Measurement of Residual Dipolar Couplings of Macromolecules Aligned in the Nematic Phase of a Colloidal Suspension of Rod-Shaped Viruses

Residual dipolar couplings provide long-range structural restraints for NMR structure determination of macromolecules1 that are not accessible by most other NMR observables, which are dependent on close spatial proximity of atoms.2 Thus, dipolar couplings provide restraints for defining the relative orientation of structural elements where the information content provided by the NOE restraints is insufficient, either due to the lack of NOEs or to the accumulation of errors over long distances.2 In addition, the use of various different dipolar couplings (e.g., DNH, DNC′, DHNC′, DCH, DCRC′) along the protein backbone narrowly restricts the backbone torsion angles.3 The measurement of residual dipolar couplings requires that the macromolecule of interest be weakly aligned in the magnetic field. Alignment can be induced in a number of ways including the magnetic field itself4 or the use of a liquid crystalline medium.5 In general, alignment arising from the former is very small and cannot be exploited on a routine basis.2,4 Moderate degrees of alignment, while retaining the resolution, sensitivity, and simplicity obtained in the isotropic phase, can be obtained by dissolving macromolecules in a very dilute liquid crystalline phase6 of lipid bicelles.7 For biological macromolecules, the liquid crystalline medium must possess a number of key features; it has to be miscible with water, it should not bind to the macromolecule of interest, it should be stable at dilute concentrations over long periods of time, and it should only induce moderate degrees of alignment. While the bicelles have been successfully applied in a number of cases,3,6 there are instances where the protein, possibly due to the presence of surface hydrophobic patches, adversely affects the stability of the bicelle, leading to phase separation of its components.8 In addition, the bicelles are thermotropic, adopting a liquid crystalline phase over a narrow range of temperatures, and are only stable over a limited pH range due to acidand base-catalyzed hydrolysis of ester bonds.6 In this paper, we show that the nematic phase of a colloidal suspension of rod-shaped viruses provides an alternative to bicelles. Suspensions of charged, rod-shaped viruses, such as the filamentous baceriophage fd and tobacco mosaic virus (TMV), are known to undergo an isotropic-nematic phase transition at relatively low concentrations.9 Figure 1 displays the residual onebond N-H (DNH) dipolar couplings for a ∼0.5 mM solution of streptococcal protein G (56 residues)10 in colloidal suspensions of ∼28 mg/mL fd and ∼50 mg/mL TMV.11 The values of DNH range from +15 to -15 Hz in the case of the fd suspension and +10 to -10 Hz in the case of the TMV suspension. The general expression for the residual dipolar coupling DAB(θ,φ) between two directly coupled nuclei A and B is given by Da{(3cos θ 1) + /2R(sin θ cos2φ)}where Da and Dr in units of hertz are the axial and rhombic components of the * To whom correspondence should be addressed. E-mail: G.M.C., clore@speck.niddk.nih.gov. A.M.G., gronenborn@vger.niddk.nih.gov. Tel.: (301) 496-0782. Fax: (301) 496-0825. (1) Tjandra, N.; Omichinski, J. G.; Gronenborn, A. M.; Clore, G. M.; Bax, A. Nat. Struct. Biol. 1997, 4, 732-738. (2) Clore, G. M.; Gronenborn, A. M. Nat. Struct. Biol. 1997, 4, 849-853. (3) (a) Bewley, C. A.; Kustafson, K. R.; Boyd, M. R., Covell, D. G.; Bax, A.; Clore, G. M.; Gronenborn, A. M. Nat. Struct. Biol. 1998, 5, 571-578. (b) Cai, M.; Huang, Y.; Zheng, R.; Wei, S. Q.; Ghirlando, R.; Lee, M. S.; Craigie, R.; Gronenborn, A. M.; Clore, G. M. Nat. Struct. Biol. 1998, 5, 903909. (4) Bothner-By, A. A. In Encyclopedia of Nuclear Magnetic Resonance; Grant, D. M., Harris, R. K., Eds.; Wiley: Chichester, 1996; pp 2932-2938. (5) Emsley, J. W.; Lindon, J. C. NMR spectroscopy using Liquid Crystal SolVents; Peregamon Press: New York, 1975. (6) (a) Tjandra, A.; Bax, A. Science 1997, 278, 1111-1114. (b) Cornilescu, G.; Marquardt, J. L.; Ottiger, M.; Bax, A. J. Am. Chem. Soc. 1998, 120, 68366837. (c) Ramirez, B. E.; Bax, A. J. Am. Chem. Soc. 1998, 120, 9106-9107. (7) Sanders, C. R.; Hare, B. J.; Howard, K. P.; Prestegard, J. H. Prog. Nucl. Magn. Reson. Spectrosc. 1994, 26, 421-444. (8) Examples at the NIH where the bicelles have proved to be unstable include enzyme I, the enzyme I-HPR complex, the N-terminal domain of HIV-1 integrase coordinated to cadmium, SIV gp41 (G.M.C. and A.M.G., unpublished data), the VR domain of a T-cell inhibitor (J. S. Hu and A. Bax, personal communication), and HIV protease (D. Torchia, personal communication). (9) (a) Fraden, S.; Maret, G.; Caspar, D. L. D.; Meyer, R. B. Phys. ReV. Lett. 1989, 63, 2068-2071. (b) Tang, J.; Fraden, S. Liq. Cryst. 1995, 4, 459467. (10) Protein G (Gronenborn, A. M.; Filpula, D. R.; Essig, N. Z.; Achari, A.; Whitlow, M., Wingfield, P. T.; Clore, G. M. Science 1991, 253, 657661) in a colloidal suspension of fd was prepared by adding the protein to a dilute (∼1-5 mg/mL) solution of fd in the appropriate buffer, followed by concentration to ∼0.5 mM protein and ∼25-28 mg/mL fd. Protein G in a colloidal suspension of TMV was prepared by adding a stock solution of TMV (210 mg/mL) in water to a protein solution in buffer to yield ∼0.5 mM in protein and ∼50 mg/mL TMV. Over a period of about 6 h, the TMV solution separated into a lower birefringent nematic phase and an upper isotropic phase. The upper isotropic phase was removed, and only the nematic phase was employed for NMR. As the pH of the solution approaches the pI of the virus particles (∼4.2 for fd and ∼3 for TMV), precipitation occurs. Once precipitation of fd has occurred, birefringence cannot be recovered, and the suspension remains isotropic, even though the fd particles can be resolubilized by raising the pH. Thus, solutions of fd should not be taken to pH values below 5.0. At this time, we have also employed suspensions of fd phage successfully for both enzyme I and the enzyme I-HPr complex, where previously a variety of lipid bicelles had proved to be unstable. Figure 1. Plot of DNH measured at 750 MHz versus residue number for the protein G domain (∼0.5 mM) dissolved in the nematic phase of a colloidal suspension of fd (∼28 mg/mL) and TMV (∼50 mg/mL) at 20 °C in 50 mM sodium phosphate buffer pH 5.4. The secondary structure and a ribbon diagram of protein G10 are shown below the figure, together with the axes for the alignment tensor obtained in the nematic phase of fd (top) and DMPC/DHPC bicelles (bottom). 10571 J. Am. Chem. Soc. 1998, 120, 10571-10572