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Louis JM, Ishima R, Nesheiwat I, Pannell LK, Lynch SM, Torchia DA, Gronenborn AM. Revisiting monomeric HIV-1 protease. Characterization and redesign for improved properties. J Biol Chem 2003; 278:6085-92. [PMID: 12468541 DOI: 10.1074/jbc.m209726200] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Interactions between the C-terminal interface residues (96-99) of the mature HIV-1 protease were shown to be essential for dimerization, whereas the N-terminal residues () and Arg(87) contribute to dimer stability (Ishima, R., Ghirlando, R., Tozser, J., Gronenborn, A. M., Torchia, D. A., and Louis, J. M. (2001) J. Biol. Chem. 276, 49110-49116). Here we show that the intramonomer interaction between the side chains of Asp(29) and Arg(87) influences dimerization significantly more than the intermonomer interaction between Asp(29) and Arg(8'). Several mutants, including T26A, destablize the dimer, exhibit a monomer fold, and are prone to aggregation. To alleviate this undesirable property, we designed proteins in which the N- and C-terminal regions can be linked intramolecularly by disulfide bonds. In particular, cysteine residues were introduced at positions 2 and 97 or 98. A procedure for the efficient preparation of intrachain-linked polypeptides is presented, and it is demonstrated that the Q2C/L97C variant exhibits a native-like single subunit fold. It is anticipated that monomeric proteases of this kind will aid in the discovery of novel inhibitors aimed at binding to the monomer at the dimerization interface. This extends the target area of current inhibitors, all of which bind across the active site formed by both subunits in the active dimer.
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Jacob J, Louis JM, Nesheiwat I, Torchia DA. Biosynthetically directed fractional 13C labeling facilitates identification of Phe and Tyr aromatic signals in proteins. JOURNAL OF BIOMOLECULAR NMR 2002; 24:231-235. [PMID: 12522310 DOI: 10.1023/a:1021662423490] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Analysis of 2D [(13)C,(1)H]-HSQC spectra of biosynthetic fractionally (13)C labeled proteins is a reliable, straightforward means to obtain stereospecific assignments of Val and Leu methyl sites in proteins. Herein we show that the same fractionally labeled protein sample facilitates observation and identification of Phe and Tyr aromatic signals. This is the case, in part, because the fractional (13)C labeling yields aromatic rings in which some of the (13)C-(13)C J-couplings, present in uniformly labeled samples, are absent. Also, the number of homonuclear J-coupling partners differs for the delta-, epsilon- and zeta-carbons. This enabled us to vary their signal intensities in distinctly different ways by appropriately setting the (13)C constant-time period in 2D [(13)C,(1)H]-HSQC spectra. We illustrate the application of this approach to an 18 kDa protein, c-VIAF, a modulator of apoptosis. In addition, we show that cancellation of the aromatic (13)C CSA and (13)C-(1)H dipolar interactions can be fruitfully utilized in the case of the fractionally labeled sample to obtain high resolution (13)C constant-time spectra with good sensitivity.
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28
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Korzhnev DM, Skrynnikov NR, Millet O, Torchia DA, Kay LE. An NMR experiment for the accurate measurement of heteronuclear spin-lock relaxation rates. J Am Chem Soc 2002; 124:10743-53. [PMID: 12207529 DOI: 10.1021/ja0204776] [Citation(s) in RCA: 117] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Rotating-frame relaxation rates, R(1)(rho), are often measured in NMR studies of protein dynamics. We show here that large systematic errors can be introduced into measured values of heteronuclear R(1)(rho) rates using schemes which are usually employed to suppress cross-correlation between dipole-dipole and CSA relaxation mechanisms. For example, in a scalar-coupled two-spin X-H spin system the use of (1)H WALTZ16 decoupling or (1)H pulses applied at regularly spaced intervals leads to a significant overestimation of heteronuclear R(1)(rho) values. The problem is studied experimentally and theoretically for (15)N-(1)H and (13)C-(1)H spin pairs, and simple schemes are described which eliminate the artifacts. The approaches suggested are essential replacements of existing methodology if accurate dynamics parameters are to be extracted from spin-lock relaxation data sets.
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29
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Torchia DA, Sparks SW, Bax A. Delineation of .alpha.-helical domains in deuteriated Staphylococcal nuclease by 2D NOE NMR spectroscopy. J Am Chem Soc 2002. [DOI: 10.1021/ja00215a063] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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30
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Bovey FA, Brewster AI, Patel DJ, Tonelli AE, Torchia DA. Determination of the solution conformations of cyclic polypeptides. Acc Chem Res 2002. [DOI: 10.1021/ar50054a001] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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31
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Lerner L, Torchia DA. An analysis of non-Lorentzian sodium-23 line shapes in two model systems. J Am Chem Soc 2002. [DOI: 10.1021/ja00275a004] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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32
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Bax A, Kay LE, Sparks SW, Torchia DA. Line narrowing of amide proton resonances in 2D NMR spectra of proteins. J Am Chem Soc 2002. [DOI: 10.1021/ja00183a082] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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33
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Torchia DA, Bovey FA. A Nuclear Magnetic Resonance Study of Poly(L-proline) in Aqueous and Aqueous Salt Solutions. Macromolecules 2002. [DOI: 10.1021/ma60020a022] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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34
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Mack JW, Torchia DA. A deuteron NMR study of the molecular dynamics of solid cyclopentane. ACTA ACUST UNITED AC 2002. [DOI: 10.1021/j100164a009] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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35
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Grzesiek S, Bax A, Nicholson LK, Yamazaki T, Wingfield P, Stahl SJ, Eyermann CJ, Torchia DA, Hodge CN. NMR Evidence for the Displacement of a Conserved Interior Water Molecule in HIV Protease by a Non-Peptide Cyclic Urea-Based Inhibitor. J Am Chem Soc 2002. [DOI: 10.1021/ja00083a058] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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36
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Hiyama Y, Niu CH, Silverton JV, Bavoso A, Torchia DA. Determination of 15N chemical shift tensor via 15N-2H dipolar coupling in Boc-glycylglycyl[15N glycine]benzyl ester. J Am Chem Soc 2002. [DOI: 10.1021/ja00216a006] [Citation(s) in RCA: 197] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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37
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Torchia DA, Sparks SW, Young PE, Bax A. Proline assignments and identification of the cis K116/P117 peptide bond in liganded staphylococcal nuclease using isotope edited 2D NMR spectroscopy. J Am Chem Soc 2002. [DOI: 10.1021/ja00203a063] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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38
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Hiyama Y, Roy S, Cohen JS, Torchia DA. Solid-state deuterium NMR study of thymidine. Base rigidity and ribose ring flexibility in deoxynucleosides. J Am Chem Soc 2002. [DOI: 10.1021/ja00205a008] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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39
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Hiyama Y, Roy S, Guo K, Butler LG, Torchia DA. Unusual asymmetry of methyl deuterium EFG in thymine: a solid state deuterium NMR and ab initio MO study. J Am Chem Soc 2002. [DOI: 10.1021/ja00242a054] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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40
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Bax A, Sparks SW, Torchia DA. Long range heteronuclear correlation. A powerful tool for the NMR analysis of medium-size proteins. J Am Chem Soc 2002. [DOI: 10.1021/ja00231a081] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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41
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Kay LE, Brooks B, Sparks SW, Torchia DA, Bax A. Measurement of NH-C.alpha.H coupling constants in staphylococcal nuclease by two-dimensional NMR and comparison with x-ray crystallographic results. J Am Chem Soc 2002. [DOI: 10.1021/ja00196a078] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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42
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Hiyama Y, Silverton JV, Torchia DA, Gerig JT, Hammond SJ. Molecular structure and dynamics of crystalline p-fluoro-D,L-phenylalanine. A combined x-ray/NMR investigation. J Am Chem Soc 2002. [DOI: 10.1021/ja00270a034] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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43
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Marion D, Kay LE, Sparks SW, Torchia DA, Bax A. Three-dimensional heteronuclear NMR of nitrogen-15 labeled proteins. J Am Chem Soc 2002. [DOI: 10.1021/ja00186a066] [Citation(s) in RCA: 462] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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44
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Roy S, Hiyama Y, Torchia DA, Cohen JS. New enzymic synthesis of 2'-deoxynucleoside-2',2'-d2 and the determination of sugar ring flexibility by solid-state deuterium NMR. J Am Chem Soc 2002. [DOI: 10.1021/ja00267a043] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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45
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Freedberg DI, Ishima R, Jacob J, Wang YX, Kustanovich I, Louis JM, Torchia DA. Rapid structural fluctuations of the free HIV protease flaps in solution: relationship to crystal structures and comparison with predictions of dynamics calculations. Protein Sci 2002; 11:221-32. [PMID: 11790832 PMCID: PMC2373438 DOI: 10.1110/ps.33202] [Citation(s) in RCA: 162] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2001] [Accepted: 10/12/2001] [Indexed: 10/16/2022]
Abstract
Crystal structures have shown that the HIV-1 protease flaps, domains that control access to the active site, are closed when the active site is occupied by a ligand. Although flap structures ranging from closed to semi-open are observed in the free protease, crystal structures reveal that even the semi-open flaps block access to the active site, indicating that the flaps are mobile in solution. The goals of this paper are to characterize the secondary structure and fast (sub-ns) dynamics of the flaps of the free protease in solution, to relate these results to X-ray structures and to compare them with predictions of dynamics calculations. To this end we have obtained nearly complete backbone and many sidechain signal assignments of a fully active free-protease construct that is stabilized against autoproteolysis by three point mutations. The secondary structure of this protein was characterized using the chemical shift index, measurements of (3h)J(NC') couplings across hydrogen bonds, and NOESY connectivities. Analysis of these measurements indicates that the protease secondary structure becomes irregular near the flap tips, residues 49-53. Model-free analysis of (15)N relaxation parameters, T(1), T(2) (T(1rho)) and (15)N-[(1)H] NOE, shows that residues in the flap tips are flexible on the sub-ns time scale, in contrast with previous observations on the inhibitor-bound protease. These results are compared with theoretical predictions of flap dynamics and the possible biological significance of the sub-ns time scale dynamics of the flap tips is discussed.
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Ishima R, Ghirlando R, Tözsér J, Gronenborn AM, Torchia DA, Louis JM. Folded monomer of HIV-1 protease. J Biol Chem 2001; 276:49110-6. [PMID: 11598128 DOI: 10.1074/jbc.m108136200] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The mature human immunodeficiency virus type 1 protease rapidly folds into an enzymatically active stable dimer, exhibiting an intricate interplay between structure formation and dimerization. We now show by NMR and sedimentation equilibrium studies that a mutant protease containing the R87K substitution (PR(R87K)) within the highly conserved Gly(86)-Arg(87)-Asn(88) sequence forms a monomer with a fold similar to a single subunit of the dimer. However, binding of the inhibitor DMP323 to PR(R87K) produces a stable dimer complex. Based on the crystal structure and our NMR results, we postulate that loss of specific interactions involving the side chain of Arg(87) destabilizes PR(R87K) by perturbing the inner C-terminal beta-sheet (residues 96-99 from each monomer), a region that is sandwiched between the two beta-strands formed by the N-terminal residues (residues 1-4) in the mature protease. We systematically examined the folding, dimerization, and catalytic activities of mutant proteases comprising deletions of either one of the terminal regions (residues 1-4 or 96-99) or both. Although both N- and C-terminal beta-strands were found to contribute to dimer stability, our results indicate that the inner C-terminal strands are absolutely essential for dimer formation. Knowledge of the monomer fold and regions critical for dimerization may aid in the rational design of novel inhibitors of the protease to overcome the problem of drug resistance.
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Sayers EW, Torchia DA. Use of the carbonyl chemical shift to relieve degeneracies in triple-resonance assignment experiments. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2001; 153:246-253. [PMID: 11740901 DOI: 10.1006/jmre.2001.2440] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
We illustrate an approach that uses the backbone carbonyl chemical shift to relieve resonance overlaps in triple-resonance assignment experiments conducted on protein samples. We apply this approach to two cases of simultaneous overlaps: those of ((1)H(N), (15)N) spin pairs and those of ((1)H(alpha), (13)C(alpha)) spin pairs in residues preceding prolines. For these cases we employed respectively CBCACO(N)H and H(CA)CON experiments, simple variants of the commonly used CBCA(CO)NH and HCA(CO)N experiments obtained by replacing one of the indirect dimensions with a carbonyl dimension. We present data collected on ribosomal protein S4 using these experiments, along with overlap statistics for four other polypeptides ranging in size from 76 to 263 residues. These data indicate that the CBCACO(N)H, in combination with the CBCA(CO)NH, can relieve >83% of the ((1)H(N), (15)N) and ((1)H(N), (13)C') overlaps for these proteins. The data also reveal how the H(CA)CON experiment successfully completed the assignment of triply and quadruply degenerate X-Pro spin systems in a mobile, proline-rich region of S4, even when X was a glycine. Finally, we discuss the relative sensitivities of these experiments compared to those of existing sequences, an analysis that reinforces the usefulness of these experiments in assigning extensively overlapped and/or proline-rich sequences in proteins.
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48
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Ishima R, Louis JM, Torchia DA. Optimized labeling of 13CHD2 methyl isotopomers in perdeuterated proteins: potential advantages for 13C relaxation studies of methyl dynamics of larger proteins. JOURNAL OF BIOMOLECULAR NMR 2001; 21:167-171. [PMID: 11727980 DOI: 10.1023/a:1012482426306] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
13CHD2 methyl isotopomers are particularly useful to study methyl dynamics in proteins because, as compared with other methyl isotopomers, the 13C relaxation mechanism for this isotopomer is straightforward. However, in the case of proteins, where (omega tau)2 >> 1, the refocused INEPT pulse sequence does not completely suppress unwanted 13CH3 signals. The presence of weak 13CH3 peaks is usually not a serious problem for smaller proteins because there are relatively few methyl signals and they are sharp; however, signal overlap becomes more common as the size of the protein increases. We overcome this problem by preparing a protein using a 98% D2O cell culture medium containing 3-(13)C pyruvic acid, 50-60% deuterated at the 3-position, and 4-(13)C 2-ketobutyric acid, 98% and 62% deuterated at the 3- and 4-positions, respectively. This approach significantly reduces the population of the CH3 isotopomer while optimizing the production of 13CHD2, the isotopomer desired for 13C relaxation measurements. In larger proteins where the deuterium T2 may be too short to measure accurately, we also suggest the alternative measurement of the proton T2 of the 13CH2D methyl isotopomer, because these protons are well-isolated from other protons in these highly deuterated samples.
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49
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Markus MA, Triantafillidou D, Choli-Papadopoulou T, Torchia DA. 1H, 15N, and 13C assignments and secondary structure identification for full-length ribosomal protein L11 from Thermus thermophilus. JOURNAL OF BIOMOLECULAR NMR 2001; 20:293-294. [PMID: 11519754 DOI: 10.1023/a:1011275602138] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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50
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Ishima R, Petkova AP, Louis JM, Torchia DA. Comparison of methyl rotation axis order parameters derived from model-free analyses of (2)H and (13)C longitudinal and transverse relaxation rates measured in the same protein sample. J Am Chem Soc 2001; 123:6164-71. [PMID: 11414851 DOI: 10.1021/ja0104711] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Recombinant HIV-1 protease was obtained from bacteria grown on a 98% D(2)O medium containing 3-(13)C pyruvic acid as the sole source of (13)C and (1)H. The purified protein is highly deuterated at non-methyl carbons, but contains significant populations of (13)CHD(2) and (13)CH(2)D methyl isotopomers. This pattern of isotope labeling permitted measurements of (1)H and (13)C relaxation rates of (13)CHD(2) isotopomers and (2)H (D) relaxation rates of (13)CH(2)D isotopomers using a single sample. The order parameters S(axis)(2), which characterize the motions of the methyl rotation axes, were derived from model-free analyses of R(1) and R(2) data sets measured for (13)C and (2)H spins. Our primary goal was to compare the S(axis)(2) values derived from the two independent types of data sets to test our understanding of the relaxation mechanisms involved. However, S(axis)(2) values derived from the analyses depend strongly on the geometry of the methyl group, the sizes of the quadrupolar and dipolar couplings, and the effects of bond vibrations and librations on these couplings. Therefore uncertainties in these basic physical parameters complicate comparison of the order parameters. This problem was circumvented by using an experimental relationship, between the methyl quadrupolar, (13)C-(13)C and (13)C-(1)H dipolar couplings, derived from independent measurements of residual static couplings of weakly aligned proteins by Ottiger and Bax (J. Am. Chem. Soc. 1999, 121, 4690-4695) and Mittermaier and Kay (J. Am. Chem. Soc. 1999, 121, 10608-10613). This approach placed a tight experimental restraint on the values of the (2)H quadrupolar and (13)C-(1)H dipolar interactions and greatly facilitated the accurate comparison of the relative values of the order parameters. When applied to our data this approach yielded satisfactory agreement between the S(axis)(2) values derived from the (13)C and (2)H data sets.
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