Cystic Fibrosis (CF) is caused by mutations in the CF transmembrane conductance regulator (CFTR). Newly developed “correctors” such as lumacaftor (VX-809) that improve CFTR maturation and trafficking and “potentiators” such as ivacaftor (VX-770) that enhance channel activity may provide important advances in CF therapy. Although VX-770 has demonstrated substantial clinical efficacy in the small subset of patients with a mutation (G551D) that affects only channel activity, a single compound is not sufficient to treat patients with the more common CFTR mutation, ΔF508. Thus, patients with ΔF508 will likely require treatment with both correctors and potentiators to achieve clinical benefit. However, whereas the effectiveness of acute treatment with this drug combination has been demonstrated in vitro, the impact of chronic therapy has not been established. In studies of human primary airway epithelial cells, we found that both acute and chronic treatment with VX-770 improved CFTR function in cells with the G551D mutation, consistent with clinical studies. In contrast, chronic VX-770 administration caused a dose-dependent reversal of VX-809-mediated CFTR correction in ΔF508 homozygous cultures. This result reflected the destabilization of corrected ΔF508 CFTR by VX-770, dramatically increasing its turnover rate. Chronic VX-770 treatment also reduced mature wild-type CFTR levels and function. These findings demonstrate that chronic treatment with CFTR potentiators and correctors may have unexpected effects that cannot be predicted from short-term studies. Combining of these drugs to maximize rescue of ΔF508 CFTR may require changes in dosing and/or development of new potentiator compounds that do not interfere with CFTR stability.

We use a long, all-atom molecular-dynamics ͑MD͒ simulation combined with theoretical modeling to investigate the dynamics of selected lipid atoms and lipid molecules in a hydrated diyristoyl-phosphatidylcholine lipid bilayer. From the analysis of a 0.1 s MD trajectory, we find that the time evolution of the mean-square displacement, ͓͗␦r͑t͔͒ 2 ͘, of lipid atoms and molecules exhibits three well-separated dynamical regions: ͑i͒ ballistic, with ͓͗␦r͑t͔͒ 2 ͘ϳt 2 for t Շ 10 fs; ͑ii͒ subdiffusive, with ͓͗␦r͑t͔͒ 2 ͘ϳt ␤ with ␤ Ͻ 1 for 10 psՇ t Շ 10 ns; and ͑iii͒ Fickian diffusion, with ͓͗␦r͑t͔͒ 2 ͘ϳt for t տ 30 ns. We propose a memory-function approach for calculating ͓͗␦r͑t͔͒ 2 ͘ over the entire time range extending from the ballistic to the Fickian diffusion regimes. The results are in very good agreement with the ones from the MD simulations. We also examine the implications of the presence of the subdiffusive dynamics of lipids on the self-intermediate scattering function and the incoherent dynamic structure factor measured in neutron-scattering experiments.

Non-canonical base pairs, mostly present in the RNA, often play a prominent role towards maintaining their structural diversity. Higher order structures like base triples are also important in defining and stabilizing the tertiary folded structure of RNA. We have developed a new program BPFIND to analyze different types of canonical and non-canonical base pairs and base triples involving at least two direct hydrogen bonds formed between polar atoms of the bases or sugar O2' only. We considered 104 possible types of base pairs, out of which examples of 87 base pair types are found to occur in the available RNA crystal structures. Analysis indicates that approximately 32.7% base pairs in the functional RNA structures are non-canonical, which include different types of GA and GU Wobble base pairs apart from a wide range of base pair possibilities. We further noticed that more than 10.4% of these base pairs are involved in triplet formation, most of which play important role in maintaining long-range tertiary contacts in the three-dimensional folded structure of RNA. Apart from detection, the program also gives a quantitative estimate of the conformational deformation of detected base pairs in comparison to an ideal planar base pair. This helps us to gain insight into the extent of their structural variations and thus assists in understanding their specific role towards structural and functional diversity.

PATH rapidly computes a path and a transition state between crystal structures by minimizing the Onsager-Machlup action. It requires input parameters whose range of values can generate different transition-state structures that cannot be uniquely compared with those generated by other methods. We outline modifications to estimate these input parameters to circumvent these difficulties and validate the PATH transition states by showing consistency between transition-states derived by different algorithms for unrelated protein systems. Although functional protein conformational change trajectories are to a degree stochastic, they nonetheless pass through a well-defined transition state whose detailed structural properties can rapidly be identified using PATH.

Errors in protein folding may result in premature clearance of structurally aberrant proteins, or in the accumulation of toxic misfolded species or protein aggregates. These pathological events lead to a large range of conditions known as conformational diseases. Several research groups have presented possible therapeutic solutions for their treatment by developing novel compounds, known as pharmacological chaperones. These cell-permeable molecules selectively provide a molecular scaffold around which misfolded proteins can recover their native folding and, thus, their biological activities. Here, we review therapeutic strategies, clinical potentials, and cost-benefit impacts of several classes of pharmacological chaperones for the treatment of a series of conformational diseases.

Access to the full text of the published version may require a subscription. An experimental examination of the properties of the Si͑100͒-SiO 2 interface measured following rapid thermal processing ͑RTP͒ is presented. The interface properties have been examined using high frequency and quasi-static capacitance-voltage ͑CV͒ analysis of metal-oxide-silicon ͑MOS͒ capacitor structures immediately following either rapid thermal oxidation ͑RTO͒ or rapid thermal annealing ͑RTA͒. The experimental results reveal a characteristic peak in the CV response measured following dry RTO and RTA (TϾ800°C), as the Fermi level at the Si͑100͒-SiO 2 interface approaches the conduction band edge. Analysis of the QSCV responses reveals a high interface state density across the energy gap following dry RTO and RTA processing, with a characteristic peak density in the range 5.5ϫ10 12 to 1.7ϫ10 13 cm Ϫ2 eV Ϫ1 located at approximately 0.85-0.88 eV above the valence band edge. When the background density of states for a hydrogen-passivated interface is subtracted, another peak of lower density (3ϫ10 12 to 7ϫ10 12 cm Ϫ2 eV Ϫ1 ͒ is observed at approximately 0.25-0.33 eV above the valence band edge. The experimental results point to a common interface state defect present after processes involving rapid cooling (10 1 -10 2°C /s) from a temperature of 800°C or above, in a hydrogen free ambient. This work demonstrates that the interface states measured following RTP (TϾ800°C) are the net contribution of the P b0 / P b1 silicon dangling bond defects for the oxidized Si͑100͒ orientation. An important conclusion arising from this work is that the primary effect of an RTA in nitrogen ͑600-1050°C͒ is to cause hydrogen desorption from pre-existing P b0 / P b1 silicon dangling bond defects. The implications of this work to the study of the Si-SiO 2 interface, and the technological implications for silicon based MOS processes, are briefly discussed. The significance of these new results to thin oxide growth and optimization by RTO are also considered. Rights

We report a high energy-resolution neutron backscattering study, combined with in-situ diffraction, to investigate slow molecular motions on nanosecond time scales in the fluid phase of phospholipid bilayers of 1,2-dimyristoyl-sn-glycero-3-phoshatidylcholine (DMPC) and DMPC/40% cholesterol (wt/wt). A cooperative structural relaxation process was observed. From the in-plane scattering vector dependence of the relaxation rates in hydrogenated and deuterated samples, combined with results from a 0.1 µs long all atom molecular dynamics simulation, it is concluded that correlated dynamics in lipid membranes occurs over several lipid distances, spanning a time interval from pico-to nanoseconds.PACS numbers: 87.16.dj, 87.14.Cc, 83.85.Hf, 87.15.ap, 83.10.Mj It is speculated that atomic and molecular motions in regions of biomolecular systems with strong local interactions are highly correlated on certain range of time and length scales [1,2]. In proteins intra-protein correlations are believed to be essential for their biological functioning, such as protein folding, domain motion and conformational changes. Very recently, inter-protein correlations in protein crystals and also membranes have been reported from experiment and simulation [3,4]. Experimental and computational effort has been invested to study collective molecular motions in phospholipid model membranes [5,6,7,8] to understand the possible impact on physiological and biological functions of the bilayers, such as transport processes [9], and eventually their implication on function of membrane-embedded proteins. While fast (picosecond) propagating collective microscopic fluctuations in the plane of the bilayer can be understood as sound waves [10,11], the slow (nanosecond) in-plane mesoscopic fluctuations (undulations) are governed by the elasticity properties of the bilayers [12].We studied dynamical modes at nearest neighbor distances of the lipid molecules using the neutron backscattering technique [13]. These modes are too fast to be accessed by x-ray photon correlation spectroscopy and the lateral length scales involved are too small to be resolved by dynamic light scattering or the neutron spinecho technique. Selective deuteration was used to discriminate relaxations due to collective molecular motions from relaxations arising from localized, single molecule excitations. In this Letter, we examine results of inelastic neutron scattering experiments that demonstrate the existence of slow coherent motion of lipid molecules in the fluid phase of phospholipid bilayers. From the inplane scattering vector dependence (q || ) of the measured relaxation rates, combined with results of a 0.1 µs long all atom molecular dynamics (MD) simulation, we find that the cooperative structural dynamics in lipid membranes occurs over several lipid distances, spanning a time interval from pico-to nanoseconds.The experiments were carried out at the cold neutron backscattering spectrometer IN16 [14] at the Institut Laue-Langevin (ILL) with an energy resolution of about 0....

Protein destabilization by amino acid substitutions is proposed to play a prominent role in widespread inherited human disorders, not just those known to involve protein misfolding and aggregation. To test this hypothesis, we computationally evaluate the effects on protein stability of all possible amino acid substitutions in 20 disease-associated proteins with multiple identified pathogenic missense mutations. For 18 of the 20 proteins studied, substitutions at known positions of pathogenic mutations are significantly more likely to destabilize the native protein fold (as indicated by more positive values of ΔΔG). Thus, positions identified as sites of disease-associated mutations, as opposed to non-disease-associated sites, are predicted to be more vulnerable to protein destabilization upon amino acid substitution. This finding supports the notion that destabilization of native protein structure underlies the pathogenicity of broad set of missense mutations, even in cases where reduced protein stability and/or aggregation are not characteristic of the disease state.