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Agarwal N, Nagar N, Raj R, Kumar D, Poluri KM. Conserved Apical Proline Regulating the Structure and DNA Binding Properties of Helicobacter pylori Histone-like DNA Binding Protein (Hup). ACS OMEGA 2022; 7:15231-15246. [PMID: 35572751 PMCID: PMC9089689 DOI: 10.1021/acsomega.2c01754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 04/06/2022] [Indexed: 06/15/2023]
Abstract
Prokaryotic cells lack a proper dedicated nuclear arrangement machinery. A set of proteins known as nucleoid associated proteins (NAPs) perform opening and closure of nucleic acids, behest cellular requirement. Among these, a special class of proteins analogous to eukaryotic histones popularly known as histone-like (HU) DNA binding proteins facilitate the nucleic acid folding/compaction thereby regulating gene architecture and gene regulation. DNA compaction and DNA protection in Helicobacter pylori is performed by HU protein (Hup). To dissect and galvanize the role of proline residue in the binding of Hup with DNA, the structure-dynamics-functional relationship of Hup-P64A variant was analyzed. NMR and biophysical studies evidenced that Hup-P64A protein attenuated DNA-binding and induced structural/stability changes in the DNA binding domain (DBD). Moreover, molecular dynamics simulations and 15N relaxation studies established the reduced conformational dynamics of P64A protein. This comprehensive study dissected the exclusive role of evolutionarily conserved apical proline residue in regulating the structure and DNA binding of Hup protein as P64 is presumed to be involved in the external leverage mechanism responsible for DNA bending and packaging, as proline rings wedge into the DNA backbone through intercalation besides their significant role in DNA binding.
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Affiliation(s)
- Nipanshu Agarwal
- Department
of Biosciences and Bioengineering, Indian
Institute of Technology Roorkee, Roorkee-247667, Uttarakhand, India
| | - Nupur Nagar
- Department
of Biosciences and Bioengineering, Indian
Institute of Technology Roorkee, Roorkee-247667, Uttarakhand, India
| | - Ritu Raj
- Centre
of Biomedical Research, SGPGIMS Campus, Lucknow-226014, India
| | - Dinesh Kumar
- Centre
of Biomedical Research, SGPGIMS Campus, Lucknow-226014, India
| | - Krishna Mohan Poluri
- Department
of Biosciences and Bioengineering, Indian
Institute of Technology Roorkee, Roorkee-247667, Uttarakhand, India
- Centre
for Nanotechnology, Indian Institute of
Technology Roorkee, Roorkee-247667, Uttarakhand, India
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Jaiswal N, Raikwal N, Pandey H, Agarwal N, Arora A, Poluri KM, Kumar D. NMR elucidation of monomer-dimer transition and conformational heterogeneity in histone-like DNA binding protein of Helicobacter pylori. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2018; 56:285-299. [PMID: 29241299 DOI: 10.1002/mrc.4701] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 12/05/2017] [Accepted: 12/06/2017] [Indexed: 05/25/2023]
Abstract
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.
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Affiliation(s)
- Nancy Jaiswal
- Centre of Biomedical Research, SGPGIMS Campus, Lucknow, 226014, India
- Dr. APJ Abdul Kalam Technical University, IET Campus, Sitapur Road, Lucknow, 226021, Uttar Pradesh, India
| | - Nisha Raikwal
- Centre of Biomedical Research, SGPGIMS Campus, Lucknow, 226014, India
| | - Himanshu Pandey
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, 226 031, India
| | - Nipanshu Agarwal
- Department of Biotechnology and Centre for Nanotechnology Indian Institute of Technology Roorkee, 247667, Uttarakhand, India
| | - Ashish Arora
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, 226 031, India
| | - Krishna Mohan Poluri
- Department of Biotechnology and Centre for Nanotechnology Indian Institute of Technology Roorkee, 247667, Uttarakhand, India
| | - Dinesh Kumar
- Centre of Biomedical Research, SGPGIMS Campus, Lucknow, 226014, India
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Altukhov DA, Talyzina AA, Agapova YK, Vlaskina AV, Korzhenevskiy DA, Bocharov EV, Rakitina TV, Timofeev VI, Popov VO. Enhanced conformational flexibility of the histone-like (HU) protein from Mycoplasma gallisepticum. J Biomol Struct Dyn 2016; 36:45-53. [PMID: 27884082 DOI: 10.1080/07391102.2016.1264893] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The histone-like (HU) protein is one of the major nucleoid-associated proteins involved in DNA supercoiling and compaction into bacterial nucleoid as well as in all DNA-dependent transactions. This small positively charged dimeric protein binds DNA in a non-sequence specific manner promoting DNA super-structures. The majority of HU proteins are highly conserved among bacteria; however, HU protein from Mycoplasma gallisepticum (HUMgal) has multiple amino acid substitutions in the most conserved regions, which are believed to contribute to its specificity to DNA targets unusual for canonical HU proteins. In this work, we studied the structural dynamic properties of the HUMgal dimer by NMR spectroscopy and MD simulations. The obtained all-atom model displays compliance with the NMR data and confirms the heterogeneous backbone flexibility of HUMgal. We found that HUMgal, being folded into a dimeric conformation typical for HU proteins, has a labile α-helical body with protruded β-stranded arms forming DNA-binding domain that are highly flexible in the absence of DNA. The amino acid substitutions in conserved regions of the protein are likely to affect the conformational lability of the HUMgal dimer that can be responsible for complex functional behavior of HUMgal in vivo, e.g. facilitating its spatial adaptation to non-canonical DNA-targets.
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Affiliation(s)
- Dmitry A Altukhov
- a National Research Centre 'Kurchatov Institute', Kurchatov Complex of NBICS-Technologies , Akad. Kurchatova sqr., 1, Moscow 123182 , Russian Federation
| | - Anna A Talyzina
- b Moscow Institute of Physics and Technology , Institutskiy per., 9, Dolgoprudny, Moscow Region 141700 , Russian Federation
| | - Yulia K Agapova
- a National Research Centre 'Kurchatov Institute', Kurchatov Complex of NBICS-Technologies , Akad. Kurchatova sqr., 1, Moscow 123182 , Russian Federation
| | - Anna V Vlaskina
- a National Research Centre 'Kurchatov Institute', Kurchatov Complex of NBICS-Technologies , Akad. Kurchatova sqr., 1, Moscow 123182 , Russian Federation
| | - Dmitry A Korzhenevskiy
- a National Research Centre 'Kurchatov Institute', Kurchatov Complex of NBICS-Technologies , Akad. Kurchatova sqr., 1, Moscow 123182 , Russian Federation
| | - Eduard V Bocharov
- a National Research Centre 'Kurchatov Institute', Kurchatov Complex of NBICS-Technologies , Akad. Kurchatova sqr., 1, Moscow 123182 , Russian Federation.,c Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry RAS , str. Miklukho-Maklaya 16/10, Moscow 117997 , Russian Federation
| | - Tatiana V Rakitina
- a National Research Centre 'Kurchatov Institute', Kurchatov Complex of NBICS-Technologies , Akad. Kurchatova sqr., 1, Moscow 123182 , Russian Federation.,c Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry RAS , str. Miklukho-Maklaya 16/10, Moscow 117997 , Russian Federation
| | - Vladimir I Timofeev
- a National Research Centre 'Kurchatov Institute', Kurchatov Complex of NBICS-Technologies , Akad. Kurchatova sqr., 1, Moscow 123182 , Russian Federation.,d Federal Scientific Research Center 'Crystallography and Photonics' RAS , Leninskii pr., 59, Moscow 119333 , Russian Federation
| | - Vladimir O Popov
- a National Research Centre 'Kurchatov Institute', Kurchatov Complex of NBICS-Technologies , Akad. Kurchatova sqr., 1, Moscow 123182 , Russian Federation.,e Bach Institute of Biochemistry , Research Center of Biotechnology of the Russian Academy of Sciences , Leninsky Prospekt. 33, bld. 2, Moscow 119071 , Russian Federation
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