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D A Torchia

Publications and source records attributed to D A Torchia.

13 recordsLinked to original sources
PubMed1992

Dynamics of methyl groups in proteins as studied by proton-detected 13C NMR spectroscopy. Application to the leucine residues of staphylococcal nuclease.

This paper describes the application of recently developed nuclear magnetic resonance (NMR) pulse sequences to obtain information about the internal dynamics of isotopically enriched hydrophobic side chains in proteins. The two-dimensional spectra provided by the pulse sequences enable one to make accurate measurements of nuclear Overhauser effects (NOE) and longitudinal (T1) and transverse (T2) relaxation times of enriched methyl carbons in proteins. Herein, these techniques are used to investigate the internal dynamics of the 11 leucine side chains of staphylococcal nuclease (SNase), a small enzyme having Mr = 16.8K, in the absence and presence of ligands thymidine 3',5'-bisphosphate (pdTp) and Ca2+. We report the synthesis of [5,5'-13C2]leucine, the preparation of SNase containing the labeled leucine, the sequential assignment of the leucine methyl carbons and protons in the liganded and unliganded proteins, and the measurement of the 13C T1, T2, and NOE values for the SNase leucine methyl carbons. Analysis of the relaxation parameters using the formalism of Lipari and Szabo shows that the internal motions of the leucine methyl carbons are characterized by effective correlation times tau f (5-80 ps) and tau s (less than 2 ns). The fast motion is identified with the rapid rotation of the methyl group about the C gamma-C delta bond axis, while the slow motion is associated with reorientation of the C gamma-C delta bond axis itself. The mean squared order parameters associated with the latter motion, Ss2, lie in the range 0.34-0.92. The values of Ss2 correlate reasonably well with the temperature factors of the leucine methyl carbons obtained from the crystal structures, but some are smaller than anticipated on the basis of the fact that nearly all leucine methyl carbons are buried and have temperature factors no larger than that of the leucine backbone atoms. Five leucine residues in liganded SNase and eight in unliganded SNase have values of Ss2 less than 0.71. These order parameters correspond to large amplitude motions (angular excursions of 27-67 degrees) of the C gamma-C delta bond axis. These results indicate that, in solution, the internal motions of the leucine side chains of SNase are significantly larger than suggested by the X-ray structures or by qualitative analysis of NOESY spectra. Comparison of Ss2 values obtained from liganded and unliganded SNase reveals a strong correlation between delta Ss2 and distance between the leucine methyl carbon and the ligands.(ABSTRACT TRUNCATED AT 400 WORDS)

Leucine↗
PubMed1992

Structural comparison of phosphorylated and unphosphorylated forms of IIIGlc, a signal-transducing protein from Escherichia coli, using three-dimensional NMR techniques.

The 18.1-kDa protein IIIGlc from Escherichia coli acts as both a phosphocarrier protein in the phosphoenolpyruvate:glycose phosphotransferase system (PTS) and as a signal-transducing protein with respect to the uptake of non-PTS sugars. Phosphorylation of IIIGlc at the N epsilon (N3) position of His-90 was effected through a regeneration system that included MgCl2, DTT, excess PEP, and catalytic amounts of Enzyme I and HPr. NH, 15N, and 13C alpha signal assignments for P-IIIGlc were made through comparison of 15N-1H correlation spectra (HSQC) of uniformly 15N-labeled preparations of phosphorylated and unphosphorylated protein and through analysis of three-dimensional triple-resonance HNCA spectra of P-IIIGlc uniformly labeled with both 15N and 13C. Backbone and side-chain 1H and 13C beta signals were assigned using 3D heteronuclear HCCH-COSY and HCCH-TOCSY spectra of P-IIIGlc. Using this approach, the assignments were made without reference to nuclear Overhauser effect data or assumptions regarding protein structure. The majority of NH, 15N, H alpha, and 13C alpha chemical shifts measured for P-IIIGlc were identical to those obtained for the unphosphorylated protein [Pelton, J. G., Torchia, D. A., Meadow, N. D., Wong, C.-Y., & Roseman, S. (1991) Biochemistry 30, 10043]. Those signals that exhibited shifts corresponded to residues within four segments (1) Leu-87-Gly-100, (2) Val-36-Val-46, (3) His-75-Ser-78, and (4) Ala-131-Val-138. These four segments are in close proximity to the active site residues His-75 and His-90 in the unphosphorylated protein [Worthylake, D., Meadow, N. D., Roseman, S., Liao, D., Hertzberg, O., & Remington, S.J. (1991) Proc. Natl. Acad. Sci. U.S.A. 88, 10382], and the chemical shift data provide strong evidence that if any structural changes accompany phosphorylation, they are confined to residues in these four segments. This conclusion is confirmed by comparing NOEs observed in 3D 15N/13C NOESY-HMQC spectra of the two forms of the protein. No NOE differences are seen for residues having the same chemical shifts in IIIGlc and P-IIIGlc. Furthermore, with the exception of residues Ala-76, Asp-94, and Val-96, the NOEs of residues (in the four segments) which exhibited chemical shift differences also had the same NOEs in IIIGlc and P-IIIGlc. In the case of residues Ala-76, Asp-94, and Val-96, minor differences in NOEs, corresponding to interproton distances changes of less than 1.5 A, were observed.(ABSTRACT TRUNCATED AT 400 WORDS)

Amino Acid Sequence↗
PubMed1979

13C NMR quantitation of polymer in deoxyhemoglobin S gels.

13C/1H magnetic double-resonance spectroscopy has been used to quantitate the amount of polymerized hemoglobin S in deoxygenated gels at 30 degrees C, for samples whose hemoglobin concentration range from 21 to 32 g/dl. Scalar- and dipolar-decoupled spectra and a 13C proton-enhanced dipolar-decoupled spectrum were recorded for each sample as was a scalar-decoupled spectrum for a matching oxyhemoglobin S control. The difference between the oxyhemoglobin S and deoxyhemoglobin S scalar-decoupled spectra was used to determine the polymer fraction, and this value was compared with the polymer fraction determined by using ultracentrifugation sedimentation on the same sample (assuming a two-phase model). The polymer fraction value determined by uncorrected sedimentation averaged 0.15 more than the value obtained from NMR. The discrepancy between the two techniques was largely removed when the analysis of the sedimentation data included a correction for depletion of hemoglobin in the supernatant or sol phase due to sedimentation of free molecules. The best fit to both the sedimentation and NMR data was obtained by using a solubility of deoxyhemoglobin S at 30 degrees C of 17.3 +/- 1 g/dl. These results indicate that the NMR techniques, which do not require separation of the sample into a sol phase and a pellet phase, provide quantitative information about the deoxyhemoglobin S polymer and will be useful for studies of sickle erythrocytes.

Erythrocytes↗
PubMed1979

Enamel matrix: structural proteins.

Cell-free, fetal bovine enamel tissue was examined intact by high resolution. 13C Fourier transform, nuclear magnetic resonance spectroscopy. Two types of protein chains were observed under these conditions, one exhibiting rapid mobility and accounting for approximately two-thirds of the enamel matrix, while the other exhibited restricted or anisotropic segmental motion and accounted for the remaining third of the matrix. Sequential extraction of this fetal enamel under non-degradative conditions with dissociative solvents yielded two biochemically distinct populations of matrix protein. As expected, the bulk of the matrix consisted of proline-rich amelogenins, although the SDS-gel electrophoresis molecular weights for these proteins were somewhat higher than those reported using other extraction methods. Approximately fifteen percent of the total matrix consisted of much higher molecular weight phosphoproteins (46,000-72,000 daltons) whose amino acid composition closely resembled that reported for mature enamel protein. These high molecular weight proteins were tightly bound to the fetal enamel apatite crystallites.

Animals↗
PubMed1977

Investigation of molecular motion of proteoglycans in cartilage by 13C magnetic resonance.

13C nmr spectral parameters were measured for intact bovine nasal cartilage tissue, the purified proteoglycan aggregate, and chondroitin 4-sulfate. A comparison of integrated intensities obtained for four different samples of fresh tissue with an ethylene glycol standard indicated that at least 80% of the total glycosaminoglycan carbons in the tissue contributed to the spectrum. This result was confirmed by intensity measurements obtained at 56 degrees on fresh tissue and at 37 degrees after extensive papain digestion of fresh tissue. Spin lattice relaxation times and nuclear Overhauser enhancements were analyzed in terms of the following models of molecular motion: (a) single correlation time; (b) log X2 distribution of correlation times; and (c) anisotropic motion. The analysis indicates that the segmental motions of glycosaminoglycan chains are characterized by a broad distribution of correlation times centered at about 50 ns. Slow motion contributions to glycosaminoglycan line widths were reduced by dipolar decoupling (gammaH2/2pi = 65 kHz). Collagen intensity was observed in dipolar decoupled spectra, but not in scalar decoupled spectra of intact tissue, showing that the type II collagen in cartilage undergoes anisotropic motion like the type I collagen in tendon. Only glycosaminoglycan resonances were observed in spectra of a solution of proteoglycan aggregate before and after chondroitinase digestion. After subsequent digestion with papain, protein resonances were observed. These results suggest that the protein portions of the proteoglycan aggregate structure, in contrast with the glycosaminoglycan chains, have restricted backbone mobility and consequently a defined backbone structure.

Amino Acids↗
PubMed1977

A 13C magnetic resonance study of embryonic chick aorta.

13C nmr spectra of defatted aorta, obtained from chick embryos, ranging in age from 13 to 20 days, showed that linewidths were independent of the age of the embryo, this, in spite of the fact that crosslinking increases with age. As expected the dipolar decoupled spectrum of defatted aorta had a larger C-H signal intensity than the scalar decoupled spectrum, since collagen in the sample contributes signal intensity only in the former case. Significantly, the dipolar decoupled spectrum of autoclaved aorta also had a larger C-H signal intensity. This result indicates that ca. 30% of the carbons in the tissue, swollen by 0.15 M NaCl, has restricted motion at 37 degrees. Preliminary data indicate that tissue culture techniques can be used to enrich specific amino acids in chick aorta with 13C, thereby affording a means to study possible differences in molecular structure of the chemically distinct regions in elastin.

Animals↗
PubMed1976

Preparation of intact monomeric collagen from rat tail tendon and skin and the structure of the nonhelical ends in solution.

Procedures for the preparation of soluble collagen from rat skin and tail tendon were reviewed and revised to permit the preparation of native monomeric collagen with intact nonhelical ends. The degree of intactness was estimated from the tyrosine content, which is present only in the nonhelical ends, and by mobility of the COOH-terminal cyanogen bromide peptide of the alpha1 chain on sodium dodecyl sulfate gels. The amount of covalently cross-linked polymeric material present was estimated by molecular sieve chromatography of denatured samples. Rapid purification in the cold was sufficient to prevent or greatly reduce proteolytic alteration. Fractionation by salt precipitation at acid pH was effective in reducing the content of polymeric material. Rat tail tendon yielded completely intact native collagen, but some high molecular weight aggregates remained. Collagen from the skin of lathyritic rats was easier to obtain free of aggregates, but contained about 1 less tyrosine residue per alpha1 chain even when isolated in the presence of enzyme inhibitors. Proton NMR spectra of denatured acidic solutions of these preparations showed that 4 to 5 tyrosine residues per alpha chain were present, confirming the chemical analysis. Spectra of the native molecule showed that about the same number of tyrosine residues per chain are in rapid motion, unlike residues in the helical portion of the molecule, a result which shows that the nonhelical ends of the native molecule are unstructured in acidic solution.

Amino Acids↗
PubMed1975

Molecular mobility and structure of elastin deduced from the solvent and temperature dependence of 13C magnetic resonance relaxation data.

13C relaxation parameters, T1, line width, and NOE, have been determined for backbone carbons of ligamentum nuchae elastin swollen by 0.15 M NaCl, 0.15 M NaCl-formamide, 0.15 M NaCl-ethanol, dimethyl sulfoxide, and formamide. The data have been analyzed in terms of (a) a single correlation time model and (b) a model employing a log-chi2 distribution of correlation times used by Schaefer (1973) to analyze solid cis-polyisoprene 13C relaxation data. Employing the latter mode, one obtains an approximately self-consistent quantitative analysis of all the elastin data. An average backbone correlation time, tau, of ca. 2 nsec is calculated for elastin swollen in the presence of polar organic solvents at 37 degrees, in approximate agreement with tau of 0.4 nsec obtained for bulk cis-polyisoprene at 35 degrees. The influence of solvent and temperature on elastin spectra indicate that the larger tau value (approximately 80 nsec) obtained for elastin swollen by 0.15 M NaCl at 37 degrees is a consequence of weak interchain polar and hydrophobic interactions, a result which is in accord with the reported viscoelastic behavior exhibited by water-swollen elastin at 37 degrees. The results obtained further suggest that Gly, Pro, and Val residues are significantly more mobile than Ala residues, which are located in the cross-link regions. Hence, the NMR data support the view that water-swollen elastin is composed of a network of mobile chains, except possibly in the cross-link regions.

Animals↗
PubMed1975

Molecular dynamics and structure of the random coil and helical states of the collagen peptide, alpha 1-CB2, as determined by 13C magnetic resonance.

Carbon-13 chemical shifts, spin-lattice (T1) and spin-spin (T2) relaxation times, and 13C-[1H] nuclear Overhauser enhancements (NOE) have been determined for the random coil and triple helical states of the alpha 1-CB2 fragment of rat skin collagen. Assignment of all aliphatic resonances of this 36 residue peptide in the random coil state (30 degrees) has been achieved with the aid of model polypeptides containing pyrrolidine residues. The chemical shifts and intensities of the Pro and Hyp C-gamma resonances show that (see article) 90% of the X-Pro and X-Hyp bonds are trans in both helix and coil conformations. From T1 measurements rotational correlation times (tau-eff) of ca. 0.45 nsec are calculated for interior C-alpha carbons in the coil, while taueff values of the side chain and near terminal carbons are found to be 2-9 times smaller. These results along with the narrow natural line widths (3-5 Hz) and maximal NOE values (2.8 plus or minus 0.3) demonstrate the high degree of backbone mobility, due to segmental motion, in the unordered state of the peptide. By contrast, the broad lines (50-90 Hz) and small NOE values (1.3 plus or minus 0.3) for the alpha carbons in the helical state (2 degrees) suggest much slower motion. The line widths and NOE values together with the C-alpha T1 values (0.025-0.040 sec) correspond to correlation times which are in reasonable agreement with those calculated for an axially symmetric rigid ellipsoid, undergoing rotational diffusion, having dimensions approximating those of a collagen-type triple helical aggregate of three alpha 1-CB2 chains. A satisfactory computer simulation of the experimental 2 degrees spectrum is obtained by assigning the narrow aliphatic resonances in the spectrum (line widths 5-40 Hz) to (a) carbons in the small amounts of alpha 1-CB2 (3 mol %) and alpha 1-CB1 (2.5 mol %) random coil conformations, (b) carbons in the flexible terminal triplets of the helix, and (c) Ala, Leu, and Phe methyl and phenyl carbons. The side chain carbon line widths obtained from the simulation--when compared with side chain line widths calculated for a rotating rigid ellipsoid with internal motion--indicate rapid axial reorientation of methyl and phenyl groups. With the exception of the Hyp residue the line widths suggest local motion for at least some carbons in most other side chain moieties. The Hyp C-beta and C-gamma line widths indicate the presence of little if any rapid Hyp ring motion.

Animals↗