Conformational dynamics

Eggeling C, Fries J R, Brand L, Gunther R and Seidel CAM 1998 Monitoring conformational dynamics of a single molecule by selective fluorescence spectroscopy Proc. Natl Acad. Sc/. USA 95 1556-61... 

Ha T, Ting A Y, Liang J, Caldwell W B, Deniz A A, Chemla D S, Schultz P G and Weiss S 1999 Single-molecule fluorescence spectroscopy of enzyme conformational dynamics and cleavage mechanism Proc. Natl Acad. Sc/. USA 96 893-8... 

Figure 8 shows a one-dimensional sketch of a small fraction of that energy landscape (bold line) including one conformational substate (minimum) as well as, to the right, one out of the typically huge number of barriers separating this local minimum from other ones. Keeping this picture in mind the conformational dynamics of a protein can be characterized as jumps between these local minima. At the MD time scale below nanoseconds only very low barriers can be overcome, so that the studied protein remains in or close to its initial conformational substate and no predictions of slower conformational transitions can be made. 

Conformational Dynamics Simulations of Proteins molecular dynamics conformational flooding... 

H. Grubmiiller, N. Ehrenhofer, and P. Tavan. Conformational dynamics of proteins Beyond the nanosecond time scale. In M. Peyard, editor. Proceedings of the Workshop Nonlinear Excitations in BiomoleculesMay 30-June 4, 1994, Houches (Prance), Seiten 231-240. Centre de Physique des Houches (France), Springer-Verlag, 1995. 

The first chapter, on Conformational Dynamics, includes discussion of several rather recent computational approaches to treat the dominant slow modes of molecular dynamical systems. In the first paper, SCHULTEN and his group review the new field of steered molecular dynamics (SMD), in which large external forces are applied in order to be able to study unbinding of ligands and conformation changes on time scales accessible to MD... 

AE Garcia, G Hummer. Conformational dynamics of cytochrome c CoiTelation to hydrogen exchange. Proteins 36 175-191, 1999. 

The binding and activation steps of receptor action have been dissected computationally, although not yet in a global fashion. The conformational dynamics of the activation of the A3AR have been approximated with respect to isolated portions of the receptor. 

The conformational dynamics of chain segments near the head groups is more restricted than that of those far from the micellar core [8]. Moreover, to avoid the presence of energetically unfavorable void space in the micellar aggregate and as a consequence of the intermolecular interactions, surfactant molecules tend to assume some preferential conformations and a staggered position with respect to the micellar core [9]. A schematic representation of a reversed micelle is shown in Figure 1. 

Shi, X Hammond, RW Morris, MD, DNA Conformational Dynamics in Polymer Solutions Above and Below the Entanglement Limit, Analytical Chemistry 67, 1132, 1995. 

Vistoli, G., Pedretti, A., Villa, L, Testa, B. The solute-solvent system solvent constraints on the conformational dynamics of acetylcholine, f Am. Chem. Soc. 2002, 124, 7472-7480. 

Schwinefus, J.J., Hammond, R.W., Oana, H., Wang, S.-C., De Carmejane, O., Bonadio, ]., and Morris, M.M., Comparative conformational dynamics of su-percoiled plasmids and linear DNA during capillary electrophoresis, Macromolecules, 32, 4625, 1999. 

The examples above serve to illustrate that the conformational dynamics of enzyme turnover create multiple, specific binding pocket configurations throughout the reaction pathway, each representing a distinct opportunity for drug binding and inhibition. 

To most effectively search chemical libraries for diverse lead molecules, enzyme assays used for HTS must take into account the conformational dynamics of enzyme catalysis and the physiological context of enzyme action in vivo. 

In recent years, a class of methods has been developed for molecular dynamics simulations to be performed with an external pH parameter, like temperature or pressure [18, 43, 44, 70], These methods treat the solution as an infinite proton bath, and are thus referred to as constant pH molecular dynamics (PHMD). In PHMD, conformational dynamics of a protein is sampled simultaneously with the protonation states as a function of pH. As a result, protein dielectric response to the... 

Three fluorescent purine analogs will be described here 2-aminopurine (2AP) [183] and 8-vinyladenine (8VAD), both of which mimic adenine, and N1,N6-ethenoadenine (e-AD). Their structures are shown in Figure 11-15. 2AP is probably the most widely used fluorescent DNA base analog, being utilized as a probe for DNA conformational dynamics [184, 185], due to the environmental specificity of... 

Bouvier B, Dognon J-P, Lavery R, Markovitsi D, Millie P, Onidas D, Zakrzewska K (2003) Influence of conformational dynamics on the exciton states of DNA oligomers. J Phys Chem B 107 13512-13522... 

Crothers D (2001) RNA, chap. RNA Conformational Dynamics, Elsevier Science Technology, Amsterdam, pp 61-71. 

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