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Ha VLT, Erlitzki N, Farahat AA, Kumar A, Boykin DW, Poon GMK. Dissecting Dynamic and Hydration Contributions to Sequence-Dependent DNA Minor Groove Recognition. Biophys J 2020; 119:1402-1415. [PMID: 32898478 DOI: 10.1016/j.bpj.2020.08.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 07/13/2020] [Accepted: 08/10/2020] [Indexed: 10/23/2022] Open
Abstract
Sequence selectivity is a critical attribute of DNA-binding ligands and underlines the need for detailed molecular descriptions of binding in representative sequence contexts. We investigated the binding and volumetric properties of DB1976, a model bis(benzimidazole)-selenophene diamidine compound with emerging therapeutic potential in acute myeloid leukemia, debilitating fibroses, and obesity-related liver dysfunction. To sample the scope of cognate DB1976 target sites, we evaluated three dodecameric duplexes spanning >103-fold in binding affinity. The attendant changes in partial molar volumes varied substantially, but not in step with binding affinity, suggesting distinct modes of interactions in these complexes. Specifically, whereas optimal binding was associated with loss of hydration water, low-affinity binding released more hydration water. Explicit-atom molecular dynamics simulations showed that minor groove binding perturbed the conformational dynamics and hydration at the termini and interior of the DNA in a sequence-dependent manner. The impact of these distinct local dynamics on hydration was experimentally validated by domain-specific interrogation of hydration with salt, which probed the charged axial surfaces of oligomeric DNA preferentially over the uncharged termini. Minor groove recognition by DB1976, therefore, generates dynamically distinct domains that can make favorable contributions to hydration release in both high- and low-affinity binding. Because ligand binding at internal sites of DNA oligomers modulates dynamics at the termini, the results suggest both short- and long-range dynamic effects along the DNA target that can influence their effectiveness as low-MW competitors of protein binding.
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Affiliation(s)
- Van L T Ha
- Department of Chemistry, Georgia State University, Atlanta, Georgia
| | - Noa Erlitzki
- Department of Chemistry, Georgia State University, Atlanta, Georgia
| | - Abdelbasset A Farahat
- Department of Chemistry, Georgia State University, Atlanta, Georgia; Department of Pharmaceutical and Medicinal Chemistry, California Northstate University, Elk Grove, California
| | - Arvind Kumar
- Department of Chemistry, Georgia State University, Atlanta, Georgia
| | - David W Boykin
- Department of Chemistry, Georgia State University, Atlanta, Georgia
| | - Gregory M K Poon
- Department of Chemistry, Georgia State University, Atlanta, Georgia; Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia.
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2
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Chalikian TV, Macgregor RB. On empirical decomposition of volumetric data. Biophys Chem 2018; 246:8-15. [PMID: 30597448 DOI: 10.1016/j.bpc.2018.12.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 12/20/2018] [Accepted: 12/21/2018] [Indexed: 11/26/2022]
Abstract
Volumetric characterization of proteins and their recognition events has been instrumental in providing information on the role of intra- and intermolecular interactions, including hydration, in stabilizing biomolecules. The credibility of molecular models and interpretation schemes used to rationalize experimental data are essential for the validity of microscopic insights derived from volumetric results. Current empirical schemes used to interpret volumetric data suffer from a lack of theoretical and computational substantiation. In this contribution, we take advantage age of recent MD simulations of proteins in solution coupled with Voronoi-Delaunay tessellation of simulated structures that have provided an exceptional level of structural detail on the nature of protein-water interfaces. We use these structural insights to re-evaluate empirical frameworks used for interpretation of volumetric data. An important issue in this respect is the actual dividing surface between water and protein atoms that is used in volumetric studies when the solute and solvent are treated as hard spheres enclosed within their respective van der Waals surfaces. In one development, using Voronoi tessellation of MD simulated protein-water systems the dividing surface has been defined as the points equidistant from the water and protein atoms. The interstitial void volume between the solute and the dividing surface corresponds to thermal volume envisaged by Scaled Particle Theory. In this communication, we explicitly account for the contributions of thermal volume to the partial molar volume, compressibility, and expansibility of proteins and re-examine and redefine the intrinsic and hydration volumetric contributions. We discuss the implications of our results for protein transitions and association events.
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Affiliation(s)
- Tigran V Chalikian
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada.
| | - Robert B Macgregor
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
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Flexibility and Hydration of Amphiphilic Hyperbranched Arabinogalactan-Protein from Plant Exudate: A Volumetric Perspective. COLLOIDS AND INTERFACES 2018. [DOI: 10.3390/colloids2010011] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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4
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Ergometric studies of proteins: New insights into protein functionality in food systems. Trends Food Sci Technol 2015. [DOI: 10.1016/j.tifs.2015.06.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Shek YL, Noudeh GD, Nazari M, Heerklotz H, Abu-Ghazalah RM, Dubins DN, Chalikian TV. Folding thermodynamics of the hybrid-1 type intramolecular human telomeric G-quadruplex. Biopolymers 2013; 101:216-27. [DOI: 10.1002/bip.22317] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Accepted: 06/04/2013] [Indexed: 12/24/2022]
Affiliation(s)
- Yuen Lai Shek
- Department of Pharmaceutical Sciences; Leslie Dan Faculty of Pharmacy, University of Toronto; 144 College Street Toronto, Ontario Canada M5S 3M2
| | - Golamreza Dehghan Noudeh
- Department of Pharmaceutical Sciences; Leslie Dan Faculty of Pharmacy, University of Toronto; 144 College Street Toronto, Ontario Canada M5S 3M2
| | - Mozhgan Nazari
- Department of Pharmaceutical Sciences; Leslie Dan Faculty of Pharmacy, University of Toronto; 144 College Street Toronto, Ontario Canada M5S 3M2
| | - Heiko Heerklotz
- Department of Pharmaceutical Sciences; Leslie Dan Faculty of Pharmacy, University of Toronto; 144 College Street Toronto, Ontario Canada M5S 3M2
| | - Rashid M. Abu-Ghazalah
- Department of Pharmaceutical Sciences; Leslie Dan Faculty of Pharmacy, University of Toronto; 144 College Street Toronto, Ontario Canada M5S 3M2
| | - David N. Dubins
- Department of Pharmaceutical Sciences; Leslie Dan Faculty of Pharmacy, University of Toronto; 144 College Street Toronto, Ontario Canada M5S 3M2
| | - Tigran V. Chalikian
- Department of Pharmaceutical Sciences; Leslie Dan Faculty of Pharmacy, University of Toronto; 144 College Street Toronto, Ontario Canada M5S 3M2
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Knoblauch M, Stubenrauch M, van Bel AJE, Peters WS. Forisome performance in artificial sieve tubes. PLANT, CELL & ENVIRONMENT 2012; 35:1419-1427. [PMID: 22348276 DOI: 10.1111/j.1365-3040.2012.02499.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
In the legume phloem, sieve element occlusion (SEO) proteins assemble into Ca(2+)-dependent contractile bodies. These forisomes presumably control phloem transport by forming reversible sieve tube plugs. This function, however, has never been directly demonstrated, and appears questionable as forisomes were reported to be too small to plug sieve tubes, and failed to block flow efficiently in artificial microchannels. Moreover, plugs of SEO-related proteins in Arabidopsis sieve tubes do not affect phloem translocation. We improved existing procedures for forisome isolation and storage, and found that the degree of Ca(2+)-driven deformation that is possible in forisomes of Vicia faba, the standard object of earlier research, has been underestimated substantially. Forisomes deform particularly strongly under reducing conditions and high sugar concentrations, as typically found in sieve tubes. In contrast to our previous inference, Ca(2+)-inducible forisome swelling certainly seems sufficient to plug sieve tubes. This conclusion was supported by 3D-reconstructions of forisome plugs in Canavalia gladiata. For a direct test, we built microfluidics chips with artificial sieve tubes. Using fluorescent dyes to visualize flow, we demonstrated the complete blockage of these biomimetic microtubes by Ca(2+)-induced forisome plugs, and concluded by analogy that forisomes are capable of regulating phloem flow in vivo.
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Affiliation(s)
- Michael Knoblauch
- School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA.
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Size dependence of cavity volume: A molecular dynamics study. Biophys Chem 2012; 161:46-9. [DOI: 10.1016/j.bpc.2011.10.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2011] [Revised: 10/14/2011] [Accepted: 10/16/2011] [Indexed: 11/18/2022]
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8
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Froelich DR, Mullendore DL, Jensen KH, Ross-Elliott TJ, Anstead JA, Thompson GA, Pélissier HC, Knoblauch M. Phloem ultrastructure and pressure flow: Sieve-Element-Occlusion-Related agglomerations do not affect translocation. THE PLANT CELL 2011; 23:4428-45. [PMID: 22198148 PMCID: PMC3269875 DOI: 10.1105/tpc.111.093179] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2011] [Revised: 11/21/2011] [Accepted: 12/07/2011] [Indexed: 05/02/2023]
Abstract
Since the first ultrastructural investigations of sieve tubes in the early 1960s, their structure has been a matter of debate. Because sieve tube structure defines frictional interactions in the tube system, the presence of P protein obstructions shown in many transmission electron micrographs led to a discussion about the mode of phloem transport. At present, it is generally agreed that P protein agglomerations are preparation artifacts due to injury, the lumen of sieve tubes is free of obstructions, and phloem flow is driven by an osmotically generated pressure differential according to Münch's classical hypothesis. Here, we show that the phloem contains a distinctive network of protein filaments. Stable transgenic lines expressing Arabidopsis thaliana Sieve-Element-Occlusion-Related1 (SEOR1)-yellow fluorescent protein fusions show that At SEOR1 meshworks at the margins and clots in the lumen are a general feature of living sieve tubes. Live imaging of phloem flow and flow velocity measurements in individual tubes indicate that At SEOR1 agglomerations do not markedly affect or alter flow. A transmission electron microscopy preparation protocol has been generated showing sieve tube ultrastructure of unprecedented quality. A reconstruction of sieve tube ultrastructure served as basis for tube resistance calculations. The impact of agglomerations on phloem flow is discussed.
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MESH Headings
- Arabidopsis/genetics
- Arabidopsis/growth & development
- Arabidopsis/metabolism
- Cloning, Molecular
- Fluorescent Dyes/metabolism
- Freeze Substitution
- Genes, Plant
- Genetic Vectors/genetics
- Genetic Vectors/metabolism
- Image Processing, Computer-Assisted
- Microscopy, Electron, Transmission
- Mutagenesis, Insertional
- Phloem/growth & development
- Phloem/metabolism
- Phloem/ultrastructure
- Plant Cells/metabolism
- Plant Physiological Phenomena
- Plant Proteins/genetics
- Plant Proteins/metabolism
- Plant Roots/genetics
- Plant Roots/growth & development
- Plant Roots/metabolism
- Plants, Genetically Modified/genetics
- Plants, Genetically Modified/growth & development
- Plants, Genetically Modified/metabolism
- Populus/growth & development
- Populus/metabolism
- Pressure
- Protein Transport
- Nicotiana/growth & development
- Nicotiana/metabolism
- Transformation, Genetic
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Affiliation(s)
- Daniel R. Froelich
- School of Biological Sciences, Washington State University, Pullman Washington 99164-4236
| | - Daniel L. Mullendore
- School of Biological Sciences, Washington State University, Pullman Washington 99164-4236
| | - Kåre H. Jensen
- Department of Physics, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Tim J. Ross-Elliott
- School of Biological Sciences, Washington State University, Pullman Washington 99164-4236
| | - James A. Anstead
- College of Agricultural Sciences, Pennsylvania State University, Pennsylvania 16802
| | - Gary A. Thompson
- College of Agricultural Sciences, Pennsylvania State University, Pennsylvania 16802
| | - Hélène C. Pélissier
- School of Biological Sciences, Washington State University, Pullman Washington 99164-4236
- Department of Plant Biology and Biotechnology, University of Copenhagen, 1871 Frederiksberg, Denmark
| | - Michael Knoblauch
- School of Biological Sciences, Washington State University, Pullman Washington 99164-4236
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Boze H, Marlin T, Durand D, Pérez J, Vernhet A, Canon F, Sarni-Manchado P, Cheynier V, Cabane B. Proline-rich salivary proteins have extended conformations. Biophys J 2010; 99:656-65. [PMID: 20643086 DOI: 10.1016/j.bpj.2010.04.050] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2010] [Revised: 04/17/2010] [Accepted: 04/21/2010] [Indexed: 10/19/2022] Open
Abstract
Three basic proline-rich salivary proteins have been produced through the recombinant route. IB5 is a small basic proline-rich protein that is involved in the binding of plant tannins in the oral cavity. II-1 is a larger protein with a closely related backbone; it is glycosylated, and it is also able to bind plant tannins. II-1 ng has the same polypeptidic backbone as II-1, but it is not glycosylated. Small angle x-ray scattering experiments on dilute solutions of these proteins confirm that they are intrinsically disordered. IB5 and II-1 ng can be described through a chain model including a persistence length and cross section. The measured radii of gyration (Rg=27.9 and 41.0+/-1 A respectively) and largest distances (rmax=110 and 155+/-10 A respectively) show that their average conformations are rather extended. The length of the statistical segment (twice the persistence length) is b=30 A, which is larger than the usual value (18 A-20 A) for unstructured polypeptide chains. These characteristics are presumably related to the presence of polyproline helices within the polypeptidic backbones. For both proteins, the radius of gyration of the chain cross-section is Rc=2.7+/-0.2A. The glycosylated protein II-1 has similar conformations but the presence of large polyoside sidegroups yields the structure of a branched macromolecule with the same hydrophobic backbone and hydrophilic branches. It is proposed that the unusually extended conformations of these proteins in solution facilitate the capture of plant tannins in the oral cavity.
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Affiliation(s)
- Hélène Boze
- INRA, Montpellier SupAgro, UMR 1083 Sciences pour l'OEnologie, F-34060 Montpellier, France
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Lau EY, Krishnan VV. Temperature dependence of protein-hydration hydrodynamics by molecular dynamics simulations. Biophys Chem 2007; 130:55-64. [PMID: 17720293 DOI: 10.1016/j.bpc.2007.07.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2007] [Revised: 07/14/2007] [Accepted: 07/18/2007] [Indexed: 11/19/2022]
Abstract
The dynamics of water molecules near the protein surface are different from those of bulk water and influence the structure and dynamics of the protein itself. To elucidate the temperature dependence hydration dynamics of water molecules, we present results from the molecular dynamic simulation of the water molecules surrounding two proteins (Carboxypeptidase inhibitor and Ovomucoid) at seven different temperatures (T=273 to 303 K, in increments of 5 K). Translational diffusion coefficients of the surface water and bulk water molecules were estimated from 2 ns molecular dynamics simulation trajectories. Temperature dependence of the estimated bulk water diffusion closely reflects the experimental values, while hydration water diffusion is retarded significantly due to the protein. Protein surface induced scaling of translational dynamics of the hydration waters is uniform over the temperature range studied, suggesting the importance protein-water interactions.
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Affiliation(s)
- Edmond Y Lau
- Biology and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
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12
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Gojło E, Gampe T, Krakowiak J, Stangret J. Hydration of Aprotic Donor Solvents Studied by Means of FTIR Spectroscopy. J Phys Chem A 2007; 111:1827-34. [PMID: 17305320 DOI: 10.1021/jp065599p] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The paper attempts to explain the mutual influence of nonpolar and electron-donor groups on solute hydration, the problem of big importance for biological aqueous systems. Aprotic organic solvents have been used as model solutes, differing in electron-donating power. Hydration of acetonitrile, acetone, 2-butanone, and triethylamine has been studied by HDO and (partially) H2O spectra. The quantitative version of difference spectra method has been applied to determine solute-affected water spectra. Analysis of the data suggests that solvent-water interaction via the donor center of the solute is averaged between water-water interactions around the solute. Such behavior can be simply explained by the model of solute rotating in a cavity of water structure, which is formed by clathratelike hydrogen-bonded water network. On the basis of the band shape of solute-affected HDO spectra and the corresponding distribution of intermolecular distances, the criterion for hydrophobic type hydration has been proposed. From that point of view, all the studied solutes could be treated as hydrophobic ones. The limiting band position and the corresponding intermolecular distance of affected water, gained with increasing electron-donating power of solutes, has been inferred from the data obtained. These observations are important for interpretation of vibrational spectra of water as well as for volumetric measurements of solutions. The simple model of hydration, proposed to better justify the results, connects the values obtained from the methods providing microscopic and macroscopic characteristics of the system studied.
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Affiliation(s)
- Emilia Gojło
- Department of Physical Chemistry, Chemical Faculty, Gdańsk University of Technology, Narutowicza 11/12, 80-952 Gdańsk, Poland
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