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Conformational analysis of processivity clamps demonstrates that tertiary structure does not correlate with structural dynamics
Author(s) -
Nevin Philip,
Fang Jing,
Engen John R,
Beuning Penny J
Publication year - 2013
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.27.1_supplement.541.1
Subject(s) - processivity , dna , dna polymerase , biophysics , molecular dynamics , polymerase , structural similarity , denaturation (fissile materials) , dynamics (music) , chemistry , biology , computational biology , biochemistry , physics , computational chemistry , nuclear chemistry , acoustics
Chromosomal replicases faithfully catalyze the polymerization of thousands of DNA bases each second without dissociating from DNA. Their remarkable processivity is attributed to sliding clamps, which are structurally conserved proteins that encircle DNA and tether the DNA polymerase to the DNA template. Here we report a comprehensive comparative study of the conformational dynamics of sliding clamps from a variety of sources ranging from phage to humans. We have probed the structural dynamics of these proteins in solution using hydrogen exchange mass spectrometry and show that sliding clamps from different species show a wide range of dynamic behavior despite highly similar three‐dimensional structures. In addition to large variations in the degree of structural fluctuations, several of the clamps undergo local unfolding events with half‐lives ranging from five minutes to several hours. Furthermore, the domains within each clamp exhibit different dynamics despite their obvious structural symmetry. Our observations reveal that the human clamp PCNA is more dynamic than other eukaryotic clamps, consistent with thermal denaturation experiments. We acknowledge generous financial support from a New Faculty Award from the Camille & Henry Dreyfus Foundation, the American Cancer Society, the NSF, the NIH, and a research collaboration with Waters Corporation.