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Sarangi MK, Zvoda V, Holte MN, Becker NA, Peters JP, Maher LJ, Ansari A. Evidence for a bind-then-bend mechanism for architectural DNA binding protein yNhp6A. Nucleic Acids Res 2019; 47:2871-2883. [PMID: 30698746 PMCID: PMC6451137 DOI: 10.1093/nar/gkz022] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 12/18/2018] [Accepted: 01/18/2019] [Indexed: 01/17/2023] Open
Abstract
The yeast Nhp6A protein (yNhp6A) is a member of the eukaryotic HMGB family of chromatin factors that enhance apparent DNA flexibility. yNhp6A binds DNA nonspecifically with nM affinity, sharply bending DNA by >60°. It is not known whether the protein binds to unbent DNA and then deforms it, or if bent DNA conformations are ‘captured’ by protein binding. The former mechanism would be supported by discovery of conditions where unbent DNA is bound by yNhp6A. Here, we employed an array of conformational probes (FRET, fluorescence anisotropy, and circular dichroism) to reveal solution conditions in which an 18-base-pair DNA oligomer indeed remains bound to yNhp6A while unbent. In 100 mM NaCl, yNhp6A-bound DNA unbends as the temperature is raised, with no significant dissociation of the complex detected up to ∼45°C. In 200 mM NaCl, DNA unbending in the intact yNhp6A complex is again detected up to ∼35°C. Microseconds-resolved laser temperature-jump perturbation of the yNhp6a–DNA complex revealed relaxation kinetics that yielded unimolecular DNA bending/unbending rates on timescales of 500 μs−1 ms. These data provide the first direct observation of bending/unbending dynamics of DNA in complex with yNhp6A, suggesting a bind-then-bend mechanism for this protein.
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Affiliation(s)
- Manas Kumar Sarangi
- Department of Physics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Viktoriya Zvoda
- Department of Physics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Molly Nelson Holte
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA
| | - Nicole A Becker
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA
| | - Justin P Peters
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA
| | - L James Maher
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA
| | - Anjum Ansari
- Department of Physics, University of Illinois at Chicago, Chicago, IL 60607, USA.,Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60607, USA
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Velmurugu Y, Vivas P, Connolly M, Kuznetsov SV, Rice PA, Ansari A. Two-step interrogation then recognition of DNA binding site by Integration Host Factor: an architectural DNA-bending protein. Nucleic Acids Res 2019; 46:1741-1755. [PMID: 29267885 PMCID: PMC5829579 DOI: 10.1093/nar/gkx1215] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 12/08/2017] [Indexed: 12/23/2022] Open
Abstract
The dynamics and mechanism of how site-specific DNA-bending proteins initially interrogate potential binding sites prior to recognition have remained elusive for most systems. Here we present these dynamics for Integration Host factor (IHF), a nucleoid-associated architectural protein, using a μs-resolved T-jump approach. Our studies show two distinct DNA-bending steps during site recognition by IHF. While the faster (∼100 μs) step is unaffected by changes in DNA or protein sequence that alter affinity by >100-fold, the slower (1–10 ms) step is accelerated ∼5-fold when mismatches are introduced at DNA sites that are sharply kinked in the specific complex. The amplitudes of the fast phase increase when the specific complex is destabilized and decrease with increasing [salt], which increases specificity. Taken together, these results indicate that the fast phase is non-specific DNA bending while the slow phase, which responds only to changes in DNA flexibility at the kink sites, is specific DNA kinking during site recognition. Notably, the timescales for the fast phase overlap with one-dimensional diffusion times measured for several proteins on DNA, suggesting that these dynamics reflect partial DNA bending during interrogation of potential binding sites by IHF as it scans DNA.
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Affiliation(s)
- Yogambigai Velmurugu
- Department of Physics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Paula Vivas
- Department of Physics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Mitchell Connolly
- Department of Physics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Serguei V Kuznetsov
- Department of Physics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Phoebe A Rice
- Department of Biochemistry & Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Anjum Ansari
- Department of Physics, University of Illinois at Chicago, Chicago, IL 60607, USA.,Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60607, USA
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Connolly M, Arra A, Zvoda V, Steinbach PJ, Rice PA, Ansari A. Static Kinks or Flexible Hinges: Multiple Conformations of Bent DNA Bound to Integration Host Factor Revealed by Fluorescence Lifetime Measurements. J Phys Chem B 2018; 122:11519-11534. [DOI: 10.1021/acs.jpcb.8b07405] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Mitchell Connolly
- Department of Physics, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Aline Arra
- Department of Physics, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Viktoriya Zvoda
- Department of Physics, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Peter J. Steinbach
- Center for Molecular Modeling, Center for Information Technology, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Phoebe A. Rice
- Department of Biochemistry & Molecular Biology, University of Chicago, Chicago, Illinois 60637, United States
| | - Anjum Ansari
- Department of Physics, University of Illinois at Chicago, Chicago, Illinois 60607, United States
- Department of Bioengineering, University of Illinois at Chicago, Chicago, Illinois 60607, United States
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Zhou HX, Pang X. Electrostatic Interactions in Protein Structure, Folding, Binding, and Condensation. Chem Rev 2018; 118:1691-1741. [PMID: 29319301 DOI: 10.1021/acs.chemrev.7b00305] [Citation(s) in RCA: 454] [Impact Index Per Article: 75.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Charged and polar groups, through forming ion pairs, hydrogen bonds, and other less specific electrostatic interactions, impart important properties to proteins. Modulation of the charges on the amino acids, e.g., by pH and by phosphorylation and dephosphorylation, have significant effects such as protein denaturation and switch-like response of signal transduction networks. This review aims to present a unifying theme among the various effects of protein charges and polar groups. Simple models will be used to illustrate basic ideas about electrostatic interactions in proteins, and these ideas in turn will be used to elucidate the roles of electrostatic interactions in protein structure, folding, binding, condensation, and related biological functions. In particular, we will examine how charged side chains are spatially distributed in various types of proteins and how electrostatic interactions affect thermodynamic and kinetic properties of proteins. Our hope is to capture both important historical developments and recent experimental and theoretical advances in quantifying electrostatic contributions of proteins.
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Affiliation(s)
- Huan-Xiang Zhou
- Department of Chemistry and Department of Physics, University of Illinois at Chicago , Chicago, Illinois 60607, United States.,Department of Physics and Institute of Molecular Biophysics, Florida State University , Tallahassee, Florida 32306, United States
| | - Xiaodong Pang
- Department of Physics and Institute of Molecular Biophysics, Florida State University , Tallahassee, Florida 32306, United States
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Mechanosensing of DNA bending in a single specific protein-DNA complex. Sci Rep 2013; 3:3508. [PMID: 24336435 PMCID: PMC3863814 DOI: 10.1038/srep03508] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Accepted: 11/29/2013] [Indexed: 01/10/2023] Open
Abstract
Many crucial biological processes are regulated by mechanical stimuli. Here, we report new findings that pico-Newton forces can drastically affect the stability of the site-specific DNA binding of a single transcription factor, the E. coli integration host factor (IHF), by stretching a short ~150 nm DNA containing a single IHF binding site. Dynamic binding and unbinding of single IHF were recorded and analyzed for the force-dependent stability of the IHF-DNA complex. Our results demonstrate that the IHF-DNA interaction is fine tuned by force in different salt concentration and temperature over physiological ranges, indicating that, besides other physiological factors, force may play equally important role in transcription regulation. These findings have broad implications with regard to general mechanosensitivity of site-specific DNA bending proteins.
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Gruebele M, Thirumalai D. Perspective: Reaches of chemical physics in biology. J Chem Phys 2013; 139:121701. [PMID: 24089712 PMCID: PMC5942441 DOI: 10.1063/1.4820139] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2013] [Accepted: 08/20/2013] [Indexed: 01/09/2023] Open
Abstract
Chemical physics as a discipline contributes many experimental tools, algorithms, and fundamental theoretical models that can be applied to biological problems. This is especially true now as the molecular level and the systems level descriptions begin to connect, and multi-scale approaches are being developed to solve cutting edge problems in biology. In some cases, the concepts and tools got their start in non-biological fields, and migrated over, such as the idea of glassy landscapes, fluorescence spectroscopy, or master equation approaches. In other cases, the tools were specifically developed with biological physics applications in mind, such as modeling of single molecule trajectories or super-resolution laser techniques. In this introduction to the special topic section on chemical physics of biological systems, we consider a wide range of contributions, all the way from the molecular level, to molecular assemblies, chemical physics of the cell, and finally systems-level approaches, based on the contributions to this special issue. Chemical physicists can look forward to an exciting future where computational tools, analytical models, and new instrumentation will push the boundaries of biological inquiry.
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Affiliation(s)
- Martin Gruebele
- Departments of Chemistry and Physics, and Center for Biophysics and Computational Biology, University of Illinois, Urbana, Illinois 61801, USA
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