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Brossard EE, Corcelli SA. Molecular Mechanism of Ligand Binding to the Minor Groove of DNA. J Phys Chem Lett 2023; 14:4583-4590. [PMID: 37163748 DOI: 10.1021/acs.jpclett.3c00635] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Although DNA-ligand binding is pervasive in biology, little is known about molecular-level binding mechanisms. Using all-atom, explicit-solvent molecular dynamics simulations in conjunction with weighted ensemble (WE)-enhanced sampling, an ensemble of 2562 binding trajectories of Hoechst 33258 (H33258) to d(CGC AAA TTT GCG) was generated from which the binding mechanism was extracted. In particular, the electrostatic interaction between the positively charged H33258 and the negatively charged DNA backbone drives the formation of initial H33258-DNA contacts. After this initial contact, a hinge-like intermediate state is formed in which one end of H33258 inserts into the minor groove of DNA. Following hinge state formation is a concerted motion whereby the second end of H33258 swings into the minor groove and the spine of hydration along the minor groove causing dehydration. This study illustrates how WE-enhanced simulations of biomolecular ligation processes can offer novel mechanistic insights by generating ensembles of binding events.
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Affiliation(s)
- E E Brossard
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - S A Corcelli
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
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2
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Hu K, Wang X, Li T. Explicit Projection of Stokes Shifts onto Solvent Motion in an Aqueous Liquid and Linear Response Theory. J Phys Chem B 2022; 126:9168-9175. [PMID: 36342144 DOI: 10.1021/acs.jpcb.2c05012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We investigate the molecular origin of the fluorescence Stokes shift in an aqueous liquid. By examining the speed of energy change, the solvation response function is explicitly projected onto the translational and rotational motions of water molecules for both nonequilibrium relaxation and equilibrium fluctuations. Molecular dynamics simulations of a tryptophan solution show that these two processes have highly consistent dynamics, not only for the total response function but also for the decomposed components in terms of specific molecular movements. We found that the rotational mode governs the relaxation of the Stokes shift, whereas the translational mode contributes non-negligibly with slower dynamics. This consistency implies the similarity of the underlying translational and rotational movements of water molecules as the system is far away from and at equilibrium, supporting the validity of the linear response theory at the molecular level. The decomposition methodology is also applicable to a rigid solvent.
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Affiliation(s)
- Kai Hu
- School of Physics, Xidian University, Xi'an 710071, People's Republic of China
| | - Xiaofang Wang
- School of Physics, Xidian University, Xi'an 710071, People's Republic of China
| | - Tanping Li
- School of Physics, Xidian University, Xi'an 710071, People's Republic of China
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3
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Wang X, Guo J, Li T, Wei Z. To unravel the connection between the non-equilibrium and equilibrium solvation dynamics of tryptophan: success and failure of the linear response theory of fluorescence Stokes shift. RSC Adv 2020; 10:18348-18354. [PMID: 35517244 PMCID: PMC9053704 DOI: 10.1039/d0ra01227k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 04/15/2020] [Indexed: 11/21/2022] Open
Abstract
The connections between the non-equilibrium solvation dynamics upon optical transitions and the system's equilibrium fluctuations are explored in aqueous liquid. Linear response theory correlates time-dependent fluorescence with the equilibrium time correlation functions. In the previous work [T. Li, J. Chem. Theory Comput., 2017, 13, 1867], Stokes shift was explicitly decomposed into the contributions of various order time correlation functions on the excited state surface. Gaussian fluctuations of the solute-solvent interactions validate linear response theory. Correspondingly, the deviation of the Gaussian statistics causes the inefficiency of linear response evaluation. The above mechanism is thoroughly tested in this study. By employing molecular simulations, multiple non-equilibrium processes, not necessarily initiated from the ground state equilibrium minimum, were examined for tryptophan. Both the success and failure of linear response theory are found for this simple system and the mechanism is analyzed. These observations, assisted by the width dynamics, the initial state linear response approach, and the variation of the solvation structures, integrally verify the virtue of the excited state Gaussian statistics on the dynamics of Stokes shift.
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Affiliation(s)
- Xiaofang Wang
- School of Physics and Optoelectronic Engineering, Xidian University Xi'an 710071 People's Republic of China
| | - Jirui Guo
- School of Physics and Optoelectronic Engineering, Xidian University Xi'an 710071 People's Republic of China
| | - Tanping Li
- School of Physics and Optoelectronic Engineering, Xidian University Xi'an 710071 People's Republic of China
| | - Zhiyi Wei
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences Beijing 100190 China
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4
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Guo J, Wang X, Li T, Wei Z. Linear Response Theory for Decomposition Energies of Stokes Shift in Proteins. J Phys Chem B 2020; 124:3540-3547. [PMID: 32212659 DOI: 10.1021/acs.jpcb.9b11519] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In aqueous solution, fluorescence Stokes shift experiments monitor the relaxation of the solute-solvent interactions upon photon excitation of the solute chromophore. Linear response (LR) theory expects the identical dynamics between the Stokes shift and the system's spontaneous fluctuations. Whether this identity guarantees similar dynamics between the nonequilibrated and equilibrium processes for the decomposition energy of the Stokes shift is the main focus of this study. In our previous work [Li, T. J. Chem. Theory Comput. 2017, 13, 1867-1873], Stokes shift is properly correlated with various order time-correlation functions. As a continuation, its decomposition energy from the subsystem is further represented as the full summation of all of the cross-time correlation functions between the decomposition energy and the total solute-solvent interactions. Gaussian statistics of the total solute-solvent interactions ensure the same decay rates among the odd orders not only for the time-correlation functions but also for the cross-time correlation functions, validating the LR of the Stokes shift and the decompositions, respectively. The above mechanism is verified by molecular dynamics simulations in the protein Staphylococcus nuclease and is robust even as the decomposed energy associated with an individual residue exhibits typical non-Gaussian properties. Further examinations reveal the consistent molecular motions for a specific residue over the nonequilibrium and equilibrium processes, which are responsible for the nonequilibrium dynamics of the associated decomposed energy. Our results show the appropriateness of LR on finer molecular scales.
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Affiliation(s)
- Jirui Guo
- School of Physics and Optoelectronic Engineering, Xidian University, Xi'an 710071, People's Republic of China
| | - Xiaofang Wang
- School of Physics and Optoelectronic Engineering, Xidian University, Xi'an 710071, People's Republic of China
| | - Tanping Li
- School of Physics and Optoelectronic Engineering, Xidian University, Xi'an 710071, People's Republic of China
| | - Zhiyi Wei
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
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5
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Hazra MK, Bagchi B. Non-linearity in dipolar solvation dynamics in water-ethanol mixture: Composition dependence of free energy landscape. J Chem Phys 2019; 151:084502. [DOI: 10.1063/1.5097751] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Milan K. Hazra
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | - Biman Bagchi
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
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6
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7
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Terranova ZL, Corcelli SA. Decompositions of Solvent Response Functions in Ionic Liquids: A Direct Comparison of Equilibrium and Nonequilibrium Methodologies. J Phys Chem B 2018; 122:6823-6828. [DOI: 10.1021/acs.jpcb.8b04235] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Z. L. Terranova
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - S. A. Corcelli
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
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8
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Heid E, Moser W, Schröder C. On the validity of linear response approximations regarding the solvation dynamics of polyatomic solutes. Phys Chem Chem Phys 2017; 19:10940-10950. [DOI: 10.1039/c6cp08575j] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Gaussian statistics and linear response predictions of the nonequilibrium solvation dynamics are tested for numerous solute/solvent combinations.
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Affiliation(s)
- Esther Heid
- University of Vienna
- Faculty of Chemistry
- Department of Computational Biological Chemistry
- A-1090 Vienna
- Austria
| | - Wanda Moser
- University of Vienna
- Faculty of Chemistry
- Department of Computational Biological Chemistry
- A-1090 Vienna
- Austria
| | - Christian Schröder
- University of Vienna
- Faculty of Chemistry
- Department of Computational Biological Chemistry
- A-1090 Vienna
- Austria
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9
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Singh MK, Shweta H, Sen S. Dispersed dynamics of solvation in G-quadruplex DNA: comparison of dynamic Stokes shifts of probes in parallel and antiparallel quadruplex structures. Methods Appl Fluoresc 2016; 4:034009. [PMID: 28355155 DOI: 10.1088/2050-6120/4/3/034009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
G-quadruplex DNA (GqDNA) structures play an important role in many specific cellular functions and are promising anti-tumor targets for small molecules (ligands). Here, we measured the dynamic Stokes shift of a ligand (Hoechst) bound to parallel c-Myc (mPu22) GqDNA over five decades of time from 100 fs to 10 ns, and compared it with the previously reported dynamics of DAPI bound to antiparallel human telomeric (hTelo22) GqDNA (Pal et al 2015 J. Phys. Chem. Lett. 6 1754). Stokes shift data from fluorescence up-conversion and time-correlated single photon counting experiments was combined to cover the broad dynamic range. The results show that the solvation dynamics of Hoechst in parallel mPu22 GqDNA follow a power law relaxation, added to fast 2 ps exponential relaxation, from 100 fs to 10 ns, with only a subtle difference of power law exponents in the two ligand-GqDNA systems (0.06 in Hoechst-mPu22 compared to 0.16 in DAPI-hTelo22). We measured steady-state fluorescence spectra and time-resolved anisotropy decays which confirm the tight binding of Hoechst to parallel mPu22 with a binding constant of ~1 × 105 M-1. The molecular docking of Hoechst in parallel GqDNA followed by a 50 ns molecular dynamics (MD) simulation on a Hoechst-GqDNA complex reveals that Hoechst binds to one of the outer G-tetrads by end-stacking near G13 and G4, which is different from the binding site of DAPI inside a groove of antiparallel hTelo22 GqDNA. Reconciling previous experimental and simulation results, we assign the 2 ps component to the hydration dynamics of only weakly perturbed water near mPu22 and the power law relaxation to the coupled motion of water and DNA (i.e. DNA backbone, unpaired bases and loops connecting G-tetrads) which come near the Hoechst inside parallel GqDNA.
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Affiliation(s)
- Moirangthem Kiran Singh
- Spectroscopy Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
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10
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Park JW, Rhee YM. Diabatic Population Matrix Formalism for Performing Molecular Mechanics Style Simulations with Multiple Electronic States. J Chem Theory Comput 2015; 10:5238-53. [PMID: 26583208 DOI: 10.1021/ct5006856] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An accurate description of nonbonded interactions is important in investigating dynamics of molecular systems. In many situations, fixed point charge models are successfully applied to explaining various chemical phenomena. However, these models with conventional formulations will not be appropriate in elucidating the detailed dynamics during nonadiabatic events. This is mainly because the chemical properties of any molecule, especially its electronic populations, significantly change with respect to molecular distortions in the vicinity of the surface crossing. To overcome this issue in molecular simulations yet within the framework of the fixed point charge model, we define a diabatic electronic population matrix and substitute it for the conventional adiabatic partial charges. We show that this matrix can be readily utilized toward attaining more reliable descriptions of Coulombic interactions, in combination with the interpolation formalism for obtaining the intramolecular interaction potential. We demonstrate how the mixed formalism with the diabatic charges and the interpolation can be applied to molecular simulations by conducting adiabatic and nonadiabatic molecular dynamics trajectory calculations of the green fluorescent protein chromophore anion in aqueous environment.
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Affiliation(s)
- Jae Woo Park
- Center for Self-Assembly and Complexity, Institute for Basic Science (IBS) , Pohang 790-784, Korea.,Department of Chemistry, Pohang University of Science and Technology (POSTECH) , Pohang 790-784, Korea
| | - Young Min Rhee
- Center for Self-Assembly and Complexity, Institute for Basic Science (IBS) , Pohang 790-784, Korea.,Department of Chemistry, Pohang University of Science and Technology (POSTECH) , Pohang 790-784, Korea
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11
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Li T, Kumar R. Role of excited state solvent fluctuations on time-dependent fluorescence Stokes shift. J Chem Phys 2015; 143:174501. [DOI: 10.1063/1.4934661] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Tanping Li
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, USA
| | - Revati Kumar
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, USA
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12
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Li T. Validity of Linear Response Theory for Time-Dependent Fluorescence in Staphylococcus Nuclease. J Phys Chem B 2014; 118:12952-9. [DOI: 10.1021/jp506599d] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tanping Li
- 700 Choppin Hall, Chemistry Department of Louisiana State University, Baton Rouge, Louisiana 70803, United States
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13
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Fresch B, Remacle F. Atomistic account of structural and dynamical changes induced by small binders in the double helix of a short DNA. Phys Chem Chem Phys 2014; 16:14070-82. [PMID: 24902052 DOI: 10.1039/c4cp01561d] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Nucleic acids are flexible molecules and their dynamical properties play a key role in molecular recognition events. Small binders interacting with DNA fragments induce both structural and dynamical changes in the double helix. We study the dynamics of a DNA dodecamer and of its complexes with Hoechst 33258, which is a minor groove binder, and with the ethidium cation, which is an intercalator, by molecular dynamics simulation. The thermodynamics of DNA-drug interaction is evaluated in connection with the structure and the dynamics of the resulting complexes. We identify and characterize the relevant changes in the configurational distribution of the DNA helix and relate them to the corresponding entropic contributions to the binding free energy. The binder Hoechst locks the breathing motion of the minor groove inducing a reduction of the configurational entropy of the helix, which amounts to 20 kcal mol(-1). In contrast, intercalations with the ethidium cation enhance the flexibility of the double helix. We show that the balance between the energy required to deform the helix for the intercalation and the gain in configurational entropy is the origin of cooperativity in the binding of a second ethidium and of anti-cooperativity in the binding of a third one. The results of our study provide an understanding of the relation between structure, dynamics and energetics in the interaction between DNA fragments and small binders, highlighting the role of dynamical changes and consequent variation of the configurational entropy of the DNA double helix for both types of binders.
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Affiliation(s)
- Barbara Fresch
- Department of Chemistry, B6c, University of Liege, B4000 Liege, Belgium.
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14
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Terranova ZL, Corcelli SA. Molecular dynamics investigation of the vibrational spectroscopy of isolated water in an ionic liquid. J Phys Chem B 2014; 118:8264-72. [PMID: 24650158 DOI: 10.1021/jp501631m] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Experimental studies examining the structure and dynamics of water in ionic liquids (ILs) have revealed local ion rearrangements that occur an order of magnitude faster than complete randomization of the liquid structure. Simulations of an isolated water molecule embedded in 1-butyl-3-methyl imidazolium hexafluorophosphate, [bmim][PF6], were performed to shed insight into the nature of these coupled water-ion dynamics. The theoretical calculations of the spectral diffusion dynamics and the infrared absorption spectra of the OD stretch of isolated HOD in [bmim][PF6] agree well with experiment. The infrared absorption line shape of the OD stretch is narrower and blue-shifted in the IL compared to those in aqueous solution. Decomposition of the OD frequency time correlation function revealed that translational motions of the anions dominate the spectral diffusion dynamics.
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Affiliation(s)
- Z L Terranova
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
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15
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Kwac K, Geva E. Solvation Dynamics of Formylperylene Dissolved in Methanol–Acetonitrile Liquid Mixtures: A Molecular Dynamics Study. J Phys Chem B 2013; 117:9996-10006. [DOI: 10.1021/jp405818f] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Kijeong Kwac
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Eitan Geva
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
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16
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Terranova ZL, Corcelli SA. On the Mechanism of Solvation Dynamics in Imidazolium-Based Ionic Liquids. J Phys Chem B 2013; 117:15659-66. [DOI: 10.1021/jp406419y] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Z. L. Terranova
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556,
United States
| | - S. A. Corcelli
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556,
United States
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17
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Garg D, Beribisky AV, Ponterini G, Ligabue A, Marverti G, Martello A, Costi MP, Sattler M, Wade RC. Translational repression of thymidylate synthase by targeting its mRNA. Nucleic Acids Res 2013; 41:4159-70. [PMID: 23423353 PMCID: PMC3627590 DOI: 10.1093/nar/gkt098] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Resistance to drugs targeting human thymidylate synthase (TS) poses a major challenge in the field of anti-cancer therapeutics. Overexpression of the TS protein has been implicated as one of the factors leading to the development of resistance. Therefore, repressing translation by targeting the TS mRNA could help to overcome this problem. In this study, we report that the compound Hoechst 33258 (HT) can reduce cellular TS protein levels without altering TS mRNA levels, suggesting that it modulates TS expression at the translation level. We have combined nuclear magnetic resonance, UV-visible and fluorescence spectroscopy methods with docking and molecular dynamics simulations to study the interaction of HT with a region in the TS mRNA. The interaction predominantly involves intercalation of HT at a CC mismatch in the region near the translational initiation site. Our results support the use of HT-like compounds to guide the design of therapeutic agents targeting TS mRNA.
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Affiliation(s)
- Divita Garg
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany.
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18
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Kim HW, Kelly A, Park JW, Rhee YM. All-Atom Semiclassical Dynamics Study of Quantum Coherence in Photosynthetic Fenna–Matthews–Olson Complex. J Am Chem Soc 2012; 134:11640-51. [DOI: 10.1021/ja303025q] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hyun Woo Kim
- Institute of Theoretical
and Computational Chemistry, Department of Chemistry, Pohang University of Science and Technology, Pohang
790-784, Korea
| | - Aaron Kelly
- Institute of Theoretical
and Computational Chemistry, Department of Chemistry, Pohang University of Science and Technology, Pohang
790-784, Korea
| | - Jae Woo Park
- Institute of Theoretical
and Computational Chemistry, Department of Chemistry, Pohang University of Science and Technology, Pohang
790-784, Korea
| | - Young Min Rhee
- Institute of Theoretical
and Computational Chemistry, Department of Chemistry, Pohang University of Science and Technology, Pohang
790-784, Korea
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19
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Woo Kim H, Rhee YM. Molecule-specific determination of atomic polarizabilities with the polarizable atomic multipole model. J Comput Chem 2012; 33:1662-72. [DOI: 10.1002/jcc.22985] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Accepted: 03/18/2012] [Indexed: 11/07/2022]
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20
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Rettig M, Germann MW, Ismail MA, Batista-Parra A, Munde M, Boykin DW, Wilson WD. Microscopic rearrangement of bound minor groove binders detected by NMR. J Phys Chem B 2012; 116:5620-7. [PMID: 22530735 DOI: 10.1021/jp301143e] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Thermodynamic and structural studies are commonly utilized to optimize small molecules for specific DNA interactions, and, thus, a significant amount of binding data is available. However, the dynamic processes that are involved in minor groove complex formation and maintenance are not fully understood. To help define the processes involved, we have conducted 1D and 2D NMR in conjunction with biosensor-SPR experiments with a variety of compounds and symmetric, as well as asymmetric, AT tract DNA sequences. Surprisingly, the NMR data clearly show exchange between equivalent binding sites for strongly binding compounds like netropsin and DB921 (Ka > 10(8) M(-1)) that does not involve dissociation off the DNA. A quantitative analysis of the data revealed that these bound exchange rates are indeed much faster than the macroscopic dissociation rates which were independently determined by biosensor-SPR. Additionally, we could show the existence of at least two 1:1 compound DNA complexes at the same site for the interaction of these compounds with an asymmetric DNA sequence. To explain this behavior we introduced a model in which the ligand is rapidly flipping between two orientations while in close association with the DNA. The ligand reorientation will contribute favorably to the binding entropy. As the potential of minor groove binders to form more than a single complex with asymmetric, as well as symmetric, duplexes is widely unknown, the consequences for binding thermodynamics and compound design are discussed.
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Affiliation(s)
- Michael Rettig
- Department of Chemistry, Georgia State University , Atlanta, Georgia 30303, United States
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21
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Perale G, Rossi F, Santoro M, Peviani M, Papa S, Llupi D, Torriani P, Micotti E, Previdi S, Cervo L, Sundström E, Boccaccini AR, Masi M, Forloni G, Veglianese P. Multiple drug delivery hydrogel system for spinal cord injury repair strategies. J Control Release 2011; 159:271-80. [PMID: 22227024 DOI: 10.1016/j.jconrel.2011.12.025] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2011] [Revised: 12/01/2011] [Accepted: 12/20/2011] [Indexed: 02/07/2023]
Abstract
The multifactorial pathological progress of spinal cord injury (SCI) is probably the main reason behind the absence of efficient therapeutic approaches. Hence, very recent highlights suggest the use of new multidrug delivery systems capable of local controlled release of therapeutic agents. In this work, a biocompatible hydrogel-based system was developed as multiple drug delivery tool, specifically designed for SCI repair strategies. Multiple release profiles were achieved by loading gel with a combination of low and high steric hindrance molecules. In vitro, in vivo and ex vivo release studies showed an independent combination of fast diffusion-controlled kinetics for smaller molecules together with slow diffusion-controlled kinetics for bigger ones. A preserved functionality of loaded substances was always achieved, confirming the absence of any chemical stable interactions between gel matrix and loaded molecules. Moreover, the relevant effect of the cerebrospinal fluid flux dynamics on the drug diffusion in the spinal cord tissue was here revealed for the first time: an oriented delivery of the released molecules in the spinal cord tract caudally to the gel site is demonstrated, thus suggesting a more efficient gel positioning rostrally to the lesion.
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Affiliation(s)
- Giuseppe Perale
- Department of Chemistry, Materials and Chemical Engineering Giulio Natta, Politecnico di Milano, via Mancinelli 7, 20131 Milan, Italy
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22
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Park JW, Kim HW, Song CI, Rhee YM. Condensed phase molecular dynamics using interpolated potential energy surfaces with application to the resolvation process of coumarin 153. J Chem Phys 2011; 135:014107. [PMID: 21744888 DOI: 10.1063/1.3605302] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Interpolated potential energy surfaces (PESs) have been used for performing reliable molecular dynamics (MD) simulations of small molecular reactions. In this article, we extend this method to MD simulations in condensed phase and show that the same scheme can also be feasibly used when it is supplemented with additional terms for describing intermolecular interactions. We then apply the approach for studying the resolvation process of coumarin 153 in a number of polar solvents. We find that the interpolated surface actually reproduces experimentally found features much better than the conventional force field based potential especially in terms of both dynamics Stokes shift in the short time limit and solute vibrational decoherence. This shows that the solute vibrational effect is important to some degree along the resolvation and should be modeled properly for accurate description of the related dynamics. The stability issue of trajectories on the interpolated PESs is also discussed, in regard to the goal of reliably performing long time simulations. Operational limitations of the present scheme are also discussed.
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Affiliation(s)
- Jae Woo Park
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang 790-784, Korea
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23
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Furse KE, Corcelli SA. Effects of an unnatural base pair replacement on the structure and dynamics of DNA and neighboring water and ions. J Phys Chem B 2011; 114:9934-45. [PMID: 20614919 DOI: 10.1021/jp105761b] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Incorporating small molecule probes into biomolecular systems to report on local structure and dynamics is a powerful strategy that underlies a wide variety of experimental techniques, including fluorescence, electron paramagnetic resonance (EPR), and Forster resonance energy transfer (FRET) measurements. When an unnatural probe is inserted into a protein or DNA, the degree to which the presence of the probe has perturbed the local structure and dynamics it was intended to study is always an important concern. Here, molecular dynamics (MD) simulations are used to systematically study the effect of replacing a DNA base pair with a fluorescent probe, coumarin 102 deoxyriboside, at six unique sites along an A-tract DNA dodecamer. While the overall structure of the DNA oligonucleotide remains intact, replacement of A*T base pairs leads to widespread structural and dynamic perturbations up to four base pairs away from the probe site, including widening of the minor groove and increased DNA flexibility. New DNA conformations, not observed in the native sequence, are sometimes found in the vicinity of the probe and its partner abasic site analog. Strong correlations are demonstrated between DNA surface topology and water mobility.
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Affiliation(s)
- K E Furse
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
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Affiliation(s)
- Kristina E. Furse
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Steven A. Corcelli
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
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Furse KE, Corcelli SA. Effects of Long-Range Electrostatics on Time-Dependent Stokes Shift Calculations. J Chem Theory Comput 2009; 5:1959-67. [DOI: 10.1021/ct9001416] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kristina E. Furse
- Department of Chemistry and Biochemistry, 251 Nieuwland Science Hall, University of Notre Dame, Notre Dame, Indiana 46556
| | - Steven A. Corcelli
- Department of Chemistry and Biochemistry, 251 Nieuwland Science Hall, University of Notre Dame, Notre Dame, Indiana 46556
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26
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Mazur AK. Kinetic and Thermodynamic DNA Elasticity at Micro- and Mesoscopic Scales. J Phys Chem B 2009; 113:2077-89. [DOI: 10.1021/jp8098945] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Alexey K. Mazur
- CNRS UPR9080, Institut de Biologie Physico-Chimique 13, rue Pierre et Marie Curie, Paris 75005, France
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Lindquist BA, Furse KE, Corcelli SA. Nitrile groups as vibrational probes of biomolecular structure and dynamics: an overview. Phys Chem Chem Phys 2009; 11:8119-32. [DOI: 10.1039/b908588b] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Furse KE, Corcelli SA. The Dynamics of Water at DNA Interfaces: Computational Studies of Hoechst 33258 Bound to DNA. J Am Chem Soc 2008; 130:13103-9. [DOI: 10.1021/ja803728g] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kristina E. Furse
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556
| | - Steven A. Corcelli
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556
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