Extending molecular dynamics with dipolar NMR tensors as constraints to chiral phosphorus compounds.

Molecular dynamics with orientational constraints (MDOC) simulations use NMR parameters as tensorial constraints in the stereochemical analysis of small molecules. C-P Residual dipolar couplings-aided MDOC simulations of small phosphorus molecules determined the relative configurations of rigid molecules after including -couplings as additional constraints. However, flexible molecules remain a problem.

Simulation of oriented NMR spectra: Combining molecular dynamics and chemical shift tensor calculations.

Solid state NMR is widely used to study the orientation and other structural features of proteins and peptides in lipid bilayers. Using data obtained by PISEMA (Polarization Inversion Spin Exchange at Magic Angle) experiments, periodic spectral patterns arise from well-aligned α-helical molecules. Significant problems in the interpretation of PISEMA spectra may arise for systems that do not form perfectly defined secondary structures, like α-helices, or the signal pattern is disturbed by molecular motion.

Residual dipolar couplings as a tool for structural analysis of ionic liquids.

An acrylonitrile/dimethylacrylamide cross-linked polymer could be swollen in different imidazolium ionic liquids. Mechanical compression of the obtained polymer gels inside an NMR tube allowed the measurement of residual dipolar couplings. Conformational analysis of the 1-methyl-3-butyl-imidazolium (BMIM) cation could be performed by including the measured RDCs as restraints in time-averaged molecular dynamics.

Structures Controlled by Entropy: The Flexibility of Strychnine as Example.

To study the flexibility of strychnine, we performed molecular dynamics simulations with orientational tensorial constraints (MDOC). Tensorial constraints are derived from nuclear magnetic resonance (NMR) interaction tensors, for instance, from residual dipolar couplings (RDCs). Used as orientational constraints, they rotate the whole molecule and molecular parts with low rotational barriers.

Statistical evaluation of simulated NMR data of flexible molecules.

A new probability score-named -probability-is introduced for evaluating the fit of mixed NMR datasets to calculate molecular model ensembles, in order to answer challenging structural questions such as the determination of stereochemical configurations. Similar to the DP4 parameter, the -probability is based on Bayes theorem and expresses the probability that an experimental NMR dataset fits to a given individual within a finite set of candidate structures or configurations. Here, the -probability is applied to single out the correct configuration in four example cases, with increasing complexity and conformational mobility.

The simulation of NMR data of flexible molecules: sagittamide A as an example for MD simulations with orientational constraints.

The recently developed MDOC (Molecular Dynamics with Orientational Constraints) simulation is applied for the first time to a fully flexible molecule. MDOC simulations aim to single out the naturally existing configuration of molecules and to elucidate conformer populations. The performance of the method was first demonstrated on a well-studied test case, the five-membered ring lactone (α-methylene-γ-butyrolactone).

Conformational Investigations in Flexible Molecules Using Orientational NMR Constraints in Combination with -Couplings and NOE Distances.

The downscaling of NMR tensorial interactions, such as dipolar couplings, from tens of kilohertz to a few hertz in low-order media is the result of dynamics spanning several orders of magnitudes, including vibrational modes (~ns-fs), whole-molecule reorientation (~ns) and higher barrier internal conformational exchange ( View Article and Find Full Text PDF

Configuration determination by residual dipolar couplings: accessing the full conformational space by molecular dynamics with tensorial constraints.

Residual dipolar couplings (RDCs) and other residual anisotropic NMR parameters provide valuable structural information of high quality and quantity, bringing detailed structural models of flexible molecules in solution in reach. The corresponding data interpretation so far is directly or indirectly based on the concept of a molecular alignment tensor, which, however, is ill-defined for flexible molecules. The concept is typically applied to a single or a small set of lowest energy structures, ignoring the effect of vibrational averaging.

Investigation of backbone dynamics and local geometry of bio-molecules using calculated NMR chemical shifts and anisotropies.

Prerequisite for chemical shift (CS) and CS tensor calculations are highly refined structures defining the molecular surroundings of the nuclei under study. Here, we present geometry optimizations with C and N CS constraints for large bio-molecules like peptides and proteins. The method discussed here provides both, refined structures and chemical shift tensors.

Molecular Dynamics with Orientational Tensorial Constraints: A New Approach to Probe the Torsional Angle Distributions of Small Rotationally Flexible Molecules.

The potential of residual dipolar couplings (RDCs) in conformational studies of small molecules is now widely recognized, but current theoretical approaches for their interpretation have several limitations and there is still the need for a general method to probe the torsional angle distributions applicable to any rotationally flexible molecule. Molecular dynamics simulations with RDC-based orientational tensorial constraints (MDOC), implemented in the software COSMOS, are presented here as a conceptually new strategy. For the cases of the fluorinated anti-inflammatory drug diflunisal and the disaccharide cellobiose, we demonstrate that MDOC simulations with one-bond RDCs as tensorial constraints unveil torsion distributions and allow the determination of relative configuration in the presence of rotational flexibility.

Insight into the chromophore of rhodopsin and its Meta-II photointermediate by F solid-state NMR and chemical shift tensor calculations.

19F nuclei are useful labels in solid-state NMR studies, since their chemical shift and tensor elements are very sensitive to the electrostatic and space-filling properties of their local environment. In this study we have exploited a fluorine substituent, strategically placed at the C-12-position of 11-cis retinal, the chromophore of visual rhodopsins. This label was used to explore the local environment of the chromophore in the ground state of bovine rhodopsin and its active photo-intermediate Meta II.

H line width dependence on MAS speed in solid state NMR - Comparison of experiment and simulation.

Recent developments in magic angle spinning (MAS) technology permit spinning frequencies of ≥100 kHz. We examine the effect of such fast MAS rates upon nuclear magnetic resonance proton line widths in the multi-spin system of β-Asp-Ala crystal. We perform powder pattern simulations employing Fokker-Plank approach with periodic boundary conditions and H-chemical shift tensors calculated using the bond polarization theory.

Molecular dynamics simulations on PGLa using NMR orientational constraints.

NMR data obtained by solid state NMR from anisotropic samples are used as orientational constraints in molecular dynamics simulations for determining the structure and dynamics of the PGLa peptide within a membrane environment. For the simulation the recently developed molecular dynamics with orientational constraints technique (MDOC) is used. This method introduces orientation dependent pseudo-forces into the COSMOS-NMR force field.

A Toxoplasma gondii Gluconeogenic Enzyme Contributes to Robust Central Carbon Metabolism and Is Essential for Replication and Virulence.

The expression of gluconeogenic enzymes is typically repressed when glucose is available. The protozoan parasite Toxoplasma gondii utilizes host glucose to sustain high rates of intracellular replication. However, despite their preferential utilization of glucose, intracellular parasites constitutively express two isoforms of the gluconeogenic enzyme fructose 1,6-bisphosphatase (TgFBP1 and TgFBP2).

Structural characterization of a peptoid with lysine-like side chains and biological activity using NMR and computational methods.

N-substituted glycine oligomers or peptoids with charged side chains are a novel class of cell penetrating peptide mimetics and have been shown to serve as drug delivery agents. Here, we investigated by NMR spectroscopy and quantum chemical calculations whether a Rhodamine B labelled peptoid [RhoB(Spiro)-Ahx]-[But](6A)NH(2) with lysine-like side chains adopts structural motifs similar to regular peptides. Due to a low chemical shift dispersion, high resolution structure determination with conventional NMR-derived distance restraints and J-couplings was not possible.

Structure simulation with calculated NMR parameters - integrating COSMOS into the CCPN framework.

The Collaborative Computing Project for NMR (CCPN) has build a software framework consisting of the CCPN data model (with APIs) for NMR related data, the CcpNmr Analysis program and additional tools like CcpNmr FormatConverter. The open architecture allows for the integration of external software to extend the abilities of the CCPN framework with additional calculation methods. Recently, we have carried out the first steps for integrating our software Computer Simulation of Molecular Structures (COSMOS) into the CCPN framework.

Rapid calculation of protein chemical shifts using bond polarization theory and its application to protein structure refinement.

Although difficult to analyze, NMR chemical shifts provide detailed information on protein structure. We have adapted the semi-empirical bond polarization theory (BPT) to protein chemical shift calculation and chemical shift driven protein structure refinement. A new parameterization for BPT amide nitrogen chemical shift calculation has been derived from MP2 ab initio calculations and successfully evaluated using crystalline tripeptides.

Irregular structure of the HIV fusion peptide in membranes demonstrated by solid-state NMR and MD simulations.

To better understand peptide-induced membrane fusion at a molecular level, we set out to determine the structure of the fusogenic peptide FP23 from the HIV-1 protein gp41 when bound to a lipid bilayer. An established solid-state (19)F nuclear magnetic resonance (NMR) approach was used to collect local orientational constraints from a series of CF(3)-phenylglycine-labeled peptide analogues in macroscopically aligned membranes. Fusion assays showed that these (19)F-labels did not significantly affect peptide function.

Analysis of the specific interactions between the lectin domain of malectin and diglucosides.

The endoplasmic reticulum malectin is a highly conserved protein in the animal kingdom that has no counterpart so far in lower organisms. We recently determined the structure of its conserved domain and found a highly selective binding to Glc(2)Man(9)GlcNAc(2), an intermediate of N-glycosylation. In our quest for putative ligands during the initial characterization of the protein, we noticed that the malectin domain is highly specific for diglucosides but quite tolerant towards the linkage of the glucosidic bond.

Two essential arginine residues in the T components of energy-coupling factor transporters.

Energy-coupling factor (ECF) transporters, a recently discovered class of importers of micronutrients, are composed of a substrate-specific transmembrane component (S component) and a conserved energy-coupling module consisting of a transmembrane protein (T component) and pairs of ABC ATPases (A proteins). Based on utilization of a dedicated (subclass I) or shared (subclass II) energy-coupling module, ECF systems fall into two subclasses. The T components are the least-characterized proteins of ECF importers, and their function is essentially unknown.

Calculation of fluorine chemical shift tensors for the interpretation of oriented (19)F-NMR spectra of gramicidin A in membranes.

A semi-empirical method for the prediction of chemical shifts, based on bond polarization theory, has recently been introduced for (13)C. Here, we extended this approach to calculate the (19)F chemical shift tensors of fluorine bound to aromatic rings and in aliphatic CF(3) groups. For the necessary parametrization, ab initio chemical shift calculations were performed at the MP2 level for a set of fluorinated molecules including tryptophan.

Transition metal complexes of a cyclic pseudo hexapeptide: synthesis, complex formation and catalytic activities.

To contribute to a better understanding of metalloenzymes, we studied ion selectivity, complex formation tendencies and catalytic activities of linear and cyclic pseudopeptides. In this contribution, a linear and cyclic pseudo hexapeptide is described. The complex with transition metal ions and the sequence were designed using the programme COSMOS.

Solid-state 19F NMR spectroscopy reveals that Trp41 participates in the gating mechanism of the M2 proton channel of influenza A virus.

The integral membrane protein M2 of influenza A virus assembles as a tetrameric bundle to form a proton-conducting channel that is activated by low pH. The side chain of His37 in the transmembrane alpha-helix is known to play an important role in the pH activation of the proton channel. It has also been suggested that Trp41, which is located in an adjacent turn of the helix, forms part of the gating mechanism.

All-atom molecular dynamics simulations using orientational constraints from anisotropic NMR samples.

Orientational constraints obtained from solid state NMR experiments on anisotropic samples are used here in molecular dynamics (MD) simulations for determining the structure and dynamics of several different membrane-bound molecules. The new MD technique is based on the inclusion of orientation dependent pseudo-forces in the COSMOS-NMR force field. These forces drive molecular rotations and re-orientations in the simulation, such that the motional time-averages of the tensorial NMR properties approach the experimentally measured parameters.

NMR chemical shift powder pattern recoupling at high spinning speed and theoretical tensor evaluation applied to silk fibroin.

The NMR pulse sequence RAI (recoupling of anisotropy information) has been improved to obtain powder patterns at high MAS spinning speeds. The 2D iso-aniso experiment displays the static chemical shift spectra on the indirect dimension and the MAS spectra on the direct dimension; hence overlapping chemical shift tensor patterns can be well resolved. This efficient technique is applicable to compounds containing (13)C sp(3) (C(alpha), C(beta)) and sp(2) (C=O) sites with higher chemical shift (CS) anisotropy (CSA), and the reliability of the method was tested here on the (13)C chemical shift tensors of polycrystalline glycine, alanine, and serine.