Terahertz spectra and normal mode analysis of the crystalline VA class dipeptide nanotubes.

Terahertz (THz) vibrational modes are characterized by nonlocal, collective molecular motions which are relevant to conformational changes and molecular functions in biological systems. We have investigated the THz spectra of a set of small bionanotubes which can serve as very simple models of membrane pores, and have examined the character of the THz modes which can impact transport processes. In this work, THz spectra of the crystalline VA class dipeptide nanotubes were calculated at both the harmonic and vibrational self-consistent field (VSCF) level using the CHARMM22 force field with periodic boundary conditions. Comparison of the calculated THz spectra against the experimental spectra revealed that the VSCF corrections generally improved the predictions in the low-frequency region. The improvements were especially manifested in the overall blue-shifts of the VSCF frequencies relative to the harmonic values, and blue shifts were attributed to the overall positive coupling strengths in all systems. Closer examination of the motions in the most significantly coupled normal mode pairs leads us to propose that, when two similar side-chain squeezing modes are coupled, the rapidly increased van der Waals interactions can lead to a stiffening of the effective potential, which in turn leads to the observed blue-shifts. However, we also noted that when the side-chain atoms become unphysically proximate and the van der Waals repulsion becomes too large, the VSCF calculations tend to deviate in the high frequency region and for the system of l-isoleucyl-l-valine. In addition, normal-mode analysis revealed a series of channel-breathing motions in all systems except l-valyl-l-alanine. We show that the inner products of the backbone vibrations between these channel-breathing motions divided the remaining VA class dipeptide systems into two subgroups. It is suggested that these modes may facilitate a pathway for the guest molecule absorption, substitution and removal in the VA class dipeptide nanotubes. Normal mode analysis also demonstrated that the THz motions may contribute to the pore permeability either directly by changing the pore size, or indirectly by affecting the solvent-host effective potentials.

Arrestin residues involved in the functional binding of arrestin to phosphorylated, photolyzed rhodopsin.

PURPOSE: The purpose of our study was to determine whether arrestin residues previously predicted by computational modeling to interact with an aspartic acid substituted rhodopsin tail are actually involved in interactions with phospho-residues on the rhodopsin cytoplasmic tail. METHODS: We generated arrestin mutants with altered charges at predicted positions. These mutants were then tested for the ability to inhibit rhodopsin using both direct binding assays, as well as functional assays involving transducin inhibition assays. RESULTS: Our results demonstrate that the computer-predicted residues are indeed involved in both the ability of the low-affinity state of arrestin to bind to rhodopsin as well as the ability of arrestin to be induced into a higher-affinity state in a phospho-residue-dependent manner. CONCLUSIONS: Our results also suggest that positions K14, K15, R29, H301, and K300 on arrestin interact with the phosphorylated carboxyl tail of rhodopsin and that this translates to the efficient activation of arrestin.

A dynamics study of the A-chain of ricin by terahertz vibrational calculation and normal modes analysis.

We studied the terahertz (THz) spectroscopy and low frequency normal modes of both apo- and holo- (adenosine monophosphate (AMP)-bound) ricin-A-chain (RTA) as a means to understand the dynamical changes that RTA undergoes upon substrate binding. The calculated THz spectra of apo- and holo-RTAs demonstrated a general intensity suppression upon substrate binding, which is attributed to the reduced number of collective motion in THz region. In normal mode analysis of RTA we find a shearing motion that is shared by both the apo- and holo-RTAs, whereas a breathing motion, and an upward hinge rising and an alpha-G bending characteristic motion are dampened significantly upon AMP binding, suggesting these motions are involved in the necessary flexibility of the active site. In contrast, we find a normal mode motion that separates domains I and II of RTA at the interface that is more common in the holo-protein. We hypothesized that the flexibility of the entrance of RTA can facilitate the entry of rRNA and allow the substrate to adjust its conformation and orientation prior to depurination. This process suggests an rRNA binding pathway which is supplemental the current RTA depurination mechanism.

THz investigations of condensed phase biomolecular systems.

Terahertz (THz) spectroscopic investigations of crystalline dipeptide nanotubes are discussed in the frequency region from 0.6 (2 cm(-1)) to 3 THz (100 cm(-1)). The THz region provides access to collective modes of biomolecular systems and is therefore sensitive to the large scale motions important for understanding the impact of environmental stimuli in biomolecular systems. The focus of this chapter is on THz spectral changes observed in this region when crystals of alanyl isoleucine (AI) and isoleucyl alanine (IA) nanotubes are exposed to water. Of biological significance is the water permeability through hydrophobic pore regions as exemplified in the disparate behavior of these two dipeptide nanotubes. AI is known from X-ray studies and confirmed here to act reversibly to the exchange of water while IA does not accept water into its pore region. Both quantum chemical and classical calculations are performed to better understand the subtle balance that determines guest molecule absorption and conduction through these hydrophobic channels. Examination of the vibrational character of the THz modes with and without water suggests water mode coupling/decoupling with collective modes of the nanotube may play an important role in the permeability dynamics.

High-resolution terahertz spectroscopy of crystalline trialanine: extreme sensitivity to beta-sheet structure and cocrystallized water.

High-resolution terahertz absorption spectra (0.06-3 THz) have been obtained at 4.2 K for three crystalline forms of trialanine [H2+-(Ala)3-O-]. The crystal structures differ in their beta-sheet forms (parallel vs antiparallel) and in their water composition (hydrated vs dehydrated antiparallel beta-sheet). The spectra are nearly vibrationally resolved, with little absorption below 1 THz. In sharp contrast to observations made in the mid-IR region, the spectral patterns of all three forms are qualitatively different, illustrating the extreme sensitivity to changes in the intermolecular hydrogen-bonding networks that stabilize peptide crystals. Predictions obtained from a classical force field model (CHARMM) and density functional theory (DFT/PW91) for periodic solids are compared with the X-ray structural data and the terahertz absorption spectra. In general, the results for the parallel beta-sheet are in better agreement with experiment than those for the antiparallel beta-sheet. For all three structures, however, most hydrogen bond distances are underestimated at both levels of theory, and the predicted absorption features are significantly red-shifted for the two antiparallel beta-sheet structures. Moreover, the nuclear motions predicted at the two levels of theory are qualitatively different. These results indicate that the PW91 functional is not sufficient to treat the weak intersheet hydrogen bonding present in the different beta-sheet forms and strongly suggest the need for improved force field models that include three-atom hydrogen-bonding terms for periodic solids.

Interaction of GroEL and GroEL/GroES complexes with a nonnative subtilisin variant: a small-angle neutron scattering study.

Small-angle neutron scattering and contrast variation were used to study the solution structure of GroEL and GroEL/GroES chaperonins complexed with a nonnative variant of the polypeptide substrate, subtilisin (PJ9). The subtilisin was 86% deuterated (dPJ9) so that it contrasted sufficiently with the chaperonin, allowing the contrast variation technique to be used to separate the scattering from the two components bound in the complex. Both the native double-ring GroEL and a single-ring mutant were used with dPJ9 bound in a 1:1 stoichiometry per GroEL toroid. This allowed both the position and the shape of dPJ9 in the GroEL/dPJ9 complexes to be determined. A single-ring GroEL/GroES variant complexed with one dPJ9 molecule was used to study the structural changes of dPJ9 in GroEL/GroES/dPJ9 complexes formed with ADP and with ATP. It was found that both the shape and the position of the bound dPJ9 in the GroEL/GroES/dPJ9 complex with ADP were the same as those in the GroEL/dPJ9 complex. However, dPJ9 assumed a more symmetric shape when bound in the GroEL/GroES/dPJ9 complex with ATP. This important observation reflects the relative ability of ATP to promote refolding of protein substrates relative to that of ADP.