And conformational changes

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... 

Rotation about single bonds and conformational changes can be studied. Amides constitute a classic example. Because of the partial double bond character of the carbon-nitrogen bond as a consequence of the contribution of 2 to the electronic structure, there is an energy barrier to rotation about this bond. 

Based on the information presented in the text and in Figures 25.4 and 25.5, suggest a model for the regulation of acetyl-CoA carboxylase. Consider the possible roles of subunit interactions, phosphorylation, and conformation changes in your model. 

These first-created enantiophores are rudimentary, but may serve as useful guidelines for a further design of more sophisticated and efficient search queries in consideration of possible alternative modes of binding and conformational changes in the CSP receptor structure. Undoubtedly, this query optimization will soon take advantage of the backgrounds of our new 3D-database project called CHIR-SOURCE. 

Exchange of counter-ions (and solvent) between the polymer and the solution in order to keep the electroneutrality in the film. In a compacted or stressed film, these kinetics are under conformational relaxation control while the structure relaxes. After the initial relaxation, the polymer swells, and conformational changes continue under counter-ion diffusion control in the gel film from the solution. 

These equations describe the full oxidation of a conducting polymer Submitted to a potential step under electrochemically stimulated confer-mational relaxation control as a function of electrochemical and structural variables. The initial term of /(f) includes the evolution of the current consumed to relax the structure. The second term indicates an interdependence between counter-ion diffusion and conformational changes, which are responsible for the overall oxidation and swelling of the polymer under diffusion control. 

Younis, H.M., Weber, G. Boyer, J.S. (1983). Activity and conformational changes in chloroplast coupling factor induced by ion binding Formation of a magnesium-enzyme-phosphate complex. Biochemistry, 22, 2505-12. 

The conformation of macro- or polyions has been defined and discussed briefly in Section 4.1.1. The conformation of a polyion is determined by a balance between contractile forces, which depend on conformation free energy, and extension forces, which arise from electrical free energy. The extent of conformational change is determined by several factors. Changes are facilitated by the degree of flexibility of the polyion, and conformational change is greatest at low concentration of polyions. 

Glucose may auto-oxidize (like other alphahydroxy-aldehydes) and generate hydroxyl radicals in a transition-metal-catalysed reaction, and induce both fragmentation and conformational changes in glycated proteins (Hunt et al., 1990). 

F. X. Schmid, Spectral methods of characterizing protein conformation and conformational changes, in Protein Structure—A Practical Approach (T.E. Creighton, ed.), IRL Press, Oxford, 1989, pp. 251-285. 

Wang S, Wang X, Shi W et al (2008) Detection of local polarity and conformational changes at the active site of rabbit muscle creatine kinase with a new arginine-specific fluorescent probe. Biochim Biophys Acta 1784 415 -22... 

The polynuclear platinum compounds stand in vivid contrast to mononuclear platinum complexes because the predominant DNA lesions are long-range inter- and intrastrand cross-links where the sites of platination may be separated by up to four base pairs. The consequent structural and conformational changes in DNA are also distinct. 

One of the most characteristic features of FRET is its sensitive dependency on the fluorophore distance. This is advantageously used to evaluate structures and conformational changes of peptides, glycopeptides, and proteins among other molecules [164-166], The conformational change of the lipopeptide antibiotic daptomycin from an inactive linear form to a biological active cyclic form... 

Danielson MA, Falke JJ (1996) Use of F-19 NMR to probe protein structure and conformational changes. Annu Rev Biophys Biomol Struct 25 163-195... 

Using molecular dynamics and free energy analyses to calculate the free energies of binding and conformational change, J. Mol. Biol. 297 1145 (2000). 

Fig. 4 Integrated molecular systems for information transduction through intermolecular electron transfer and conformation change...

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