Molecular conformations in a phospholipid bilayer extracted from dipolar couplings: a computer simulation study

This paper describes an analysis of NMR dipolar couplings in a bilayer formed by dimyristoylphosphatidylcholine (DMPC). The couplings are calculated from a trajectory generated in a molecular dynamics (MD) simulation based on a realistic atom-atom interaction potential. The analysis is carried out employing a recently developed approach that focuses on the construction of the conformational distribution function. This approach is a combination of two models, the additive potential (AP) model and the maximum entropy (ME) method, and is therefore called APME. In contrast to the AP model, the APME procedure does not require an intuition-based choice of the functional form of the torsional potential and is, unlike the ME method, applicable to weakly ordered systems. The conformational distribution function for the glycerol moiety of the DMPC molecule derived from the APME analysis of the dipolar couplings is in reasonable agreement with the "true" distributions calculated from the trajectory. Analyses of dipolar couplings derived from MD trajectories can, in general, serve as guidelines for experimental investigations of bilayers and other complex biological systems.     

On the analysis of Liquid Crystal NMR dipolar coupling data via mixed a priori-maximum entropy methods

In this Letter, a general expression is derived for the conformational distribution function of a molecule dissolved in an anisotropic condensed fluid medium by combining an a priori model with the maximum entropy principle applied to treatment of liquid crystalline-NMR data. The recently proposed additive potential maximum entropy (APME) method is recovered as a special case, when the AP is chosen as the a priori model and the orientational order is low.     

Toward a four-toothed molecular bevel gear with C2-symmetrical rotors

The design, synthesis, conformational analysis, and variable-temperature NMR studies of pentiptycene-based molecular gears Pp(2)X, where Pp is the unlabeled (in 1H) or methoxy groups-labeled (in 1OM) pentiptycene rotor and X is the phenylene stator containing ortho-bridged ethynylene axles, are reported. The approach of using shape-persistent rotors of four teeth but C(2) symmetry for constructing four-toothed molecular gears is unprecedented. In addition, the first example of enantioresolution of chiral pentiptycene scaffolds is demonstrated. Density functional theory (DFT) and AM1 calculations on these Pp(2)X systems suggest two possible correlated torsional motions, geared rocking and four-toothed geared rotations, which compete with the uncorrelated gear slippage. The DFT-derived torsional barriers in 1H for rocking, four-toothed rotation, and gear slippage are approximately 2.9, 5.5, and 4.7 kcal mol(-1), respectively. The low energy barriers for these torsional motions result from the low energy cost of bending the ethynylene axles. Comparison of the NMR spectra of 1OM in a mixture of stereoisomers (1OM-mix) and in an enantiopure form (1OM-op) confirms a fast gear slippage in these Pp(2)X systems. The effect of the methoxy labels on rotational potential energy surface and inter-rotor dynamics is also discussed.     

Computer‐Assisted 3D Structure Elucidation of Natural Products using Residual Dipolar Couplings

An enhanced computer‐assisted procedure for the determination of the relative configuration of natural products, which starts from the molecular formula and uses a combination of conventional 1D and 2D NMR spectra, and residual dipolar couplings (RDCs), is reported. Having already the data acquired (1D/2D NMR and RDCs), the procedure begins with the determination of the molecular constitution using standard computer‐assisted structure elucidation (CASE) and is followed by fully automated determination of relative configuration through RDC analysis. In the case of moderately flexible molecules the simplest data‐explaining conformational model is selected by the use of the Akaike information criterion.     

Jet spectroscopy of arylmethyl radicals in the visible region: assignment of low-frequency vibrational modes in diphenylmethyl and chlorodiphenylmethyl radicals

The D(1)-D(0) transitions of diphenylmethyl (DPM) and chlorodiphenylmethyl (CDPM) radicals were studied by laser induced fluorescence (LIF) spectroscopy in a supersonic jet. Laser induced fluorescence excitation and dispersed fluorescence (DF) spectra were obtained for DPM and CDPM radicals produced by ArF excimer laser (193 nm) photolyses of their chlorides. With the aid of the density functional theory (DFT) calculation, vibronic bands are assigned by comparing the observed LIF excitation spectra of the jet-cooled radicals with the single vibronic level DF spectra. Low-frequency vibrations of 55 and 53 cm(-1) in the ground and excited states, respectively, are assigned to the symmetric phenyl torsional mode of the DPM radical. The geometries of DPM in the ground and excited states are discussed with regards to observed spectra and DFT calculations. Similarly for the CDPM radical, symmetric phenyl torsional and Ph-C-Ph bending modes are assigned and the halogen-substitution effect in equilibrium geometry is discussed.     

Probing motions between equivalent RNA domains using magnetic field induced residual dipolar couplings: accounting for correlations between motions and alignment

Approaches developed thus for extracting structural and dynamical information from RDCs have rested on the assumption that motions do not affect molecular alignment. However, it is well established that molecular alignment in ordered media is dependent on conformation, and slowly interconverting conformational substates may exhibit different alignment properties. Neglecting these correlation effects can lead to aberrations in the structural and dynamical analysis of RDCs and diminish the utility of RDCs in probing motions between domains having similar alignment propensities. Here, we introduce a new approach based on measurement of magnetic field induced residual dipolar couplings in nucleic acids which can explicitly take into account such correlations and demonstrate measurements of motions between two "magnetically equivalent" domains in the transactivation response element (TAR) RNA.     

Effects of ligands and spin-polarization on the preferred conformation of distannynes

Recent experimental and theoretical evidence has shown that distannynes, RSnSnR, can adopt either a singly bonded or a multiply bonded structure. Within calculations on small models, such as MeSnSnMe, apparently dramatic differences in conformational preference have been reported. We show that these differences arise due to the treatment of spin-polarization in density functional theory (DFT), and review stability analysis; a diagnostic for the need to include spin-polarization. The low-energy singly bonded structure can only be reached when spin-polarization is allowed. Additional DFT calculations on PhSnSnPh show that the singly bonded structure is the global minimum, leading to a flat torsional potential. The role of electronic effects is further probed by changing the donor-acceptor properties of R. Implications for the structural preference of experimentally synthesized species are discussed.     

Torsion sensitivity in NMR of aligned molecules: study on various substituted biphenyls

To estimate the torsion sensitivity of dipolar coupling, biphenylic molecules were chosen as probes due to their relatively simple structure and the surprisingly high ambiguity of the only flexible parameter-the interring torsion angle. Solution structures of 4,4'-dibromobiphenyl and 4,4'-diiodobiphenyl are reported for the first time in two liquid crystals I52 and ZLI 1695. The comparison of NMR structures of various para-substituted biphenyls (BPs), calculated by the additive potential maximum entropy (APME) approach, shows that the small spread of torsion angle values in case of different solvents and para-substituents is in good agreement with theoretical expectations from hybrid density functional theory (DFT) methods. Furthermore, the real structural changes of interring torsion and the prevalence of solvent effects over para-halosubstitution can be correctly revealed from these small fluctuations.     

Highly populated turn conformations in natively unfolded tau protein identified from residual dipolar couplings and molecular simulation

Tau, a natively unstructured protein that regulates the organization of neuronal microtubules, is also found in high concentrations in neurofibrillary tangles of Alzheimer's disease and other neurodegenerative disorders. The conformational transition between these vastly different healthy and pathological forms remains poorly understood. We have measured residual dipolar couplings (RDCs), J-couplings, and nuclear Overhauser enhancement (NOE) in construct K18 of tau, containing all four repeat domains R1-R4. NHN RDCs were compared with prediction on the basis of a statistical model describing the intrinsic conformational sampling of unfolded proteins in solution. While local variation and relative amplitude of RDCs agrees with propensity-based prediction for most of the protein, homologous sequences in each repeat domain (DLKN, DLSN, DLSK, and DKFD in repeats R1-R4) show strong disagreement characterized by inversion of the sign of the central couplings. Accelerated molecular dynamic simulations (AMD) in explicit solvent revealed strong tendencies to form turns, identified as type I beta-turns for repeats R1-R3. Incorporation of the backbone dihedral sampling resulting from AMD into the statistical coil model closely reproduces experimental RDC values. These localized sequence-dependent conformational tendencies interrupt the propensity to sample more extended conformations in adjacent strands and are remarkably resistant to local environmental factors, as demonstrated by the persistence of the RDC signature even under harsh denaturing conditions (8 M urea). The role that this specific conformational behavior may play in the transition to the pathological form is discussed.     

Mapping the potential energy landscape of intrinsically disordered proteins at amino Acid resolution

Intrinsically disordered regions are predicted to exist in a significant fraction of proteins encoded in eukaryotic genomes. The high levels of conformational plasticity of this class of proteins endows them with unique capacities to act in functional modes not achievable by folded proteins, but also places their molecular characterization beyond the reach of classical structural biology. New techniques are therefore required to understand the relationship between primary sequence and biological function in this class of proteins. Although dependences of some NMR parameters such as chemical shifts (CSs) or residual dipolar couplings (RDCs) on structural propensity are known, so that sampling regimes are often inferred from experimental observation, there is currently no framework that allows for a statistical mapping of the available Ramachandran space of each amino acid in terms of conformational propensity. In this study we develop such an approach, combining highly efficient conformational sampling with ensemble selection to map the backbone conformational sampling of IDPs on a residue specific level. By systematically analyzing the ability of NMR data to map the conformational landscape of disordered proteins, we identify combinations of RDCs and CSs that can be used to raise conformational degeneracies inherent to different data types, and apply these approaches to characterize the conformational behavior of two intrinsically disordered proteins, the K18 domain from Tau protein and N(TAIL) from measles virus nucleoprotein. In both cases, we identify the enhanced populations of turn and helical regions in key regions of the proteins, as well as contiguous strands that show clear and enhanced polyproline II sampling.     

Detection of Significant Aprotic Solvent Effects on the Conformational Distribution of Methyl 4‐Nitrophenyl Sulfoxide: From Gas‐Phase Rotational to Liquid‐Crystal NMR Spectroscopy

The conformational equilibrium of methyl 4‐nitrophenyl sulfoxide (MNPSO) was experimentally investigated in the gas phase by using microwave spectroscopy and in isotropic and nematic liquid‐crystal solutions, in which the solvents are nonaqueous and aprotic, by using NMR spectroscopy; moreover, it was theoretically studied in vacuo and in solution at different levels of theory. The overall set of results indicates a significant dependence of the solute conformational distribution on the solvent dielectric permittivity constant: when dissolved in low‐polarity media, the most stable conformation of MNPSO proved to be strongly twisted with respect to that in more polar solvents, in which the conformational distribution maximum essentially coincides with that obtained in the gas phase. We discuss a possible explanation of this behavior, which rests on electrostatic solute–solvent interactions and is supported by calculations of the solute electric dipole moment as a function of the torsional angle. This function shows that the least polar conformation of MNPSO is located at a twist angle close to that of the conformational distribution maximum found in less‐polar solvents. This fact, associated with a relatively flat torsional potential, can justify the stabilization of the twisted conformation by the less‐polar solvents.     

Paramagnetic-based NMR restraints lift residual dipolar coupling degeneracy in multidomain detergent-solubilized membrane proteins

Residual dipolar couplings (RDCs) are widely used as orientation-dependent NMR restraints to improve the resolution of the NMR conformational ensemble of biomacromolecules and define the relative orientation of multidomain proteins and protein complexes. However, the interpretation of RDCs is complicated by the intrinsic degeneracy of analytical solutions and protein dynamics that lead to ill-defined orientations of the structural domains (ghost orientations). Here, we illustrate how restraints from paramagnetic relaxation enhancement (PRE) experiments lift the orientational ambiguity of multidomain membrane proteins solubilized in detergent micelles. We tested this approach on monomeric phospholamban (PLN), a 52-residue membrane protein, which is composed of two helical domains connected by a flexible loop. We show that the combination of classical solution NMR restraints (NOEs and dihedral angles) with RDC and PRE constraints resolves topological ambiguities, improving the convergence of the PLN structural ensemble and giving the depth of insertion of the protein within the micelle. The combination of RDCs with PREs will be necessary for improving the accuracy and precision of membrane protein conformational ensembles, where three-dimensional structures are dictated by interactions with the membrane-mimicking environment rather than compact tertiary folds common in globular proteins.     

The use of residual dipolar coupling for conformational analysis of structurally related natural products

Determining the conformational preferences of molecules in solution remains a considerable challenge. Recently, the use of residual dipolar coupling (RDC) analysis has emerged as a key method to address this. Whilst to date the majority of the applications have focused on biomolecules including proteins and DNA, the use of RDCs for studying small molecules is gaining popularity. Having said that, the method continues to develop, and here, we describe an early case study of the quantification of conformer populations in small molecules using RDC analysis. Having been inspired to study conformational preferences by unexpected differences in the NMR spectra and the reactivity of related natural products, we showed that the use of more established techniques was unsatisfactory in explaining the experimental observations. The use of RDCs provided an improved understanding that, following use of methods to quantify conformer populations using RDCs, culminated in a rationalisation of the contrasting diastereoselectivities observed in a ketone reduction reaction. Copyright © 2015 John Wiley & Sons, Ltd.     

Conformational behaviour and molecular similarity of some β1-adrenergic ligands

Summary The conformational behaviour of a series of aryloxypropanolamines was investigated by means of a new procedure which allows the sampling of the molecular torsional surface in a very efficient way. The combination of such a procedure with the standard molecular mechanics algorithms for the geometry optimization gives, as a result, the definition of a powerful computational scheme for the detailed analysis of the potential energy surface of complex molecules. The compounds studied show a remarkable tendency to form intramolecular hydrogen bonds, which seem to play a key role in determining the lowest energy structures. The indices of molecular similarity proposed by Carbó, computed for the most stable conformers, do not account for differences between diastereoisomers, and, as a consequence, can hardly be used to attempt a structure-activity correlation.     

Theoretical study on the properties of linear and cyclic amides in gas phase and water solution

The structural and energetic properties of a group of selected amides, of well-known importance for the design of efficient clathrate inhibitors, are calculated with Hartree-Fock and density functional theory, B3LYP, theoretical levels, and a 6-311++g** basis set in the gas phase and a water solution. The conformational behavior of the molecules is studied through the scanning of the torsional potential energy surfaces and by the analysis of the differences in the energetic and structural properties between the isomers. The properties of the amides in water solution are determined within a self-consistent reaction field approach with a polarizable continuum model that allows the calculation of the different contributions to the free energy of solvation. The calculated barriers to rotation are in good agreement with the available experimental data and the comparison of the gas and water results shows the strong effect of the solute polarization. The properties of different amide-water complexes are calculated and compared with available experimental information.     

Computer-assisted study on the reaction between pyruvate and ylide in the pathway leading to lactyl–ThDP

In this study the formation of the lactyl-thiamin diphosphate intermediate (L-ThDP) is addressed using density functional theory calculations at X3LYP/6-31++G(d,p) level of theory. The study includes potential energy surface scans, transition state search, and intrinsic reaction coordinate calculations. Reactivity is analyzed in terms of Fukui functions. The results allow to conclude that the reaction leading to the formation of L-ThDP occurs via a concerted mechanism, and during the nucleophilic attack on the pyruvate molecule, the ylide is in its AP form. The calculated activation barrier for the reaction is 19.2?kcal/mol, in agreement with the experimental reported value.