Mutational approaches

Whiteaker, P., Marks, M.J., Grady, S.R. et al. Pharmacological and null mutation approaches reveal nicotinic receptor diversity. Eur. J. Pharmacol. 393 123, 2000. 

A MUTATIONAL APPROACH TO DISSECTION OF FLAVONOID BIOSYNTHESIS IN ARABIDOPSIS... 

Holmes A (2001) Targeted gene mutation approaches to the study of anxiety-like behavior in mice. Neurosci fiiobehav Rev 25 261-273... 

Winkel-Shirley, B., A mutational approach to dissection of fiavonoid biosynthesis in Arabidopsis, in Phytochemistry in the Genomics and Post-Genomics Eras, Romeo, J.T. and Dixon, R.A., Eds., Pergamon, New York, 2002, 95. 

Figure 11. The error threshold of replication and mutation in genotype space. Asexually reproducing populations with sufficiently accurate replication and mutation, approach stationary mutant distributions which cover some region in sequence space. The condition of stationarity leads to a (genotypic) error threshold. In order to sustain a stable population the error rate has to be below an upper limit above which the population starts to drift randomly through sequence space. In case of selective neutrality, i.e. the case of equal replication rate constants, the superiority becomes unity, Om = 1, and then stationarity is bound to zero error rate, pmax = 0. Polynucleotide replication in nature is confined also by a lower physical limit which is the maximum accuracy which can be achieved with the given molecular machinery. As shown in the illustration, the fraction of mutants increases with increasing error rate. More mutants and hence more diversity in the population imply more variability in optimization. The choice of an optimal mutation rate depends on the environment. In constant environments populations with lower mutation rates do better, and hence they will approach the lower limit. In highly variable environments those populations which approach the error threshold as closely as possible have an advantage. This is observed for example with viruses, which have to cope with an immune system or other defence mechanisms of the host.

The structure-based thermodynamic method combines the derived binding free energy model with the formalism which computes probabilities of individual amino acids being folded in native-like conformations and thereby allows to determine structural stability of different protein regions [48-53]. In a single site thermodynamic mutation approach, the cooperativity of in-... 

The PS-I core protein and its reconstitution with the PsaC subunit will also be discussed in more detail in Chapter 31 in connection with another PS-I iron-sulfur cluster, FeS-X. As we will see, the forward electron transfer from FeS-X to [FeS-A/FeS-B] can be very efficient in the reconstituted complex. It suffices to say that the PS-I core protein is utilized here as a natural reducing vehicle to carry out photochemical reduction of the secondary electron acceptors FeS-A and FeS-B so they may be characterized by EPR spectroscopy. The premise of the mutation approach was that replacement of a given cysteine might cause an alteration of a specific [4Fe 4S] cluster and thus lead to some interference in the functioning of that iron-sulfur cluster. 

The success of the chemical mutation approach described above depends on the ability to transform the energy function, U, from one state to another during the MD simulations. This may not be applicable if the two states are very different, or for a QM... 

Aside from the ability to mimic the experimental design and conditions, the mutational approach can be a useful probe of the interactions involved in a particular folding process. Oftentimes straightforward energetic, dynamic, or structural analysis fails to uncover the important nonlocal or indirect interactions that drive a process. But the consequence of mutating a residue, in either a conservative or dramatic manner, can serve as an important computational test of the broader hypothesis about particular events in folding. 

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