NMR elucidation of monomer–dimer transition and conformational heterogeneity in histone‐like DNA binding protein of Helicobacter pylori

• Published in: Magnetic resonance in chemistry 2018-04, Vol.56 (4), p.285-299
• Main Authors: Jaiswal, Nancy, Raikwal, Nisha, Pandey, Himanshu, Agarwal, Nipanshu, Arora, Ashish, Poluri, Krishna Mohan, Kumar, Dinesh
• Format: Article
• Language: English
• Subjects: Acidic oxides; Denaturation; Deoxyribonucleic acid; Dimerization; DNA; Helicobacter pylori; histone like DNA binding protein; Monomers; multiple conformations; NMR; NMR resonance assignments; Nuclear magnetic resonance; Oxidative stress; Proteins; secondary structure
• ISSN: 0749-1581; 1097-458X
• DOI: 10.1002/mrc.4701

Helicobacter pylori (H. pylori) colonizes under harsh acidic/oxidative stress conditions of human gastrointestinal tract and can survive there for infinitely longer durations of host life. The bacterium expresses several harbinger proteins to facilitate its persistent colonization under such conditions. One such protein in H. pylori is histone‐like DNA binding protein (Hup), which in its homo‐dimeric form binds to DNA to perform various DNA dependent cellular activities. Further, it also plays an important role in protecting the genomic DNA from oxidative stress and acidic denaturation. Legitimately, if the binding of Hup to DNA is suppressed, it will directly impact on the survival of the bacterium, thus making Hup a potential therapeutic target for developing new anti‐H. pylori agents. However, to inhibit the binding of Hup to DNA, it is necessary to gain detailed insights into the molecular and structural basis of Hup‐dimerization and its binding mechanism to DNA. As a first step in this direction, we report here the nuclear magnetic resonance (NMR) assignments and structural features of Hup at pH 6.0. The study revealed the occurrence of dynamic equilibrium between its monomer and dimer conformations. The dynamic equilibrium was found to shifting towards dimer both at low temperature and low pH; whereas DNA binding studies evidenced that the protein binds to DNA in its dimeric form. These preliminary investigations correlate very well with the diverse functionality of protein and will form the basis for future studies aiming to develop novel anti‐H. pylori agents employing structure‐based‐rational drug discovery approach. The study revealed dynamic equilibrium between monomeric and dimeric conformations of H. pylori Hup at near physiological temperature and pH. The dynamic equilibrium shifts more towards dimeric state at low pH and low temperature. Compared to monomer, the dimeric state confers conformationally stable β‐arms and binding to DNA.