Lysozyme hinge bending

Figure 36. Stereo views of residue displacements in the lysozyme hinge bending. The thin line on each C shows the direction and magnitude of the mass-weighted rms residue displacements for a closing, 2-A mass-weighted rms step along the normalized mode, (a) Rigid model (i>) normal mode that has the best overlap with the rigid model.

In an early study of lysozyme ([McCammon et al. 1976]), the two domains of this protein were assumed to be rigid, and the hinge-bending motion in the presence of solvent was described by the Langevin equation for a damped harmonic oscillator. The angular displacement 0 from the equilibrium position is thus governed by... 

B. R. Brooks and M. Karplus. Normal modes for specific motions of macromolecules Application to the hinge-bending mode of lysozyme. Proc. Natl. Acad. Sci. USA, 82 4995-4999, 1985. 

Figure 4 DynDom [67] analysis of the first two normal modes of human lysozyme. Dark grey and white indicate the two dynamic domains, separated by the black hinge bending region. The vertical line represents a hinge axis that produces a closure motion in the first normal mode. The horizontal line represents a hinge axis that produces a twisting motion in the second normal mode. (Adapted from Ref. 68.) The DynDom program is available from the Internet at http //md. chem.rug.nl/ steve/dyndom.html.

The internal motion of T4 lysozyme in the crystal was interpreted as an inter-domain motion corresponding to opening and closing of the active site cleft (Weaver et al., 1989). Hinge-bending and substrate-induced conformational transition in T4 lysozyme in solution were confirmed in a study by site-directed labelling (Mchaourban et al., 1997). 

Neutron spectroscopy is becoming a principal tool for the study of protein dynamics (Cusack, 1986, 1989 Middendorf, 1984 Middendorf et al., 1984). Current instruments cover motions with characteristic times from 10 to 10 sec. This range embraces essentially all protein modes excited at room temperature (the soft modes), including motions of the solvent shell and also low-frequency large-scale domain motions, like the hinge-bending motion of the lysozyme domains that form the... 

Comparison of neutron scattering of lysozyme at 0.07 and 0.20 h (Smith et al., 1987) showed that hydration decreased elastic scattering and increased inelastic scattering between 0.8 and 4.0 cm". This observation is consistent with an increase in the number of low-frequency modes. Normal mode analysis indicates that the lowest frequency mode of lysozyme and the hinge-bending mode fall in this frequency range (Brooks and Karplus, 1985 Bruccoleri et al., 1986 Levitt et al., 1985). Hydration of a protein has little effect on the scattering spectrum, outside of that noted above (Cusack, 1989). 

Figure 24.2a shows dual fluorescence intensity trajectories simultaneously recorded from a donor-acceptor labeled T4 lysozyme in the presence of substrate at pH 7.2. The anticorrelated fluctuations (Fig. 24.2a and b) are due to spFRET, reporting the donor-acceptor distance change associated with the protein conformational motion. Likewise, fluorescence trajectories of donor-acceptor labeled T4 lysozyme without substrates did not show anticorrelated behavior (Fig. 24.2c and d). We attribute this conformational motion to an enzymatic-related motion, most likely the open-closed hinge-bending motion... 

Fig. 24.4. Simultaneous probing of a single T4 lysozyme enzymatic reaction turnover trajectory with correlated hinge-bending conformational motions of the enzyme under hydroiysis of polysaccharide of a cell wall. The data in the three panels were recorded in 0.65 ms per chaimel at the same enzymatic reaction condition. The upper panei shows an expanded portion of a trajectory (middie panel) from donor fluorescence of a donor-acceptor labeled single-T4 lysozyme. Intensity wiggles in the trajectory are evident beyond the measurement shot noise. The lower panel shows a portion of a trajectory recorded from a donor-aione-iabeied enzyme. The fluorescence intensity distributions derived from the two trajectories are shown in the insets of the middle and lower panels. The solid lines are fit using bimodal and Gaussian functions, respectively. The T4 lysozyme was covalently linked to a hydrocarbon-modified glass cover slip by the bi-fimctional linker SIAXX (Molec-uiar Probes, Inc.) (Adapted with permission from [12]. Copyright 2003 American Chemicai Society)...

E-fS ES ES. The standard deviation of the distribution, (Atopen ) = 8.3 2ms, reflects the distribution bandwidth. For the individual T4 lysozyme molecules examined under the same enz unatic reaction conditions, we found that the first and second moments of the single-molecule topen distributions are homogeneous, within the error bars. The hinge-bending motion allows sufficient structural flexibility for the enzyme to optimize its domain conformation the donor fluorescence essentially reaches the same intensity in each turnover, reflecting the domain conformation reoccurrence. The distribution with a defined first moment and second moment shows typical oscillatory conformational motions. The nonequilibrium conformational motions in forming the active enzymatic reaction intermediate states intrinsically define a recurrence of the essentially similar potential surface for the enzymatic reaction to occur, which represents a memory effect in the enzymatic reaction conformational dynamics [12,41,42]. 

Figure 5. The hinge-bending potential for free and bound lysozyme systems (from Bruccoleri et al. 1986) (a) steepest descents protocol (b) spatially constrained protocol. The circles are the points calculated by the protocols, the line is the least-squares fit parabola. All plots are on the same scale with energies in units of kcal/mole and angles in degrees. Positive angles correspond to closing.

Brooks, B. R. and Kamlus, M. (1985) Normal Modes for Specific Motions of Macromolecules Application to the Hinge-Bending Mode of Lysozyme, Proc. Natl Acad. Sci. USA 82, 4995-4999. 

Bruccoleri, R. E., Karplus, M. and McCammon, J. A. (1986) The Hinge-Bending Mode of a Lysozyme-Inhibitor Complex, Biopolymers 25, 1767-1802. 

Bruccoleri, R.E., Karpins, M., McCammon, J.A. The hinge-bending mode of a lysozyme-inhibitor complex. Biopolymers 25, 1767-1802 (1986)... 

Mouse epidermal growth factor (EOF) is a relatively small protein consisting of 53 amino acids with three disulfide bonds. EGF can be described as a right-handed mitten where the thumb and palm represent separate domains and the hollow is postulated as the site where the EGF receptor binds. Ikura and Go have carried out a normal mode analysis of this protein. As was the case with lysozyme, the lowest frequency mode (4.1 cm" ) corresponds to a hinge-bending motion. This finding helps to rationalize the difference between two NMR structures which have been solved for this molecule. These two structures differed in terms of the distance between the two domains, due to the paucity of interdomain NOEs. Normal modes have also been incorporated into the structure determination process, as described in Sections 3.4 and 3.5. 

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