Effect on DNA relaxation of the single Thr718Ala mutation in human topoisomerase I: a functional and molecular dynamics study

• Published in: Nucleic acids research 2005-01, Vol.33 (10), p.3339-3350
• Main Authors: Chillemi, Giovanni, Fiorani, Paola, Castelli, Silvia, Bruselles, Alessandro, Benedetti, Piero, Desideri, Alessandro
• Format: Article
• Language: English
• Subjects: Alanine - genetics; Amino Acid Substitution; Computer Simulation; DNA - chemistry; DNA - metabolism; DNA Topoisomerases, Type I - chemistry; DNA Topoisomerases, Type I - genetics; DNA Topoisomerases, Type I - metabolism; Humans; Hydrogen Bonding; Kinetics; Models, Molecular; Mutation; Principal Component Analysis; Threonine - genetics
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gki642

The functional and dynamical properties of the human topoisomerase I Thr718Ala mutant have been compared to that of the wild-type enzyme using functional assays and molecular dynamics (MD) simulations. At physiological ionic strength, the cleavage and religation rates, evaluated on oligonucleotides containing the preferred topoisomerase I DNA sequence, are almost identical for the wild-type and the mutated enzymes, as is the cleavage/religation equilibrium. On the other hand, the Thr718Ala mutant shows a decreased efficiency in a DNA plasmid relaxation assay. The MD simulation, carried out on the enzyme complexed with its preferred DNA substrate, indicates that the mutant has a different dynamic behavior compared to the wild-type enzyme. Interestingly, no changes are observed in the proximity of the mutation site, whilst a different flexibility is detected in regions contacting the DNA scissile strand, such as the linker and the V-shaped α helices. Taken together, the functional and simulation results indicate a direct communication between the mutation site and regions located relatively far away, such as the linker domain, that with their altered flexibility confer a reduced DNA relaxation efficiency. These results provide evidence that the comprehension of the topoisomerase I dynamical properties are an important element in the understanding of its complex catalytic cycle.