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Nasou AG, Pantatosaki E, Papadopoulos GK. A Simulation Study of the Effect of Naturally Occurring Point Mutations on the SRY-DNA Complex. J Phys Chem B 2022; 126:8921-8930. [PMID: 36315187 DOI: 10.1021/acs.jpcb.2c04852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Molecular dynamics (MD) simulations were conducted in order to investigate the effect of the naturally occurring point mutations of the transcription factor (TF) sex-determining region Y (SRY) on the structure and dynamics of the SRY-DNA complex. The normal SRY, along with the two mutants I13T and G40R, comprising point mutations on the SRY chain, which have been clinically identified in patients with sex developmental disorders, were modeled as DNA complexes. Our modeling work aims at elucidating atomic-level structural determinants of the aberrant SRY-DNA complexation by means of μs-long MD. The results suggest that the observed disorders brought about by the G40R-DNA and I13T-DNA may arise predominantly from the destabilization of the complex being in accord with in vitro assays found elsewhere and from modifications of the DNA bending as revealed in this study. Comparative potential of mean force computations, over a sequence of short separation distances for the three complexes, verified a higher stability of the normal SRY-DNA. Examining the way the SRY mutations modulate the SRY-DNA complex dynamics at the microscopic level is important also toward elucidating molecular determinants of function for proteins capable of binding to DNA.
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Affiliation(s)
- Angeliki-Georgia Nasou
- School of Chemical Engineering, National Technical University of Athens, 157 80 Athens, Greece
| | - Evangelia Pantatosaki
- School of Chemical Engineering, National Technical University of Athens, 157 80 Athens, Greece
| | - George K Papadopoulos
- School of Chemical Engineering, National Technical University of Athens, 157 80 Athens, Greece
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Guo J, Wang D, Pantatosaki E, Kuang H, Papadopoulos GK, Tsapatsis M, Kokkoli E. A Localized Enantioselective Catalytic Site on Short DNA Sequences and Their Amphiphiles. JACS Au 2022; 2:483-491. [PMID: 35252997 PMCID: PMC8889555 DOI: 10.1021/jacsau.1c00513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Indexed: 06/14/2023]
Abstract
A DNA-based artificial metalloenzyme (ArM) consisting of a copper(II) complex of 4,4'-dimethyl-2,2'-bipyridine (dmbipy-Cu) bound to double-stranded DNA (dsDNA) as short as 8 base pairs with only 2 contiguous central pairs (G for guanine and C for cytosine) catalyzes the highly enantioselective Diels-Alder reaction, Michael addition, and Friedel-Crafts alkylation in water. Molecular simulations indicate that these minimal sequences provide a single site where dmbipy-Cu is groove-bound and able to function as an enantioselective catalyst. Enantioselective preference inverts when d-DNA is replaced with l-DNA. When the DNA is conjugated to a hydrophobic tail, the obtained ArMs exhibit enantioselective performance in a methanol-water mixture superior to that of non-amphiphilic dsDNA, and dsDNA-amphiphiles with more complex G•C-rich sequences.
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Affiliation(s)
- Jun Guo
- Institute
for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Danyu Wang
- Institute
for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department
of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Evangelia Pantatosaki
- School
of Chemical Engineering, National Technical
University of Athens, 15780 Athens, Greece
| | - Huihui Kuang
- Institute
for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - George K. Papadopoulos
- School
of Chemical Engineering, National Technical
University of Athens, 15780 Athens, Greece
- Institute
for Medical Engineering and Science, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Michael Tsapatsis
- Institute
for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department
of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Applied
Physics Laboratory, Johns Hopkins University, Laurel, Maryland 20723, United States
| | - Efrosini Kokkoli
- Institute
for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department
of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
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Pantatosaki E, Papadopoulos GK. Binding Dynamics of siRNA with Selected Lipopeptides: A Computer-Aided Study of the Effect of Lipopeptides' Functional Groups and Stereoisomerism. J Chem Theory Comput 2020; 16:3842-3855. [PMID: 32324997 DOI: 10.1021/acs.jctc.9b01261] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The engineering issues pertaining to nanoparticle systems toward targeted gene therapies have not been fully probed. Recent experiments have identified specific structural characteristics of a novel class of lipopeptides (LP) that may lead to potent nanocarriers intended as RNAi therapeutics, albeit the molecular mechanism that underlies their performance remains unexplored. We conducted molecular dynamics simulations in atomistic detail coupled with free energy computations to study the dynamics and thermodynamics of an acrylate- and an epoxide-derived LP, members of the aforesaid class, upon their binding to siRNA in aqueous solution aiming at examining structure-potency relations. We found that the entropic part of the free energy of binding predominates; moreover, the first LP class tends to disrupt the Watson-Crick base pairing of siRNA, whereas the latter leaves the double helix intact. Moreover, the identified tug-of-war effect between LP-water and LP-siRNA hydrogen bonding in the supramolecular complex can underpin synthesis routes toward tuning the association dynamics. Our simulations on two diastereomers of the epoxide-derived LP showed significant structural and energetics differences upon binding, as a result of steric effects imposed by the different absolute configurations at their chiral centers. These findings may serve as crucial design parameters toward modulating the interplay between complex stability and ease of releasing the nucleic acid drug into the cell.
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Affiliation(s)
- Evangelia Pantatosaki
- School of Chemical Engineering, National Technical University of Athens, 15780 Athens, Greece
| | - George K Papadopoulos
- School of Chemical Engineering, National Technical University of Athens, 15780 Athens, Greece.,Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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Stallmach F, Splith T, Chmelik C, Füldner G, Henninger SK, Kolokathis PT, Pantatosaki E, Papadopoulos GK. Wasseradsorption und -diffusion in SAPO-34 für die adsorptive Wärmetransformation. CHEM-ING-TECH 2016. [DOI: 10.1002/cite.201500140] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Kolokathis PD, Pantatosaki E, Gatsiou CA, Jobic H, Papadopoulos GK, Theodorou DN. Dimensionality reduction of free energy profiles of benzene in silicalite-1: calculation of diffusion coefficients using transition state theory. Molecular Simulation 2013. [DOI: 10.1080/08927022.2013.840895] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Panagiotis D. Kolokathis
- School of Chemical Engineering, National Technical University of Athens, Zografou Campus, GR-15780, Athens, Greece
| | - Evangelia Pantatosaki
- School of Chemical Engineering, National Technical University of Athens, Zografou Campus, GR-15780, Athens, Greece
| | - Christina-Anna Gatsiou
- School of Chemical Engineering, National Technical University of Athens, Zografou Campus, GR-15780, Athens, Greece
| | - Hervé Jobic
- Institut de Recherches sur la Catalyse et l' Environnement de Lyon, CNRS, 2 av. Albert Einstein, 69626, Villeurbanne, France
| | - George K. Papadopoulos
- School of Chemical Engineering, National Technical University of Athens, Zografou Campus, GR-15780, Athens, Greece
| | - Doros N. Theodorou
- School of Chemical Engineering, National Technical University of Athens, Zografou Campus, GR-15780, Athens, Greece
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Kowalczyk P, Gauden PA, Terzyk AP, Pantatosaki E, Papadopoulos GK. Constant Pressure Path Integral Gibbs Ensemble Monte Carlo Method. J Chem Theory Comput 2013; 9:2922-9. [PMID: 26583975 DOI: 10.1021/ct400110c] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present the implementation of a real-space constant pressure path integral Gibbs ensemble Monte Carlo (CP-PIGEMC) method for the simulation of one-component fluid consists of distinguishable quantum particles (henceforth referred to as Boltzmannons) in an external potential field at finite temperatures. We apply this simulation method to study the para-H2 adsorption in NaX zeolite at 77 K and pressures up to 100 bar. We present a new set of effective solid-fluid parameters optimized for path integral simulations of hydrogen isotope adsorption and separation in synthetic zeolites. The agreement among CP-PIGEMC, experiment, and the path integral grand canonical Monte Carlo method (PIGCMC) is very good, even at high pressures. CP-PIGEMC is a particularly useful method for simulation of one-component quantum fluid composed of Boltzmannons at finite temperatures, when the chemical potential is difficult to measure or calculate explicitly.
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Affiliation(s)
- Piotr Kowalczyk
- Nanochemistry Research Institute, Department of Chemistry, Curtin University of Technology , P.O. Box U1987, Perth, 6845 Western Australia, Australia
| | - Piotr A Gauden
- Department of Chemistry, Physicochemistry of Carbon Materials Research Group, N. Copernicus University , Gagarin St. 7, 87-100 Torun, Poland
| | - Artur P Terzyk
- Department of Chemistry, Physicochemistry of Carbon Materials Research Group, N. Copernicus University , Gagarin St. 7, 87-100 Torun, Poland
| | - Evangelia Pantatosaki
- School of Chemical Engineering, National Technical University of Athens , 9 Heroon Polytechniou Street, 157 80 Athens, Greece
| | - George K Papadopoulos
- School of Chemical Engineering, National Technical University of Athens , 9 Heroon Polytechniou Street, 157 80 Athens, Greece
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Pantatosaki E, Jobic H, Kolokolov DI, Karmakar S, Biniwale R, Papadopoulos GK. Probing the hydrogen equilibrium and kinetics in zeolite imidazolate frameworks via molecular dynamics and quasi-elastic neutron scattering experiments. J Chem Phys 2013; 138:034706. [PMID: 23343292 DOI: 10.1063/1.4774375] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The problem of simulating processes involving equilibria and dynamics of guest sorbates within zeolitic imidazolate frameworks (ZIF) by means of molecular dynamics (MD) computer experiments is of growing importance because of the promising role of ZIFs as molecular "traps" for clean energy applications. A key issue for validating such an atomistic modeling attempt is the possibility of comparing the MD results, with real experiments being able to capture analogous space and time scales to the ones pertained to the computer experiments. In the present study, this prerequisite is fulfilled through the quasi-elastic neutron scattering technique (QENS) for measuring self-diffusivity, by elaborating the incoherent scattering signal of hydrogen nuclei. QENS and MD experiments were performed in parallel to probe the hydrogen motion, for the first time in ZIF members. The predicted and measured dynamics behaviors show considerable concentration variation of the hydrogen self-diffusion coefficient in the two topologically different ZIF pore networks of this study, the ZIF-3 and ZIF-8. Modeling options such as the flexibility of the entire matrix versus a rigid framework version, the mobility of the imidazolate ligand, and the inclusion of quantum mechanical effects in the potential functions were examined in detail for the sorption thermodynamics and kinetics of hydrogen and also of deuterium, by employing MD combined with Widom averaging towards studying phase equilibria. The latter methodology ensures a rigorous and efficient way for post-processing the dynamics trajectory, thereby avoiding stochastic moves via Monte Carlo simulation, over the large number of configurational degrees of freedom a nonrigid framework encompasses.
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Affiliation(s)
- Evangelia Pantatosaki
- School of Chemical Engineering, National Technical University of Athens, 9 Heroon Polytechniou Street, 157 80 Athens, Greece
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Pantatosaki E, Pazzona FG, Megariotis G, Papadopoulos GK. Atomistic Simulation Studies on the Dynamics and Thermodynamics of Nonpolar Molecules within the Zeolite Imidazolate Framework-8. J Phys Chem B 2010; 114:2493-503. [DOI: 10.1021/jp911477a] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Evangelia Pantatosaki
- IRCELYON, Institut de Recherches sur la Catalyse et l’Environnement de Lyon, CNRS, Université de Lyon, 2 Avenue A. Einstein, 69626 Villeurbanne, France, School of Chemical Engineering, National Technical University of Athens, 9 Heroon Polytechniou Street, 157 80 Athens, Greece
| | - Federico G. Pazzona
- IRCELYON, Institut de Recherches sur la Catalyse et l’Environnement de Lyon, CNRS, Université de Lyon, 2 Avenue A. Einstein, 69626 Villeurbanne, France, School of Chemical Engineering, National Technical University of Athens, 9 Heroon Polytechniou Street, 157 80 Athens, Greece
| | - Gregory Megariotis
- IRCELYON, Institut de Recherches sur la Catalyse et l’Environnement de Lyon, CNRS, Université de Lyon, 2 Avenue A. Einstein, 69626 Villeurbanne, France, School of Chemical Engineering, National Technical University of Athens, 9 Heroon Polytechniou Street, 157 80 Athens, Greece
| | - George K. Papadopoulos
- IRCELYON, Institut de Recherches sur la Catalyse et l’Environnement de Lyon, CNRS, Université de Lyon, 2 Avenue A. Einstein, 69626 Villeurbanne, France, School of Chemical Engineering, National Technical University of Athens, 9 Heroon Polytechniou Street, 157 80 Athens, Greece
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Pantatosaki E, Papadopoulos GK, Jobic H, Theodorou DN. Combined Atomistic Simulation and Quasielastic Neutron Scattering Study of the Low-Temperature Dynamics of Hydrogen and Deuterium Confined in NaX Zeolite. J Phys Chem B 2008; 112:11708-15. [DOI: 10.1021/jp8018342] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Evangelia Pantatosaki
- IRCELYON, Institut de Recherches sur la Catalyse et l’Environnement de LYON, CNRS, Université de Lyon, UMR5256, 2 Avenue A. Einstein, 69626 Villeurbanne, France, and School of Chemical Engineering, National Technical University of Athens, 9 Heroon Polytechniou Street, 157 80 Athens, Greece
| | - George K. Papadopoulos
- IRCELYON, Institut de Recherches sur la Catalyse et l’Environnement de LYON, CNRS, Université de Lyon, UMR5256, 2 Avenue A. Einstein, 69626 Villeurbanne, France, and School of Chemical Engineering, National Technical University of Athens, 9 Heroon Polytechniou Street, 157 80 Athens, Greece
| | - Hervé Jobic
- IRCELYON, Institut de Recherches sur la Catalyse et l’Environnement de LYON, CNRS, Université de Lyon, UMR5256, 2 Avenue A. Einstein, 69626 Villeurbanne, France, and School of Chemical Engineering, National Technical University of Athens, 9 Heroon Polytechniou Street, 157 80 Athens, Greece
| | - Doros N. Theodorou
- IRCELYON, Institut de Recherches sur la Catalyse et l’Environnement de LYON, CNRS, Université de Lyon, UMR5256, 2 Avenue A. Einstein, 69626 Villeurbanne, France, and School of Chemical Engineering, National Technical University of Athens, 9 Heroon Polytechniou Street, 157 80 Athens, Greece
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Pantatosaki E, Papadopoulos GK. On the computation of long-range interactions in fluids under confinement: Application to pore systems with various types of spatial periodicity. J Chem Phys 2007; 127:164723. [DOI: 10.1063/1.2799986] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Pantatosaki E, Psomadopoulos D, Steriotis T, Stubos A, Papaioannou A, Papadopoulos G. Micropore size distributions from CO2 using grand canonical Monte Carlo at ambient temperatures: cylindrical versus slit pore geometries. Colloids Surf A Physicochem Eng Asp 2004. [DOI: 10.1016/j.colsurfa.2004.04.026] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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