The principles and parameters to consider when choosing an NMR probe for analysis of a volume- or mass-limited sample are identified and discussed. In particular, a capillary-based microflow probe is described which has a mass sensitivity comparable to cryoprobes (observe volume approximately 40 microL), but with several distinct advantages. The microflow probe has a flowcell volume of 5 microL and an observe volume of 1.5 microL and is equipped with proton and carbon observe channels, deuterium lock, and z-gradient capability. The entire flow path is fused silica; inlet and outlet capillary inner diameters are 50 microm to minimize sample dispersion, making it well-suited to volume-limited samples. An injected sample of 1 nmol of sucrose (0.34 microg in 3 microL, 0.33 mM; MW = 342 g/mol) yields a 1D proton spectrum in 10 min on a spectrometer of 500 MHz or higher. In another example, 15 microg of sucrose (in 3 microL; 15 mM, 45 nmol) is injected and parked in the probe to yield a heteronuclear multiple-quantum coherence (HMQC) spectrum in less than 15 h. The natural product muristerone A (75 microg in 3 microL, 50 mM, 150 nmol; MW = 497 g/mol) was delivered to the flow cell, and a gradient correlation spectroscopy spectrum was acquired in 7 min, a gradient HMQC in 4 h, and a gradient heteronuclear multiple-bond correlation in 11 h. Four basic modes of sample injection into the probe vary in degree of user intervention, speed, solvent consumption, and sample delivery efficiency. Manual, manual-assisted (employing a micropump), automated (using an autosampler), and capillary HPLC modes of operation are described.
The solution structure of Fe(II) cytochrome c551 from Pseudomonas aeruginosa based on 2D 1H NMR data is reported. Two sets of structure calculations were completed with a combination of simulated annealing and distance geometry calculations: one set of 20 structures included the heme-peptide covalent linkages, and one set of 10 structures excluded them. The main-chain atoms were well constrained within the two structural ensembles (1.30 and 1.35 A average RMSD, respectively) except for two regions spanning residues 30-40 and 60-70. The results were essentially the same when global fold comparisons were made between the ensembles with an average RMSD of 1.33 A. In total, 556 constraints were used, including 479 NOEs, 53 volume constraints, and 24 other distances. This report represents the first solution structure determination of a heme protein by 2D 1H NMR and should provide a basis for the application of these techniques to other proteins containing large prosthetic groups or cofactors.
The 21-amino acid peptides siamycin II (BMY-29303) and siamycin I (BMY-29304), derived from Streptomyces strains AA3891 and AA6532, respectively, have been found to inhibit HIV-1 fusion and viral replication in cell culture. The primary sequence of siamycin II is CLGIGSCNDFAGCGYAIVCFW. Siamycin I differs by only one amino acid; it has a valine residue at position 4. In both peptides, disulfide bonds link Cys1 with Cys13 and Cys7 with Cys19, and the side chain of Asp9 forms an amide bond with the N-terminus. Siamycin II, when dissolved in a 50:50 mixture of DMSO and H2O, yields NOESY spectra with exceptional numbers of cross peaks for a peptide of this size. We have used 335 NOE distance constraints and 13 dihedral angle constraints to generate an ensemble of 30 siamycin II structures; these have average backbone atom and all heavy atom rmsd values to the mean coordinates of 0.24 and 0.52 A, respectively. The peptide displays an unusual wedge-shaped structure, with one face being predominantly hydrophobic and the other being predominantly hydrophilic. Chemical shift and NOE data show that the siamycin I structure is essentially identical to siamycin II. These peptides may act by preventing oligomerization of the HIV transmembrane glycoprotein gp41, or by interfering with interactions between gp41 and the envelope glycoprotein gp120, the cell membrane or membrane-bound proteins [Frèchet, D. et al. (1994) Biochemistry, 33, 42-50]. The amphipathic nature of siamycin II and siamycin I suggests that a polar (or apolar) site on the target protein may be masked by the apolar (or polar) face of the peptide upon peptide/protein complexation.
Wehave previously reported on the preparation and initial characterization of the structure and biological activity of siamycins I and II1}. Here, we report on the novel strategy used to rapidly determine the primary, secondary and preliminary solution structure of siamycin I using a multidisciplinary approach that utilized primarily MSand NMRdata. The presence of three internal covalent cross-linkages found in siamycin I made structure analysis by traditional methods difficult, particularly in the TV-terminal region.Lowresolution full scan and product ion mass spectra were acquired on a Sciex API /// tandem quadrupole mass spectrometer equipped with an Ionspray (pneumatically assisted electrospray) interface. Samples were analyzed in the flow injection mode using a 0.1% trifluoroacetic acid in methanol mobile phase at a flow rate of 60/d/minute. The ionspray tip was operated at +5300V. Full scan mass spectra were obtained using an orifice voltage of 75 eV while scanning from m/z 800 to 2250 with a step size of 0.4D and a dwell time of 1.5msec. Product ion spectra were obtained from collision induced dissociation (CID) with an argon collision gas at 450x 1012atoms/cm2 and a collision energy of 65 eV. NMRdata were collected on a Varian Unity 500 spectrometer and processed on a SiliconGraphics Crimson workstation using Felix (Biosym).Spectra were collected on a 3.5mMsample of siamycin I in 99% DMSO-J6. Double quantum filtered COSY spectra (DQF-COSY)2), 2D total correlation spectra (TOCSY)3) and NOESY4) two-dimensional XH NMR datasets were collected with 512 tx values and 2K complex t2 data points using the hyercomplex method for frequency discrimination in col 5). Crosspeak intensities were measured by counting contours on a 500ms
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
hi@scite.ai
10624 S. Eastern Ave., Ste. A-614
Henderson, NV 89052, USA
Copyright © 2024 scite LLC. All rights reserved.
Made with 💙 for researchers
Part of the Research Solutions Family.