Tuning ion coordination preferences to enable selective permeation

Potassium (K-) channels catalyze K+ ion permeation across cellular membranes while simultaneously discriminating their permeation over Na+ ions by more than a factor of a thousand. Structural studies show bare K+ ions occupying the narrowest channel regions in a state of high coordination by all 8 surrounding oxygen ligands from the channel walls. As in most channels, the driving force for selectivity occurs when one ion is preferentially stabilized or destabilized by the channel compared to water. In the common view of mechanism, made vivid by textbook graphics, the driving force for selectivity in K- channels arises by a fit, whereby the channel induces K+ ions to leave water by offering an environment like water for K+, in terms of both energy and local structure. The implication that knowledge of local ion coordination in a liquid environment translates to design parameters in a protein ion channel, producing similar energetic stabilities, has gone unchallenged, presumably due in part to lack of consensus regarding ion coordination structures in liquid water. Growing evidence that smaller numbers and different arrangements of ligands coordinate K+ ions in liquid water, however, raises new questions regarding mechanism: how and why should ion coordination preferences change, and how does that alter the current notions of ion selectivity? Our studies lead to a new channelcentric paradigm for the mechanism of K+ ion channel selectivity. Because the channel environment is not liquid-like, the channel necessarily induces local structural changes in ion coordination preferences that enable structural and energetic differentiation between ions.Comment: Main manuscript: 12 pages, 6 figures. Supplementary information: 10 pages, 7 figure

Agential Obligation as Non-Agential Personal Obligation plus Agency

I explore various ways of integrating the framework for predeterminism, agency, and ability in[P.McNamara, Nordic J. Philos. Logic 5 (2)(2000) 135] with a framework for obligations. However,the agential obligation operator explored here is defined in terms of a non-agential yet personal obligation operator and a non-deontic (and non-normal) agency operator. This is contrary to the main current trend, which assumes statements of personal obligation always take agential complements. Instead, I take the basic form to be an agent’s being obligated to be such that p. I sketch some logics for agential obligation based on personal obligation and agency, first in a fairly familiar context that rules out conflicting personal obligations (and derivatively, conflicting agential obligations), and then in contexts that do allow for conflicts (of both sorts)

Model Channel Ion Currents in NaCl - SPC/E Solution with Applied-Field Molecular Dynamics

Using periodic boundary conditions and a constant applied field, we have simulated current flow through an 8.125 Angstrom internal diameter, rigid, atomistic channel with polar walls in a rigid membrane using explicit ions and SPC/E water. Channel and bath currents were computed from ten 10-ns trajectories for each of 10 different conditions of concentration and applied voltage. An electric field was applied uniformly throughout the system to all mobile atoms. On average, the resultant net electric field falls primarily across the membrane channel, as expected for two conductive baths separated by a membrane capacitance. The channel is rarely occupied by more than one ion. Current-voltage relations are concentration-dependent and superlinear at high concentrations.Comment: Accepted for publication in Biophysical Journa

Incommensurability as vagueness: a burden-shifting argument

Two options are ‘incommensurate’ when neither is better than the other, but they are not equally good. Typically, we will say that one option is better in some ways, and the other in others, but neither is better ‘all things considered’. It is tempting to think that incommensurability is vagueness—that it is (perhaps) indeterminate which is better—but this ‘vagueness view’ of incommensurability has not proven popular. I set out the vagueness view and its implications in more detail, and argue that it can explain most of the puzzling features of incommensurability. This argument proceeds without appeal to John Broome’s ‘collapsing principle’

Impact of an extruded nucleotide on cleavage activity and dynamic catalytic core conformation of the hepatitis delta virus ribozyme

The self-cleaving hepatitis delta virus (HDV) ribozyme is essential for the replication of HDV, a liver disease causing pathogen in humans. The catalytically critical nucleotide C75 of the ribozyme is buttressed by a trefoil turn pivoting around an extruded G76. In all available crystal structures, the conformation of G76 is restricted by stacking with G76 of a neighboring molecule. To test whether this crystal contact introduces a structural perturbation into the catalytic core, we have analyzed ∼200 ns of molecular dynamics (MD) simulations. In the absence of crystal packing, the simulated G76 fluctuates between several conformations, including one wherein G76 establishes a perpendicular base quadruplet in the major groove of the adjacent P1 stem. Second-site mutagenesis experiments suggest that the identity of the nucleotide in position 76 (N76) indeed contributes to the catalytic activity of a trans-acting HDV ribozyme through its capacity for hydrogen bonding with P1. By contrast, in the cis-cleaving genomic ribozyme the functional relevance of N76 is less pronounced and not correlated with the P1 sequence. Terbium(III) footprinting and additional MD show that the activity differences between N76 mutants of this ribozyme are related instead to changes in average conformation and modified cross-correlations in the trefoil turn. © 2007 Wiley Periodicals, Inc. Biopolymers 85: 392–406, 2007. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at [email protected] Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/55986/1/20693_ftp.pd

Mechanism of activation at the selectivity filter of the KcsA K(+) channel

Potassium channels are opened by ligands and/or membrane potential. In voltage-gated K(+) channels and the prokaryotic KcsA channel, conduction is believed to result from opening of an intracellular constriction that prevents ion entry into the pore. On the other hand, numerous ligand-gated K(+) channels lack such gate, suggesting that they may be activated by a change within the selectivity filter, a narrow region at the extracellular side of the pore. Using molecular dynamics simulations and electrophysiology measurements, we show that ligand-induced conformational changes in the KcsA channel removes steric restraints at the selectivity filter, thus resulting in structural fluctuations, reduced K(+) affinity, and increased ion permeation. Such activation of the selectivity filter may be a universal gating mechanism within K(+) channels. The occlusion of the pore at the level of the intracellular gate appears to be secondary

Chemical feasibility of the general acid/base mechanism of glmS ribozyme self‐cleavage

In numerous Gram‐positive bacteria, the glmS ribozyme or catalytic riboswitch regulates the expression of glucosamine‐6‐phosphate (GlcN6P) synthase via site‐specific cleavage of its sugar‐phosphate backbone in response to GlcN6P ligand binding. Biochemical data have suggested a crucial catalytic role for an active site guanine (G40 in Thermoanaerobacter tengcongensis, G33 in Bacillus anthracis). We used hybrid quantum chemical/molecular mechanical (QM/MM) calculations to probe the mechanism where G40 is deprotonated and acts as a general base. The calculations suggest that the deprotonated guanine G40− is sufficiently reactive to overcome the thermodynamic penalty arising from its rare protonation state, and thus is able to activate the A‐1(2′‐OH) group toward nucleophilic attack on the adjacent backbone. Furthermore, deprotonation of A‐1(2′‐OH) and nucleophilic attack are predicted to occur as separate steps, where activation of A‐1(2′‐OH) precedes nucleophilic attack. Conversely, the transition state associated with the rate‐determining step corresponds to concurrent nucleophilic attack and protonation of the G1(O5′) leaving group by the ammonium moiety of the GlcN6P cofactor. Overall, our calculations help to explain the crucial roles of G40 (as a general base) and GlcN6P (as a general acid) during glmS ribozyme self‐cleavage. In addition, we show that the QM/MM description of the glmS ribozyme self‐cleavage reaction is significantly more sensitive to the size of the QM region and the quality of the QM‐MM coupling than that of other small ribozymes. © 2015 Wiley Periodicals, Inc. Biopolymers 103: 550–562, 2015.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/112240/1/bip22657.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/112240/2/bip22657-sup-0004-suppinfo04.pd

Structural Rigidity of Paranemic (PX) and Juxtapose (JX) DNA Nanostructures

Crossover motifs are integral components for designing DNA based nanostructures and nanomechanical devices due to their enhanced rigidity compared to the normal B-DNA. Although the structural rigidity of the double helix B-DNA has been investigated extensively using both experimental and theoretical tools, to date there is no quantitative information about structural rigidity and the mechanical strength of parallel crossover DNA motifs. We have used fully atomistic molecular dynamics simulations in explicit solvent to get the force-extension curve of parallel DNA nanostructures to characterize their mechanical rigidity. In the presence of mono-valent Na+ ions, we find that the stretch modulus (\gamma_1) of the paranemic crossover (PX) and its topo-isomer JX DNA structure is significantly higher (~ 30%) compared to normal B-DNA of the same sequence and length. However, this is in contrast to the original expectation that these motifs are almost twice rigid compared to the double-stranded B-DNA. When the DNA motif is surrounded by a solvent with Mg2+ counterions, we find an enhanced rigidity compared to Na+ environment due to the electrostatic screening effects arising from the divalent nature of Mg2+ ions. This is the first direct determination of the mechanical strength of these crossover motifs which can be useful for the design of suitable DNA for DNA based nanostructures and nanomechanical devices with improved structural rigidity.Comment: 30 pages, 7 figure