Dynamics, ligand complexes

To enable an atomic interpretation of the AFM experiments, we have developed a molecular dynamics technique to simulate these experiments [49], Prom such force simulations rupture models at atomic resolution were derived and checked by comparisons of the computed rupture forces with the experimental ones. In order to facilitate such checks, the simulations have been set up to resemble the AFM experiment in as many details as possible (Fig. 4, bottom) the protein-ligand complex was simulated in atomic detail starting from the crystal structure, water solvent was included within the simulation system to account for solvation effects, the protein was held in place by keeping its center of mass fixed (so that internal motions were not hindered), the cantilever was simulated by use of a harmonic spring potential and, finally, the simulated cantilever was connected to the particular atom of the ligand, to which in the AFM experiment the linker molecule was connected. 

Schmidtke H-H, Degan J (1989) A Dynamic Ligand Field Theory for Vibronic Structures Rationalizing Electronic Spectra of Transition Metal Complex Compounds. 71 99-124 Schneider W (1975) Kinetics and Mechanism of Metalloporphyrin Formation. 23 123-166... 

Molecular simulation methods can be a complement to surface complexation modeling on metal-bacteria adsorption reactions, which provides a more detailed and atomistic information of how metal cations interact with specific functional groups within bacterial cell wall. Johnson et al., (2006) applied molecular dynamics (MD) simulations to analyze equilibrium structures, coordination bond distances of metal-ligand complexes. 

NMR is a powerful and versatile tool for structural studies of biological RNAs and complexes they form with other nucleic acids, proteins, and small molecules. The goal of these studies is to determine the role that structure and dynamics play in biological function. NMR has the capacity to determine high-resolution structures, as well as to map RNAiligand interfaces at low resolution. Most structures of RNA and RNA-ligand complexes are under 20 KDa in size however, recent advances allow for determination of solution structures of complexes up to 40 kDa. NMR can also probe dynamic motions in RNA on micro- to millisecond time scales. A number of biologically relevant internal motions such as... 

Hegener, O., Prenner, L., Runkel, F., Baader, S. L., Kappler, J., and Haberlein, H. (2004). Dynamics of b2-adrenegic receptor-ligand complexes on living cells. Biochemistry 43, 6190-6199. 

In the pharamaceutical industry, NMR spectroscopy has demonstrated itself to be a powerful, highly versatile tool that has impact throughout the drug discovery process. NMR is frequently used as an assay to screen compound collections, to facilitate the assessment of hits, and to provide detailed structural and dynamical characterization of protein-ligand complexes. Because NMR can provide information in discrete units, the spectroscopist can fine tune data collection strategies. 

Walter, N. G., and Burke, J. M. (2000). Fluorescence assays to study structure, dynamics, and function of RNA and RNA-ligand complexes. Methods Enzymol. 317, 409-440. Walter, F., Murchie, A. I. H., Duckett, D. R., and Lilley, D. M. J. (1998a). Global structure of four-way RNA junctions studied using fluorescence resonance energy transfer. RNA 4, 719-728. 

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