Secondary structure of ?-hydroxydecanoyl thiol ester dehydrase, a 39-kDa protein, derived from H?, C?, C? and CO signal assignments and the Chemical Shift Index: Comparison with the crystal structure

Abstract

Nearly complete backbone 1H, 15N and 13C signal assignments are reported for beta-hydroxydecanoyl thiol ester dehydrase, a 39-kDa homodimer containing 342 amino acids. Although 15N relaxation data show that the protein has a rotational correlation time of 18 ns, assignments were derived from triple-resonance experiments recorded at 500 MHz and pH 6.8, without deuteration. The Chemical Shift Index, CSI, identified two long helices and numerous beta-strands in dehydrase. The CSI predictions are in close agreement with the secondary structure identified in the recently derived crystal structure, particularly when one takes account of the numerous bulges in the beta-strands. The assignment of dehydrase and a large deuterated protein [Yamazaki et al. (1994) J. Am. Chem. Soc., 116, 11655-11666] suggest that assignment of 40-60 kDa proteins is feasible. Hence, further progress in understanding the chemical shift/structure relationship could open the way to determine the structures of such large proteins.

Solution NMR Analyses of the C-type Carbohydrate Recognition Domain of DC-SIGNR Protein Reveal Different Binding Modes for HIV-derived Oligosaccharides and Smaller Glycan Fragments

“…from the average (and thus experience a significant contribution from either chemical exchange or internal motion (53)) and then calculating as described (54). A value for the relaxation-derived c of 10.4 Ϯ 0.4 ns was obtained for the holo-CRD, which is only slightly longer than the expected value of 8.55 ns obtained using the general rule of 0.5 ns c per 1 kDa of molecular mass (53)(54)(55). This deviation from the ideal value is not large enough to infer oligomerization of the CRD, but it may reflect a non-spherical shape of the monomeric protein.…”

NMR studies of the structure and dynamics of peptide E, an endogenous opioid peptide that binds with high affinity to multiple opioid receptor subtypes

“…Secondary structure elements can be quite flexible and m determined from their R 2 /R 1 value may be underestimated. The value of the optimized m calculated here relative to the effective molecular weight is higher than some investigators have reported; for example, in studies of Staphylococcal nuclease, 44 interleukin-1␤, 45 and ␤-hydroxydecanoyl thiol ester dehydrase, 48 the optimized m is generally in the range of 0.5 ns per kDa molecular weight. However, observations similar in magnitude to that reported here for adrenal peptide E have been reported by other investigators.…”

Solution NMR Studies of a 42 KDa Escherichia Coli Maltose Binding Protein/β-Cyclodextrin Complex: Chemical Shift Assignments and Analysis

“…1 This limit was extended approximately 2-fold through the subsequent development of heteronuclear triple resonance NMR methods optimized for application to uniformly 15 N, 13 C-labeled protein samples. 2 Although chemical shift assignments have been obtained for a number of fully protonated 15 N, 13 C-labeled pro-teins larger than 25 kDa, [3][4][5][6] rapid aliphatic 13 C relaxation rates limit the sensitivity, and hence the utility, of many triple resonance methods.…”