title: Optimal numbers of residues in linkers of DNA polymerase I, T7 primase and DNA polymerase IV.
abstract: DNA polymerase I (PolI), T7 primase and DNA polymerase IV (Dpo4) have a common feature in their structures that the two main domains are connected by an unstructured polypeptide linker. To perform their specific enzymatic activities, the enzymes are required to rearrange the position and orientation of one domain relative to the other into an active mode. Here, we show that the three enzymes share the same mechanism of the transition from the inert to active modes and use the minimum numbers of residues in their linkers to achieve the most efficient transitions. The transition time to the finally active mode is sensitively dependent on the stretched length of the linker in the finally active mode while is insensitive to the position and orientation in the initially inert state. Moreover, we find that for any enzyme whose two domains are connected by an unstructured flexible linker, the stretched length (L) of the linker in the finally active mode and the optimal number (Nopt) of the residues in the linker satisfy relation L ≈ αNopt, with α = 0.24-0.27 nm being a constant insensitive to the system.
authors.affiliation: Key Laboratory of Soft Matter Physics and Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China.
authors.forename: Yi-Ben
authors.initials: YB
authors.lastname: Fu
authors.affiliation: Key Laboratory of Soft Matter Physics and Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China.
authors.forename: Zhan-Feng
authors.initials: ZF
authors.lastname: Wang
authors.affiliation: Key Laboratory of Soft Matter Physics and Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China.
authors.forename: Peng-Ye
authors.initials: PY
authors.lastname: Wang
authors.affiliation: Key Laboratory of Soft Matter Physics and Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China.
authors.forename: Ping
authors.initials: P
authors.lastname: Xie
mesh_terms: D000595:Amino Acid Sequence / Q000235:genetics; D017123:Bacteriophage T7 / Q000201:enzymology / Q000235:genetics; D004256:DNA Polymerase I / Q000737:chemistry / Q000235:genetics*; D019951:DNA Polymerase beta / Q000737:chemistry / Q000235:genetics*; D019915:DNA Primase / Q000235:genetics*
chemical_list: D019915:DNA Primase; D004256:DNA Polymerase I; D019951:DNA Polymerase beta