Instantaneous ion configurations in the K+ ion channel selectivity filter revealed by 2D IR spectroscopy.

Potassium channels are responsible for the selective permeation of K+ ions across cell membranes. K+ ions permeate in single file through the selectivity filter, a narrow pore lined by backbone carbonyls that compose four K+ binding sites. Here, we report on the two-dimensional infrared (2D IR) spectra of a semisynthetic KcsA channel with site-specific heavy (13C18O) isotope labels in the selectivity filter. The ultrafast time resolution of 2D IR spectroscopy provides an instantaneous snapshot of the multi-ion configurations and structural distributions that occur spontaneously in the filter. Two elongated features are resolved, revealing the statistical weighting of two structural conformations. The spectra are reproduced by molecular dynamics simulations of structures with water separating two K+ ions in the binding sites, ruling out configurations with ions occupying adjacent sites.

Increased task demand during spatial memory testing recruits the anterior cingulate cortex.

We examined whether increasing retrieval difficulty in a spatial memory task would promote the recruitment of the anterior cingulate cortex (ACC) similar to what is typically observed during remote memory retrieval. Rats were trained on the hidden platform version of the Morris Water Task and tested three or 30 d later. Retrieval difficulty was manipulated by removing several prominent extra-pool cues from the testing room. Immediate early gene expression (c-Fos) in the ACC was greater following the cue removal and comparable to remote memory retrieval (30-d retention interval) levels, supporting the view of increased ACC contribution during high cognitive-demand memory processes.

Theoretical Sum Frequency Generation Spectroscopy of Peptides.

Vibrational sum frequency generation (SFG) has become a very promising technique for the study of proteins at interfaces, and it has been applied to important systems such as anti-microbial peptides, ion channel proteins, and human islet amyloid polypeptide. Moreover, so-called "chiral" SFG techniques, which rely on polarization combinations that generate strong signals primarily for chiral molecules, have proven to be particularly discriminatory of protein secondary structure. In this work, we present a theoretical strategy for calculating protein amide I SFG spectra by combining line-shape theory with molecular dynamics simulations. We then apply this method to three model peptides, demonstrating the existence of a significant chiral SFG signal for peptides with chiral centers, and providing a framework for interpreting the results on the basis of the dependence of the SFG signal on the peptide orientation. We also examine the importance of dynamical and coupling effects. Finally, we suggest a simple method for determining a chromophore's orientation relative to the surface using ratios of experimental heterodyne-detected signals with different polarizations, and test this method using theoretical spectra.

Structural motif of polyglutamine amyloid fibrils discerned with mixed-isotope infrared spectroscopy.

Polyglutamine (polyQ) sequences are found in a variety of proteins, and mutational expansion of the polyQ tract is associated with many neurodegenerative diseases. We study the amyloid fibril structure and aggregation kinetics of K2Q24K2W, a model polyQ sequence. Two structures have been proposed for amyloid fibrils formed by polyQ peptides. By forming fibrils composed of both (12)C and (13)C monomers, made possible by protein expression in Escherichia coli, we can restrict vibrational delocalization to measure 2D IR spectra of individual monomers within the fibrils. The spectra are consistent with a ß-turn structure in which each monomer forms an antiparallel hairpin and donates two strands to a single ß-sheet. Calculated spectra from atomistic molecular-dynamics simulations of the two proposed structures confirm the assignment. No spectroscopically distinct intermediates are observed in rapid-scan 2D IR kinetics measurements, suggesting that aggregation is highly cooperative. Although 2D IR spectroscopy has advantages over linear techniques, the isotope-mixing strategy will also be useful with standard Fourier transform IR spectroscopy.

2D IR spectra of cyanide in water investigated by molecular dynamics simulations.

Using classical molecular dynamics simulations, the 2D infrared (IR) spectroscopy of CN(-) solvated in D2O is investigated. Depending on the force field parametrizations, most of which are based on multipolar interactions for the CN(-) molecule, the frequency-frequency correlation function and observables computed from it differ. Most notably, models based on multipoles for CN(-) and TIP3P for water yield quantitatively correct results when compared with experiments. Furthermore, the recent finding that T1 times are sensitive to the van der Waals ranges on the CN(-) is confirmed in the present study. For the linear IR spectrum, the best model reproduces the full widths at half maximum almost quantitatively (13.0 cm(-1) vs. 14.9 cm(-1)) if the rotational contribution to the linewidth is included. Without the rotational contribution, the lines are too narrow by about a factor of two, which agrees with Raman and IR experiments. The computed and experimental tilt angles (or nodal slopes) α as a function of the 2D IR waiting time compare favorably with the measured ones and the frequency fluctuation correlation function is invariably found to contain three time scales: a sub-ps, 1 ps, and one on the 10-ps time scale. These time scales are discussed in terms of the structural dynamics of the surrounding solvent and it is found that the longest time scale (≈10 ps) most likely corresponds to solvent exchange between the first and second solvation shell, in agreement with interpretations from nuclear magnetic resonance measurements.

Heterogeneous translational dynamics of rhodamine B in polyelectrolyte multilayer thin films observed by single molecule microscopy.

The lateral diffusion dynamics of rhodamine B (RB) in polyelectrolyte multilayer (PEM) thin films has been studied with single-molecule confocal fluorescence microscopy. The films were made with sodium poly(sodium 4-styrenesulfonate) (PSS) and poly(diallydimethlyammonium chloride) (PDDA). Analysis of the real-time emission intensity traces reveals three diverse components of translational motion: (1) fast diffusion of RB through the confocal detection volume; (2) reversible tracer adsorption processes; and (3) nanoconfined diffusion. These processes cover a wide range of time scales. Analysis via fluorescence correlation spectroscopy (FCS) involves multicomponent fitting of the autocorrelated emission data. The model includes a free Brownian diffusion parameter, D, and two rate constants of desorption, k(-1) and k(-2). For RB in a PSS/PDDA thin film made with 0.01 M NaCl in the polyelectrolyte buildup solutions, D = 1.7 x 10(-7) cm(2)/s, k(-1) = 30 s(-1), and k(-2) = 0.1 s(-1). FCS was also performed on RB/PEM samples made with NaCl concentrations of the buildup solutions ranging from 0.01 to 0.7 M. A weak dependence of D and k(-1) on NaCl concentration was observed while k(-2) increased linearly with [NaCl].