Open/closed motion

P. Derreumaux and T. Schlick. The loop opening/closing motion of the enzyme triosephosphate isomerase. Biophys. J., 74 72-81, 1998. 

Vajda S, Camacho CJ. Protein-protein docking is the glass half-full or half-empty Trends Biotechnol. 2004 22 110-116. Derreumaux P, Schlick T. The loop opening/closing motion of the enzyme triosephosphate isomerase. Biophys. J. 1998 74 72-81. Gerstein M, Chothia C. Analysis of protein loop closure. Two types of hinges produce one motion in lactate dehydrogenase. J. Mol Biol 1991 220 133-149. 

The total drifting distance of the conformational open-close motion in one enzymatic reaction turnover, (Xjv(f)), is about 9 A, based on our MD simulation (Fig. 24.6). The mean open-time, (fopen) and the standard deviation... 

UV light irradiation at 350 nm of a THF solution of the trans isomer resulted in a typical trans to cis isomerization of the azobenzene moiety (89% conversion), whereas irradiation with a visible light gave back to a transjcis isomer ratio of 46 54. Absorption, circular dichroism (CD) and NMR spectra of an enantiomer of 4 agreed well with the prediction by DFT calculations that the blade parts are opened when the azobenzene unit adopts a cis configuration while they are closed in the case of the trans isomer. Interestingly, the oxidation state of the ferrocene pivot was found to affect the PSSs of 4 and thus to allow a reversible open-closed motion by use of redox and UV light [20] (Scheme 3). 

Scheme 3 Open/closed motion of 4 induced by redox and ITV ...

Takahashi E, Takaya H, Naota T (2010) Dynamic vapochromic behaviors of oiganic crysttds on the open-close motions of S-shaped donor-acceptor folding units. Chem Eur J 16 4793-4802. doi 10.1002/chem.200903403... 

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... 

Figure 93 Molecular structures of the molecular scissor and cartoon representation of its open and close motion induced by photoisomerization of the azobenzene unit. (Reproduced from Ref. 154. American Chemical Society, 2003.)...

The kinematics of the opening and closing motion of a snuff-back valve is precisely the reverse of that of a needle seat valve (O Fig. 38.8). To open the valve, the piston is moved forward and this opens the valve cross section. To close the valve, the piston is retracted until the free cross section of the valve seat is closed. This generates a slight vacuum in the outlet needle, allowing... 

Fig. 5. Rigid-body analysis of citrate synthase, using two X-ray structures (after Hayward and Berendsen, Proteins 30 (1998) 144). The decomposition of the protein into two domains (dark gray and white) and two interconnecting regions (light gray) is shown, together with the hinge axis for the closing/opening motion between them.

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