Functional and Conformational Analysis of TmMutS2 Figure 5. SAXS analysis for the structures of TmMutS2 and its complexes with nucleotides and DNAs. (A) SAXS scattering curves of apo- TmMutS2 at a concentration range of 1 to 5 mg/mL. The insert exhibits the Guinier approximation for the scattering data of TmMutS2 (5 mg/mL). (B) SAXS scattering curves of apo-TmMutS2 and its complexes with nucleotides (ADP and ADPnP) and DNAs (dsDNA and FWJ-DNA) as calculated by the PRIMUS program. (C) P(R) function plots estimated by GNOM program. (D) SAXS data parameters from a GNOM analysis and DAMMIN modeling. TmS2 is T. maritima TmMutS2. Rpre* was calculated from the Guinier approximation using AutoRg program. Rcal1 and Dmax" (the maximum diameter) were calculated from the P(r) function by GNOM program. FDNA represents four-way junction DNA. Dmax is the longest distance of the SAXS models $ as determined by the DAMMIN program. Using DLS analysis, the hydrodynamic radii (Rhydro ) were calculated at various temperatures. doi:10.1371/journal.pone.0034529.g005 conformational changes in TmMutS2 (Figure 8C, circle dash- lines). These results were in accordance with the DNA-binding activities experiments (Figure 1C). Discussion Studies on the conformational alterations of proteins containing conserved domains, such as ATPase and DNA-association domains, provide important clues for biological mechanisms [40]. To validate the conformational changes of TmMutS2, proteolytic digestion was carried out. As shown in Figure 1D, while the conformational changes of TmMut2 were weakly induced in the presence of FWJ-DNA, the addition of nucleotides resulted in the decrease of digested TmMutS2 fragments. These results indicate that the structure of TmMutS2 is altered through nucleotide binding. A similar phenomenon has been previously PLoS ONE | www.plosone.org 8 April 2012 | Volume 7 | Issue 4 | e34529