On the design principles of metabolic flux sensing

Metabolism is precisely coordinated, with the goal of balancing fluxes to maintain robust growth. However, coordinating fluxes requires information about rates, which can only be inferred through concentrations. While flux-sensitive metabolites have been reported, the design principles underlying such sensing have not been clearly elucidated. Here we use kinetic modeling to show that substrate concentrations of thermodynamically constrained reactions reflect upstream flux and therefore carry information about rates. Then we use untargeted multi-omic data from Escherichia coli and Saccharomyces cerevisiae to show that the concentrations of some metabolites in central carbon metabolism reflect fluxes as a result of thermodynamic constraints. We then establish, using 37 real concentration-flux relationships across both organisms, that in vivo $\text{Δ}{G}^{°}\ge ?4$ kJ/mol is the threshold above which substrates are likely to be sensitive to upstream flux(es).     

Significant compaction of H4 histone tail upon charge neutralization by acetylation and its mimics,possible effects on chromatin structure

The intrinsically disordered, positively charged H4 histone tail is important for chromatin structure and function. We have explored conformational ensembles of human H4 tail in solution, with varying levels of charge neutralization via acetylation or amino-acid substitutions such as $K\to Q$. We have employed an explicit water model shown recently to be well suited for simulations of intrinsically disordered proteins.Upon progressive neutralization of the H4, its radius of gyration decreases linearly with the tail charge q, the trend is explained using a simple polymer model. While the wild type state ($q=+8$) is essentially a random coil, hyper-acetylated H4 ($q=+3$) is virtually as compact and stable as a globular protein of the same number of amino-acids.Conformational ensembles of acetylated H4 match the corresponding $K\to X$ substitutions only approximately: based on the ensemble similarity, we propose $K\to M$ as a possible alternative to the commonly used $K\to Q$.Possible effects of the H4 tail compaction on chromatin structure are discussed within a qualitative model in which the chromatin is highly heterogeneous, easily inter-converting between various structural forms. We predict that upon progressive charge neutralization of the H4 tail, the least compact sub-states of chromatin de-condense first, followed by de-condensation of more compact structures, e.g. those that harbor a high fraction of stacked di-nucleosomes. The predicted hierarchy of DNA accessibility increase upon progressive acetylation of H4 might be utilized by the cell for selective DNA accessibility control.     

Crowding-induced protein destabilization in the absence of soft attractions

It is generally assumed that volume exclusion by macromolecular crowders universally stabilizes the native states of proteins and destabilization suggests soft attractions between crowders and protein. Here we show that proteins can be destabilized even by crowders that are purely repulsive. With a coarse-grained sequence-based model, we study the folding thermodynamics of two sequences with different native folds, a helical hairpin and a β-barrel, in a range of crowder volume fractions, ${\phi }_{\text{c}}$. We find that the native state, N, remains structurally unchanged under crowded conditions, while the size of the unfolded state, U, decreases monotonically with ${\phi }_{\text{c}}$. Hence, for all ${\phi }_{\text{c}}>0$, U is entropically disfavored relative to N. This entropy-centric view holds for the helical hairpin protein, which is stabilized under all crowded conditions as quantified by changes in either the folding midpoint temperature, $T_{\text{m}}$, or the free energy of folding. We find, however, that the β-barrel protein is destabilized under low-T, low-${\phi }_{\text{c}}$ conditions. This destabilization can be understood from two characteristics of its folding: 1) a relatively compact U at $T<T_{\text{m}}$, such that U is only weakly disfavored entropically by the crowders; and 2) a transient, compact, and relatively low-energy nonnative state that has a maximum population of only a few percent at ${\phi }_{\text{c}}=0$, but increasing monotonically with ${\phi }_{\text{c}}$. Overall, protein destabilization driven by hard-core effects appears possible when a compaction of U leads to even a modest population of compact nonnative states that are energetically competitive with N.     

Characterization of the pace-and-drive capacity of the human sinoatrial node: A 3D in silico study

The sinoatrial node (SAN) is a complex structure that spontaneously depolarizes rhythmically (“pacing”) and excites the surrounding non-automatic cardiac cells (“drive”) to initiate each heart beat. However, the mechanisms by which the SAN cells can activate the large and hyperpolarized surrounding cardiac tissue are incompletely understood. Experimental studies demonstrated the presence of an insulating border that separates the SAN from the hyperpolarizing influence of the surrounding myocardium, except at a discrete number of sinoatrial exit pathways (SEPs). We propose a highly detailed 3D model of the human SAN, including 3D SEPs to study the requirements for successful electrical activation of the primary pacemaking structure of the human heart. A total of 788 simulations investigate the ability of the SAN to pace and drive with different heterogeneous characteristics of the nodal tissue (gradient and mosaic models) and myocyte orientation. A sigmoidal distribution of the tissue conductivity combined with a mosaic model of SAN and atrial cells in the SEP was able to drive the right atrium (RA) at varying rates induced by gradual If block. Additionally, we investigated the influence of the SEPs by varying their number, length, and width. SEPs created a transition zone of transmembrane voltage and ionic currents to enable successful pace and drive. Unsuccessful simulations showed a hyperpolarized transmembrane voltage (?66 mV), which blocked the L-type channels and attenuated the sodium-calcium exchanger. The fiber direction influenced the SEPs that preferentially activated the crista terminalis (CT). The location of the leading pacemaker site (LPS) shifted toward the SEP-free areas. LPSs were located closer to the SEP-free areas (3.46 $\pm$ 1.42 mm), where the hyperpolarizing influence of the CT was reduced, compared with a larger distance from the LPS to the areas where SEPs were located (7.17$\pm$ 0.98 mm). This study identified the geometrical and electrophysiological aspects of the 3D SAN-SEP-CT structure required for successful pace and drive in silico.