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Peluffo RD, Hernández JA. The Na +,K +-ATPase and its stoichiometric ratio: some thermodynamic speculations. Biophys Rev 2023; 15:539-552. [PMID: 37681108 PMCID: PMC10480117 DOI: 10.1007/s12551-023-01082-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 06/18/2023] [Indexed: 09/09/2023] Open
Abstract
Almost seventy years after its discovery, the sodium-potassium adenosine triphosphatase (the sodium pump) located in the cell plasma membrane remains a source of novel mechanistic and physiologic findings. A noteworthy feature of this enzyme/transporter is its robust stoichiometric ratio under physiological conditions: it sequentially counter-transports three sodium ions and two potassium ions against their electrochemical potential gradients per each hydrolyzed ATP molecule. Here we summarize some present knowledge about the sodium pump and its physiological roles, and speculate whether energetic constraints may have played a role in the evolutionary selection of its characteristic stoichiometric ratio.
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Affiliation(s)
- R. Daniel Peluffo
- Group of Biophysical Chemistry, Department of Biological Sciences, CENUR Litoral Norte, Universidad de La República, Rivera 1350, CP: 50000 Salto, Uruguay
| | - Julio A. Hernández
- Biophysics and Systems Biology Section, Department of Cell and Molecular Biology, Facultad de Ciencias, Universidad de La República, Iguá 4225, CP: 11400 Montevideo, Uruguay
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2
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Mantela M, Morphis A, Lambropoulos K, Simserides C, Di Felice R. Effects of Structural Dynamics on Charge Carrier Transfer in B-DNA: A Combined MD and RT-TDDFT Study. J Phys Chem B 2021; 125:3986-4003. [PMID: 33857373 DOI: 10.1021/acs.jpcb.0c11489] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Hole transfer along the axis of duplex DNA has been the focus of physical chemistry research for decades, with implications in diverse fields, from nanotechnology to cell oxidative damage. Computational approaches are particularly amenable for this problem, to complement experimental data for interpretation of transfer mechanisms. To be predictive, computational results need to account for the inherent mobility of biological molecules during the time frame of experimental measurements. Here, we address the structural variability of B-DNA and its effects on hole transfer in a combined molecular dynamics (MD) and real-time time-dependent density functional theory (RT-TDDFT) study. Our results show that quantities that characterize the charge transfer process, such as the time-dependent dipole moment and hole population at a specific site, are sensitive to structural changes that occur on the nanosecond time scale. We extend the range of physical properties for which such a correlation has been observed, further establishing the fact that quantitative computational data on charge transfer properties should include statistical averages. Furthermore, we use the RT-TDDFT results to assess an efficient tight-binding method suitable for high-throughput predictions. We demonstrate that charge transfer, although affected by structural variability, on average, remains strong in AA and GG dimers.
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Affiliation(s)
- Marilena Mantela
- Department of Physics, National and Kapodistrian University of Athens, Panepistimiopolis, Zografos GR-15784, Athens, Greece
| | - Andreas Morphis
- Department of Physics, National and Kapodistrian University of Athens, Panepistimiopolis, Zografos GR-15784, Athens, Greece
| | - Konstantinos Lambropoulos
- Department of Physics, National and Kapodistrian University of Athens, Panepistimiopolis, Zografos GR-15784, Athens, Greece
| | - Constantinos Simserides
- Department of Physics, National and Kapodistrian University of Athens, Panepistimiopolis, Zografos GR-15784, Athens, Greece
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Aggarwal A, Vinayak V, Bag S, Bhattacharyya C, Waghmare UV, Maiti PK. Predicting the DNA Conductance Using a Deep Feedforward Neural Network Model. J Chem Inf Model 2020; 61:106-114. [PMID: 33320660 DOI: 10.1021/acs.jcim.0c01072] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Double-stranded DNA (dsDNA) has been established as an efficient medium for charge migration, bringing it to the forefront of the field of molecular electronics and biological research. The charge migration rate is controlled by the electronic couplings between the two nucleobases of DNA/RNA. These electronic couplings strongly depend on the intermolecular geometry and orientation. Estimating these electronic couplings for all the possible relative geometries of molecules using the computationally demanding first-principles calculations requires a lot of time and computational resources. In this article, we present a machine learning (ML)-based model to calculate the electronic coupling between any two bases of dsDNA/dsRNA and bypass the computationally expensive first-principles calculations. Using the Coulomb matrix representation which encodes the atomic identities and coordinates of the DNA base pairs to prepare the input dataset, we train a feedforward neural network model. Our neural network (NN) model can predict the electronic couplings between dsDNA base pairs with any structural orientation with a mean absolute error (MAE) of less than 0.014 eV. We further use the NN-predicted electronic coupling values to compute the dsDNA/dsRNA conductance.
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Affiliation(s)
- Abhishek Aggarwal
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
| | - Vinayak Vinayak
- Undergraduate Program, Indian Institute of Science, Bangalore 560012, India
| | - Saientan Bag
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
| | - Chiranjib Bhattacharyya
- Department of Computer Science and Automation, Indian Institute of Science, Bangalore 560012, India
| | - Umesh V Waghmare
- Theoretical Sciences Unit, Jawaharlal Nehru Center for Advanced Scientific Research, Jakkur P.O., Bangalore 560064, India
| | - Prabal K Maiti
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
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Behnia S, Fathizadeh S, Javanshour E, Nemati F. Light-Driven Modulation of Electrical Current through DNA Sequences: Engineering of a Molecular Optical Switch. J Phys Chem B 2020; 124:3261-3270. [DOI: 10.1021/acs.jpcb.0c00073] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- S. Behnia
- Department of Physics, Urmia University of Technology, Urmia 5716693187, Iran
| | - S. Fathizadeh
- Department of Physics, Urmia University of Technology, Urmia 5716693187, Iran
| | - E. Javanshour
- Department of Physics, Urmia University of Technology, Urmia 5716693187, Iran
| | - F. Nemati
- Department of Physics, Urmia University of Technology, Urmia 5716693187, Iran
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Mantela M, Lambropoulos K, Theodorakou M, Simserides C. Quasi-Periodic and Fractal Polymers: Energy Structure and Carrier Transfer. MATERIALS (BASEL, SWITZERLAND) 2019; 12:E2177. [PMID: 31284609 PMCID: PMC6651379 DOI: 10.3390/ma12132177] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 07/02/2019] [Accepted: 07/04/2019] [Indexed: 12/23/2022]
Abstract
We study the energy structure and the coherent transfer of an extra electron or hole along aperiodic polymers made of N monomers, with fixed boundaries, using B-DNA as our prototype system. We use a Tight-Binding wire model, where a site is a monomer (e.g., in DNA, a base pair). We consider quasi-periodic (Fibonacci, Thue-Morse, Double-Period, Rudin-Shapiro) and fractal (Cantor Set, Asymmetric Cantor Set) polymers made of the same monomer (I polymers) or made of different monomers (D polymers). For all types of such polymers, we calculate the highest occupied molecular orbital (HOMO) eigenspectrum and the lowest unoccupied molecular orbital (LUMO) eigenspectrum, the HOMO-LUMO gap and the density of states. We examine the mean over time probability to find the carrier at each monomer, the frequency content of carrier transfer (Fourier spectra, weighted mean frequency of each monomer, total weighted mean frequency of the polymer), and the pure mean transfer rate k. Our results reveal that there is a correspondence between the degree of structural complexity and the transfer properties. I polymers are more favorable for charge transfer than D polymers. We compare k ( N ) of quasi-periodic and fractal sequences with that of periodic sequences (including homopolymers) as well as with randomly shuffled sequences. Finally, we discuss aspects of experimental results on charge transfer rates in DNA with respect to our coherent pure mean transfer rates.
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Affiliation(s)
- Marilena Mantela
- Department of Physics, National and Kapodistrian University of Athens, Panepistimiopolis, Zografos, GR-15784 Athens, Greece
| | - Konstantinos Lambropoulos
- Department of Physics, National and Kapodistrian University of Athens, Panepistimiopolis, Zografos, GR-15784 Athens, Greece
| | - Marina Theodorakou
- Department of Physics, National and Kapodistrian University of Athens, Panepistimiopolis, Zografos, GR-15784 Athens, Greece
| | - Constantinos Simserides
- Department of Physics, National and Kapodistrian University of Athens, Panepistimiopolis, Zografos, GR-15784 Athens, Greece.
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Lambropoulos K, Simserides C. Periodic, quasiperiodic, fractal, Kolakoski, and random binary polymers: Energy structure and carrier transport. Phys Rev E 2019; 99:032415. [PMID: 30999536 DOI: 10.1103/physreve.99.032415] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Indexed: 05/26/2023]
Abstract
We study periodic, quasiperiodic (Thue-Morse, Fibonacci, period doubling, Rudin-Shapiro), fractal (Cantor, generalized Cantor), Kolakoski, and random binary sequences using a tight-binding wire model, where a site is a monomer (e.g., in DNA, a base pair). We use B-DNA as our prototype system. All sequences have purines, guanine (G) or adenine (A), on the same strand, i.e., our prototype binary alphabet is {G,A}. Our aim is to examine the influence of sequence intricacy and magnitude of parameters on energy structure, localization, and charge transport. We study quantities such as autocorrelation function, eigenspectra, density of states, Lyapunov exponents, transmission coefficients, and current-voltage curves. We show that the degree of sequence intricacy and the presence of correlations decisively affect the aforementioned physical properties. Periodic segments have enhanced transport properties. Specifically, in homogeneous sequences transport efficiency is maximum. There are several deterministic aperiodic sequences that can support significant currents, depending on the Fermi level of the leads. Random sequences is the less efficient category.
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Affiliation(s)
- K Lambropoulos
- Department of Physics, National and Kapodistrian University of Athens, Panepistimiopolis, 15784 Zografos, Athens, Greece
| | - C Simserides
- Department of Physics, National and Kapodistrian University of Athens, Panepistimiopolis, 15784 Zografos, Athens, Greece
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Tassi M, Morphis A, Lambropoulos K, Simserides C. RT-TDDFT study of hole oscillations in B-DNA monomers and dimers. ACTA ACUST UNITED AC 2017. [DOI: 10.1080/23311940.2017.1361077] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- M. Tassi
- Department of Physics, National and Kapodistrian University of Athens, Panepistimiopolis, Zografos GR-15784, Athens, Greece
| | - A. Morphis
- Department of Physics, National and Kapodistrian University of Athens, Panepistimiopolis, Zografos GR-15784, Athens, Greece
| | - K. Lambropoulos
- Department of Physics, National and Kapodistrian University of Athens, Panepistimiopolis, Zografos GR-15784, Athens, Greece
| | - C. Simserides
- Department of Physics, National and Kapodistrian University of Athens, Panepistimiopolis, Zografos GR-15784, Athens, Greece
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