The refinement of a molecular model is a computational procedure by which the atomic model is fitted to the diffraction data. The commonly used target in the refinement of macromolecular structures is the maximum-likelihood (ML) function, which relies on the assessment of model errors. The current ML functions rely on cross-validation. They utilize phase-error estimates that are calculated from a small fraction of diffraction data, called the test set, that are not used to fit the model. An approach has been developed that uses the work set to calculate the phase-error estimates in the ML refinement from simulating the model errors via the random displacement of atomic coordinates. It is called ML free-kick refinement as it uses the ML formulation of the target function and is based on the idea of freeing the model from the model bias imposed by the chemical energy restraints used in refinement. This approach for the calculation of error estimates is superior to the cross-validation approach: it reduces the phase error and increases the accuracy of molecular models, is more robust, provides clearer maps and may use a smaller portion of data for the test set for the calculation of Rfree or may leave it out completely
COBISS.SI-ID: 1537009860
FK506 (tacrolimus) is a clinically important immunosuppressant, produced in industrial fermentation processes by various Streptomyces species. Yields of FK506 in these processes remain relatively low and their efficiency is further reduced by the presence of structurally similar impurities in fermentation broths. Biosynthetic processes of secondary metabolites are often affected by regulatory genes, located in biosynthetic gene clusters. In this article we describe the identification and characterization of two regulatory elements present in the FK506 biosynthetic gene cluster fkbR and fkbN, belonging to the LysR and LAL family, respectively. Inactivation of these genes caused a dramatic reduction in FK506 yield whereas their overexpression significantly improved the yield of this compound. The results show a promising potential of the obtained genetically modified strains of to improve the yield of FK506 as well as FK506 analogues which are being produced in the scope of this project in S. tsukubaensis by chemobiosynthetic approach.
COBISS.SI-ID: 4146808