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. 2017 Mar 14;112(5):933-942.
doi: 10.1016/j.bpj.2016.12.049.

Moving in the Right Direction: Protein Vibrations Steering Function

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Free PMC article

Moving in the Right Direction: Protein Vibrations Steering Function

Katherine A Niessen et al. Biophys J. .
Free PMC article

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Abstract

Nearly all protein functions require structural change, such as enzymes clamping onto substrates, and ion channels opening and closing. These motions are a target for possible new therapies; however, the control mechanisms are under debate. Calculations have indicated protein vibrations enable structural change. However, previous measurements found these vibrations only weakly depend on the functional state. By using the novel technique of anisotropic terahertz microscopy, we find that there is a dramatic change to the vibrational directionality with inhibitor binding to lysozyme, whereas the vibrational energy distribution, as measured by neutron inelastic scattering, is only slightly altered. The anisotropic terahertz measurements provide unique access to the directionality of the intramolecular vibrations, and immediately resolve the inconsistency between calculations and previous measurements, which were only sensitive to the energy distribution. The biological importance of the vibrational directions versus the energy distribution is revealed by our calculations comparing wild-type lysozyme with a higher catalytic rate double deletion mutant. The vibrational energy distribution is identical, but the more efficient mutant shows an obvious reorientation of motions. These results show that it is essential to characterize the directionality of motion to understand and control protein dynamics to optimize or inhibit function.

Figures

Figure 1
Figure 1
ATM measurements of the change in protein vibration directionality with inhibitor binding. Measured Δabs of (a) a free CEWL crystal and (b) a bound CEWL-3NAG inhibitor crystal. The THz light is incident perpendicular to the (110) tetragonal crystal face, with alignment of the THz polarization along the [001] axis at 0°. To see this figure in color, go online.
Figure 2
Figure 2
Measured dynamical structure factor and change in vibrational density of states of free and 3NAG inhibitor bound CEWL. (a) Dynamical structure factor measured with INS at Q = 2.85 Å−1 and at a temperature of 100 K for free (solid circles) and 3NAG bound (open circles) CEWL. The spectra have been normalized with respect to the elastic peak at the lowest Q value. (b) (Left axis) Vibrational density of states from INS measurements of free (blue solid circles) and 3NAG bound (blue open circles) CEWL. (Right axis) The difference in density of states between bound and free CEWL (red circles). To see this figure in color, go online.
Figure 3
Figure 3
Changes in vibrational direction with binding. Protein vibrations indicating (a) a clamping motion around the binding site at 55 cm−1 from NMA of free CEWL and (b) a twisting around the binding site at 56 cm−1 for 3NAG bound CEWL. (Orange) 3NAG inhibitor; (fuchsia) transition dipole direction. To see this figure in color, go online.
Figure 4
Figure 4
Increasing spectral definition with anisotropic optical absorption for CEWL and CEWL-3NAG. Calculated (a) VDOS and (b) isotropic absorbance show small changes with inhibitor binding, whereas the (c) calculated anisotropic absorbance show a large sensitivity to the binding. (d) ATM measurements indeed show narrow band resonant changes with binding. The free CEWL (black solid lines) and CEWL-3NAG bound (gray dashed lines) spectra are shown on the left axes, and the difference between bound and free spectra (blue solid lines) are shown on the right axes. The symmetry for the anisotropic calculations reflects the experimental configuration. To see this figure in color, go online.
Figure 5
Figure 5
Sensitivity of intramolecular vibrations to mutations. Calculated (a) VDOS and (b) isotropic absorbance for free and inhibitor bound WT and DD CEWL. The units for the difference (right axis) are the same as the left axis. These calculations reveal little difference in the dynamics for the two proteins, whereas (c) the relative anisotropic absorbance at 90°, shows the directionality of vibrations clearly changes. The spectra (a–c) are calculated for free WT CEWL (black solid line), 3NAG bound WT CEWL (green solid line), for free DD CEWL (gray dashed line), 3NAG bound DD CEWL (green dashed line), and the difference spectra with binding for WT CEWL (blue solid line) and DD CEWL (blue dashed line). Calculated Δabs spectra of (d) a free WT CEWL, (e) a bound WT CEWL-3NAG inhibitor, (f) a free CEWL mutant, and (g) a bound CEWL-3NAG inhibitor mutant. The color scale follows that in Fig. 1; however, the range here is [−30, +15]. The symmetry for the anisotropic calculations reflects the experimental configuration. To see this figure in color, go online.

Comment in

  • Pickin' Up Good Vibrations.
    Smith JC. Smith JC. Biophys J. 2017 Mar 14;112(5):829-830. doi: 10.1016/j.bpj.2017.01.008. Biophys J. 2017. PMID: 28297641 Free PMC article. No abstract available.

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