A Transferrable Model for Chromatin Folding
Jose N. Onuchic
Center for Theoretical Biological Physics, Rice University, Houston TX
In vivo, the human genome folds into a characteristic ensemble of 3D structures. The mechanism driving the folding process remains unknown. A theoretical model for chromatin (minimal chromatin model) that explains the folding of interphase chromosomes and generates chromosome conformations consistent with experimental data will be presented. The energy landscape of the model was derived by using the maximum entropy principle and relies on two experimentally derived inputs: a classification of loci into chromatin types and a catalog of the positions of chromatin loops. First, we trained our energy function using the Hi-C contact map of chromosome 10 from human GM12878 lymphoblastoid cells. Then, we used the model to perform molecular dynamics simulations producing an ensemble of 3D structures for all GM12878 autosomes. Finally, we used these 3D structures to generate contact maps. We found that simulated contact maps closely agree with experimental results for all GM12878 autosomes. The ensemble of structures resulting from these simulations exhibited unknotted chromosomes, phase separation of chromatin types, and a tendency for open chromatin to lie at the periphery of chromosome territories.
Bridge-mediated exciton transport: pathway analysis of the donor-acceptor exciton coupling
Spiros S. Skourtis
Department of Physics, University of Cyprus, Nicosia Cyprus
Dexter energy transfer (triplet-exciton transfer), is important in solar energy harvesting assemblies, damage protection schemes of photobiology, and organometallic opto-electronic materials. Triplet-exciton transfer between chemically linked donors and acceptors is bridge-mediated. If the bridge is a tunneling barrier for the transferring exciton, exciton transfer presents an enticing analogy with bridge-mediated superexchange electron transfer. We formulate a theory for exciton-transfer coupling pathways by analogy to electron-transfer coupling pathways . We show that virtual exciton intermediates with one electron or one hole on the bridge dominate the donor-acceptor coupling at shorter distances and/or high tunneling energy gaps, while virtual intermediates with an electron and a hole on the bridge (virtual bridge excitons) dominate at longer distances and /or low energy gaps. The effects of virtual bridge excitons have been neglected in earlier descriptions and may alter the distance dependence of the Dexter rate. Spiros S. Skourtis, Charoen Liu, Panayiotis Antoniou, Aaron M. Virshup and David N. Beratan. Proc. Nat. Acad. Sci. USA, 2016, 113 8115-8120.
Molecular Conductance and Electrochemical Studies of Nucleic Acids and Peptides
David H. Waldeck, Edward Beall, and Emil Wierzbinski
University of Pittsburgh
We present new results on charge transport in nucleic acids and chiral symmetry effects on electron transfer. Molecular conductance and electrochemical charge transfer are different manifestations of a molecule’s ability to transmit electric charge, and we report on experiments that compare the molecular conductance to the charge transfer rates. We present recent findings on the chiral induced spin-selectivity effect and its importance for understanding the fundamental nature of charge transfer and charge displacement
MANIPULATION OF ELECTRON TRANSFER RATES IN MOLECULES WITH SHORT MID INFRARED PULSES
Igor V. Rubtsov
Department of Chemistry, Tulane University, New Orleans LA 70118, USA
It was recently proposed theoretically by D. Beratan and co-workers that electron transfer rate in donor-bridge-acceptor molecules can be changed by manipulating interferences of inelastic pathways through the bridge. Experimental attempts to accomplishing this goal by exciting vibrational modes at the bridge with a mid-IR radiation are discussed. Several molecular systems were interrogated featuring bridges of different types, including hydrogen bonded bridges and bridges involving coordination bonds. The results show that vibrational excitation may increase or reduce the rate of electron transfer. It is demonstrated that vibrational excitation of the bridge modes could reduce the electron transfer rate while heat accelerates it.
U-Turn Electron Transfer: A New Strategy to Control Photo-triggered Energy Conversion Reactions of Coordination Compounds
Nicholas F. Polizzi, Ting Jiang, David N. Beratan, and Michael J. Therien
Department of Chemistry, French Family Science Center, 124 Science Drive, Duke University, Durham, North Carolina 27708, USA
Efficient energy conversion requires quantitative, light-driven formation of high-energy, charge-separated states. Conventional artificial photosystem designs seek to promote electron transfer (ET) by polarizing excited donor electron density toward the acceptor (“one-way” ET). Enigmatically, the excited donor of the archetypal R. sphaeroides reaction center polarizes its electron density away from its electron acceptor: light absorption by the reaction center thus triggers a “U-turn” ET event. Whatever mechanistic importance lies behind this biological U-turn ET has been obscured by the inability to experimentally reverse donor excited-state polarization within the reaction center. We describe how U-turn ET produces a strikingly larger yield of high-energy photo-products compared to a conventional one-way ET scheme, by minimizing intersystem crossing to the donor triplet state. We directly compare one-way vs. U-turn ET strategies via linked donor-acceptor (DA) assemblies based on highly conjugated (porphinato)metal-(polypyridyl)metal constructs, in which selective optical excitation produces donor excited states polarized either toward or away from the acceptor. Ultrafast spectroscopic studies of these DA assemblies pinpoint the importance of realizing donor singlet and triplet excited states that have opposite electronic polarizations to shut down intersystem crossing, a scheme exploited by the reaction center of R. sphaeroides. These results offer an unexpected U-turn design principle, heralded by Nature, that averts intersystem crossing and dramatically increases the yield of high-energy photo-products critical for light-driven energy conversion reactions.