Structural representations of extended crystalline calmodulin.

<p>The crystal structure (a) and contact map (b) of calcium-bound calmodulin (3cln <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002168#pcbi.1002168-Babu1" target="_blank">[39]</a>). The calcium ions are shown in yellow, and several residues are labeled in both panels for reference. The distance between each pair of atoms is indicated by color (see scale bar) in (b), where - and -axes run over residue labels. The residue labeling corresponds to the full sequence, however residues that do not possess torsional degrees of freedom in our model (A, G, P, and all residues bound to the calcium ions) are excluded from the contact map.</p

Mutual information of residue pairs in calmodulin.

<p>The mutual information, , associated with side-chain fluctuations of residue pairs in calmodulin. Plots (b)–(f) display the mutual information signal∶noise ratio, (upper left triangles) and the excess mutual information (lower right triangles), as indicated in (a). The - and -axes run over labels, and respectively, of residues in the amino acid sequence, excluding those lacking rotameric freedom in our model. Scale bars for the signal∶noise ratio and the excess mutual information are presented on the top and bottom left, respectively. Results are shown for the following combinations of interactions: (b) repulsive sterics (S), (c) implicit solvent (IS) (d) Lennard-Jones (LJ) interaction comprising repulsive sterics and van der Waals attractions, (e) hydrogen bonding and salt-bridges (HBSB), and (f) the full potential (LJ+HBSB+IS). Residue 30K, which we scrutinize in detail later (see <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002168#pcbi-1002168-g005" target="_blank">Fig. 5</a>), is highlighted in (f) for reference.</p

Single-residue perturbations in barstar.

<p>Changes in the Gibbs entropy of each residue in barstar (1a19 <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002168#pcbi.1002168-Ratnaparkhi1" target="_blank">[47]</a>) that resulted from perturbations to single side-chains. Residues whose entropy changes by a significant amount, according to Student's t-test at the 90% level, are shown in color. Red indicates increased entropy, blue indicates decreased entropy (see scale bar). Although side-chains are depicted in their crystallographic arrangements for graphical simplicity, note that is a measure of the extent of fluctuations among a wide variety of distinct packings. For the results presented in panel (a), I86 (shown in black and circled) was mutated to G. For those of panel (b) E46 (shown in black and circled) was constrained to its crystallographic configuration.</p

Distance dependence of mutual information in different NMR models of barstar.

<p>The average excess mutual information per residue pair is plotted here for various atomic interactions, binned according to the - inter-residue distance, for the crystal structure (1a19 <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002168#pcbi.1002168-Ratnaparkhi1" target="_blank">[47]</a>) and four NMR model structures (1btb <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002168#pcbi.1002168-Lubienski1" target="_blank">[43]</a>) of barstar, using the full LJ+IS+HBSB potential. See <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002168#s4" target="_blank">Methods</a> for details.</p

Mutual information by residue type.

<p>The average excess mutual information per interaction, , for all twenty amino acids. In each case data was pooled from all applicable pairs of fluctuating residues within a set of twelve small globular proteins (see <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002168#s4" target="_blank">Methods</a>).</p

Correlation between residue 30 and other residues in calmodulin.

<p>The extent of correlation between residue 30 (shown in black and circled) and all other side-chains in calmodulin (3cln <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002168#pcbi.1002168-Babu1" target="_blank">[39]</a>) is shown here. In (a) each residue is colored according to the magnitude of its excess mutual information with 30K (see left scale bar and <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002168#pcbi-1002168-g003" target="_blank">Fig. 3</a>). Coloring in (b) indicates the change in each residue's side chain entropy effected by the mutation K30G. Here, red represents increased entropy and blue decreased entropy (see right scale bar). See <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002168#s4" target="_blank">Methods</a> for details.</p

Impact of Molecular Symmetry on Single-Molecule Conductance

We have measured the single-molecule conductance of a family of bithiophene derivatives terminated with methyl sulfide gold-binding linkers using a scanning tunneling microscope based break-junction technique. We find a broad distribution in the single-molecule conductance of bithiophene compared with that of a methyl sulfide terminated biphenyl. Using a combination of experiments and calculations, we show that this increased breadth in the conductance distribution is explained by the difference in 5-fold symmetry of thiophene rings as compared to the 6-fold symmetry of benzene rings. The reduced symmetry of thiophene rings results in a restriction on the torsion angle space available to these molecules when bound between two metal electrodes in a junction, causing each molecular junction to sample a different set of conformers in the conductance measurements. In contrast, the rotations of biphenyl are essentially unimpeded by junction binding, allowing each molecular junction to sample similar conformers. This work demonstrates that the conductance of bithiophene displays a strong dependence on the conformational fluctuations accessible within a given junction configuration, and that the symmetry of such small molecules can significantly influence their conductance behaviors

Construction of Donor–Acceptor Polymers via Cyclopentannulation of Poly(arylene ethynylene)s

A one-step postpolymerization modification that converts three high bandgap poly­(arylene ethynylene)­s into low bandgap donor–acceptor copolymers is described. The strategy relies on a palladium-catalyzed cyclopentannulation reaction between the main-chain ethynylene functionality and a small molecule aryl bromide (6-bromo-1,2-dimethylaceanthrylene). The reaction installs new cyclopenta­[<i>hi</i>]­aceanthrylene electron-accepting groups between the electron rich arylenes along the polymer backbone. The modified polymers include poly­(9,9-didodecyl-fluorene-2,7-ethynylene), poly­(9-dodecyl-carbazole-2,7-ethynylene), and poly­(2,5-dioctyloxyphenylene-1,4-ethynylene). The functionalization efficiency was evaluated via isotopic ¹³C labeling of the polymeric ethynylene carbons and then monitoring the chemical environment of those carbons via NMR spectroscopy. Near complete conversion of the sp carbon species to sp² carbon species was observed, which demonstrates the high efficiency of the modification strategy. Gel permeation chromatography shows that the hydrodynamic radius of the polymers is reduced considerably going from linear to kinked polymer morphology upon functionalization, and molecular dynamics simulations illustrate the underlying morphological change. The newly formed donor–acceptor polymers showed dramatically different optical and electrochemical properties from the precursor poly­(arylene ethynylene) polymers. A new absorption band centered at ∼650 nm represents a red-shift of >300 nm for the onset of absorption compared with that of precursor polymers and cyclic voltammetry shows two new low-lying reduction peaks that coincide with the cyclopenta­[<i>hi</i>]­aceanthrylene moiety