Kinetics of conformational change

Kinetic information on the molecular conformational change can be extracted from dynamic mechanical studies, as described in Chapter 10, from the closely related acoustic relaxation experiments described in Chapter 11, and from dielectric relaxation covered in Chapter 12. In all of these, the observation of a transition in the frequency dependence of the property under study yields a relaxation time for the molecular process. This in turn transforms into the kinetics of the movement. Again, the activation energy associated with the conformational change is obtained from the effect of temperature on the relaxation time, using either the Arrhenius equation or a related analysis. 

Much of what is known about the dynamics of molecular movement has come from such studies. However, these relaxation techniques have an intrinsic problem. They indicate the way in which the rate of a process changes with temperature, but, unlike resonance spectroscopic methods, do not identify the particular molecular transformations which are responsible. 

Information on the reorientation of specific groups in a polymer molecule can be obtained by extending the time dependent photo processes, described in 

Chapter 13, using polarised exciting light. Examination of the depolarisation of the resulting luminescence allows orientation of a specific chromophore to be selected and its rotation studied. This can be done in steady state experiments which yield the amount of rotation of the excited state during its lifetime. More informative are time dependent observations of the polarised and depolarised emissions. Unfortunately, most common polymers do not have chromophores that can easily be studied in this way. Luminescent probes can be attached to the polymer backbone and these used to monitor the motion. However, such measurements usually indicate the way in which the probe is attached to the polymer rather than the intrinsic motion of the polymer chain. 

In both the spectroscopic and the relaxation measurements, the most direct time resolved information about rapid processes is obtained using pulsed excitation. This allows the collection of data from multiple pulses extending over convenient measurement times. 

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Evidence indicates that microwaves affect the kinetics of conformation changes of proteins such as P-lactoglobulin (Bohr and Bohr, 2000). It is thought that even approximately a few GHz can excite protein molecules. Consequently, the kinetics of conformational changes of the protein molecule are enhanced, and this denaturing effect is... 

Nevertheless, the ability to constrain dihedral angles can be useful in simulations in which one needs to assess the behavior of a molecule as a function of conformation. An important application of this type of constraint is the evaluation of potentials of mean force (PMF), which provide the work required to move the system along a predefined dihedral coordinate. The thermal probability is directly related to this free energy profile. PMF provide a means of estimating relative stabilities of conformers as well as the kinetics of conformational changes. 

Van Tassel P R, Guemourl L, Ramsden J J, Tar]us G, VIot P and Talbot J 1998 A model for the Influence of conformational change on protein adsorption kinetics J. Colloid Interfaoe Sc/. 207 317-23... 

The possibility of conformational changes in chains between chemical junctions for weakly crosslinked CP in ionization is confirmed also by the investigation of the kinetic mobility of elements of the reticular structure by polarized luminescence [32, 33]. Polarized luminescence is used for the study of relaxation properties of structural elements with covalently bonded luminescent labels [44,45]. For a microdisperse form of a macroreticular MA-EDMA (2.5 mol% EDMA) copolymer (Fig. 9 a, curves 1 and 2), as compared to linear PM A, the inner structure of chain parts is more stable and the conformational transition is more distinct. A similar kind of dependence is also observed for a weakly crosslinked AA-EDMA (2.5 mol%) copolymer (Fig. 9b, curves 4 and 5). 

Kane DJ, Fendler K, Grell E et al (1997) Stopped-flow kinetic investigations of conformational changes of pig kidney Na+,K+-ATPase. Biochemistry 36 13406-13420... 

Seeman, J. I. Effect of conformational change on reactivity in organic chemistry. Evaluations, applications, and extensions of Curtin-Ham-mett/Winstein-Holness kinetics. Chem. Rev. 1983, 83, 83-134. 

The chromophoric pyridoxal phosphate coenzyme provides a useful spectrophotometric probe of catalytic events and of conformational changes that occur at the pyridoxal phosphate site of the P subunit and of the aiPi complex. Tryptophan synthase belongs to a class of pyridoxal phosphate enzymes that catalyze /3-replacement and / -elimination reactions.3 The reactions proceed through a series of pyridoxal phosphate-substrate intermediates (Fig. 7.6) that have characteristic spectral properties. Steady-state and rapid kinetic studies of the P subunit and of the aiPi complex in solution have demonstrated the formation and disappearance of these intermediates.73-90 Fig. 7.7 illustrates the use of rapid-scanning stopped-flow UV-visible spectroscopy to investigate the effects of single amino acid substitutions in the a subunit on the rate of reactions of L-serine at the active site of the P subunit.89 Formation of enzyme-substrate intermediates has also been observed with the 012P2 complex in the crystalline state.91 ... 

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