Atomic-Resolution Structure of the Protein Encoded by Gene V of fd Bacteriophage in Complex with Viral ssDNA Determined by Magic-Angle Spinning Solid-State NMR

Abstract

F-specific filamentous phages, elongated particles with circular single-stranded DNA encased in a symmetric protein capsid, undergo an intermediate step, where thousands of homodimers of a non-structural protein, gVp, bind to newly synthesized strands of DNA, preventing further DNA replication and preparing the circular genome in an elongated conformation for assembly of a new virion structure at the membrane. While the structure of the free homodimer is known, the ssDNA-bound conformation has yet to be determined. We report an atomic-resolution structure of the gVp monomer bound to ssDNA of fd phage in the nucleoprotein complex elucidated via magic-angle spinning solid-state NMR. The model presents significant conformational changes with respect to the free form. These modifications facilitate the binding mechanism and possibly promote cooperative binding in the assembly of the gVp–ssDNA complex.

Recent Progress in Phage‐Based Nanoplatforms for Tumor Therapy

“…M13 phage is a typical representative of the ssDNA phages. [ 40 ] The M13 phage particle is a filamentous long tubular structure about 880 nm in length and 6–7 nm in diameter, which is mainly composed of the major coat protein (gp/pVIII) and four minor coat proteins (gp/pIII, VI, VII, and IX). Several thousand copies of the major coat protein and four minor coat proteins are located in pairs at the ends of the virus with an odd number of copies.…”

Interaction of a Dimeric Single-Stranded DNA-Binding Protein (G5P) with DNA Hairpins. A Molecular Beacon Study

“…G5P was chosen since it is a well-studied SBP prototype. Its properties, structure, and complex formation with ssDNA were previously examined by electron microscopy, circular dichroism, surface plasmon resonance, , Raman spectroscopy, fluorescence, small-angle X-ray scattering (SAXS), NMR, and mass spectrometry methods. G5P also serves as a model system in radiation research for investigations of the chemistry of DNA–protein crosslink formation, as can be found in cancerous tissue with high radiation resistance. ,, The G5P protein monomer has a molecular weight of 9.7 kDa and consists of 87 amino acids in a single polypeptide chain, which are mostly in the β-conformation, organized as a five-stranded antiparallel β-sheet and two antiparallel β-ladder loops with a broad connecting loop .…”

“…G5P was chosen since it is a well-studied SBP prototype. Its properties, structure, and complex formation with ssDNA were previously examined by electron microscopy, 10 circular dichroism, 11 surface plasmon resonance, 12,13 Raman spectroscopy, 13 fluorescence, 12 small-angle X-ray scattering (SAXS), 14 NMR, 15 and mass spectrometry 16 methods. G5P also serves as a model system in radiation research for investigations of the chemistry of DNA−protein crosslink formation, as can be found in cancerous tissue with high radiation resistance.…”