Local protein backbone folds determined by calculated NMR chemical shifts

NMR chemical shifts (CSs: δN(NH), δC(α), δC(β), δC', δH(NH), and δH(α)) were computed for the amino acid backbone conformers (α(L), β(L), γ(L), δ(L), ε(L), α(D), γ(D), δ(D), and ε(D) [Perczel et al., J Am Chem Soc 1991, 113, 6256]) modeled by oligoalanine structures. Topological differences of the extended fold were investigated on single β-strands, hairpins with type I and II β-turns, as well as double- and triple-stranded β-sheet models. The so-called "capping effect" was analyzed: residues at the termini of a homoconformer sequence unit usually have different CSs than the central residues of an adequately long homoconformer model. In heteroconformer sequences capping effect ruins the direct applicability of several chemical shift types (δH(NH), δC', and δN(NH)) for backbone structure determination of the parent residue. Experimental δH(α), δC(α), and δC(β) values retrieved from protein database are in good agreement with the relevant computed data in the case of the common backbone conformers (α(L), β(L), γ(L), and ε(L)), even though neighboring residue effects were not accounted for. Experimental and computed ΔδH(α)-ΔδC(α), ΔδH(α)-ΔδC(β), and ΔδC(α)-ΔδC(β) maps give qualitatively the same picture, that is, the positions of the backbone conformers relative to each other are very similar. This indicates that the H(α), C(α), and C(β) chemical shifts of alanine depend considerably on the backbone fold of the parent residue also in proteins. We provide tabulated CSs of the chiral amino acids that may predict the various structures of the residues.     

Observation of dimethylaminoethyl methacrylate–myoglobin binding reaction using laser spray mass spectrometry

Covalent bonds are often created by a reaction between chemicals and protein before causing various adverse effects in a cell. Dimethylaminoethyl methacrylate (DMAEMA), which has moderate toxicity, causes skin inflammation and throat irritation. For this study, we investigated a reaction mechanism between myoglobin and (DMAEMA) using a new analytical tool developed at our laboratory: laser spray mass spectrometry technique. It was found that initially DMAEMA was added to the amino group of protein by the Michael addition mechanism; the added DMAEMA was hydrolyzed to methacrylic acid using an autocatalytic system. The results of this study indicate the feasibility of the laser spray technique in analyses of reaction dynamics. Copyright © 2012 John Wiley & Sons, Ltd.     

Complexation between nickel(II), cobalt(III) and hydrazones derived from pyridoxal 5′-phosphate and hydrazides of 2-,3-,4-pyridinecarboxylic acids in aqueous solution

abstract

The present work reports on stoichiometry, apparent stability constants of biologically relevant complexes of nickel(II), cobalt(III) with hydrazones derived from pyridoxal 5′-phosphate and hydrazides of 2-,3-,4-pyridinecarboxylic acids at pH 7.4, T?=?25.0?°C, I?=?0.25 determined using UV-Vis spectroscopy. The thermodynamic constants of some complexes formation (NiL, NiL₂, NiL₂H) were estimated. Cobalt(II) ion was found to be oxidized to cobalt(III). Co(II) and Co(III) form low-spin state complexes. Hydrazones binding ability (pL_0.5) in the medium mimicking biological ones towards Ni(II) and Co(III) was estimated.     

Physicochemical properties of new cellulosic Artisdita hystrix leaf fiber

The characterization of new natural fiber is increasing due to its excellent properties. This drives investigators to create high performance composites. The present investigation was designed to study the physicochemical properties of fibers obtained from the leaf of the Artistida hystrix. The Artistida hystrix fibers (AHFs) had crystallinity index (44.85%), cellulose (59.54 wt%), hemicellulose (11.35 wt%), lignin (8.42 wt%), and density (540 kg m^?3). The tensile strength of AHFs was 440 ± 13.4 MPa with an average strain rate of 1.57 ± 0.04%. The calculated microfibril angle of AHFs was 12.64 ± 0.45°, which influenced the mechanical properties.     

A sequence-based computational model for the prediction of the solvent accessible surface area for α-helix and β-barrel transmembrane residues

Predicting the solvent accessible surface area (ASA) of transmembrane (TM) residues is of great importance for experimental researchers to elucidate diverse physiological processes. TM residues fall into two major structural classes (α-helix membrane protein and β-barrel membrane protein). The reported solvent ASA prediction models were developed for these two types of TM residues respectively. However, this prevents the general use of these methods because one cannot determine which model is suitable for a given TM residue without information of its type. To conquer this limitation, we developed a new computational model that can be used for predicting the ASA of both TM α-helix and β-barrel residues. The model was developed from 78 α-helix membrane protein chains and 24 β-barrel membrane protein. Its prediction ability was evaluated by cross validation method and its prediction result on an independent test set of 20 membrane protein chains. The results show that our model performs well for both types of TM residues and outperforms other prediction model which was developed for the specific type of TM residues. The prediction results also proved that the random forest model incorporating conservation score is an effective sequence-based computational approach for predicting the solvent ASA of TM residues.     

载体表面氧化程度对Ni/SiC甲烷化催化剂性能的影响

采用等体积浸渍法制备了Ni/SiC甲烷化催化剂, 研究了SiC载体表面氧化程度对催化剂低温活性和高温稳定性的影响, 并采用热重-差示扫描量热、N₂物理吸附、傅立叶变换红外光谱、氨程序升温脱附、X射线衍射、氢程序升温还原和氢化学吸附技术对样品进行了表征. 结果表明, 随着载体氧化温度的提高, 催化剂的比表面积和镍分散度降低, 但还原性和反应稳定性提高. 未氧化载体所负载催化剂的高温稳定性最差, 其原因在于载体对镍粒子的固定作用最弱. 负载于500和700℃处理的SiC载体上的催化剂具有较好的低温活性和高温稳定性, 这是因为适度氧化后的载体能较好地分散并固定镍粒子. 900℃处理的载体因过度氧化形成了低活性的氧化层, 使负载的镍粒子变大, 因而催化剂的低温活性最差.     

Single‐Molecule Detection Reveals Knot Sliding in TrmD Denaturation

An increasing number of proteins are found to contain a knot in their polypeptide chain. Although some studies have looked into the folding mechanism of knotted proteins, why and how these complex topologies form are still far from being fully answered. Moreover, no experimental information about how the knot moves during the protein‐folding process is available. Herein, by combining single‐molecule fluorescence resonance energy transfer (smFRET) experiments with molecular dynamics (MD) simulations, we performed a detailed study to characterize the knot in the denatured state of TrmD, a knotted tRNA (guanosine‐1) methyltransferase from Escherichia coli, as a model system. We found that the knot still existed in the unfolded state of TrmD, consistent with the results for two other knotted proteins, YibK and YbeA. More interestingly, both smFRET experiments and MD simulations revealed that the knot slid towards the C‐terminal during the unfolding process, which could be explained by the relatively strong interactions between the β‐sheet core at the N terminal of the native knot region. The size of the knot in the unfolded state is not larger than that in the native state. In addition, the knot slid in a “downhill” mode with simultaneous chain collapse in the denatured state.     

DOT2: Macromolecular docking with improved biophysical models

Computational docking is a useful tool for predicting macromolecular complexes, which are often difficult to determine experimentally. Here, we present the DOT2 software suite, an updated version of the DOT intermolecular docking program. DOT2 provides straightforward, automated construction of improved biophysical models based on molecular coordinates, offering checkpoints that guide the user to include critical features. DOT has been updated to run more quickly, allow flexibility in grid size and spacing, and generate an infinitive complete list of favorable candidate configurations. Output can be filtered by experimental data and rescored by the sum of electrostatic and atomic desolvation energies. We show that this rescoring method improves the ranking of correct complexes for a wide range of macromolecular interactions and demonstrate that biologically relevant models are essential for biologically relevant results. The flexibility and versatility of DOT2 accommodate realistic models of complex biological systems, improving the likelihood of a successful docking outcome. © 2013 Wiley Periodicals, Inc.     

Synthesis of PAF,an Antifungal Protein from P. chrysogenum,by Native Chemical Ligation: Native Disulfide Pattern and Fold Obtained upon Oxidative Refolding

The folding of disulfide proteins is of considerable interest because knowledge of this may influence our present understanding of protein folding. However, sometimes even the disulfide pattern cannot be unequivocally determined by the available experimental techniques. For example, the structures of a few small antifungal proteins (PAF, AFP) have been disclosed recently using NMR spectroscopy but with some ambiguity in the actual disulfide pattern. For this reason, we carried out the chemical synthesis of PAF. Probing different approaches, the oxidative folding of the synthetic linear PAF yielded a folded protein that has identical structure and antifungal activity as the native PAF. In contrast, unfolded linear PAF was inactive, a result that may have implications concerning its redox state in the mode of action.