Average solution structure

The preceding sections highlighted the similarities and differences between the static crystal structure and the average solution structure of rhodopsin in the cytoplasmic domain. This section considers fluctuations in the structure of the cytoplasmic domain relative to the average. This is of interest, because dynamics sequences are often correlated with function, and that appears to be the case in rhodopsin. 

In conclusion, NMR has become a routine and reliable technique for the determination of average solution structures of moderately sized nucleic acids of up to about 30-40 nt the challenges for structure determination increase more than linearly as molecular size increases. It is expected that development of experimental and computational techniques will lead to rapid progress in two directions a better understanding of flexibility and dynamics of nucleic acids in solution,342 343 and increasing the size limit of nucleic acids amenable to structure determination.254,259,261,265,275,296... 

Dgk is also available.The average solution structure calculated from NMR data is shown in Figure 3.25 See color plate section, page C-10.)... 

Ftg. 14. Proposed average, solution structure of the trimer consisting of pyrochlorophyllide a, pyrochlorophyllide b, and pyropheophorbide a in the presence of hydroxylic solvents. (From ref. 85)... 

Additional data in ref derived H.--H distances derived backbone torsion angles of average solution structure. 

For gas-phase molecules the assumption of electronic adiabaticity leads to the usual Bom-Oppenheimer approximation, in which the electronic wave function is optimized for fixed nuclei. For solutes, the situation is more complicated because there are two types of heavy-body motion, the solute nuclear coordinates, which are treated mechanically, and the solvent, which is treated statistically. The SCRF procedures correspond to optimizing the electronic wave function in the presence of fixed solute nuclei and for a statistical distribution of solvent coordinates, which in turn are in equilibrium with the average electronic structure. The treatment of the solvent as a dielectric material by the laws of classical electrostatics and the treatment of the electronic charge distribution of the solute by the square of its wave function correctly embodies the result of... 

Recently, Sivakolundu and Mabrouk published an NMR solution structure of horse heart ferrocytochrome c in which the heme contains an Fe(II) ion. This solution structure was the first in which the cytochrome c protein was dissolved in a nonaqueous solvent a solvent mix of 70% water and 30% acetonitrile (ACN). The data obtained from the NMR study are deposited in the protein data bank (PDB) as (1) ILCl, the minimized average NMR structure and (2) 1LC2, the 30 lowest energy NMR structures. 

At room temperature, the complexes are extremely fluxional and in fact the proton spectrum shows a doublet (due to coupling with Rh, spin 1/2) of triplets due to the averaged coupling constants of the two phosphorus nuclei. The details of chemical shifts and coupling constants are now well known and can be used for the determination of the solution structures [14]. 

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