Domain movement

Molecular dynamics simulations ([McCammon and Harvey 1987]) propagate an atomistic system by iteratively solving Newton s equation of motion for each atomic particle. Due to computational constraints, simulations can only be extended to a typical time scale of 1 ns currently, and conformational transitions such as protein domains movements are unlikely to be observed. 

Ion channels open or close upon relative movement of internal domains, movements that can be elicited by... 

Fig. 7.3. Conformational changes and E2-binding specificity of the HECTdomain. (A) Schematic diagram of the structures of E6AP and WWPl HECT domains with their N-lobes superimposed indicating the potential large domain movement of the HECT E3. (B)...

This extrinsic domain movement is explained using a combination of two rotations (i) whole domain rotations against the rest of the complex and (ii) the relative rotations within the domain between base and cluster binding folds. Between these, the rotation of the whole domain is more prominent than the rotation within the domain. Therefore, as a first approximation, the conformational change of ISP is well described by rotation of the whole extrinsic domain. 

Mould, A. P., Barton, S. J., Askari, J. A., McEwan, P. A., Buckley, P. A., Craig, S. E., and Humphries, M.J. (2003b). Conformational changes in the integrin j3A domain provide a mechanism for signal transduction via hybrid domain movement. / Biol. Chem. 278, 17028-17035. 

Darrouzet, E.,Valkova-Valchanova, M., Moser, C. C., Dutton, P. L., and Daldal, F., 1999, Uncovering the [2Fe2S] domain movement in cytochrome bcG implications for energy conversion and a target for antibiotics submitted. 

Tian, H., White, S., Yu, L., and Yu, C. A., 1999, Evidence for the head domain movement of the rieske iron-sulfur protein in electron transfer reaction of the cytochrome bcl complex, J. Biol. Chem. 274 7146n7152. 

Magnetostriction is the dimensional change (strain) which accompanies the domain movement and rotation of magnetization. When the magnetio field vibrates so does mag-netostriotion, and as a result ultrasonic waves are produced. A magnetostrictive transducer (MART) is a transducer in a non-contact US instrument where the coated sample... 

Proper substrate binding allows for the hound (closed) state (EzS) to be in dynamic equilibrium with free substrate. Upon domain closure, catalytic reaction can occur to transform the bound state (EzS) to an energetically less stable state than the open state of the protein (F.zP) by altering the interactions between the protein and the bound molecule. Note that the upper limit on the rate of catalytic reaction should, therefore, be fixed by the rate of domain movements. Since the open state is more energetically favored, the product will desorb to return the enzyme to the open state. 

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