Domain motions hinge-bending

Interestingly, there are many proteins with two domains that show a very clear hinge-bending motion with an obvious functional significance. Such domains have often been reported in the literature, but were never detected on an automated basis. 

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... 

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). 

A physical technique for the study of conformation based on measuring changes in heat capacity of a molecule under various conditions. See Zecchinon, L., Oriol, A., Netzel, U. et al.. Stability domains, substrate-induced conformational changes, and hinge-bending motions in a psychro-philic phosphoglycerate kinase. A microcalorimetric study, J. Biol. Chem. 280, 41307-41314, 2005. 

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... 

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]. 

Early modelling of this system was carried out by Miaskiewicz and Orstein [96] who performed dynamic simulations on isolated TBP and on its complex with DNA. Their study showed that the protein underwent large hinge-bending movements between the two domains of the protein. These motions changed the angle between the domains from 150° (its value in the complex) to roughly 90°. 

One of the most common applications of protein normal mode analysis is to the study of hinge-bending in certain multi-domain proteins. Because functional sites are often found in the clefts between domains in such proteins, hinge-bending motions have been postulated to be integral to their function. An understanding of the dynamics of such systems is then critical to understanding their mechanism of action. 

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. 

An example of a protein that has multiple domains but which was not necessarily expected to undergo a hingebending motion is that of human CD4, the receptor for the human immunodeficiency virus (HIV), Hinge bending was not anticipated in this protein because the crystal structure of the two amino terminal domains showed them to be tightly abutting. Furthermore, no crystal structure was available for the complex between CD4 and gpl20, the HIV envelope protein. 

The hinge-bending motion of domains has been reported for several kinases. Thus, it is tempting as a working hypothesis to assume a correlation between this motion and the characteristic enzyme memory described for wheat germ hexokinase acting as a mnemonic enzyme (Ricard et al. 1974). 

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