Lysozyme hinge-bending mode

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. 

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). 

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. 

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.

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

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.

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... 

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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