Dynamics of conformational change

Since we are concerned with the dynamics, we have to ask how long it takes for a monomer unit to hop between the various states. The time can be of the order of 10 to 10 s. So the step interval in the computation is often taken as 10 ° s to allow the changes to be accurately mapped. This is extremely laborious and so an alternative approach is required. We achieve this with a molecular kinetic model. 

Kinetic studies of the interchange process allow rate and energy values for specific changes to be measured. In the usual case, where there is more than one higher energy state, an average value is observed. Of course, if the technique can identify a specific conformation, then an exact value can be measured. However, in the case of a polymer molecule, average values are observed. 

Alternatively, if we were to attempt to achieve rotation about one single backbone bond, the motion would require a large element of the polymer chain to move through space. This is very unlikely to occur. So we next look at the coupled nature of the motions in polymers. 

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Wiberg KB, Boyd RH (1972) Application of strain energy minimization to the dynamics of conformational change. J Am Chem Soc 94 8426- 8430... 

Irie, M. and Schnabel, W. (1981) Photoresponsive polymers - on the dynamics of conformational-changes of polyamides with backbone azobenzene groups. Macromolecules, 14, 1246-1249. 

Schlitter et al., 1993] Schlitter, J., Engels, M., Kruger, P., Jacoby, E., and Wollmer, A. Targeted molecular dynamics simulation of conformational change - application to the t <- r transition in insulin. Molecular Simulation. 10 (1993) 291-308... 

The classical microscopic description of molecular processes leads to a mathematical model in terms of Hamiltonian differential equations. In principle, the discretization of such systems permits a simulation of the dynamics. However, as will be worked out below in Section 2, both forward and backward numerical analysis restrict such simulations to only short time spans and to comparatively small discretization steps. Fortunately, most questions of chemical relevance just require the computation of averages of physical observables, of stable conformations or of conformational changes. The computation of averages is usually performed on a statistical physics basis. In the subsequent Section 3 we advocate a new computational approach on the basis of the mathematical theory of dynamical systems we directly solve a... 

The authors believe that electron exchange occurs at every intramolecular collision . Thus, their work should provide the first quantitative measurements of the frequency of intramolecular collision between end-groups attached to flexible chains. According to these authors such frequency reflects an intrinsic property of chain molecules, referred to as the dynamic flexibility, which is a measure of the rate of conformational change. It should be distinguished from the static flexibility, which depends on the multitude of... 

D. Genest and P. Wahl, in Dynamic Aspects of Conformational Change in Biological Macromolecules (C. Sadron, ed.), pp. 367-379, D. Reidel, Dordrecht, Holland (1973). 

For ribonuclease A the occurrence of conformational changes and the occurrence of acid-base catalysis has been well documented. The overall mechanism can be envisaged as follows. The enzyme exists in dynamic equilibrium between two forms differing in the structure of the active site groove. The substrate is bound almost as rapidly as it can diffuse to the active site. Binding of the substrate induces a conformational change that... 

Any one of the five methylene groups of cyclopentane can be bent out of plane thus cyclopentane is a dynamic system which undergoes a series of conformational changes between different envelope conformations. 

Several biophysical tools can provide information on the stmcture, dynamics, and conformational changes of membrane proteins. Many of these methods are beyond the scope of this review and were not mentioned here. However, each of these approaches has strengths and weaknesses to investigate membrane protein stmcture and functional dynamics fully, a multitude of techniques is required. Static high-resolution stmctures... 

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