Browsing by Author "Phillips, G.N."
Now showing 1 - 2 of 2
Results Per Page
Sort Options
Item Molecular-replacement phasing using predicted protein structures from AWSEM-Suite(International Union of Crystallography, 2020) Jin, S.; Miller, M.D.; Chen, M.; Schafer, N.P.; Lin, X.; Chen, X.; Phillips, G.N.; Wolynes, P.G.; Center for Theoretical Biological PhysicsThe phase problem in X-ray crystallography arises from the fact that only the intensities, and not the phases, of the diffracting electromagnetic waves are measured directly. Molecular replacement can often estimate the relative phases of reflections starting with those derived from a template structure, which is usually a previously solved structure of a similar protein. The key factor in the success of molecular replacement is finding a good template structure. When no good solved template exists, predicted structures based partially on templates can sometimes be used to generate models for molecular replacement, thereby extending the lower bound of structural and sequence similarity required for successful structure determination. Here, the effectiveness is examined of structures predicted by a state-of-the-art prediction algorithm, the Associative memory, Water-mediated, Structure and Energy Model Suite (AWSEM-Suite), which has been shown to perform well in predicting protein structures in CASP13 when there is no significant sequence similarity to a solved protein or only very low sequence similarity to known templates. The performance of AWSEM-Suite structures in molecular replacement is discussed and the results show that AWSEM-Suite performs well in providing useful phase information, often performing better than I-TASSER-MR and the previous algorithm AWSEM-Template.Item The crystal structure of DynF from the dynemicin-biosynthesis pathway of Micromonospora chersina(International Union of Crystallography, 2022) Kosgei, A.J.; Miller, M.D.; Bhardwaj, M.; Xu, W.; Thorson, J.S.; Van Lanen, S.G.; Phillips, G.N.Dynemicin is an enediyne natural product from Micromonospora chersina ATCC53710. Access to the biosynthetic gene cluster of dynemicin has enabled the in vitro study of gene products within the cluster to decipher their roles in assembling this unique molecule. This paper reports the crystal structure of DynF, the gene product of one of the genes within the biosynthetic gene cluster of dynemicin. DynF is revealed to be a dimeric eight-stranded β-barrel structure with palmitic acid bound within a cavity. The presence of palmitic acid suggests that DynF may be involved in binding the precursor polyene heptaene, which is central to the synthesis of the ten-membered ring of the enediyne core.