Looping motion

Loop motion Active site conformation adap- Nanoseconds (ns) to micro-... 

EGS and sulfo-EGS also have been used to study the surface loop motion in FepA (Scott et al., 2002), to characterize the high affinity copper transporter in Saccharomyces cerevi-siae (Pena et al., 2000), and in the study of protein interactions and large protein complexes (Petrotchenko et al., 2005(2005 a or b ). 

Positioning systems can use either an open-loop or a closed-loop control system. In closed-loop motion control, such as the optimized positioning of solar collectors based on measuring their shadows, the positions of both the collector and the shadow are continuously detected. Based on this feedback, the position and velocity of the collector can both be controlled. The reported position is continuously compared to the desired one, and the collector is moved to reduce the error between the two. This is called servo control (Figure 3.154). 

Basic block diagram of a closed-loop motion control system. 

Gryk, M.R., Abseher, R., Simon, B., Nilges, M., and Oshkinat, H. (1998) Heteronuclearrelaxation study ofthe pH domain ofb-spectrin restriction of loop motion upon binding inisitol triphosphate, J. Mol. Biol. 280, 879-986. 

Rozovscy, S. and McDermott, A. E. (2001) The times scale of the catalytic loop motion in triosephosphate isomerazey. Mol. Biol. 310, 259-270. 

Williams, J. C. and McDermott, A. E. (1995) Dynamics of the Flexible Loop of Triosephosphate Isomerase The Loop Motion is Not Ligand Gated, Biochemistry 34, 8309-8319. 

Rurkcuoglu Z, Bakan A, Kocaman D et al (2012) Coupling between catalytic loop motions and enzyme global dynamics. PLoS Comput Biol 8 el002705... 

In both studies, the flexible loops of TIM were held fixed in the open position. Therefore the effect the motion of the loops may have in binding is still unknown. To address this issue, a simulation of the loop motion in TIM was carried out and is described in the next section. 

Numerous experimental and theoretical studies have documented the direct correlation between internal motions of an enzyme and its activity. For example, the catalytic activities of many enzymes are closely associated with loop motions, which open and close the active site and also position key residues into contact with the substrate [7, 8]. X-ray crystal structmes of hgand-bound and fi-ee enzymes show that substantial conformational changes can be induced by ligand binding and by chemical transformation during an enzymatic reaction [9, 10]. The reaction catalyzed by thymidylate synthase has been shown to couple directly with the protein s conformation-... 

Williams, J.C. McDermott, A.E. Dynamics of the flexible loop of triose-phosphate isomerase—The loop motion is not ligand-gated. Biochemistry 1995, 34. 8309-8319. Holbrook, J.J. Liljas, A. Steindel, S.J.. et al. Lactate dehpdrogenase. Enzymes 1975,11, 191-292. 3rd ed. Wilks, H.M. Halsall. D.J. Atkinson, T., et al. Designs for a broad substrate-specificity keto acid dehydrogenase. Biochemistry 1990, 29. 8587-8591. 

The normal case with a molten or dissolved polymer is that its conformational jumps are quite rapid, compared with the tumbling and looping motions of entire chains. A typical barrier to a conformational jump in a vinyl polymer chain without external constraints is only approximately 12-20 kJ mol and is therefore readily surmounted at room temperature, typically at least 10 times per second. In this case, the local motions will contribute to the NMR relaxation parameters of the polymer, such as T, T2 and NOE. Similar motions will occur in the gel state and in the flexible solid, above Tg. 

If the molecule also undergoes slow isotropic rotation as before, then this will also tend to reduce G(t) towards zero, but much more slowly than the timescale for libration. (The same will often turn out to be true for the looping motions of a polymer chain). Thus,... 

Rozovsky, S., Jogl, G., Tong, L., and McDermott, A.E. 2001. Solution-state NMR investigations of triosephos-phate isomerase active site loop motion Ligand release in relation to active site loop dynamics. J. Mol. Biol. 310 271-280. 

FIGURE 18.64 A typical closed loop motion control or servo system. 

The closed-loop stability of the batch motion can be established with the application of the standard singular perturbation [25] or small gain theorems [8, 10] available in the nonlinear dynamical systems literature, in eonjunction with the definition (7) of finite-time motion stability. In a chemical process context this closed-loop stability assessments can be seen in the cascade control of a continuous reactor [22], the cascade control of a continuous distillation [21, 24], and in the calorimetric estimation [15] of a batch polymer reactor. The closed-loop motion stability is ensured if the observer gain ( o) is tuned slower than the characteristic frequency ( j) of the fastest unmodeled dynamics, and the observer ( ), secondary ( ,.), and primary ( p) gains are sufficiently separated. This is. 

Since the reactor motion determines the product properties, the nominal operation and its control must be such that the closed-loop motion variability over the batch-to-batch operation is kept within specifications. 

The formal analysis of the closed-loop dynamics can be done with an extension of the nonlocal closed-loop stability analysis of a continuous reactor with temperature cascade controller presented before [22] in conjunction with the stability definitions (Eq. 7) given in section 2. Here it suffices to mention that, the closed-loop motion is stable if the filter and estimator gains are chosen not faster than the characteristic frequency Oj of the jacket hydraulic dynamics [26], and the secondary and primary control gains are chosen so that there is adequate dynamic separation between coj, coj and 0). This is,(Eq. 30),... 

A slow 11-hour semibatch (shown in [11]) exhibits an open-loop motion with a large degree of stability and a small product variability. As the semibatch time is decreased by... 

Troy, J.T., C.A Erignac, and P. Murray. 2007. Closed-loop Motion Capture Feedback Control of Small-scale Aerial Vehicles. AIAA Paper 2007-2905. Infotech Aerospace 2007 Conference and Exhibit, Rohnert Park, Calif., May 7-10, 2007. Reston, Va. American Institute of Aeronautics and Astronautics. 

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