Protein strain

With Warshel s or our definition of strain, we have shown without any doubts that the cupric structure of the blue copper proteins is not strained to any signifi- 

Another problem with small models is that molecules from the solution (e.g. water) may come in and stabilise tetragonal structures and higher coordination numbers [224]. It is illustrative that very few inorganic con5)lexes reproduce the properties of the blue copper proteins [66,67], whereas typical blue-copper sites have been constructed in several proteins and peptides by metal substitution, e.g. insulin, alcohol dehydrogenase, and superoxide dismutase [66]. This shows that the problem is more related to protection from water and dimer formation than to strain. 

it is clear that the surrounding protein and solvent have an important influence on the structure and spectra of the copper sites. For reduction potentials and outer-sphere reorganisadon energies, these effects are of the same magnitude as the electronic effects and therefore essendal. We have used three different levels of approximadons for these effects an array of point charges, condnuum models, and combined quantum chemical and classical simuladons. We andcipate that this will be an area of intensive development in the future. 

In conclusion, we have shown that theoredcal calculadons can be used to successfully solve biochemical problems. In similarity with experimental methods, they involve assumptions and interpretadon, and they have their limitadons, but there are many problems that are best studied by theory. Thus, theoredcal meth- 

Williams (1963) in Molecular basis of enzyme action and inhibition (P.A.E. Desnuelle, ed), p. 133, Pergamon Press, Oxford. 

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We observed that addition of free biotin to the growth medium increases the extent of biotinylation of the recombinant BCCP fusion protein. Strains overexpressing the E. coli biotin ligase are also available from Avidity (www.avidity.com) if desired, although we have not found this necessary when using the BCCP tag. The wash step prior to cell lysis is needed to remove free biotin before array fabrication if the protein is purified before array fabrication, this is not necessary. 

Fluorescent protein strains Thyl-TFP-16 3709 YFP expression in all motor neurons (166)... 

Total synthesis of peptides is rarely an economical method for their commercial production. Important peptides are usually derived from biological sources. For example, insulin for diabetics was originally taken from pork pancreas. Now, recombinant DNA techniques have improved the quality and availability of peptide pharmaceuticals. It is possible to extract the piece of DNA that contains the code for a particular protein, insert it into a bacterium, and induce the bacterium to produce the protein. Strains of Escherichia coli have been developed to produce human insulin that avoids dangerous reactions in people who are allergic to pork products. 

According to the induced-rack and the entatic state hypotheses [10,12], the Cu(II) coordination sphere in the blue copper proteins is strained into a Cu(I)-like structure. Such hypotheses are hard to test experimentally, but with theoretical methods it is quite straightforward. The actual coordination preferences of the copper ion can be determined by optimising the geometry of the ion and its ligands in vacuum if the optimised structure is almost the same as in the proteins, strain is probably of minor importance for the geometry. 

At first, these improved structures could be taken as evidence for protein strain. However, the ComQum calculations involve effects that are normally not considered as strain, e.g. the change in the dielectric surrounding of the copper... 

During electron transfer, the Cua site alternates between the fully reduced and the mixed-valence (Cu +Cu ) forms. Interestingly, the unpaired electron in the mixed-valence form seems to be delocalised between the two copper ions. Several theoretical investigations of the electronic structure and spectrum of the Cua dimer have been published [138-144]. In similarity to the blue copper proteins, it has been suggested that the structure and the properties of the Cua site is determined by protein strain. More precisely, it has been proposed [136] that Cua in its natural state is similar to an inorganic model studied by Tolman and coworkers [145]. This complex has a long Cu-Cu bond (293 pm) and short axial interactions (-212 pm). The protein is said to enforce weaker axial interactions, which is conpensated by shorter bonds to the other ligands and the formation of a Cu-Cu bond. This should allow the protein to modulate the reduction potential of the site [136,146]. 

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