arXiv subjects

Tatiana Domratcheva

Publications and source records attributed to Tatiana Domratcheva.

3 recordsLinked to original sources

arXiv2026

The arrangement of anisotropic spin couplings can optimize sensitivity of the cryptochrome radical pair to the direction of geomagnetic field

Sensing of the geomagnetic field direction by many living organisms is commonly thought to involve radical pairs, such as those formed photochemically between the flavin and tryptophan radicals in the cryptochrome proteins. Previous theoretical studies have shown that strongly axial hyperfine couplings in the cryptochrome radicals greatly enhance the formation of a signaling state of the protein when the magnetic field is directed perpendicular to the hyperfine axis of either of the radicals. However, further analysis led to the conclusion that sharpness of detecting those magnetic directions is strongly suppressed by the inter-radical electron spin coupling. Here, we perform theoretical simulations of the compass function for a set of arrangements of the intra- and inter-radical spin couplings in the idealized cryptochrome radical pair, and find certain arrangements that preserve the sharpness in detecting the direction of the geomagnetic field. One particular arrangement, with the hyperfine axes of the radicals orthogonal to the symmetry axis of inter-radical coupling, provides even sharper field-direction sensitivity than that contributed solely by the anisotropy of the hyperfine coupling.

physics.bio-ph↗

arXiv2019

Three-dimensional view of ultrafast dynamics in photoexcited bacteriorhodopsin

Bacteriorhodopsin (bR) is a light-driven proton pump. We use time-resolved crystallography at an X-ray free-electron laser to follow the structural changes in multiphoton-excited bR from 250 femtoseconds to 10 picoseconds. Quantum chemistry and ultrafast spectroscopy allow identifying a sequential two-photon absorption process, leading to excitation of a tryptophan residue flanking the retinal chromophore, as a first manifestation of multi-photon effects. We resolve distinct stages in the structural dynamics of the all-trans retinal in photoexcited bR to a highly twisted 13-cis conformation. Other active site sub-picosecond rearrangements include correlated vibrational motions of the electronically excited retinal chromophore, the surrounding amino acids and water molecules as well as their hydrogen bonding network. These results show that this extended photo-active network forms an electronically and vibrationally coupled system in bR, and most likely in all retinal proteins.

physics.bio-ph↗

arXiv2016

Nuclear dynamics investigation of the initial electron transfer in the cyclobutane pyrimidine dimer lesion repair process by photolyases

Photolyases are proteins capable of harvesting the sunlight to repair DNA damages caused by UV light. In this work we focus on the first step in the repair process of the cyclobutane pyrimidine dimer photoproduct (CPD) lesion, which is an electron transfer (ET) from a flavine cofactor to CPD, and study the role of various nuclear degrees of freedom (DOF) in this step. The ET step has been experimentally studied using transient spectroscopy and the corresponding data provide excellent basis for testing the quality of quantum dynamical models. Based on previous theoretical studies of electronic structure and conformations of the protein active site, we present a procedure to build a diabatic Hamiltonian for simulating the ET reaction in a molecular complex mimicking the enzyme's active site. We generate a reduced nuclear dimensional model that provides a first non-empirical quantum dynamical description of the structural features influencing the ET rate. By varying the nuclear DOF parametrization in the model to assess the role of different nuclear motions, we demonstrate that the low frequency flavin butterfly bending mode slows ET by reducing Franck-Condon overlaps between donor and acceptor states and also induces decoherence.

physics.chem-ph↗