Complete 1H, 13C and 15N NMR assignments and secondary structure of the 269-residue serine protease PB92 from Bacillus alcalophilus

Summary The ¹H, ¹³C and ¹⁵N NMR resonances of serine protease PB92 have been assigned using 3D tripleresonance NMR techniques. With a molecular weight of 27 kDa (269 residues) this protein is one of the largest monomeric proteins assigned so far. The side-chain assignments were based mainly on 3D H(C)CH and 3D (H)CCH COSY and TOCSY experiments. The set of assignments encompasses all backbone carbonyl and CH_n carbons, all amide (NH and NH₂) nitrogens and 99.2% of the amide and CH_n protons. The secondary structure and general topology appear to be identical to those found in the crystal structure of serine protease PB92 [Van der Laan et al. (1992) Protein Eng., 5, 405–411], as judged by chemical shift deviations from random coil values, NH exchange data and analysis of NOEs between backbone NH groups.Abbreviations 2D/3D/4D two-/three-/four-dimensional - HSQC heteronuclear single-quantum coherence - HMQC heteronuclear multiple-quantum coherence - COSY correlation spectroscopy - TOCSY total correlation spectroscopy - NOE nuclear Overhauser enhancement (connectivity) - NOESY 2D NOE spectroscopy Experiment nomenclature (H(C)CH, etc.) follows the conventions used elsewhere [e.g. Ikura et al. (1990) Biochemistry, 29, 4659–4667].     

A suite of Mathematica notebooks for the analysis of protein main chain 15N NMR relaxation data

A suite of Mathematica notebooks has been designed to ease the analysis of protein main chain ¹⁵N NMR relaxation data collected at a single magnetic field strength. Individual notebooks were developed to perform the following tasks: nonlinear fitting of ¹⁵N-T ₁ and -T ₂ relaxation decays to a two parameter exponential decay, calculation of the principal components of the inertia tensor from protein structural coordinates, nonlinear optimization of the principal components and orientation of the axially symmetric rotational diffusion tensor, model-free analysis of ¹⁵N-T ₁, -T ₂, and {¹H}–¹⁵N NOE data, and reduced spectral density analysis of the relaxation data. The principle features of the notebooks include use of a minimal number of input files, integrated notebook data management, ease of use, cross-platform compatibility, automatic visualization of results and generation of high-quality graphics, and output of analyses in text format.L. Spyracopoulos is an AHFMR Medical Research Senior Scholar     

Correlation between 15N NMR chemical shifts in proteins and secondary structure

Summary An empirical correlation between the peptide ¹⁵N chemical shift, ¹⁵N_i, and the backbone torsion angles _i, _i–1 is reported. By using two-dimensional shielding surfaces (_i1–1), it is possible in many cases to make reasonably accurate predictions of ¹⁵N chemical shifts for a given structure. On average, the rms error between experiment and prediction is about 3.5 ppm. Results for threonine, valine and isoleucine are worse (4.8 ppm), due presumably to ₁-distribution/-gauche effects. The rms errors for the other amino acids are 3 ppm, for a typical maximal chemical shift range of 15–20 ppm. Thus, there is a significant correlation between ¹⁵N chemical shift and secondary structure.     

1H, 15N, 13C and 13CO assignments and secondary structure determination of basic fibroblast growth factor using 3D heteronuclear NMR spectroscopy

Summary The assignments of the ¹H, ¹⁵N, ¹³CO and ¹³C resonances of recombinant human basic fibroblast growth factor (FGF-2), a protein comprising 154 residues and with a molecular mass of 17.2 kDa, is presented based on a series of three-dimensional triple-resonance heteronuclear NMR experiments. These studies employ uniformly labeled ¹⁵N- and ¹⁵N-/¹³C-labeled FGF-2 with an isotope incorporation >95% for the protein expressed in E. coli. The sequence-specific backbone assignments were based primarily on the interresidue correlation of C, C and H to the backbone amide ¹H and ¹⁵N of the next residue in the CBCA(CO)NH and HBHA(CO)NH experiments and the intraresidue correlation of C, C and H to the backbone amide ¹H and ¹⁵N in the CBCANH and HNHA experiments. In addition, C and C chemical shift assignments were used to determine amino acid types. Sequential assignments were verified from carbonyl correlations observed in the HNCO and HCACO experiments and C correlations from the carbonyl correlations observed in the HNCO and HCACO experiments and C correlations from the HNCA experiment. Aliphatic side-chain spin systems were assigned primarily from H(CCO)NH and C(CO)NH experiments that correlate all the aliphatic ¹H and ¹³C resonances of a given residue with the amide resonance of the next residue. Additional side-chain assignments were made from HCCH-COSY and HCCH-TOCSY experiments. The secondary structure of FGF-2 is based on NOE data involving the NH, H and H protons as well as ³J_H n _H coupling constants, amide exchange and ¹³C and ¹³C secondary chemical shifts. It is shown that FGF-2 consists of 11 well-defined antiparallel -sheets (residues 30–34, 39–44, 48–53, 62–67, 71–76, 81–85, 91–94, 103–108, 113–118, 123–125 and 148–152) and a helix-like structure (residues 131–136), which are connected primarily by tight turns. This structure differs from the refined X-ray crystal structures of FGF-2, where residues 131–136 were defined as -strand XI. The discovery of the helix-like region in the primary heparin-binding site (residues 128–138) instead of the -strand conformation described in the X-ray structures may have important implications in understanding the nature of heparin-FGF-2 interactions. In addition, two distinct conformations exist in solution for the N-terminal residues 9–28. This is consistent with the X-ray structures of FGF-2, where the first 17–19 residues were ill defined.     

Addressing the overlap problem in the quantitative analysis of two dimensional NMR spectra: Application to <Superscript>15</Superscript>N relaxation measurements

A quantitative analysis of 2D ¹H-¹⁵N spectra is often complicated by resonance overlap. Here a simple method is presented for resolving overlapped correlations by recording 2D projection planes from HNCO data sets. Applications are presented involving the measurement of ¹⁵N T₁ relaxation rates in a high molecular weight protein, malate synthase G, and in a system that exchanges between folded and unfolded states, the drkN SH3 domain. By supplementing relaxation data recorded in the conventional way as a series of 2D ¹H-¹⁵N data sets with a series of a pair of projection planes the number of dynamics probes is increased significantly for both systems studied.     

Complete 1H, 13C, and 15N NMR resonance assignments and secondary structure of human glutaredoxin in the fully reduced form.

Human glutaredoxin is a member of the glutaredoxin family, which is characterized by a glutathione binding site and a redox-active dithiol/disulfide in the active site. Unlike Escherichia coli glutaredoxin-1, this protein has additional cysteine residues that have been suggested to play a regulatory role in its activity. Human glutaredoxin (106 amino acid residues, M(r) = 12,000) has been purified from a pET expression vector with both uniform 15N labeling and 13C/15N double labeling. The combination of three-dimensional 15N-edited TOCSY, 15N-edited NOESY, HNCA, HN(CO)CA, and gradient sensitivity-enhanced HNCACB and HNCO spectra were used to obtain sequential assignments for residues 2-106 of the protein. The gradient-enhanced version of the HCCH-TOCSY pulse sequence and HCCH-COSY were used to obtain side chain 1H and 13C assignments. The secondary structural elements in the reduced protein were identified based on NOE information, amide proton exchange data, and chemical shift index data. Human glutaredoxin contains five helices extending approximately from residues 4-10, 24-36, 53-64, 83-92, and 94-104. The secondary structure also shows four beta-strands comprised of residues 15-19, 43-48, 71-75, 78-80, which form a beta-sheet almost identical to that found in E. coli glutaredoxin-1. Complete 1H, 13C, and 15N assignments and the secondary structure of fully reduced human glutaredoxin are presented. Comparison to the structures of other glutaredoxins is presented and differences in the secondary structure elements are discussed.     

Performance of a neural-network-based determination of amino acid class and secondary structure from 1H-15N NMR data

A neural network which can determine both amino acid class andsecondary structure using NMR data from ¹⁵N-labeled proteinsis described. We have included nitrogen chemical shifts,³J_HN_H coupling constants, -protonchemical shifts, and side-chain proton chemical shifts as input to athree-layer feed-forward network. The network was trained with 456 spinsystems from several proteins containing various types of secondarystructure, and tested on human ubiquitin, which has no sequence homologywith any of the proteins in the training set. A very limited set of data,representative of those from a TOCSY-HSQC and HNHA experiment, was used.Nevertheless, in 60% of the spin systems the correct amino acid classwas among the top two choices given by the network, while in 96% ofthe spin systems the secondary structure was correctly identified. Theperformance of this network clearly shows the potential of the neuralnetwork algorithm in the automation of NMR spectral analysis.     

Nuclear Magnetic Resonance Studies on Huwentoxin-XI from the Chinese Bird Spider Ornithoctonus huwena： ^15N Labeling and Sequence-specific ^1H, ^15N Nuclear Magnetic Resonance Assignments

Huwentoxin-XI purified from the Chinese bird spider Ornithoctonus huwena is a toxin with both antiprotease activity and potassium channel blocking activity. To determine its solution structure, huwentoxin-XI was expressed in a yeast eukaryotic expression system and studied by NMR. The ^15N labeling strategy was used to facilitate the process of resonance assignments. The nearly complete sequence-specific assignments of proton and nitrogen resonances were obtained by analyzing a series of two-dimensional （2D） and three-dimensional （3D） spectra, including DQF-COSY, TOCSY, NOESY, ^15N-^1H HSQC, ^15N-^1H HNHA, ^15N-^1H HNHB, ^15N-^1H TOCSY-HSQC and ^15N-^1H NOESY-HSQC spectra. Secondary structure analysis of huwentoxin-XI showed that it mainly contains an N-terminal 310-helix from Thr3 to Arg5 and a C-terminal α-helix from Gln45 to Cys52, plus a triple-stranded antiparallel β-sheet of Glu18-Asn23, Thr26-Ile31 and Asn40-Lys41. These studies provide a solid basis for the final structure determination of huwentoxin-XI.     

Bacterial siderophores: structure elucidation, and 1H, 13C and 15N two-dimensional NMR assignments of azoverdin and related siderophores synthesized by Azomonas macrocytogenes ATCC 12334

Two major azoverdins were isolated from the cultures of Azomonas macrocytogenes ATCC 12334 grown in irondeficient medium. Their structures have been established using fast atom bombardment-mass spectroscopy, homonuclear and heteronuclear two-dimensional ¹⁵N, ¹³C and ¹H NMR, and circular dichroism techniques. These siderophores are chromopeptides possessing at the N-terminal end of their peptide chain the chromophore derived from 2,3-diamino-6,7-dihydroxyquinoline common to pyoverdins. The linear peptide chain (l)-Hse-(d)-AcOHOrn-(d)-Ser-(l)-AcOHOrn-(d)-Hse-(l)-CTHPMD has at its C-terminal end a new natural amino acid which is the result of the condensation of 1 mol of homoserine and 1 mol of 2,4-diaminobutyric acid forming a cyclic amidine belonging to the tetrahydropyrimidine family: 2-homoseryl-4-carboxyl-3,4,5,6-tetrahydropyrimidine. The azoverdins differ only by a substitutent bound to the nitrogen on C-3 of the chromophore: azoverdin, the most abundant one, possesses a succinamide moiety, whereas azoverdin A bears a succinic acid moiety. ¹⁵N-labelled azoverdin afforded readily, after the complete assignment of the ¹⁵N spectrum of the siderophore, a sequence determination of the peptidic part of the molecule and gave evidence for the presence of two tetrahydropyrimidine groups on the molecule: one on the chromophore and the second at the C-terminal end of the siderophore.     

The relative orientation of the fibronectin 6F11F2 module pair: A 15N NMR relaxation study

The structure of a pair of modules (⁶F1¹F2), that forms part of the collagen-binding region of fibronectin, is refined using heteronuclear relaxation data. A structure of the pair was previously derived from ¹H-¹H NOE and ³ J _HHN data [Bocquier et al. (1999) Structure, 7, 1451–1460] and a weak module–module interface, comprising Leu19 and Leu28, in ⁶F1, and Tyr68 in ²F1, was identified. In this study, the definition of the average relative orientation of the two modules is improved using the dependence of ¹⁵N relaxation on rotational diffusion anisotropy. This structure refinement is based on the selection of a subset of structures from sets calculated with NOE and ³ J _HHN data alone, using the quality of the fits to the relaxation data as the selection criterion. This simple approach is compared to a refinement strategy where ¹⁵N relaxation data are included in the force field as additional restraints [Tjandra et al. (1997) Nat. Struct. Biol., 4, 443–449].