Protein structure validation and refinement using amide proton chemical shifts derived from quantum mechanics

We present the ProCS method for the rapid and accurate prediction of protein backbone amide proton chemical shifts - sensitive probes of the geometry of key hydrogen bonds that determine protein structure. ProCS is parameterized against quantum mechanical (QM) calculations and reproduces high level QM results obtained for a small protein with an RMSD of 0.25 ppm (r = 0.94). ProCS is interfaced with the PHAISTOS protein simulation program and is used to infer statistical protein ensembles that reflect experimentally measured amide proton chemical shift values. Such chemical shift-based structural refinements, starting from high-resolution X-ray structures of Protein G, ubiquitin, and SMN Tudor Domain, result in average chemical shifts, hydrogen bond geometries, and trans-hydrogen bond (h3JNC') spin-spin coupling constants that are in excellent agreement with experiment. We show that the structural sensitivity of the QM-based amide proton chemical shift predictions is needed to refine protein structures to this agreement. The ProCS method thus offers a powerful new tool for refining the structures of hydrogen bonding networks to high accuracy with many potential applications such as protein flexibility in ligand binding.Comment: PLOS ONE accepted, Nov 201

Measuring the interior of in-use sewage pipes using 3D vision

Sewage pipes may be renovated using tailored linings. However, the interior diameter of the pipes must be measured prior to renovation. This paper investigates the use of 3D vision sensors for measuring the interior diameter of sewage pipes, removing the need for human entry in the pipes. The 3D sensors are residing in a waterproof box that is lowered into the well. A RANSAC-based method is used for cylinder estimation from the acquired point clouds of the pipe and the diameter of these cylinders is used as a measure of the interior pipe diameter. The method is tested in 74 real-world sewage pipes with diameters between 150- and 1100 mm. The diameter of 68 pipes is measured within a tolerance of ±20mm whereas 8 pipes are above. It was found that the faulty estimates can be detected in the field using a combination of human-in-the-loop qualitative and quantitative data-driven measures.</p

Regulation of brain-derived neurotrophic factor (BDNF) in the chronic unpredictable stress rat model and the effects of chronic antidepressant treatment

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Ab initio linear scaling response theory: Electric polarizability by perturbed projection

A linear scaling method for calculation of the static {\em ab inito} response within self-consistent field theory is developed and applied to calculation of the static electric polarizability. The method is based on density matrix perturbation theory [Niklasson and Challacombe, cond-mat/0311591], obtaining response functions directly via a perturbative approach to spectral projection. The accuracy and efficiency of the linear scaling method is demonstrated for a series of three-dimensional water clusters at the RHF/6-31G** level of theory. Locality of the response under a global electric field perturbation is numerically demonstrated by approximate exponential decay of derivative density matrix elements.Comment: 4.25 pages in PRL format, 2 figure

Holocene ice marginal fluctuations of the Qassimiut lobe in South Greenland

Knowledge about the Holocene evolution of the Greenland ice sheet (GrIS) is important to put the recent observations of ice loss into a longer-term perspective. In this study, we use six new threshold lake records supplemented with two existing lake records to reconstruct the Holocene ice marginal fluctuations of the Qassimiut lobe (QL) – one of the most dynamic parts of the GrIS in South Greenland. Times when the ice margin was close to present extent are characterized by clastic input from the glacier meltwater, whereas periods when the ice margin was behind its present day extent comprise organic-rich sediments. We find that the overall pattern suggests that the central part of the ice lobe in low-lying areas experienced the most prolonged ice retreat from ~9–0.4 cal. ka BP, whereas the more distal parts of the ice lobe at higher elevation re-advanced and remained close to the present extent during the Neoglacial between ~4.4 and 1.8 cal. ka BP. These results demonstrate that the QL was primarily driven by Holocene climate changes, but also emphasises the role of local topography on the ice marginal fluctuations

Noncatalytic Direct Liquefaction of Biorefinery Lignin by Ethanol

There is a growing interest in lignin valorization to biofuels and chemicals. Here, we propose a novel and simple noncatalytic process to directly liquefy lignin rich solid residual from second generation bioethanol production by solvolysis with ethanol. Through an extensive parameter study in batch autoclaves assessing the effects of varying reaction temperature, reaction time, and solvent:lignin ratio, it is shown that hydrothermally pretreated enzymatic hydrolysis lignin solvolysis in supercritical ethanol can produce a heptane soluble bio-oil without the need for exhaustive deoxygenation. The process does not require addition of catalyst or a reducing agent such as hydrogen. The process is advantageously carried out with a low reaction period (<1 h) and with a reduced amount of solvent to lignin feedstock (ethanol:lignin (w/w) ratio of 2:1) which is a previously unexplored domain for lignin solvolysis. The resulting bio-oil product is mainly a mixture of di- and monomeric lignin species where the original lignin unit linkages have been broken. The oxygen content is lowered to <10 wt % (corresponding to an HHV of 36 MJ/kg) and the bio-oil is stable and acid free (verified by NMR), and due to the use of sulfur free lignin rich residual as feedstock, the resulting oil product is equally sulfur free. The residual solid product (char) has a reduced oxygen content relative to the lignin feed and equally increased higher heating value, making it a candidate for use as a biochar