state emerges as an isola of limit cycles, i.e. a closed loop of periodic solutions disconnected from the branch of SD fixed points. This bifurcation structure endows the model with the ability to reproduce the $\text{F}\to \text{SD}$ F → SD transition triggered by hyperpolarizing current pulses. The model also reproduces the $\text{F}\to \text{SD}$ F → SD transition induced by blocking Ca currents and ascribes this transition to the blocking of the high-threshold Ca current. The model suggests that intracellular current injections can trigger fully reversible $\text{F}\leftrightarrow \text{SD}$ F ↔ SD transitions. Investigation of low-dimension reduced models suggests that the voltage-dependent Na current is prominent for these dynamical features. Finally, simulations of the model suggest that physiological synaptic inputs may trigger $\text{F}\leftrightarrow \text{SD}$ F ↔ SD transitions. These transitions could explain the puzzling observation of positively correlated activities of connected Purkinje cells and DCNn despite the former inhibit the latter.

Prediction study on the spatiotemporal distribution of Yesso scallop larvae based on a coupled biophysical model

Aquaculture ◽  
2021 ◽  
pp. 736598
Author(s):  
Qiaofeng Ma ◽  
Yunkuan Han ◽  
Yanbin Xi ◽  
Jingming Huang ◽  
Zhaojun Sheng ◽  
...  
Keyword(s):  
Spatiotemporal Distribution ◽  
Biophysical Model ◽  
Yesso Scallop ◽  
Scallop Larvae

scholarly journals Dynamic modulation of spike timing-dependent calcium influx during corticostriatal upstates

2013 ◽  
Vol 110 (7) ◽  
pp. 1631-1645 ◽  
Author(s):  
R. C. Evans ◽  
Y. M. Maniar ◽  
K. T. Blackwell
Keyword(s):  
Synaptic Plasticity ◽  
Slow Wave Sleep ◽  
Calcium Influx ◽  
Spike Timing ◽  
Medium Spiny Neuron ◽  
Calcium Transients ◽  
Biophysical Model ◽  
Published Data ◽  
High Calcium

The striatum of the basal ganglia demonstrates distinctive upstate and downstate membrane potential oscillations during slow-wave sleep and under anesthetic. The upstates generate calcium transients in the dendrites, and the amplitude of these calcium transients depends strongly on the timing of the action potential (AP) within the upstate. Calcium is essential for synaptic plasticity in the striatum, and these large calcium transients during the upstates may control which synapses undergo plastic changes. To investigate the mechanisms that underlie the relationship between calcium and AP timing, we have developed a realistic biophysical model of a medium spiny neuron (MSN). We have implemented sophisticated calcium dynamics including calcium diffusion, buffering, and pump extrusion, which accurately replicate published data. Using this model, we found that either the slow inactivation of dendritic sodium channels (NaSI) or the calcium inactivation of voltage-gated calcium channels (CDI) can cause high calcium corresponding to early APs and lower calcium corresponding to later APs. We found that only CDI can account for the experimental observation that sensitivity to AP timing is dependent on NMDA receptors. Additional simulations demonstrated a mechanism by which MSNs can dynamically modulate their sensitivity to AP timing and show that sensitivity to specifically timed pre- and postsynaptic pairings (as in spike timing-dependent plasticity protocols) is altered by the timing of the pairing within the upstate. These findings have implications for synaptic plasticity in vivo during sleep when the upstate-downstate pattern is prominent in the striatum.

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