Mannose‐Binding Geometry of Pradimicin A

Pradimicins (PRMs) and benanomicins are the only family of non‐peptidic natural products with lectin‐like properties, that is, they recognize D ‐mannopyranoside (Man) in the presence of Ca²⁺ ions. Coupled with their unique Man binding ability, they exhibit antifungal and anti‐HIV activities through binding to Man‐containing glycans of pathogens. Notwithstanding the great potential of PRMs as the lectin mimics and therapeutic leads, their molecular basis of Man recognition has yet to be established. Their aggregate‐forming propensity has impeded conventional interaction analysis in solution, and the analytical difficulty is exacerbated by the existence of two Man binding sites in PRMs. In this work, we investigated the geometry of the primary Man binding of PRM‐A, an original member of PRMs, by the recently developed analytical strategy using the solid aggregate composed of the 1:1 complex of PRM‐A and Man. Evaluation of intermolecular distances by solid‐state NMR spectroscopy revealed that the C2–C4 region of Man is in close contact with the primary binding site of PRM‐A, while the C1 and C6 positions of Man are relatively distant. The binding geometry was further validated by co‐precipitation experiments using deoxy‐Man derivatives, leading to the proposal that PRM‐A binds not only to terminal Man residues at the non‐reducing end of glycans, but also to internal 6‐substituted Man residues. The present study provides new insights into the molecular basis of Man recognition and glycan specificity of PRM‐A.     

Noise reduction by dynamic signal preemphasis

In this work we propose an approach to reduce the digitization noise for a given dynamic range, i.e., the number of bits, of an analog to digital converter used in an NMR receiver. In this approach, the receiver gain is dynamically increased so that the free induction decay is recorded in such an emphasized way that the decaying signal is digitized using as many number of bits as possible, and at the stage of data processing, the original signal profile is restored by applying the apodization that compensates the effect of the preemphasis. This approach, which we call APodization after Receiver gain InCrement during Ongoing sequence with Time (APRICOT), is performed in a solid-state system containing a pair of (13)C spins, one of which is fully isotopically labeled and the other is naturally abundant. It is demonstrated that the exceedingly smaller peak buried in the digitization noise in the conventional approach can be revealed by employing APRICOT.     

Mapping of the primary mannose binding site of pradimicin A

Pradimicin A (PRM-A) is an actinomycete-derived antibiotic with the lectin-like property of being able to recognize D-mannopyranoside (Man) in the presence of Ca(2+) ion. PRM-A and its derivatives have been attracting a great deal of attention as the only family of natural carbohydrate receptors with nonpeptidic skeleton and, more recently, as conceptually novel drug candidates for human immunodeficiency virus (HIV). Despite its scientific interest and potential therapeutic importance, understanding how PRM-A recognizes Man has been severely limited. Conventional interaction analysis of PRM-A with Man in solution has been frustrated by aggregation of PRM-A and the three-component equilibrium consisting of the [PRM-A(2)/Ca(2+)], [PRM-A(2)/Ca(2+)/Man(2)], [PRM-A(2)/Ca(2+)/Man(4)] complexes, and their mixed oligomers. In this Article, we demonstrate the interaction analysis of PRM-A with methyl α-D-mannopyranoside (Man-OMe) in the solid state, which benefits from aggregate-forming propensity of PRM-A and eliminates the problem associated with the complicated equilibrium in solution. Isothermal titration calorimetry (ITC) analysis and coprecipitation experiments revealed that the primary Man binding of PRM-A is markedly tighter than the secondary one, leading to preparation of the solid aggregate solely composed of the [PRM-A(2)/Ca(2+)/Man-OMe(2)] complex. The simple 1:1 complexes of biosynthetically (13)C-enriched PRM-As and [(13)C(6)]Man-OMe facilitated the analysis of the primary Man binding of PRM-A by two-dimensional dipolar-assisted rotational resonance (2D-DARR), which clearly identified that the cavity consisted of D-alanine moiety and ABC rings of PRM-A is the Man binding site. Interestingly, the proposed Man binding site of PRM-A seems to resemble the typical architecture of artificial carbohydrate receptors.     

Compensation of effect of field instability by reference deconvolution with phase reconstruction

A compensation method based on reference deconvolution is developed to obtain high-resolution NMR spectra under an unstable magnetic field. It is shown that the applicability of the original deconvolution method is limited for small fluctuation, and a process what may be called phase reconstruction is proposed to compensate large field fluctuation. We demonstrate the method using a probe with a coil that can generate a fluctuation field artificially. A high-resolution 1H NMR spectrum of ethylbenzene was obtained under the unstable field after compensation with this method.     

Inhomogeneous NMR line shape as a probe of microscopic organization of bicontinuous cubic phases

NMR line shapes of the lipid and aqueous species in bicontinuous cubic phase (BCP) samples prepared by centrifugation are inhomogeneously broadened. The broadening of the lipid peaks is removed by magic-angle spinning (MAS). In this work, we studied the mechanism of this broadening using (1)H and (13)C NMR spectroscopy of a myverol/water BCP. It is demonstrated that the inhomogeneity possesses an intrinsic contribution that is independent of instrumental or setup factors and can be attributed to the microscopic organization of the BCP bilayer. A mechanism of the inhomogeneous broadening is proposed, which involves a spatially nonuniform diamagnetically induced magnetic field determined by the mesoscopic structure and the diamagnetic susceptibilities of the two BCP domains. The proposed mechanism does not require that molecular reorientation of the lipid be slow for the inhomogeneous broadening to survive. We discuss how this inhomogeneous broadening can be employed as a probe of compositional uniformity and microscopic organization of BCP samples.     

C–H dipolar recoupling under very fast magic-angle spinning using virtual pulses

A new solid-state NMR pulse sequence for recoupling ¹³C–¹H dipolar interactions under magic-angle spinning is proposed, which works under a spinning speed of a few to several tens kilohertz. The sequence is composed of two different frequency switched Lee–Goldburg sequences, and the modulation of the spin part of the ¹³C–¹H dipolar interaction is introduced by a virtual pulse sequence consisting of unitary operators connecting the rotating frame and the tilted rotating frame. When the cycle time of the spinning is equal to or twice the cycle time of the sequence, the ¹³C–¹H dipolar interactions can be recoupled. The sequence is insensitive to experimental imperfections such as rf inhomogeneity or frequency offset, and the resulting lineshape can be represented by a simple analytical equation based on the zeroth-order average Hamiltonian. Experimental results for [2-¹³C] -valine·HCl are reported.