Comb macromolecules with attracting functional groups in side chains

The conformational behavior of a single comb-shaped macromolecule with associating groups in side chains was studied by means of Monte Carlo simulation. The side chains contain two types of units, type A representing nonfunctional units (main chain units are likewise classified with type A) and type B representing functional (attracting) units. As a result of an increase in attraction energy between associating groups, the transition of the macromolecule from coil to the globule state takes place. The coil-globule transition is accompanied by segregation of unlike units; as a result, the globule has a complex structure: the core of the globule is formed by attracting groups of side chains, and the envelope is formed from soluble units of both main and side chains. The dependence of the size and shape of the macromolecule on its structural parameters, such as the length of main and side chains and the graft density of side chains, and on the position of the functional groups in side chains was examined. Along with the single globule, conformations in which the attracting units of side chains formed several bead globules were observed.     

Solid-state NMR detection of 14N-13C dipolar couplings between amino acid side groups provides constraints on amyloid fibril architecture

Solid‐state nuclear magnetic resonance (SSNMR) is a powerful technique for the structural analysis of amyloid fibrils. With suitable isotope labelling patterns, SSNMR can provide constraints on the secondary structure, alignment and registration of β‐strands within amyloid fibrils and identify the tertiary and quaternary contacts defining the packing of the β‐sheet layers. Detection of ¹⁴N? ¹³C dipolar couplings may provide potentially useful additional structural constraints on β‐sheet packing within amyloid fibrils but has not until now been exploited for this purpose. Here a frequency‐selective, transfer of population in double resonance SSNMR experiment is used to detect a weak ¹⁴N? ¹³C dipolar coupling in amyloid‐like fibrils of the peptide H₂N‐SNNFGAILSS‐COOH, which was uniformly ¹³C and ¹⁵N labelled across the four C‐terminal amino acids. The ¹⁴N? ¹³C interatomic distance between leucine and asparagine side groups is constrained between 2.4 and 3.8 Å, which allows current structural models of the β‐spine arrangement within the fibrils to be refined. This procedure could be useful for the general structural analysis of other proteins in condensed phases and environments, such as biological membranes. Copyright © 2011 John Wiley & Sons, Ltd.     

Direct analysis of 15N-label in amino and amide groups of glutamine and asparagine

A novel method for on-line determination of the amount and position of 15N-labeling in complex mixtures of amino acids is presented. Underivatized amino acids were analyzed by ion-pair chromatography in combination with mass spectrometry. This enables the direct determination of the 15N label distribution. The fragmentation pathways of the nitrogen moieties of glutamine (Gln) and asparagine (Asn) were studied in detail using all mono 15N isotopomers, which led to a method for differentiating between 15N-amide and 15N-amino labeling. The fragmentation involving the amino and amide groups of Gln led to distinct ion structures. The equivalent fragmentation pattern was not observed for Asn. Instead, the amide group of Asn was eliminated as HNCO in a secondary process. The developed analytical method was evaluated by analysis of a range of standard mixtures taking into account different levels of 15N abundance and distribution between the amino and amide groups. The detection limit (3 SD) for the presence of a 15N label was 0.7 and 1.0% for Gln and Asn, respectively. The determination of the positional labeling follows a nonlinear function. A representative example at 30% 15N was used as a benchmark resulting in average relative standard deviations of 2.7 and 15% for Gln and Asn, respectively. The corresponding expectation windows for the positional labeling were found to be 2 and 12%, respectively.     

Measurement of carbon-proton dipolar couplings in liquid crystals using DAPT

Dipolar couplings provide valuable information on order and dynamics in liquid crystals. For measuring heteronuclear dipolar couplings in oriented systems, a new separated local field experiment is presented here. The method is based on the dipolar assisted polarization transfer (DAPT) pulse sequence proposed recently (Chem. Phys. Lett. 2007, 439, 407) for transfer of polarization between two spins I and S. DAPT utilizes the evolution of magnetization of the I and S spins under two blocks of phase shifted BLEW-12 pulses on the I spin separated by a 90 degree pulse on the S spin. Compared to the rotating frame techniques based on Hartmann-Hahn match, this approach is easy to implement and is independent of any matching conditions. DAPT can be utilized either as a proton encoded local field (PELF) technique or as a separated local field (SLF) technique, which means that the heteronuclear dipolar coupling can be obtained by following either the evolution of the abundant spin like proton (PELF) or that of the rare spin such as carbon (SLF). We have demonstrated the use of DAPT both as a PELF and as a SLF technique on an oriented liquid crystalline sample at room temperature and also have compared its performance with PISEMA. We have also incorporated modifications to the original DAPT pulse sequence for (i) improving its sensitivity and (ii) removing carrier offset dependence.     

Probing the diastereotopicity of methylene protons in strychnine using residual dipolar couplings

Residual dipolar couplings were successfully used to distinguish between the two diastereotopic protons on C-20 of strychnine dissolved in an organic liquid crystal (PBLG/CDCl(3)). The results presented here strongly suggest that this method will be of help in organic structure determination, making the determination of relative stereochemistry in the absence of NOE data possible.     

具有极性大侧基乙烯基聚合物的分子尺寸和均方二极矩

基于旋转异构态模型和生成矩阵代数方法,重新推导了大侧基聚合物均方回转半径和均方二极矩等基础量公式,应用于对聚乙烯咔唑（PVK）、聚对氯苯乙烯（PPCS）、聚乙烯砒啶（P2VP）和聚乙烯砒咯烷酮（PVP）链构象-构型依赖性质的研究.计算得到其无规链的均方二极矩特征比分别为0.55、0.57、0.48和0.37,均方回转半径特征比分别为2.07、1.74、1.11和1.52,全同链温度系数在？6.1×10？3～2.1×10？3K？1之间,范围比间同和无规链大.比较各特征比变化曲线规律,发现PPCS、PVP和P2VP的基础量分别受聚合物聚合度、规整程度和构象能的影响相对比较明显,而大侧基使PVK的均方二极矩和均方回转半径特征差异显著;对照改进的计算结果表明,在计算均方二极矩和回转半径时考虑极性侧基的方向和尺寸是十分重要的,在聚合物极性和柔性分析中不能忽略极性大侧基的影响.     

Conformational analysis of a flexible oligosaccharide using residual dipolar couplings.

We present a new approach to the analysis of the conformational and the motional properties of an oligosaccharide, methyl 3,6-di-O-(alpha-D-mannopyranosyl)-alpha-D-mannopyranoside. The approach relies on an order matrix analysis of residual dipolar couplings in the solution state. By combining a number of different types of couplings, (1)D(CH), (2)D(CH), and D(HH), an order matrix is solved for each ring of the trimannoside. The resulting order parameters indicate the internal motion at the alpha (1,3) linkage to be limited, while significant motion is suggested at the alpha (1,6) linkage. Two structures for the trimannoside were determined by aligning the order tensor principal axes obtained from two different orienting media, bicelles and phage. The very similar conformations at the alpha (1,3) linkage of these two structures confirm that the internal motion at the alpha (1,3) linkage is small and the conformation is a good representation of a single preferred structure. The different conformations at the alpha (1,6) linkage suggest that the motional amplitudes are large and the conformations must be viewed as virtual conformers. Compared with traditional NMR methods, data acquisition is easy and data analysis is straightforward.     

Complete relative stereochemistry of multiple stereocenters using only residual dipolar couplings

Residual dipolar couplings (RDCs), in combination with molecular order matrix calculations, were used to unambiguously determine the complete relative stereochemistry of an organic compound with five stereocenters. Three simple one-dimensional experiments were utilized for the measurements of (13)C-(1)H, (13)C-(19)F, (19)F-(1)H, and (1)H-(1)H RDCs. The order matrix calculation was performed on each chiral isomer independently. The fits were evaluated by the comparison of the root-mean-square deviation (rmsd) of calculated and measured RDCs. The order tensor simulations based on two different sets of RDC data collected with phage and bicelles are consistent. The resulting stereochemical assignments of the stereocenters obtained from using only RDCs are in perfect agreement with those obtained from the single-crystal X-ray structure. Six RDCs are found to be necessary to run the simulation, and seven are the minimum to get an acceptable result for the investigated compound. It was also shown that (13)C-(1)H and (1)H-(1)H RDCs, which are the easiest to measure, are also the most important and information-rich data for the order matrix calculation. The effect of each RDC on the calculation depends on the location of the corresponding vector in the structure. The direct RDC of a stereocenter is important to the configuration determination, but the configuration of stereocenters devoid of protons can also be obtained from analysis of nearby RDCs.     

Probing the proton-transfer coordinate of complexes with F--H...P hydrogen bonds using one- and two-bond spin-spin coupling constants

Scalar coupling constants have been computed using the EOM-CCSD method for equilibrium structures of complexes stabilized by F--H...P hydrogen bonds, as well as structures along the proton-transfer coordinates of these complexes. Variations in the signs and absolute values of (1)J(F--H), (1h)J(H--P) and (2h)J(F--P) have been analyzed and interpreted in terms of changing hydrogen bond type. Of the three phosphorus bases (phosphine, trimethylphosphine and phosphinine) investigated in this study, trimethylphosphine forms the strongest complex with FH, and has the largest two-bond F--P coupling constant. Among the relatively simple phosphorus bases, it would appear to be a leading candidate for experimental NMR study. Similarities and differences are noted between the corresponding coupling constants (J) and the reduced coupling constants (K) across F--H...P and F--H...N hydrogen bonds.     

Calculation of residual dipolar couplings from disordered state ensembles using local alignment

Residual dipolar couplings (RDCs) have been observed in disordered states of several proteins. While their nonuniform values were initially surprising, it has been shown that reasonable approximation of experimental RDCs can be obtained using simple statistical coil models and assuming global alignment of each structure, provided that many thousands of conformers are averaged. Here we show that, by using short local alignment tensors, we can achieve good agreement between experimental and simulated RDCs with far fewer structures than required when using global alignment. This makes the possibility of using RDCs as direct restraints in structural calculations of disordered proteins much more feasible. In addition, it provides insight into the nature of RDCs in disordered states, suggesting that they are primarily reporting on local structure.     

Magnetic self-assembly of gold nanoparticle chains using dipolar core-shell colloids

The preparation of gold nanoparticle (AuNP) assemblies was conducted by the synthesis and dipolar assembly of ferromagnetic core-shell nanoparticles composed of AuNP cores and cobalt NP shells. Dissolution of metallic Co phases with mineral acids afforded self-assembled AuNP chains and bracelets.     

The synthesis of biodegradable polymers with functional side chains

Trifunctional hydroxy-terminated oligomeric polyesters, M_n 500, 1000, and 2000, were prepared by initiating ring-opening copolymerization of δ-valerolactone and ε-caprolactone with glycerol. The prepolymers were converted to crosslinked polyester-urethanes by their reaction with hexane-1,6-diisocyanate in proportions corresponding to 70, 80, 90, and 100% of the hydroxyl content. The moduli of the resulting elastomers varied between 0.12 MPa and 3.83 MPa, and the elongation at break between 60 and 2000%. The residual hydroxyl groups were derivatized by heterogeneous reaction with chloroacetic anhydride or excess hexane-1,6-diisocyanate, and these and further transformations of the functional groups were verified by infrared spectroscopy and electron probe x-ray microanalysis. A second series of hydroxy-substituted elastomers was synthesized by copolymerization of δ-valerolactone, ε-caprolactone, and 4-(t-butyldimethylsilyloxy)-ε-caprolactone, using different amounts of 2,2-bis(caprolacton-4-yl)propane as the crosslinking agent; removal of the t-butyldimethylsilyl group to liberate pendant hydroxyl groups was achieved with acetic acid but not fluoride ion. The hydroxylated polyester (but not the polyesterurethanes) was shown to undergo enzymatic surface erosion in rabbit. The biodegradation data were compared with results previously obtained with low-modulus elastomeric polyesters.     

De novo determination of protein backbone structure from residual dipolar couplings using Rosetta

As genome-sequencing projects rapidly increase the database of protein sequences, the gap between known sequences and known structures continues to grow exponentially, increasing the demand to accelerate structure determination methods. Residual dipolar couplings (RDCs) are an attractive source of experimental restraints for NMR structure determination, particularly rapid, high-throughput methods, because they yield both local and long-range orientational information and can be easily measured and assigned once the backbone resonances of a protein have been assigned. While very extensive RDC data sets have been used to determine the structure of ubiquitin, it is unclear to what extent such methods will generalize to larger proteins with less complete data sets. Here we incorporate experimental RDC restraints into Rosetta, an ab initio structure prediction method, and demonstrate that the combined algorithm provides a general method for de novo determination of a variety of protein folds from RDC data. Backbone structures for multiple proteins up to approximately 125 residues in length and spanning a range of topological complexities are rapidly and reproducibly generated using data sets that are insufficient in isolation to uniquely determine the protein fold de novo, although ambiguities and errors are observed for proteins with symmetry about an axis of the alignment tensor. The models generated are not high-resolution structures completely defined by experimental data but are sufficiently accurate to accelerate traditional high-resolution NMR structure determination and provide structure-based functional insights.     

Preparation of a bacterial polyester with carboxy groups in side chains

Unsaturated biopolyesters were produced by Pseudomonas oleovorans from two mixtures of sodium octanoate and 10-undecenoic acid (90:10 and 80:20 mol/mol) as a reserve of carbon and energy. Chemical modification of double bonds into carboxyl groups was carried out with potassium permanganate (KMnO₄). Oxidation reaction was proved by ¹H and ¹³C NMR spectroscopy. Molecular weights of modified biopolyesters were not highly affected by the oxidation reaction. Hydrophilicity was enhanced; polyester containing 25 % of repeating units pendant carboxylic acid end groups was soluble in polar solvents such as methanol, dimethylsulfoxide or a 85:15 (v/v) acetone/water mixture. Moreover, the presence of carboxy pendant groups was important with respect to the hydrolytic degradation. A fast hydrolysis was observed at pH = 11 in 24 hours for the carboxylated modified polyester containing 25 % of carboxyl groups.