Derivation of the Bound-State Conformation of a Ligand in a Weakly Aligned Ligand−Protein Complex

Exploiting Uniformly 13C-Labeled Carbohydrates for Probing Carbohydrate-Protein Interactions by NMR Spectroscopy

NMR of a uniformly ¹³C-labeled carbohydrate was used to elucidate the atomic details of a sugar-protein complex. The structure of the ¹³C-labeled Manα(1-2)Manα(1-2)ManαOMe trisaccharide ligand, when bound to cyanovirin-N (CV-N), was characterized and revealed that in the complex the glycosidic linkage torsion angles between the two reducing-end mannoses are different from the free trisaccharide. Distances within the carbohydrate were employed for conformational analysis, and NOE-based distance mapping between sugar and protein revealed that Manα(1-2)Manα(1-2)ManαOMe is bound more intimately with its two reducing-end mannoses into the domain A binding site of CV-N than with the nonreducing end unit. Taking advantage of the ¹³C spectral dispersion of ¹³C-labeled carbohydrates in isotope-filtered experiments is a versatile means for a simultaneous mapping of the binding interactions on both, the carbohydrate and the protein.

A conformational study of N-acetyl glucosamine derivatives utilizing residual dipolar couplings

The conformational analyses of six non-rigid N-acetyl glucosamine (NAG) derivatives employing residual dipolar couplings (RDCs) and NOEs together with molecular dynamics (MD) simulations are presented. Due to internal dynamics we had to consider different conformer ratios existing in solution. The good quality of the correlation between theoretically and experimentally obtained RDCs show the correctness of the calculated conformers even if the ratios derived from the MD simulations do not exactly meet the experimental data. If possible, the results were compared to former published data and commented.

Kinetic analyses of bindings of Shiga-like toxin to clustered and dispersed Gb3 glyco-arrays on a quartz-crystal microbalance

One-, two-, four-, and eight-branched globotriaosyl saccharides (Gb(3): Gal-alpha1,4-Gal-beta1,4-Glc), whose reducing ends were biotinylated, were prepared (1Gb(3)-bio, 2Gb(3)-bio, 4Gb(3)-bio, and 8Gb(3)-bio, respectively). They are dispersively immobilized as a glyco-array in the matrix of biotinylated maltotriose (Glc(3)-bio) on a streptavidin-covered 27 MHz quartz-crystal microbalance (QCM). The binding kinetics of the verotoxin B subunit (VTB) to various branched Gb(3)-bio ligands in the Glc(3)-bio matrix could be obtained from frequency decreases (mass increases) of the QCM. VTB can recognize the Gb(3) unit but not the Glc(3) unit, where VTB is a pentamer having five binding sites for one Gb(3) unit per each B subunit (having a total of 15 binding sites for Gb(3)). By changing the Gb(3) multivalency, the Gb(3) packing density, and the Gb(3) cluster size in the Glc(3) matrix, association constants (K(a)), maximum amounts bound (Delta m(max)), and binding and dissociation rate constants (k(on) and k(off)) were obtained. When 15 sites of VTB were recognized by 16 Gb(3) units, K(a) was 100 times larger than that when 15 sites of VTB were recognized by only 2 Gb(3) units, with a 6-fold-larger k(on) and a 25-fold-smaller k(off). When the Gb(3) multivalency was changed by covering with two 1Gb(3)-bio, 2Gb(3)-bio, 4Gb(3)-bio, or 8Gb(3)-bio ligands on two pockets of one streptavidin, the K(a) values increased with increasing branch number from one to eight. When the Gb(3) cluster size was changed from eight 1Gb(3)-bio units to one 8Gb(3)-bio unit in the matrix, the K(a) values increased but the Delta m(max) values decreased with increasing cluster size from eight 1Gb(3)-bio units to one 8Gb(3)-bio unit. This is the first example of systematically obtaining all kinetic parameters of sugar-binding proteins to sugars on a glyco-array by changing the sugar multivalency, the sugar packing density, and the sugar cluster size in the matrix.

Solution NMR structure of putidaredoxin-cytochrome P450cam complex via a combined residual dipolar coupling-spin labeling approach suggests a role for Trp106 of putidaredoxin in complex formation

The 58-kDa complex formed between the [2Fe-2S] ferredoxin, putidaredoxin (Pdx), and cytochrome P450cam (CYP101) from the bacterium Pseudomonas putida has been investigated by high-resolution solution NMR spectroscopy. Pdx serves as both the physiological reductant and effector for CYP101 in the enzymatic reaction involving conversion of substrate camphor to 5-exo-hydroxycamphor. In order to obtain an experimental structure for the oxidized Pdx-CYP101 complex, a combined approach using orientational data on the two proteins derived from residual dipolar couplings and distance restraints from site-specific spin labeling of Pdx has been applied. Spectral changes for residues in and near the paramagnetic metal cluster region of Pdx in complex with CYP101 have also been mapped for the first time using (15)N and (13)C NMR spectroscopy, leading to direct identification of the residues strongly affected by CYP101 binding. The new NMR structure of the Pdx-CYP101 complex agrees well with results from previous mutagenesis and biophysical studies involving residues at the binding interface such as formation of a salt bridge between Asp38 of Pdx and Arg112 of CYP101, while at the same time identifying key features different from those of earlier modeling studies. Analysis of the binding interface of the complex reveals that the side chain of Trp106, the C-terminal residue of Pdx and critical for binding to CYP101, is located across from the heme-binding loop of CYP101 and forms non-polar contacts with several residues in the vicinity of the heme group on CYP101, pointing to a potentially important role in complex formation.

Structure determination of a Galectin-3-carbohydrate complex using paramagnetism-based NMR constraints

The determination of the location and conformation of a natural ligand bound to a protein receptor is often a first step in the rational design of molecules that can modulate receptor function. NMR observables, including NOEs, often provide the basis for these determinations. However, when ligands are carbohydrates, interactions mediated by extensive hydrogen-bonding networks often reduce or eliminate NOEs between ligand and protein protons. In these cases, it is useful to look to other distance- and orientation-dependent observables that can constrain the geometry of ligand-protein complexes. Here we illustrate the use of paramagnetism-based NMR constraints, including pseudo-contact shifts (PCS) and field-induced residual dipolar couplings (RDCs). When a paramagnetic center can be attached to the protein, field-induced RDCs and PCS reflect only bound-state properties of the ligand, even when averages over small fractions of bound states and large fractions of free states are observed. The effects can also be observed over a long range, making it possible to attach a paramagnetic center to a remote part of the protein. The system studied here is a Galectin-3-lactose complex. A lanthanide-binding peptide showing minimal flexibility with respect to the protein was integrated into the C terminus of an expression construct for the Galectin-3-carbohydrate-binding domain. Dysprosium ion, which has a large magnetic susceptibility anisotropy, was complexed to the peptide, making it possible to observe both PCSs and field-induced RDCs for the protein and the ligand. The structure determined from these constraints shows agreement with a crystal structure of a Galectin-3-N-acetyllactosamine complex.

Bound-state residual dipolar couplings for rapidly exchanging ligands of His-tagged proteins

The study of bound-state conformations of ligands interacting with proteins is important to the understanding of protein function and the design of drugs that alter function. Traditionally, transferred nuclear Overhauser effects (trNOEs), measured from NMR spectra of ligands in rapid exchange between bound and free states, have been used in these studies, owing to the inherent heavy weighting of bound-state data in the averaged ligand signals. In principle, residual dipolar couplings (RDCs) provide a useful complement to NOE data in that they provide orientational constraints as opposed to distance constraints, but use in ligand-binding applications has been limited due to the absence of heavy weighting of bound-state data. A widely applicable approach to increasing the weighting of bound-state data in averaged RDCs measured on ligands is presented. The approach rests on association of a His-tagged protein with a nickel-chelate-carrying lipid inserted into the lipid bilayer-like alignment media used in the acquisition of RDCs. The approach is validated through the observation of bound-state RDCs for the disaccharide, lactose, bound to the carbohydrate recognition domain of the mammalian lectin, galectin-3.

NMR spectroscopic characterization of the membrane affinity of polyols

Residual dipolar couplings (RDCs) are applied here for the analysis of weak, transient binding events between phosphatidylcholine bilayers and polyols. Large signal responses are observed even for low percentages of 'ligand-receptor complexes', making RDCs a sensitive tool for the analysis of molecular recognition events. The different degree of alignment in solution can be compared as a result of the calculation of the alignment tensor elements. By varying polarity and/or charge of the molecules under investigation, nonspecific hydrophobic effects can be excluded.

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.

Structural characterization of a mannose-binding protein-trimannoside complex using residual dipolar couplings

The ligand-binding properties of a 53 kDa homomultimeric trimer from mannose-binding protein (MBP) have been investigated using residual dipolar couplings (RDCs) that are easily measured from NMR spectra of the ligand and isotopically labeled protein. Using a limited set of 1H-15N backbone amide NMR assignments for MBP and orientational information derived from the RDC measurements in aligned media, an order tensor for MBP has been determined that is consistent with symmetry-based predictions of an axially symmetric system. 13C-1H couplings for a bound trisaccharide ligand, methyl 3,6-di-O-(alpha-D-mannopyranosyl)-alpha-D-mannopyranoside (trimannoside) have been determined at natural abundance and used as orientational constraints. The bound ligand geometry and orientational constraints allowed docking of the trimannoside ligand in the binding site of MBP to produce a structural model for MBP-oligosaccharide interactions.

Partial alignment of biomolecules: an aid to NMR characterization

Partial alignment of biomolecules in solution has added a new dimension to structural investigation by high-resolution NMR methods. Applications to proteins, nucleic acids and carbohydrates now abound. Limitations initially associated with compatibility of biomolecules with the liquid-crystal media commonly used to achieve alignment have begun to disappear. This is, in part, a result of the introduction of a wide variety of new media. Future applications to biologically important problems such as the structural organization of multi-domain proteins and multi-protein assemblies look very promising.

Free and protein-bound carbohydrate structures

Several areas of research in the study of the structure and dynamics of free and protein-bound carbohydrates have experienced considerable advances during the past year. These include the application of state-of-the-art NMR techniques using (13)C-labeled sugars to obtain conformational information, the full structural characterization of several saccharides that either form part of glycoproteins or form noncovalent complexes, both in solution and in the solid state, the description of several enzyme-carbohydrate complexes at the atomic level and last, but not least, the development and analysis of calculation protocols to predict the dynamical and conformational behavior of oligosaccharides.