Conformational studies of blood group A and blood group B oligosaccharides using NMR residual dipolar couplings

Prediction of anisotropic NMR data without knowledge of alignment medium structure by surface decomposition

Prediction of anisotropic NMR data directly from solute-medium interaction is of significant theoretical and practical interest, particularly for structure elucidation, configurational analysis and conformational studies of complex organic molecules and natural products. Current prediction methods require an explicit structural model of the alignment medium: a requirement either impossible or impractical on a scale necessary for small organic molecules. Here we formulate a comprehensive mathematical framework for a parametrization protocol that deconvolutes an arbitrary surface of the medium into several simple local landscapes that are distributed over the medium's surface by specific orientational order parameters. The shapes and order parameters of these local landscapes are determined via fitting that maximizes the congruence between experimentally determined anisotropic NMR measurables and their predicted counterparts, thus avoiding the need for an a priori knowledge of the global medium morphology. This method achieves substantial improvements in the accuracy of predicted anisotropic NMR values compared to current methods, as demonstrated herein with sixteen natural products. Furthermore, because this formalism extracts structural commonalities of the medium by combining anisotropic NMR data from different compounds, its robustness and accuracy are expected to improve as more experimental data become available for further re-optimization of fitting parameters.

Concurrent Identification and Characterization of Protein Structure and Continuous Internal Dynamics with REDCRAFT

Internal dynamics of proteins can play a critical role in the biological function of some proteins. Several well documented instances have been reported such as MBP, DHFR, hTS, DGCR8, and NSP1 of the SARS-CoV family of viruses. Despite the importance of internal dynamics of proteins, there currently are very few approaches that allow for meaningful separation of internal dynamics from structural aspects using experimental data. Here we present a computational approach named REDCRAFT that allows for concurrent characterization of protein structure and dynamics. Here, we have subjected DHFR (PDB-ID 1RX2), a 159-residue protein, to a fictitious, mixed mode model of internal dynamics. In this simulation, DHFR was segmented into 7 regions where 4 of the fragments were fixed with respect to each other, two regions underwent rigid-body dynamics, and one region experienced uncorrelated and melting event. The two dynamical and rigid-body segments experienced an average orientational modification of 7° and 12° respectively. Observable RDC data for backbone C′-N, N-HN, and C′-HN were generated from 102 uniformly sampled frames that described the molecular trajectory. The structure calculation of DHFR with REDCRAFT by using traditional Ramachandran restraint produced a structure with 29 Å of structural difference measured over the backbone atoms (bb-rmsd) over the entire length of the protein and an average bb-rmsd of more than 4.7 Å over each of the dynamical fragments. The same exercise repeated with context-specific dihedral restraints generated by PDBMine produced a structure with bb-rmsd of 21 Å over the entire length of the protein but with bb-rmsd of less than 3 Å over each of the fragments. Finally, utilization of the Dynamic Profile generated by REDCRAFT allowed for the identification of different dynamical regions of the protein and the recovery of individual fragments with bb-rmsd of less than 1 Å. Following the recovery of the fragments, our assembly procedure of domains (larger segments consisting of multiple fragments with a common dynamical profile) correctly assembled the four fragments that are rigid with respect to each other, categorized the two domains that underwent rigid-body dynamics, and identified one dynamical region for which no conserved structure could be defined. In conclusion, our approach was successful in identifying the dynamical domains, recovery of structure where it is meaningful, and relative assembly of the domains when possible.

Minimizing the Entropy Penalty for Ligand Binding: Lessons from the Molecular Recognition of the Histo Blood-Group Antigens by Human Galectin-3

Ligand conformational entropy plays an important role in carbohydrate recognition events. Glycans are characterized by intrinsic flexibility around the glycosidic linkages, thus in most cases, loss of conformational entropy of the sugar upon complex formation strongly affects the entropy of the binding process. By employing a multidisciplinary approach combining structural, conformational, binding energy, and kinetic information, we investigated the role of conformational entropy in the recognition of the histo blood‐group antigens A and B by human galectin‐3, a lectin of biomedical interest. We show that these rigid natural antigens are pre‐organized ligands for hGal‐3, and that restriction of the conformational flexibility by the branched fucose (Fuc) residue modulates the thermodynamics and kinetics of the binding process. These results highlight the importance of glycan flexibility and provide inspiration for the design of high‐affinity ligands as antagonists for lectins.

High-resolution crystal structures and STD NMR mapping of human ABO(H) blood group glycosyltransferases in complex with trisaccharide reaction products suggest a molecular basis for product release

The human ABO(H) blood group A- and B-synthesizing glycosyltransferases GTA and GTB have been structurally characterized to high resolution in complex with their respective trisaccharide antigen products. These findings are particularly timely and relevant given the dearth of glycosyltransferase structures collected in complex with their saccharide reaction products. GTA and GTB utilize the same acceptor substrates, oligosaccharides terminating with α-l-Fucp-(1→2)-β-d-Galp-OR (where R is a glycolipid or glycoprotein), but use distinct UDP donor sugars, UDP-N-acetylgalactosamine and UDP-galactose, to generate the blood group A (α-l-Fucp-(1→2)[α-d-GalNAcp-(1→3)]-β-d-Galp-OR) and blood group B (α-l-Fucp-(1→2)[α-d-Galp-(1→3)]-β-d-Galp-OR) determinant structures, respectively. Structures of GTA and GTB in complex with their respective trisaccharide products reveal a conflict between the transferred sugar monosaccharide and the β-phosphate of the UDP donor. Mapping of the binding epitopes by saturation transfer difference NMR measurements yielded data consistent with the X-ray structural results. Taken together these data suggest a mechanism of product release where monosaccharide transfer to the H-antigen acceptor induces active site disorder and ejection of the UDP leaving group prior to trisaccharide egress.

Structure Calculation and Reconstruction of Discrete-State Dynamics from Residual Dipolar Couplings

Residual dipolar couplings (RDCs) acquired by nuclear magnetic resonance (NMR) spectroscopy are an indispensable source of information in investigation of molecular structures and dynamics. Here, we present a comprehensive strategy for structure calculation and reconstruction of discrete-state dynamics from RDC data that is based on the singular value decomposition (SVD) method of order tensor estimation. In addition to structure determination, we provide a mechanism of producing an ensemble of conformations for the dynamical regions of a protein from RDC data. The developed methodology has been tested on simulated RDC data with ±1 Hz of error from an 83 residue α protein (PDB ID 1A1Z ) and a 213 residue α/β protein DGCR8 (PDB ID 2YT4 ). In nearly all instances, our method reproduced the structure of the protein including the conformational ensemble to within less than 2 Å. On the basis of our investigations, arc motions with more than 30° of rotation are identified as internal dynamics and are reconstructed with sufficient accuracy. Furthermore, states with relative occupancies above 20% are consistently recognized and reconstructed successfully. Arc motions with a magnitude of 15° or relative occupancy of less than 10% are consistently unrecognizable as dynamical regions within the context of ±1 Hz of error.

Improvements to REDCRAFT: a software tool for simultaneous characterization of protein backbone structure and dynamics from residual dipolar couplings

Within the past two decades, there has been an increase in the acquisition of residual dipolar couplings (RDC) for investigations of biomolecular structures. Their use however is still not as widely adopted as the traditional methods of structure determination by NMR, despite their potential for extending the limits in studies that examine both the structure and dynamics of biomolecules. This is in part due to the difficulties associated with the analysis of this information-rich data type. The software analysis tool REDCRAFT was previously introduced to address some of these challenges. Here we describe and evaluate a number of additional features that have been incorporated in order to extend its computational and analytical capabilities. REDCRAFT's more traditional enhancements integrate a modified steric collision term, as well as structural refinement in the rotamer space. Other, non-traditional improvements include: the filtering of viable structures based on relative order tensor estimates, decimation of the conformational space based on structural similarity, and forward/reverse folding of proteins. Utilizing REDCRAFT's newest features we demonstrate de-novo folding of proteins 1D3Z and 1P7E to within less than 1.6 Å of the corresponding X-ray structures, using as many as four RDCs per residue and as little as two RDCs per residue, in two alignment media. We also show the successful folding of a structure to less than 1.6 Å of the X-ray structure using {C(i-1)-N(i), N(i)-H(i), and C(i-1)-H(i)} RDCs in one alignment medium, and only {N(i)-H(i)} in the second alignment medium (a set of data which can be collected on deuterated samples). The program is available for download from our website at http://ifestos.cse.sc.edu .

Dynafold: a dynamic programming approach to protein backbone structure determination from minimal sets of Residual Dipolar Couplings

Residual Dipolar Couplings (RDCs) are a source of NMR data that can provide a powerful set of constraints on the orientation of inter-nuclear vectors, and are quickly becoming a larger part of the experimental toolset for molecular biologists. However, few reliable protocols exist for the determination of protein backbone structures from small sets of RDCs. DynaFold is a new dynamic programming algorithm designed specifically for this task, using minimal sets of RDCs collected in multiple alignment media. DynaFold was first tested utilizing synthetic data generated for the N--H , C(α)--H(α), and C--N vectors of 1BRF, 1F53, 110M, and 3LAY proteins, with up to ±1 Hz error in three alignment media, and was able to produce structures with less than 1.9 Å of the original structures. DynaFold was then tested using experimental data, obtained from the Biological Magnetic Resonance Bank, for proteins PDBID:1P7E and 1D3Z using RDC data from two alignment media. This exercise yielded structures within 1.0 Å of their respective published structures in segments with high data density, and less than 1.9 Å over the entire protein. The same sets of RDC data were also used in comparisons with traditional methods for analysis of RDCs, which failed to match the accuracy of DynaFold's approach to structure determination.

Enhanced conformational sampling of carbohydrates by Hamiltonian replica-exchange simulation

Knowledge of the structure and conformational flexibility of carbohydrates in an aqueous solvent is important to improving our understanding of how carbohydrates function in biological systems. In this study, we extend a variant of the Hamiltonian replica-exchange molecular dynamics (MD) simulation to improve the conformational sampling of saccharides in an explicit solvent. During the simulations, a biasing potential along the glycosidic-dihedral linkage between the saccharide monomer units in an oligomer is applied at various levels along the replica runs to enable effective transitions between various conformations. One reference replica runs under the control of the original force field. The method was tested on disaccharide structures and further validated on biologically relevant blood group B, Lewis X and Lewis A trisaccharides. The biasing potential-based replica-exchange molecular dynamics (BP-REMD) method provided a significantly improved sampling of relevant conformational states compared with standard continuous MD simulations, with modest computational costs. Thus, the proposed BP-REMD approach adds a new dimension to existing carbohydrate conformational sampling approaches by enhancing conformational sampling in the presence of solvent molecules explicitly at relatively low computational cost.

Advances in the REDCAT software package

Background

Residual Dipolar Couplings (RDCs) have emerged in the past two decades as an informative source of experimental restraints for the study of structure and dynamics of biological macromolecules and complexes. The REDCAT software package was previously introduced for the analysis of molecular structures using RDC data. Here we report additional features that have been included in this software package in order to expand the scope of its analyses. We first discuss the features that enhance REDCATs user-friendly nature, such as the integration of a number of analyses into one single operation and enabling convenient examination of a structural ensemble in order to identify the most suitable structure. We then describe the new features which expand the scope of RDC analyses, performing exercises that utilize both synthetic and experimental data to illustrate and evaluate different features with regard to structure refinement and structure validation.

Results

We establish the seamless interaction that takes place between REDCAT, VMD, and Xplor-NIH in demonstrations that utilize our newly developed REDCAT-VMD and XplorGUI interfaces. These modules enable visualization of RDC analysis results on the molecular structure displayed in VMD and refinement of structures with Xplor-NIH, respectively. We also highlight REDCAT’s Error-Analysis feature in reporting the localized fitness of a structure to RDC data, which provides a more effective means of recognizing local structural anomalies. This allows for structurally sound regions of a molecule to be identified, and for any refinement efforts to be focused solely on locally distorted regions.

Conclusions

The newly engineered REDCAT software package, which is available for download via the WWW from http://ifestos.cse.sc.edu, has been developed in the Object Oriented C++ environment. Our most recent enhancements to REDCAT serve to provide a more complete RDC analysis suite, while also accommodating a more user-friendly experience, and will be of great interest to the community of researchers and developers since it hides the complications of software development.

Typing of blood-group antigens on neutral oligosaccharides by negative-ion electrospray ionization tandem mass spectrometry

Blood-group antigens, such as those containing fucose and bearing the ABO(H)- and Lewis-type determinants expressed on the carbohydrate chains of glycoproteins and glycolipids, and also on unconjugated free oligosaccharides in human milk and other secretions, are associated with various biological functions. We have previously shown the utility of negative-ion electrospay ionization tandem mass spectrometry with collision-induced dissociation (ESI-CID-MS/MS) for typing of Lewis (Le) determinants, for example, Le(a), Le(x), Le(b), and Le(y) on neutral and sialylated oligosaccharide chains. In the present report, we extended the strategy to characterization of blood-group A-, B-, and H-determinants on type 1 and type 2 and also on type 4 globoside chains to provide a high sensitivity method for typing of all the major blood-group antigens, including the A, B, H, Le(a), Le(x), Le(b), and Le(y) determinants, present in oligosaccharides. Using the principles established, we identified two minor unknown oligosaccharide components present in the products of enzymatic synthesis by bacterial fermentation. We also demonstrated that the unique fragmentations derived from the D- and (0,2)A-type cleavages observed in ESI-CID-MS/MS, which are important for assigning blood-group and chain types, only occur under the negative-ion conditions for reducing sugars but not for reduced alditols or under positive-ion conditions.

Constant time INEPT CT-HSQC (CTi-CT-HSQC) - A new NMR method to measure accurate one-bond J and RDCs with strong 1H-1H couplings in natural abundance

Strong (1)H-(1)H coupling can significantly reduce the accuracy of (1)J(CH) measured from frequency differences in coupled HSQC spectra. Although accurate (1)J(CH) values can be extracted from spectral simulation, it would be more convenient if the same accurate (1)J(CH) values can be obtained experimentally. Furthermore, simulations reach their limit for residual dipolar coupling (RDC) measurement, as many significant, but immeasurable RDCs are introduced into the spin system when a molecule is weakly aligned, thus it is impossible to have a model spin system that truly represents the real spin system. Here we report a new J modulated method, constant-time INEPT CT-HSQC (CTi-CT-HSQC), to accurately measure one-bond scalar coupling constant and RDCs without strong coupling interference. In this method, changing the spacing between the two 180° pulses during a constant time INEPT period selectively modulates heteronuclear coupling in quantitative J fashion. Since the INEPT delays for measuring one-bond carbon-proton spectra are short compared to (3)J(HH), evolution due to (strong) (1)H-(1)H coupling is marginal. The resulting curve shape is practically independent of (1)H-(1)H coupling and only correlated to the heteronuclear coupling evolution. Consequently, an accurate (1)J(CH) can be measured even in the presence of strong coupling. We tested this method on N-acetyl-glucosamine and mannose whose apparent isotropic (1)J(CH) values are significantly affected by strong coupling with other methods. Agreement to within 0.5Hz or better is found between (1)J(CH) measured by this method and previously published simulation data. We further examined the strong coupling effects on RDC measurements and observed an error up to 100% for one bond RDCs using coupled HSQC in carbohydrates. We demonstrate that RDCs can be obtained with higher accuracy by CTi-CT-HSQC, which compensates the limitation of simulation method.

Simultaneous structure and dynamics of a membrane protein using REDCRAFT: membrane-bound form of Pf1 coat protein

A strategy for simultaneous study of the structure and internal dynamics of a membrane protein is described using the REDCRAFT algorithm. The membrane-bound form of the Pf1 major coat protein (mbPf1) was used as an example. First, synthetic data is utilized to validate the simultaneous study of structure and dynamics with REDCRAFT using dihedral restraints and backbone N-H RDCs from two different alignments. Subsequently, the validated analysis is applied to experimental data and confirms that REDCRAFT produces meaningful structures from sparse RDC data. Furthermore, simulated data from a two-state jump motion is used to illustrate the necessity for simultaneous consideration of structure and dynamics. Disregarding internal dynamics during the course of structure determination is shown to produce an average-state that is not related to the two intermediate states. During the analysis of RDC data from the dynamic model, REDCRAFT appropriately identifies the region separating the static and dynamic domains of the protein. Finally, analysis of experimental data strongly suggests the existence of internal motion between the amphipathic and the transmembrane helices of the membrane-bound form of the protein. The ability to perform fragmented structure determination of each domain without a priori assumption of the order tensors allows an independent determination of the order tensors, which yields a more comprehensive description of protein structure and dynamics and is particularly relevant to the study of membrane proteins.

Structural assembly of molecular complexes based on residual dipolar couplings

We present and evaluate a rigid-body molecular docking method, called PATIDOCK, that relies solely on the three-dimensional structure of the individual components and the experimentally derived residual dipolar couplings (RDCs) for the complex. We show that, given an accurate ab initio predictor of the alignment tensor from a protein structure, it is possible to accurately assemble a protein-protein complex by utilizing the RDCs' sensitivity to molecular shape to guide the docking. The proposed docking method is robust against experimental errors in the RDCs and computationally efficient. We analyze the accuracy and efficiency of this method using experimental or synthetic RDC data for several proteins, as well as synthetic data for a large variety of protein-protein complexes. We also test our method on two protein systems for which the structure of the complex and steric-alignment data are available (Lys48-linked diubiquitin and a complex of ubiquitin and a ubiquitin-associated domain) and analyze the effect of flexible unstructured tails on the outcome of docking. The results demonstrate that it is fundamentally possible to assemble a protein-protein complex solely on the basis of experimental RDC data and the prediction of the alignment tensor from 3D structures. Thus, despite the purely angular nature of RDCs, they can be converted into intermolecular distance/translational constraints. Additionally, we show a method for combining RDCs with other experimental data, such as ambiguous constraints from interface mapping, to further improve structure characterization of protein complexes.

Improvement and analysis of computational methods for prediction of residual dipolar couplings

We describe a new, computationally efficient method for computing the molecular alignment tensor based on the molecular shape. The increase in speed is achieved by re-expressing the problem as one of numerical integration, rather than a simple uniform sampling (as in the PALES method), and by using a convex hull rather than a detailed representation of the surface of a molecule. This method is applicable to bicelles, PEG/hexanol, and other alignment media that can be modeled by steric restrictions introduced by a planar barrier. This method is used to further explore and compare various representations of protein shape by an equivalent ellipsoid. We also examine the accuracy of the alignment tensor and residual dipolar couplings (RDC) prediction using various ab initio methods. We separately quantify the inaccuracy in RDC prediction caused by the inaccuracy in the orientation and in the magnitude of the alignment tensor, concluding that orientation accuracy is much more important in accurate prediction of RDCs.

Conformational analysis of thioglycoside derivatives of histo-blood group ABH antigens using an ab initio-derived reparameterization of MM4: implications for design of non-hydrolysable mimetics

Histo-blood group ABH antigens serve as recognition sites for infectious microorganisms and tissue lectins in intercellular communication, e.g. in tumor progression. Thus, they are of interest as a starting point for drug design. In this respect, potent non-hydrolysable derivatives such as thioglycosides are of special interest. As prerequisite to enable estimations of ligand properties relative to their natural counterparts, conformational properties of the thioglycosidic derivatives of ABH trisaccharides and their disaccharide units were calculated using systematic and filtered systematic searches with the MM4 force field. Parameters for the glycosidic torsions of thioglycosides were independently derived from ab initio calculations. The resulting energy deviations required a reparameterization of MM4 to a new parameter set called MM4R. The data sets obtained using MM4R reveal that the thioglycosides have somewhat increased levels of flexibility about the major low-energy conformations shared with the corresponding O-glycosides. In the trisaccharides, the thiosubstitution of the Gal[NAc]alpha1-3Gal linkage leads to a preference for a conformation which is the secondary minimum of the natural counterparts. This conformation also generates contacts between the N-acetyl group and the fucose moiety in the blood group A derivative. Calculations further indicate that thiosubstitution of only the Fucalpha1-2Gal linkage does not affect the conformational preferences compared to the natural trisaccharide. Thiosubstitution of both linkages in the trisaccharide results in increased flexibility but the favored conformation of the natural trisaccharides is preferred. The study suggests that thioglycoside derivatives of ABH antigens could have pharmaceutical interest as ligands of lectins and other carbohydrate-binding proteins.

Efficient and accurate estimation of relative order tensors from lambda-maps

The rapid increase in the availability of RDC data from multiple alignment media in recent years has necessitated the development of more sophisticated analyses that extract the RDC data's full information content. This article presents an analysis of the distribution of RDCs from two media (2D-RDC data), using the information obtained from a lambda-map. This article also introduces an efficient algorithm, which leverages these findings to extract the order tensors for each alignment medium using unassigned RDC data in the absence of any structural information. The results of applying this 2D-RDC analysis method to synthetic and experimental data are reported in this article. The relative order tensor estimates obtained from the 2D-RDC analysis are compared to order tensors obtained from the program REDCAT after using assignment and structural information. The final comparisons indicate that the relative order tensors estimated from the unassigned 2D-RDC method very closely match the results from methods that require assignment and structural information. The presented method is successful even in cases with small datasets. The results of analyzing experimental RDC data for the protein 1P7E are presented to demonstrate the potential of the presented work in accurately estimating the principal order parameters from RDC data that incompletely sample the RDC space. In addition to the new algorithm, a discussion of the uniqueness of the solutions is presented; no more than two clusters of distinct solutions have been shown to satisfy each lambda-map.

Stereochemical identification of (R)- and (S)-ibuprofen using residual dipolar couplings, NMR, and modeling

In this work, we describe an NMR-based method that utilizes an orientation media composed of the chiral polypeptide liquid crystal poly-gamma-benzyl-L-glutamate (PBLG) dissolved in CDCl(3), to measure the (1)H-(1)H, (1)H-(13)C and (13)C-(13)C residual dipolar couplings (RDCs) of (R) and (S)-ibuprofen. Calculated RDCs, obtained from the lowest energy conformers, are then compared with the experimentally measured RDCs to predict the stereochemistry of each enantiomer. Excellent agreement between calculated and experimental RDCs was found when the lowest energy structure of each enantiomer, obtained in a simulated PBLG/CDCl(3) environment, was used to back-calculate the RDCs. This method is generally useful for small molecular weight molecules that possess either one or two chiral centers, are soluble in low viscosity organic solvents, and will not crystallize (Clegg, Crystal Structure Analysis. Principles and Practice. New York: Oxford University Press; 2002) or cannot be derivatized with a Mosher's reagent (Dale and Mosher, J Am Chem Soc 1973;95:512-519).

Activity–structure correlations in divergent lectin evolution: fine specificity of chicken galectin CG-14 and computational analysis of flexible ligand docking for CG-14 and the closely related CG-16

Gene duplication and sequence divergence are driving forces toward establishing protein families. To examine how sequence changes affect carbohydrate specificity, the two closely related proto-type chicken galectins CG-14 and CG-16 were selected as models. Binding properties were analyzed using a highly sensitive solid-phase assay. We tested 56 free saccharides and 34 well-defined glycoproteins. The two galectins share preference for the II (Galbeta1-4GlcNAc) versus I (Galbeta1-3GlcNAc) version of beta-galactosides. A pronounced difference is found owing to the reactivity of CG-14 with histo-blood group ABH active oligosaccharides and A/B active glycoproteins. These experimental results prompted to determine activity-structure correlations by modeling. Computational analysis included consideration of the flexibility of binding partners and the presence of water molecules. It provided a comparative description of complete carbohydrate recognition domains, which had so far not been characterized in animal galectins. The structural models assigned II, I selectivity to a region downstream of the central Trp moiety. Docking revealed that the tetrasaccharides can be accommodated in their free-state low-energy conformations. CG-14's preference for A versus B epitopes could be attributed to a contact between His124 and the N-acetyl group of GalNAc. Regarding intergalectin comparison, the Ala53/Cys51 exchange affects the interaction potential of His54/His52. Close inspection of simulated dynamic interplay revealed reorientation of His124 at the site of the His124/Glu123 substitution, with potential impact on ligand dissociation. In summary, this study identifies activity differences and provides information on their relation to structural divergence, epitomizing the value of this combined approach beyond galectins.

Determination of natural abundance 15N-1H and 13C-1H dipolar couplings of molecules in a strongly orienting media using two-dimensional inverse experiments

NMR spectra of molecules oriented in liquid crystals provide homo- and heteronuclear dipolar couplings and thereby the geometry of the molecules. Several inequivalent dilute spins such as 13C and 15N coupled to protons form different coupled spin systems in their natural abundance and appear as satellites in the proton spectra. Identification of transitions belonging to each spin system is essential to determine heteronuclear dipolar couplings, which is a formidable task. In the present study, using 15N-1H and 13C-1H HSQC, and HMQC experiments we have selectively detected spectra of each rare spin coupled to protons. The 15N-1H and 13C-1H dipolar couplings have been determined in the natural abundance of 13C and 15N for the molecules pyrazine, pyrimidine and pyridazine oriented in a thermotropic liquid crystal.

Reconciling solvent effects on rotamer populations in carbohydrates - A joint MD and NMR analysis

The rotational preferences of the hydroxymethyl group in pyranosides is known to depend on the local environment, whether in solid, solution, or gas phase. By combining molecular dynamics (MD) simulations with NMR spectroscopy the rotational preferences for the ω angle in methyl 2,3-di-O-methyl-α-D-glucopyranoside (3) and methyl 2,3-di-O-methyl-α-D-galactopyranoside (6) in a variety of solvents, with polarities ranging from 80 to 2.3 D have been determined. The effects of solvent polarity on intramolecular hydrogen bonding have been identified and quantified. In water, the internal hydrogen bonding networks are disrupted by competition with hydrogen bonds to the solvent. When the internal hydrogen bonds are differentially disrupted, the rotamer populations associated with the ω angle may be altered. In the case of 3 in water, the preferential disruption of the interaction between HO6 and O4 destabilizes the tg rotamer, leading to the observed preference for gauche rotamers. Without the hydrogen bond enhancement offered by a low polarity environment, both 3 and 6 display rotamer populations that are consistent with expectations based on the minimization of repulsive intramolecular oxygen-oxygen interactions. In a low polarity environment, HO6 prefers to interact with O4, however, in water these interactions are markedly weakened, indicating that HO6 acts as a hydrogen bond donor to water.

Two different O-polysaccharides from Escherichia coli O86 are produced by different polymerization of the same O-repeating unit

The structure of a new O-polysaccharide from Escherichia coli O86:K62:B7 was determined using NMR and methylation analysis. The structure is as follows: [carbohydrate: see text]. Comparison with the previously published structure from E. coli O86:K2:H2 revealed that the O-polysaccharides from these two E. coli O86 serotypes share the same branched pentasaccharide repeating unit. However, they differ in the anomeric configuration of the linkage, the linkage position, and the identity of the residue through which polymerization occurs. The immunochemical activity of these two forms of LPS toward anti-B antibody was studied and compared. The results showed that LPS from E. coli O86:K2:H2 strain possesses higher blood group B reactivity. The immunoreactivity difference was explained by modeling of the O-repeating unit tetrasaccharide fragments. This finding provides a good system for the further study of O-polysaccharide biosynthesis especially the repeating unit polymerization mechanism.

Prediction of charge-induced molecular alignment: residual dipolar couplings at pH 3 and alignment in surfactant liquid crystalline phases

Recently we reported that the alignment tensor of a biological macromolecule, which was dissolved in a dilute suspension of highly negatively charged filamentous phage at close to neutral pH, can be predicted from the molecule's 3D charge distribution and shape (Zweckstetter et al. 2004). Here it is demonstrated that this approach is also applicable to alignment of proteins in liquid crystalline phases formed by filamentous phage at low pH. Residual dipolar couplings (RDCs) predicted by our simple electrostatic model for the B1 domain of protein G in fd phage at pH 3 fit very well with the experimental values. The sign of charge-shape predicted one-bond (1)H-(15)N dipolar couplings for the B1 domain of protein G (GB1) was inverted at pH 3 compared to neutral pH, in agreement with experimental observations. Our predictions indicate that this is a feature specific for GB1. In addition, it is shown that RDCs induced in the protein ubiquitin by the presence of a positively charged surfactant system comprising cetylpyridinium bromide/hexanol/sodium bromide can be predicted accurately by a simple electrostatic alignment model. This shows that steric and electrostatic interactions dominate weak alignment of biomolecules for a wide range of pH values both in filamentous phage and in surfactant liquid crystalline phases.

Simultaneous determination of 1H-1H and 1H-13C residual dipolar couplings in a chiral liquid crystal solvent using a natural abundance HSQC experiment

A high-resolution, phase-sensitive, natural abundance F2-coupled 1H-13C HSQC (F2HSQC) NMR experiment was developed to measure simultaneously both (n)D(HH) and 1D(CH) residual dipolar couplings (RDCs) of small molecules present in a chiral polypeptide liquid crystal solvent system composed of poly-gamma-benzyl-L-glutamate (PBLG) in CDCl3. Because this is an indirect-detection NMR experiment, the relatively small amount of sample (7.5 mg in this study) and short acquisition times (5 h) that are required make this HSQC experiment well suited for samples that are either limited in solubility or in quantity or require short analysis times. The F2HSQC experiment can be performed without any specialized equipment or sample modification and can enhance our ability to measure RDCs accurately and rapidly in polypeptide liquid crystal solvents.

Orientational Properties of Stretched Polystyrene Gels in Organic Solvents and the Suppression of Their Residual 1H NMR Signals

While residual dipolar couplings (RDCs) are an established method in high-resolution biomolecular NMR, their use for structure determination of small molecules in organic solvents is limited by the alignment media available. Only recently stretched polystyrene (PS) gels were introduced for the measurement of RDCs on small compounds that allowed urgently needed free scalability of the induced anisotropy. Here, the properties of such stretched PS gels in different organic solvents as well as for different magnetic field strengths and temperatures are studied and practical NMR-spectroscopic aspects are discussed.

Design of the blood group AB glycotope

Although the nature of the blood groups A and B has been comprehensively studied for a long time, it is still unclear as to what exactly is the epitope that is recognized by antibodies having AB specificity, i.e. monoclonal and polyclonal antibodies which are capable of interacting equally well with the antigens GalNAcalpha 1-3(Fucalpha 1-2)Gal (A trisaccharide) and Galalpha 1-3(Fucalpha 1-2)Gal (B trisaccharide), but do not react with their common fragment Fucalpha 1-2Gal. We have supposed that besides Fucalpha 1-2Gal, A and B antigens have one more shared epitope. The trisaccharides A and B are practically identical from the conformational point of view, the only difference being situated at position 2 of Galalpha residue, i.e. trisaccharide A has a NHAc group, whereas trisaccharide B has a hydroxyl group (see formulas). We have hypothesized that the AB-epitope should be situated in the part of the molecule that is opposite to the NHAc group of GalNAc residue. In order to test this hypothesis we have synthesized a polymeric conjugate in such a way that de-N-acetylated A-trisaccharide is attached to a polymer via the nitrogen in position C-2 of the galactosamine residue. In this conjugate the supposed AB-epitope should be maximally accessible for antibodies from the solution, whereas the discrimination site of antigens A and B by the antibodies should be maximally hidden due to the close proximity of the polymer. Interaction with several anti-AB monoclonal antibodies revealed that a part of them really interacted with the synthetic AB-glycotope, thus confirming our hypothesis. Moreover, similar antibodies were revealed in the blood of healthy blood group 0 donors. Analysis of spatial models was performed in addition to identify the hydroxyl groups of Fuc, Galalpha, and Galbeta residues, which are particularly involved in the composition of the AB-glycotope.

Prediction of charge-induced molecular alignment of biomolecules dissolved in dilute liquid-crystalline phases

Alignment of macromolecules in nearly neutral aqueous lyotropic liquid-crystalline media such as bicelles, commonly used in macromolecular NMR studies, can be predicted accurately by a steric obstruction model (Zweckstetter and Bax, 2000). A simple extension of this model is described that results in improved predictions for both the alignment orientation and magnitude of protein and DNA solutes in charged nematic media, such as the widely used medium of filamentous phage Pf1. The extended model approximates the electrostatic interaction between a solute and an ordered phage particle as that between the solute's surface charges and the electric field of the phage. The model is evaluated for four different proteins and a DNA oligomer. Results indicate that alignment in charged nematic media is a function not only of the solute's shape, but also of its electric multipole moments of net charge, dipole, and quadrupole. The relative importance of these terms varies greatly from one macromolecule to another, and evaluation of the experimental data indicates that these terms scale differently with ionic strength. For several of the proteins, the calculated alignment is sensitive to the precise position of the charged groups on the protein surface. This suggests that NMR alignment measurements can potentially be used to probe protein electrostatics. Inclusion of electrostatic interactions in addition to steric effects makes the extended model applicable to all liquid crystals used in biological NMR to date.

Application of residual dipolar couplings in organic compounds

Residual dipolar couplings (RDCs) induced by anisotropic media are a powerful tool for the structure determination of biomolecules through NMR spectroscopy. Recent advances have proven it to be a valuable tool for determination of the stereochemistry of organic molecules. By simple inspection or order matrix calculations, RDCs provide unambiguous information about the relative configurations or complete stereochemistry of organic compounds.

A clostridial endo-beta-galactosidase that cleaves both blood group A and B glycotopes: the first member of a new glycoside hydrolase family, GH98

We have isolated an endo-beta-galactosidase designated E-ABase from Clostridium perfringens ATCC 10543 capable of liberating both the A trisaccharide (A-Tri; GalNAcalpha1-->3(Fucalpha1-->2)Gal) and B trisaccharide (B-Tri; Galalpha1-->3(Fucalpha1-->2)Gal) from glycoconjugates containing blood group A and B glycotopes, respectively. We have subsequently cloned the gene (eabC) that encodes E-ABase from this organism. This gene was found to be identical to the CPE0329 gene of C. perfringens strain 13, whose product was labeled as a hypothetical protein (Shimizu, T., Ohtani, K., Hirakawa, H., Ohshima, K., Yamashita, A., Shiba, T., Ogasawara, N., Hattori, M., Kuhara, S., and Hayashi, H. (2002) Proc. Natl. Acad. Sci. U. S. A. 99, 996-1001). Since the amino acid sequence of E-ABase does not bear detectable similarity to any of the 97 existing families of glycoside hydrolases, we have proposed to assign this unusual enzyme to a new family, GH98. We also expressed eabC in Escherichia coli BL21(DE3) and obtained 27 mg of fully active recombinant E-ABase from 1 liter of culture. Recombinant E-ABase not only destroyed the blood group A and B antigenicity of human type A and B erythrocytes, but also released A-Tri and B-Tri from blood group A(+)- and B(+)- containing glycoconjugates. The structures of A-Tri and B-Tri liberated from A(+) porcine gastric mucin and B(+) human ovarian cyst glycoprotein were established by NMR spectroscopy. The unique specificity of E-ABase should make it useful for studying the structure and function of blood group A- and B-containing glycoconju-gates as well as for identifying other glycosidases belonging to the new GH98 family.

Structure and disorder in the ribonuclease S-peptide probed by NMR residual dipolar couplings

NMR residual dipolar couplings for the S-peptide of ribonuclease A aligned in C8E5/n-octanol liquid crystals are consistent with the presence of a native-like alpha-helix structure undergoing dynamic fraying. Residues 3-13, which correspond to the first alpha-helix of ribonuclease A, show couplings that become more negative at low temperature and in the presence of salt, conditions which stabilize alpha-helical structure in the S-peptide. By contrast, dipolar couplings from the N and C termini of the peptide are close to zero and remain nearly invariant with changes in solution conditions. Torsion angle dynamics simulations using a gradient of dihedral restraint bounds that increase from the center to the ends of the peptide reproduce the experimentally observed sequence dependence of dipolar couplings. The magnitudes of residual dipolar couplings depend on the anisotropy of the solute. Native proteins often achieve nearly spherical shapes due to the hydrophobic effect. Embryonic partially folded structures such as the S-peptide alpha-helix have an intrinsically greater potential for anisotropy that can result in sizable residual dipolar couplings in the absence of long-range structure.

REDCAT: a residual dipolar coupling analysis tool

Recent advancements in the utilization of residual dipolar couplings (RDCs) as a means of structure validation and elucidation have demonstrated the need for, not only a more user friendly, but also a more powerful RDC analysis tool. In this paper, we introduce a software package named REsidual Dipolar Coupling Analysis Tool (REDCAT) designed to address the above issues. REDCAT is a user-friendly program with its graphical-user-interface developed in Tcl/Tk, which is highly portable. Furthermore, the computational engine behind this GUI is written in C/C++ and its computational performance is therefore excellent. The modular implementation of REDCAT's algorithms, with separation of the computational engine from the graphical engine allows for flexible and easy command line interaction. This feature can be utilized for the design of automated data analysis sessions. Furthermore, this software package is portable to Linux clusters for high throughput applications. In addition to basic utilities to solve for order tensors and back calculate couplings from a given order tensor and proposed structure, a number of improved algorithms have been incorporated. These include the proper sampling of the Null-space (when the system of linear equations is under-determined), more sophisticated filters for invalid order-tensor identification, error analysis for the identification of the problematic measurements and simulation of the effects of dynamic averaging processes.

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.

A novel method for the determination of stereochemistry in six-membered chairlike rings using residual dipolar couplings

A novel method for the determination of the relative stereochemistry of six-membered chairlike ring molecules by residual dipolar couplings is presented. C-H residual dipolar couplings were used to investigate the relative stereochemistry of 4,6-O-ethylidene-d-glucopyranose. For this and similar systems it is not necessary to acquire redundant dipolar couplings and to calculate the orientation order tensor. The presented methodology is a paradigmatic leap for the determination of the relative stereochemistry or remote stereochemistry in this kind of fused ring system. Residual dipolar coupling data were collected by 1D and 2D direct-measurement heteronuclear multiple quantum coherence (HMQC) spectroscopy. It was demonstrated that direct measurement of HMQC was quick and accurate for small molecules at natural abundance.

Experimental evidence for the existence of non-exo-anomeric conformations in branched oligosaccharides: the neomycin-B case

For the first time in natural O-glycosides, a large amount of non-exo-anomeric conformation is experimentally detected, in solution.