Jumping Over the Wall

<p>Cation channels from the voltage-gated like family [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0138679#pone.0138679.ref007" target="_blank">7</a>] (represented here by NavAb; PDB 3RVY) [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0138679#pone.0138679.ref013" target="_blank">13</a>] consist of a four domain transmembrane protein with an ion conduction pore (yellow), a cation selective filter at the extracellular pore mouth (SF, pink) and a gate region at the intracellular pore end (green). Inward pointing carbonyl oxygens from the backbone amide groups provide a lining of the SF [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0138679#pone.0138679.ref005" target="_blank">5</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0138679#pone.0138679.ref006" target="_blank">6</a>]. The charged side chains present in the SFs of the bacterial Na⁺ channels and the Ca²⁺ selective CavAb [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0138679#pone.0138679.ref018" target="_blank">18</a>] structure are embedded in the pore lining. Hydrated (large) and fully dehydrated (small) Na⁺ (blue) and K⁺ (green) cations are shown to scale as spheres. Black bars are 5 Å.</p

Simulated cation profile (as moving average over 2Å) in the K⁺ (KcsA) ion channel SF.

<p>[Na⁺·<i>X</i>] pink, [K⁺·<i>X</i>] black, [<math>NH<msubsup><mrow></mrow><mn>4</mn><mo>+</mo></msubsup></math>·<i>X</i>] red and [Rb⁺·<i>X</i>] or [Tl⁺·<i>X</i>] light blue. Concentration minimum region used to calculate selectivity [−6.5 : −2.5].</p

Local Fluctuations and Conformational Transitions in Proteins

The intrinsic plasticity of protein residues, along with the occurrence of transitions between distinct residue conformations, plays a pivotal role in a variety of molecular recognition events in the cell. Analysis aimed at identifying both of these features has been limited so far to protein-complex structures. We present a computationally efficient tool (T-pad), which quantitatively analyzes protein residues’ flexibility and detects backbone conformational transitions. T-pad is based on directional statistics of NMR structural ensembles or molecular dynamics trajectories. T-pad is here applied to human ubiquitin (hU), a paradigmatic cellular interactor. The calculated plasticity is compared to hU’s Debye–Waller factors from the literature as well as those from experimental work carried out for this paper. T-pad is able to identify most of the key residues involved in hU’s molecular recognition, also in the absence of its cellular partners. Indeed, T-pad identified as many as 90% of ubiquitin residues interacting with their cognate proteins. Hence, T-pad might be a useful tool for the investigation of interactions between proteins and their cellular partners at the genome-wide level

Simulated cation profile (as moving average over 2Å) in the Ca²⁺ (CavAb) ion channel SF.

<p>[Mn²⁺·<i>X</i>] green, [Ca²⁺·<i>X</i>] blue, [Na⁺·<i>X</i>] pink and [Ba²⁺·<i>X</i>] orange. Concentration minimum region used to calculate selectivity [−5.5 : −2.5].</p

Predicted selectivity from simulations based on the CavAb [18] ion channel X-ray structures using cations with radii of the fully hydrated (α^sim,hyd) and fully dehydrated (α^sim,dehyd) species.

<p>Predicted selectivity from simulations based on the CavAb [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0138679#pone.0138679.ref018" target="_blank">18</a>] ion channel X-ray structures using cations with radii of the fully hydrated (<math><msub><mi>α</mi><mo>^</mo>sim,hyd</msub></math>) and fully dehydrated (<math><msub><mi>α</mi><mo>^</mo>sim,dehyd</msub></math>) species.</p

Schematic for the circumcircles that give the partially hydrated cation diameters, <i>d</i>_<i>M</i>⁺, used in the CSC simulations (not drawn to scale).

<p>They follow the replacement of four waters of hydration (dashed circles) in a plane perpendicular to the channel axis. Removal of one water does not change the diameter (0, 1 = orange). Loss of more waters reduces the diameter (2 = blue, 3 = pink) to a minimum when four (or more) waters are lost (4 = black). The actual dimensions are calculated from the experimental cation–water oxygen distance (r(MO)) and water oxygen–water oxygen distance (r(OO)).</p

Comparison of change in maximum concentration and selectivity from simulations based on the KcsA X-ray structure [6] with and without “polarization” charges on the SF oxygen atoms.

<p>Comparison of change in maximum concentration and selectivity from simulations based on the KcsA X-ray structure [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0138679#pone.0138679.ref006" target="_blank">6</a>] with and without “polarization” charges on the SF oxygen atoms.</p

Simulated cation profile (as moving average over 2Å) in the Na⁺ (NavAb) ion channel SF.

<p>[Na⁺·<i>X</i>] pink and [K⁺·<i>X</i>] black. Concentration minimum region used to calculate selectivity [−4.0 : −2.0].</p

Variation of [A ⋅ <i>X</i>]_min (at maximum [A]_bulk) in KcsA K⁺ channel simulation with “polarization” charge (red = 0:0, blue = −0.1) as a function of cation diameter.

<p>Variation of [A ⋅ <i>X</i>]_min (at maximum [A]_bulk) in KcsA K⁺ channel simulation with “polarization” charge (red = 0:0, blue = −0.1) as a function of cation diameter.</p

Schematic view of the simulation cell used here.

<p>The cell is a cylinder divided by a virtual membrane perpendicular to the cylinder’s axis of rotation. The model cation channel forms the only pore through the membrane and is located at the cylinder’s axis of rotation. The blue outline shows the dielectric boundary surface of the protein. The pink region shows where the spheres modelling the atoms lining the SF are located.</p