Arc repressor-operator DNA interactions and contribution of Phe10 to binding specificity.
Solution properties of Arc repressors (wild-type and F10H variant) from Salmonella bacteriophage P22 and their complexes with operator DNA (Arc-wt-DNA and Arc-F10H-DNA) were characterized by circular dichroism, fluorescence, and Raman difference spectroscopy and compared with the crystal structures of free and DNA-bound Arc repressors (wild-type and F10V variant). From the crystal structure of Arc-wt-operator DNA complex, it is known that amino acids Phe10/10' flip out of the hydrophobic protein core, and in the Arc-F10V-DNA complex, the methyl groups of Val10/10' rotate toward the DNA. Arc-wt and Arc-F10H significantly perturb the Raman signatures of the operator DNA upon complex formation. The two proteins induce similar changes in the DNA spectra. Raman markers in the difference spectra (spectrum of the complex minus spectra of DNA and Arc) indicate binding of Arc in the major groove, several direct contacts, e.g., hydrogen bonds of protein residues with bases, and slight perturbations of the deoxyribose ring systems that are consistent with bending of the operator DNA. Trp14, the only one tryptophan of Arc repressor monomers, serves as a very sensitive tool for changes of the hydrophobic core of the protein. The Raman spectra identify in the free Arc-F10H variant a largely different chi(2,1) rotation angle of Trp14 compared to that in wild-type Arc. In the Arc-wt-DNA and Arc-F10H-DNA complexes, however, the Trp14 chi(2,1) rotation angles are similar in both proteins. Furthermore, in both complexes, a strengthening of the van der Waals interactions of the aromatic ring of Trp14 is indicated compared to these interactions in the free proteins. According to the fluorescence and Raman data, His10 is buried in the hydrophobic core of free Arc-F10H, resembling the "core" conformation of Phe10 in Arc-wt, but His10 is looped out in the complex with DNA resembling the "bound" conformation of Phe10 in the Arc-wt-operator DNA complex.
Dostál
Lubomír
L
AG Biopolymerspektroskopie, Max-Delbrück-Centrum für Molekulare Medizin Berlin-Buch, Robert-Rössle-Strasse 10, D-13092 Berlin, Germany.
Misselwitz
Rolf
R
Welfle
Heinz
H
D019943:Amino Acid Substitution / Q000235:genetics; D002942:Circular Dichroism; D018360:Crystallography, X-Ray; D004279:DNA, Viral / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D003853:Deoxyribonucleosides / Q000737:chemistry; D003855:Deoxyribose / Q000737:chemistry; D006639:Histidine / Q000235:genetics; D057927:Hydrophobic and Hydrophilic Interactions; D009690:Nucleic Acid Conformation; D009875:Operator Regions, Genetic; D010649:Phenylalanine / Q000737:chemistry* / Q000235:genetics; D011687:Purines / Q000737:chemistry; D011743:Pyrimidines / Q000737:chemistry; D012097:Repressor Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D012475:Salmonella / Q000737:chemistry / Q000821:virology; D013050:Spectrometry, Fluorescence; D013059:Spectrum Analysis, Raman; D013816:Thermodynamics; D014364:Tryptophan / Q000737:chemistry; D014443:Tyrosine / Q000737:chemistry / Q000235:genetics; D014764:Viral Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D054334:Viral Regulatory and Accessory Proteins
D004279:DNA, Viral; D004268:DNA-Binding Proteins; D003853:Deoxyribonucleosides; D011687:Purines; D011743:Pyrimidines; D012097:Repressor Proteins; D014764:Viral Proteins; D054334:Viral Regulatory and Accessory Proteins; C016649:phage repressor proteins; D014443:Tyrosine; D010649:Phenylalanine; D006639:Histidine; D003855:Deoxyribose; D014364:Tryptophan; C030986:pyrimidine