Direct structure determination using residual dipolar couplings: reaction-site conformation of methionine sulfoxide reductase in solution

Residual dipolar couplings (RDC) from partially aligned molecules provide long-range structural data and are thus particularly well adapted to rapid structure validation or protein fold recognition. Extensive measurements in two alignment media can also provide precise de novo structure from RDC alone. We have applied a novel combination of these approaches to the study of methionine sulfoxide reductase (MsrA) from Erwinia chrysanthemi, a 27 kDa enzyme essential for repairing oxidative stress damage. The tertiary fold was initially validated by comparing backbone RDC to expected values from the crystal structure of the homologous MsrA from Escherichia coli. Good agreement was found throughout the chain, verifying the overall topology of the molecule, with the exception of the catalytically important peptide P196-L202, where strong and systematic RDC violation was observed. No evidence for local differential mobility in this region was detected, implying that the structure of the strand differs in the two molecules. We have therefore applied the de novo approach meccano to determine the conformation of this peptide using only RDC. A single conformation is found that is in agreement with all measured data. The aligned peptide can be docked onto the expected covalence of the rest of the template molecule while respecting its strictly defined relative orientation. In contrast to the structure of MsrA from E. coli, the reactive side chain of Cys200 is oriented toward the interior of the molecule and therefore closer to the catalytic Cys53, obviating the need for previously proposed conformational reorganization prior to formation of this disulfide intermediate. This analysis requires only backbone assignment and uses unambiguously assigned and readily measurable structural data, thereby greatly economizing investigation time compared to established nuclear Overhauser effect- (nOe-) based structure calculation methods.     

NMR assessment of the global shape of a non-labelled DNA dodecamer containing a tandem of G-T mismatches

We have carried out a solution study of two non-labelled self-complementary DNA dodecamers d(GACTGTACAGTC)2 and d(GACTGTGCAGTC)2 by NMR, the second sequence composed of two G-T mismatches. Structures were determined using distances extracted from NOE effects alone or using both NOE and RDC constraints, measured in three different liquid crystalline media. We ensured that our data on the influence of the mesogen on the DNA structures, and the way in which the RDCs were incorporated as constraints in the protocol refinement, were consistent. We also tested the influence of different sets of RDCs and the best means of optimizing the calculation of D(a) and R. Resolution and accuracy of the ten best energy final structures were compared. The addition of a small set of RDC constraints significantly improves the final determined structures. We took advantage of the specificity of the RDC, i.e. it contains orientational information, and explored the global shape of the DNA duplexes; it was found that the duplexes do not have a large curvature. For the G-T base pair, we observed, in this particular sequence (tandem of G-T mismatches), a new pattern of base pairing, which involved the formation of a bifurcated hydrogen bond.     

Side chain orientation from methyl 1H-1H residual dipolar couplings measured in highly deuterated proteins

High-level deuteration is a prerequisite for the study of high molecular weight systems using liquid-state NMR. Here, we present new experiments for the measurement of proton-proton dipolar couplings in CH(2)D methyl groups of (13)C labeled, highly deuterated (70-80%) proteins. (1)H-(1)H residual dipolar couplings (RDCs) have been measured in two alignment media for 57 out of 70 possible methyl containing residues in the 167-residue flavodoxin-like domain of the E. coli sulfite reductase. These data yield information on the orientation of the methyl symmetry axis with respect to the molecular alignment frame. The alignment tensor characteristics were obtained very accurately from a set of backbone RDCs measured on the same protein sample. To demonstrate that accurate structural information is obtained from these data, the measured methyl RDCs for Valine residues are analyzed in terms of chi(1) torsion angles and stereospecific assignment of the prochiral methyl groups. On the basis of the previously determined backbone solution structure of this protein, the methyl RDC data proved sufficient to determine the chi(1) torsion angles in seven out of nine valines, assuming a single-rotamer model. Methyl RDCs are complementary to other NMR data, for example, methyl-methyl NOE, to determine side chain conformation in high molecular weight systems.     

Conformation of ionizable poly Para phenylene ethynylene in dilute solutions

The conformation of dinonyl poly para phenylene ethynylenes (PPEs) with carboxylate side chains, equilibrated in solvents of different quality have been studied using molecular dynamics simulations. PPEs are of interest because of their tunable electro‐optical properties, chemical diversity, and functionality which are essential in wide range of applications. The polymer conformation determines the conjugation length and their assembly mode and affects electro‐optical properties which are critical in current and potential uses. This study investigates the effect of carboxylate fraction on PPEs side chains on the conformation of chains in the dilute limit, in solvents of different quality. The dinonyl PPE chains are modeled atomistically, where the solvents are modeled both implicitly and explicitly. Dinonyl PPEs maintained a stretched out conformation up to a carboxylate fraction f of 0.7 in all solvents studied. The nonyl side chains are extended and oriented away from the PPE backbone in toluene and in implicit good solvent, whereas in water and implicit poor solvent, the nonyl side chains are collapsed toward the PPE backbone. Rotation around the aromatic ring is fast and no long range correlations are seen within the backbone. © 2015 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2016 , 54, 582–588     

RDC‐enhanced structure calculation of a β‐heptapeptide in methanol

Residual dipolar couplings (RDCs) are a rich source of structural information that goes beyond the range covered by the nuclear Overhauser effect or scalar coupling constants. They can only be measured in partially oriented samples. RDC studies of peptides in organic solvents have so far been focused on samples in chloroform or DMSO. Here, we show that stretched poly(vinyl acetate) can be used for the partial alignment of a linear β‐peptide with proteinogenic side chains in methanol. ¹D_CH, ¹D_NH, and ²D_HH RDCs were collected with this sample and included as restraints in a simulated annealing calculation. Incorporation of RDCs in the structure calculation process improves the long‐range definition in the backbone of the resulting 3₁₄‐helix and uncovers side‐chain mobility. Experimental side‐chain RDCs of the central leucine and valine residues are in good agreement with predicted values from a local three‐state model. Copyright © 2016 John Wiley & Sons, Ltd.     

Structural studies of laterally attached liquid crystalline polymers

Abstract

Structural studies of a series of laterally attached side chain liquid crystalline polysiloxanes have been made by X-ray diffraction. All but one exhibit a nematic phase with S_C-like short range ordering. The diffraction has been interpreted in terms of a model in which the mesogenic units form a ‘jacket’ around the polymer backbone. The backbone conformation has been studied by small angle X-ray scattering from oriented samples of mesomorphic solutions and by infrared dichroism measurements on oriented samples of the polymers. In both cases the results were consistent with the mesogens being oriented parallel to the backbone which is consistent with the ‘mesogen jacket’ model.     

Elucidation of mechanism for living radical polymerization of styrene with N,N-diethyldithiocarbamate derivatives as iniferters by the use of spin trapping technique

The photodissociation of several N,N-diethyldithiocarbamate derivatives (RDC), i.e., benzyl, 1-phenylethyl, 2-phenylethyl, n-butyl, sec-, and tert-butyl N,N-diethyldithiocarbamates, was investigated by the spin trapping technique to elucidate the polymerization mechanism of styrene (St) with RDC as iniferters. The scission of RDC occured at two different C? S bonds depending on the structure of the alkyl groups of RDC and the cleavage manner was dominated by both resonance and steric effects. It has been confirmed that RDC generating an N,N-diethyldithiocarbamyl radical acts as an effective iniferter and induces the living radical polymerization of St in homogeneous system. The polymerizations of St with tetraethylthiuram disulfide and p-xylylene bis(N,N-diethyldithiocarbamate) were also discussed on the basis of the results of the spin trapping for RDC as the model compounds of the poly(St) chain ends. © 1994 John Wiley & Sons, Inc.     

Development of New Supramolecular Lyotropic Liquid Crystals and Their Application as Alignment Media for Organic Compounds

Most alignment media for the residual dipolar coupling (RDC) based molecular structure determination of small organic compounds consist of rod‐like polymers dissolved in organic solvents or of swollen cross‐linked polymer gels. Thus far, the synthesis of polymer‐based alignment media has been a challenging process, which is often followed by a time‐consuming sample preparation. We herein propose the use of non‐polymeric alignment media based on benzenetricarboxamides (BTAs), which self‐assemble into rod‐like supramolecules. Our newly found supramolecular lyotropic liquid crystals (LLCs) are studied in terms of their LLC properties and their suitability as alignment media in NMR spectroscopy. Scalable enantiodifferentiating properties are introduced through a sergeant‐and‐soldier principle by blending achiral with chiral substituted BTAs.     

An Alignment Medium for Measuring Residual Dipolar Couplings in Pure DMSO: Liquid Crystals from Graphene Oxide Grafted with Polymer Brushes

Residual dipolar couplings (RDCs) have attracted attention in light of their great impact on the structural elucidation of organic molecules. However, the effectiveness of RDC measurements is limited by the shortage of alignment media compatible with widely used organic solvents, such as DMSO. Herein, we present the first liquid crystal (LC) based alignment medium that is compatible with pure DMSO, thus enabling RDC measurements of polar and intermediate polarity molecules. The liquid crystals were obtained by grafting polymer brushes onto graphene oxide (GO) using free radical polymerization. The resulting new medium offers several advantages, such as absence of background signals, narrow line shapes, and tunable alignment. Importantly, this medium is compatible with π‐conjugated molecules. Moreover, sonication‐induced fragmentation can reduce the size of GO sheets. The resulting anisotropic medium has moderate alignment strength, which is a prerequisite for an accurate RDC measurement.     

Meshed tert-butyl gears on a quasirigid backbone

MM3-based calculations showed that bicycles and polycycles with four- to six-membered rings-components of the bi- and polycyclic backbone are sufficiently rigid to keep a syn-periplanar orientation of vicinal tert-butyl substituents. As a result of the spatial proximity of these groups, their rotation occurs in a concerted manner as demonstrated by conformational schemes that are built using MM3-derived methodology. Only correlated disrotation in saturated systems with four- to five-membered rings-components and in the adamantane system leads to isochronism for Me groups of the tert-Bu substituents (i.e., to dynamic gearing in Mislow's terms). Moreover, correlated rotation of these substituents is coupled with a change of the backbone geometry (pseudorotation) except in the most rigid bicyclo[2.1.1]hexa-2-ene system. Thus, a new type of dynamic gearing, correlated rotation–rotation–pseudorotation, is predicted for quasirigid bi- and polycycles with syn-periplanar oriented tert-Bu substituents. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1786–1794, 1998     

Composite spectral density functions for the interpretation of the 13C NMR relaxation behavior of polymers containing hydrocarbon side chains. Free and restricted side chain motion

¹³C NMR NT₁ and NOE have been calculated by using composite spectral density functions describing polymer chain segmental motion and internal rotation of a hydrocarbon side chain attached to the polymer backbone. Numerical results at two magnetic fields are presented as a function of the various motional parameters characterizing the various models. NT₁ and NOE relaxation parameters are well behaved and appear to have practical value for describing the dynamics of these systems. The models have been applied to the relaxation data of poly(n-butyl methacrylate) and poly(n-hexyl methacrylate) in toluene solutions. The dynamics of the two polymers are characterized by a very localized backbone motion and restricted internal rotation about successive C? C bonds of the side chains. © 1995 John Wiley & Sons, Inc.     

NMR experimental evidence of the differentiation of enantiotopic directions in C(s) and C(2v) molecules using partially oriented, chiral media.

We report new and explicit experimental evidence of the differentiation of (1)H-(1)H, (13)C-(1)H, and (13)C-(2)H enantiotopic directions in prochiral molecules with C(s) and C(2v)symmetry dissolved in a chiral liquid-crystalline phase using (13)C and (2)H-[(1)H] NMR spectroscopy at the natural abundance level. The case of endo-bicyclo[2.2.2]oct-5-ene-2,3-dicarboxylic anhydride, bicyclo[2.2.1]hepta-2,5-diene, and ethyl alcohol oriented in organic solutions of poly-gamma-benzyl-L-glutamate (PBLG) or poly-epsilon-carbobenzyloxy-L-lysine (PCBLL) is investigated and discussed. Next, we describe the first NMR differentiation of enantiotopic directions in a C(2v) molecule with no prostereogenic carbon using malononitrile as a model. The various results presented in this work experimentally validate our recent theoretical arguments which predict that NMR spectra of nonplanar C(s) and C(2v) compounds embedded in a chiral oriented solvent should differ from those recorded in nonchiral oriented media, because their effective molecular symmetry point group (interacting molecule) is different from their molecular point group (isolated molecule). In addition, the differentiation of enantiotopic directions in C(2v) molecules exhibiting no prostereogenic tetrahedral center illustrates for the first time an old stereochemical hypothesis which speculates that "for molecules of the type CXXYY. the two X groups as well as the Y groups are equivalent and cannot be distinguished in chiral or achiral circumstances. However, the relationships between X and Y groups are not all equivalent. The four X-Y relationships may be ordered into two enantiotopic sets of two equivalent relationships" (Mislow, K.; Raban, M. Top. Stereochem. 1967, 1, 1) and validate the stereogenicity concepts proposed more recently by Fujita (Fujita, S. J. Am. Chem. Soc. 1990, 112, 3390).     

Structural studies of laterally attached liquid crystalline polymers

Structural studies of a series of laterally attached side chain liquid crystalline polysiloxanes have been made by X-ray diffraction. All but one exhibit a nematic phase with S_C-like short range ordering. The diffraction has been interpreted in terms of a model in which the mesogenic units form a 'jacket' around the polymer backbone. The backbone conformation has been studied by small angle X-ray scattering from oriented samples of mesomorphic solutions and by infrared dichroism measurements on oriented samples of the polymers. In both cases the results were consistent with the mesogens being oriented parallel to the backbone which is consistent with the 'mesogen jacket' model.     

Effect of matrix domination in PANI interpolymer complexes with polyamidosulfonic acids

Various polyaniline (PANI) interpolymer complexes with polyacids in the form of molecular solutions were synthesized by chemical oxidative polymerization of aniline in the presence of water-soluble poly-(2-acrylamido-2-methyl-1-propanesulfonic acid) (flexible backbone), poly-p,p′-(2,2′-disulfoacid)-diphenylene-terephthalamide (t-PASA, rigid backbone), and their mixtures in different ratios. The complexes were characterized by UV-Vis-near infrared spectroscopy in solutions; also, the films’ drop-casts from these solutions were investigated by cyclic voltammetry, spectroelectrochemical, direct current (DC) conductivity, and atomic force microscopy (AFM) measurements. It was shown that the nature of polyacid affects the shape of spectra and the dynamics of their changes. The character of spectral changes during the matrix synthesis of PANI in the presence of mixtures of the rigid-chain and flexible-chain matrixes and the study of spectral properties of the obtained PANI solutions demonstrates the existence of the rigid-matrix domination effect in the process of formation of PANI interpolymer complexes. Spectral properties of the obtained PANI complexes with the mixtures of flexible-chain and rigid-chain polyacids of different ratios (3:1, 1:1, 1:3, and 1:6) are very similar to those ones for the complex with rigid-chain t-PASA. At the same time, there is a correlation between the electrical conductivity and morphology of the films of PANI complexes and their composition, the conductivity passing through a minimum for the complexes with the polyacid mixtures (6:1, 3:1, and 1:1).     

Repeat Space Theory Applied to Carbon Nanotubes and Related Molecular Networks. I

The present article is the first part of a series devoted to extending the Repeat Space Theory (RST) to apply to carbon nanotubes and related molecular networks. Four key problems are formulated whose affirmative solutions imply the formation of the initial investigative bridge between the research field of nanotubes and that of the additivity and other network problems studied and solved by using the RST. All of these four problems are solved affirmatively by using tools from the RST. The Piecewise Monotone Lemmas (PMLs) are cornerstones of the proof of the Fukui conjecture concerning the additivity problems of hydrocarbons. The solution of the fourth problem gives a generalized analytical formula of the pi-electron energy band curves of nanotube (a, b), with two new complex parameters c and d. These two parameters bring forth a broad class of analytic curves to which the PMLs and associated theoretical devices apply. Based on the above affirmative solutions of the problems, a central theorem in the RST, called the asymptotic linearity theorem (ALT) has been applied to nanotubes and monocyclic polyenes. Analytical formulae derived in this application of the ALT illuminate in a new global context (i) the conductivity of nanotubes and (ii) the aromaticity of monocyclic polyenes; moreover an analytical formula obtained by using the ALT provides a fresh insight into Hückel’s (4n+2) rule. The present article forms a foundation of the forthcoming articles in this series. The present series of articles is closely associated with the series of articles entitled ‘Proof of the Fukui conjecture via resolution of singularities and related methods’ published in the JOMC.     

Aqueous solution behavior of new thermoassociative polymers

A new kind of water-soluble polymer was obtained by grafting side chains, characterized by a phase separation on heating (Lower Critical Solution Temperature LCST), on a hydrosoluble backbone. For semidilute solutions, the side chains associate as the temperature exceeds a critical temperature (T _ass), which is close to their LCST. Microdomains are formed which act like physical crosslinking units between the main chains, and an increase in the aqueous solution viscosity is observed. Systems based on 2-Acrylamido-2-methyl propane sulfonic acid (AMPS) backbone and polyethylene oxide (PEO) side chains were developed. Their rheological behavior in both dilute and semi-dilute states was studied by varying differents parameters such as polymer and salt concentrations, grafting ratio, etc. Fluorescence measurements indicate the formation of hydrophobic microdomains on heating, in agreement with the thickening properties of the solutions.     

Extraction of mercury from aqueous iodide solutions by trilaurylamine N-oxide and its subsequent determination by atomic absorption spectrometry

A solvent extraction technique using 0.01M solution of trilaurylamine N-oxide in benzene as extractant has been used to concentrate mercury efficiently from water solutions with or without the presence of 0.02M KI in weakly acidic media. In addition to unmodified aqueous solutions, mercury can be extracted quantitatively from aqueous iodide solutions that are up to 1M in HCl, H₂SO₄, and HNO₃ in a single equilibration. Distribution coefficients and separation factors of several elements relative to mercury(II) are reported for media that contain 0.1 M HCl and 0.02M KI. The reagent is superior to aliphatic amines and quaternary amines for the extraction of mercury from aqueous iodide solutions.     

From secondary structure to three-dimensional structure: Improved dihedral angle probability distribution function for use with energy searches for native structures of polypeptides and proteins

An improved scheme to help in the prediction of protein structure is presented. This procedure generates improved starting conformations of a protein suitable for energy minimization. Trivariate gaussian distribution functions for the π, ψ, and χ¹ dihedral angles have been derived, using conformational data from high resolution protein structures selected from the Protein Data Bank (PDB). These trivariate probability functions generate initial values for the π, ψ, and χ¹ dihedral angles which reflect the experimental values found in the PDB. These starting structures speed the search of the conformational space by focusing the search mainly in the regions of native proteins. The efficiency of the new trivariate probability distributions is demonstrated by comparing the results for the α-class polypeptide fragment, the mutant Antennapedia (C39 → S) homeodomain (2HOA), with those from two reference probability functions. The first reference probability function is a uniform or flat probability function and the second is a bivariate probability function for π and ψ. The trivariate gaussian probability functions are shown to search the conformational space more efficiently than the other two probability functions. The trivariate gaussian probability functions are also tested on the binding domain of Streptococcal protein G (2GB1), an α/β class protein. Since presently available energy functions are not accurate enough to identify the most native-like energy-minimized structures, three selection criteria were used to identify a native-like structure with a 1.90-Å rmsd from the NMR structure as the best structure for the Antennapedia fragment. Each individual selection criterion (ECEPP/3 energy, ECEPP/3 energy-plus-free energy of hydration, or a knowledge-based mean field method) was unable to identify a native-like structure, but simultaneous application of more than one selection criterion resulted in a successful identification of a native-like structure for the Antennapedia fragment. In addition to these tests, structure predictions are made for the Antennapedia polypeptide, using a Pattern Recognition-based Importance-Sampling Minimization (PRISM) procedure to predict the backbone conformational state of the mutant Antennapedia homeodomain. The ten most probable backbone conformational state predictions were used with the trivariate and bivariate gaussian dihedral angle probability distributions to generate starting structures (i.e., dihedral angles) suitable for energy minimization. The final energy-minimized structures show that neither the trivariate nor the bivariate gaussian probability distributions are able to overcome the inaccuracies in the backbone conformational state predictions to produce a native-like structure. Until highly accurate predictions of the backbone conformational states become available, application of these dihedral angle probability distributions must be limited to problems, such as homology modeling, in which only a limited portion of the backbone (e.g., surface loops) must be explored. © 1996 John Wiley & Sons, Inc.