@article{12724, abstract = {We use general symmetry-based arguments to construct an effective model suitable for studying optical properties of lead halide perovskites. To build the model, we identify an atomic-level interaction between electromagnetic fields and the spin degree of freedom that should be added to a minimally coupled k⋅p Hamiltonian. As a first application, we study two basic optical characteristics of the material: the Verdet constant and the refractive index. Beyond these linear characteristics of the material, the model is suitable for calculating nonlinear effects such as the third-order optical susceptibility. Analysis of this quantity shows that the geometrical properties of the spin-electric term imply isotropic optical response of the system, and that optical anisotropy of lead halide perovskites is a manifestation of hopping of charge carriers. To illustrate this, we discuss third-harmonic generation.}, author = {Volosniev, Artem and Shiva Kumar, Abhishek and Lorenc, Dusan and Ashourishokri, Younes and Zhumekenov, Ayan and Bakr, Osman M. and Lemeshko, Mikhail and Alpichshev, Zhanybek}, issn = {2469-9969}, journal = {Physical Review B}, number = {12}, publisher = {American Physical Society}, title = {{Effective model for studying optical properties of lead halide perovskites}}, doi = {10.1103/physrevb.107.125201}, volume = {107}, year = {2023}, } @article{12759, abstract = {Stereological methods for estimating the 3D particle size and density from 2D projections are essential to many research fields. These methods are, however, prone to errors arising from undetected particle profiles due to sectioning and limited resolution, known as ‘lost caps’. A potential solution developed by Keiding, Jensen, and Ranek in 1972, which we refer to as the Keiding model, accounts for lost caps by quantifying the smallest detectable profile in terms of its limiting ‘cap angle’ (ϕ), a size-independent measure of a particle’s distance from the section surface. However, this simple solution has not been widely adopted nor tested. Rather, model-independent design-based stereological methods, which do not explicitly account for lost caps, have come to the fore. Here, we provide the first experimental validation of the Keiding model by comparing the size and density of particles estimated from 2D projections with direct measurement from 3D EM reconstructions of the same tissue. We applied the Keiding model to estimate the size and density of somata, nuclei and vesicles in the cerebellum of mice and rats, where high packing density can be problematic for design-based methods. Our analysis reveals a Gaussian distribution for ϕ rather than a single value. Nevertheless, curve fits of the Keiding model to the 2D diameter distribution accurately estimate the mean ϕ and 3D diameter distribution. While systematic testing using simulations revealed an upper limit to determining ϕ, our analysis shows that estimated ϕ can be used to determine the 3D particle density from the 2D density under a wide range of conditions, and this method is potentially more accurate than minimum-size-based lost-cap corrections and disector methods. Our results show the Keiding model provides an efficient means of accurately estimating the size and density of particles from 2D projections even under conditions of a high density.}, author = {Rothman, Jason Seth and Borges Merjane, Carolina and Holderith, Noemi and Jonas, Peter M and Angus Silver, R.}, issn = {1932-6203}, journal = {PLoS ONE}, number = {3 March}, publisher = {Public Library of Science}, title = {{Validation of a stereological method for estimating particle size and density from 2D projections with high accuracy}}, doi = {10.1371/journal.pone.0277148}, volume = {18}, year = {2023}, } @article{12756, abstract = {ESCRT-III family proteins form composite polymers that deform and cut membrane tubes in the context of a wide range of cell biological processes across the tree of life. In reconstituted systems, sequential changes in the composition of ESCRT-III polymers induced by the AAA–adenosine triphosphatase Vps4 have been shown to remodel membranes. However, it is not known how composite ESCRT-III polymers are organized and remodeled in space and time in a cellular context. Taking advantage of the relative simplicity of the ESCRT-III–dependent division system in Sulfolobus acidocaldarius, one of the closest experimentally tractable prokaryotic relatives of eukaryotes, we use super-resolution microscopy, electron microscopy, and computational modeling to show how CdvB/CdvB1/CdvB2 proteins form a precisely patterned composite ESCRT-III division ring, which undergoes stepwise Vps4-dependent disassembly and contracts to cut cells into two. These observations lead us to suggest sequential changes in a patterned composite polymer as a general mechanism of ESCRT-III–dependent membrane remodeling.}, author = {Hurtig, Fredrik and Burgers, Thomas C.Q. and Cezanne, Alice and Jiang, Xiuyun and Mol, Frank N. and Traparić, Jovan and Pulschen, Andre Arashiro and Nierhaus, Tim and Tarrason-Risa, Gabriel and Harker-Kirschneck, Lena and Löwe, Jan and Šarić, Anđela and Vlijm, Rifka and Baum, Buzz}, issn = {2375-2548}, journal = {Science Advances}, number = {11}, publisher = {American Association for the Advancement of Science}, title = {{The patterned assembly and stepwise Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell division}}, doi = {10.1126/sciadv.ade5224}, volume = {9}, year = {2023}, } @article{12758, abstract = {AlphaFold changed the field of structural biology by achieving three-dimensional (3D) structure prediction from protein sequence at experimental quality. The astounding success even led to claims that the protein folding problem is “solved”. However, protein folding problem is more than just structure prediction from sequence. Presently, it is unknown if the AlphaFold-triggered revolution could help to solve other problems related to protein folding. Here we assay the ability of AlphaFold to predict the impact of single mutations on protein stability (ΔΔG) and function. To study the question we extracted the pLDDT and metrics from AlphaFold predictions before and after single mutation in a protein and correlated the predicted change with the experimentally known ΔΔG values. Additionally, we correlated the same AlphaFold pLDDT metrics with the impact of a single mutation on structure using a large scale dataset of single mutations in GFP with the experimentally assayed levels of fluorescence. We found a very weak or no correlation between AlphaFold output metrics and change of protein stability or fluorescence. Our results imply that AlphaFold may not be immediately applied to other problems or applications in protein folding.}, author = {Pak, Marina A. and Markhieva, Karina A. and Novikova, Mariia S. and Petrov, Dmitry S. and Vorobyev, Ilya S. and Maksimova, Ekaterina and Kondrashov, Fyodor and Ivankov, Dmitry N.}, issn = {1932-6203}, journal = {PLoS ONE}, number = {3}, publisher = {Public Library of Science}, title = {{Using AlphaFold to predict the impact of single mutations on protein stability and function}}, doi = {10.1371/journal.pone.0282689}, volume = {18}, year = {2023}, } @article{12757, abstract = {My group and myself have studied respiratory complex I for almost 30 years, starting in 1994 when it was known as a L-shaped giant ‘black box' of bioenergetics. First breakthrough was the X-ray structure of the peripheral arm, followed by structures of the membrane arm and finally the entire complex from Thermus thermophilus. The developments in cryo-EM technology allowed us to solve the first complete structure of the twice larger, ∼1 MDa mammalian enzyme in 2016. However, the mechanism coupling, over large distances, the transfer of two electrons to pumping of four protons across the membrane remained an enigma. Recently we have solved high-resolution structures of mammalian and bacterial complex I under a range of redox conditions, including catalytic turnover. This allowed us to propose a robust and universal mechanism for complex I and related protein families. Redox reactions initially drive conformational changes around the quinone cavity and a long-distance transfer of substrate protons. These set up a stage for a series of electrostatically driven proton transfers along the membrane arm (‘domino effect'), eventually resulting in proton expulsion from the distal antiporter-like subunit. The mechanism radically differs from previous suggestions, however, it naturally explains all the unusual structural features of complex I. In this review I discuss the state of knowledge on complex I, including the current most controversial issues.}, author = {Sazanov, Leonid A}, issn = {1470-8728}, journal = {The Biochemical Journal}, number = {5}, pages = {319--333}, publisher = {Portland Press}, title = {{From the 'black box' to 'domino effect' mechanism: What have we learned from the structures of respiratory complex I}}, doi = {10.1042/BCJ20210285}, volume = {480}, year = {2023}, }