The role of the C-domain of bacteriophage T4 gene 32 protein in ssDNA binding and dsDNA helix-destabilization: Kinetic, single-molecule, and cross-linking studies

PLoS One. 2018 Apr 10;13(4):e0194357. doi: 10.1371/journal.pone.0194357. eCollection 2018.

Abstract

The model single-stranded DNA binding protein of bacteriophage T4, gene 32 protein (gp32) has well-established roles in DNA replication, recombination, and repair. gp32 is a single-chain polypeptide consisting of three domains. Based on thermodynamics and kinetics measurements, we have proposed that gp32 can undergo a conformational change where the acidic C-terminal domain binds internally to or near the single-stranded (ss) DNA binding surface in the core (central) domain, blocking ssDNA interaction. To test this model, we have employed a variety of experimental approaches and gp32 variants to characterize this conformational change. Utilizing stopped-flow methods, the association kinetics of wild type and truncated forms of gp32 with ssDNA were measured. When the C-domain is present, the log-log plot of k vs. [NaCl] shows a positive slope, whereas when it is absent (*I protein), there is little rate change with salt concentration, as expected for this model.A gp32 variant lacking residues 292-296 within the C-domain, ΔPR201, displays kinetic properties intermediate between gp32 and *I. The single molecule force-induced DNA helix-destabilizing activitiesas well as the single- and double-stranded DNA affinities of ΔPR201 and gp32 truncated at residue 295 also fall between full-length protein and *I. Finally, chemical cross-linking of recombinant C-domain and gp32 lacking both N- and C-terminal domains is inhibited by increasing concentrations of a short single-stranded oligonucleotide, and the salt dependence of cross-linking mirrors that expected for the model. Taken together, these results provide the first evidence in support of this model that have been obtained through structural probes.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacteriophage T4 / metabolism*
  • Binding Sites
  • Cross-Linking Reagents / chemistry
  • DNA Repair
  • DNA Replication
  • DNA, Single-Stranded / chemistry*
  • DNA-Binding Proteins / metabolism*
  • Escherichia coli / metabolism
  • Kinetics
  • Linear Models
  • Mutation
  • Protein Binding
  • Protein Domains
  • Recombination, Genetic
  • Thermodynamics
  • Viral Proteins / metabolism*

Substances

  • Cross-Linking Reagents
  • DNA, Single-Stranded
  • DNA-Binding Proteins
  • Viral Proteins
  • gp32 protein, Enterobacteria phage T4