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Intermolecular hydrogen bonding behavior of amino acid radical cations
No full textAmino acid and peptide radicals are of broad interest due to their roles in biochemical oxidative damage, pathogenesis and protein radical catalysis, among others. Using density functional theory (DFT) calculations at the ωB97X-D/def2-QZVPPD//ωB97X-D/def2-TZVPP level of theory, we systematically investigated the hydrogen bonding between water and fourteen α-amino acids (Ala, Asn, Cys, Gln, Gly, His, Met, Phe, Pro, Sel, Ser, Thr, Trp, and Tyr) in both neutral and radical cation forms. For all amino acids surveyed, stronger hydrogen-bonding interactions with water were observed upon single-electron oxidation, with the greatest increases in hydrogen-bonding strength occurring in Gly, Ala and His. We demonstrate that the side chain has a significant impact on the most favorable hydrogen-bonding modes experienced by amino acid radical cations. Our computations also explored the fragmentation of amino acid radical cations through the loss of a COOH radical facilitated by hydrogen bonding. The most favorable pathways provided stabilization of the resulting cationic fragments through hydrogen bonding, resulting in more favorable thermodynamics for the fragmentation process. These results indicate that non-covalent interactions with the environment have a profound impact on the structure and chemical fate of oxidized amino acids
Myosin mutations suppress Twitchin and troponin by altering the rate constant for attachment/detachment
No full textOur research focuses on understanding the regulation of muscle force production, particularly concerning force, velocity, work, and power, which are mediated by two protein switches. Mutations in these switches can lead to lethal heart diseases. Caenorhabditis elegans’ muscle is similar to human skeletal and cardiac muscle, allowing us to conduct physiological experiments regarding the mutations of the switches. In C. elegans, one of the switches is termed Twitchin, as mutations of it causes worms to twitch uncontrollably, and the other is termed troponin. We induced a mutation in myosin, altering the 462nd amino acid from alanine to valine. Interestingly, this mutation suppresses the twitching of a Twitchin mutant and the hypercontraction of a troponin mutant. Our study tested whether the myosin mutation reduces the number of interactions between actin and myosin, thus suppressing the twitching and hypercontraction of the Twitchin and troponin mutants. Myosin and actin interactions could be altered by decreasing the rate constant for attachment of myosin to actin or by increasing the detachment rate constant. We found diminished force and either normal or reduced fatigability in the mutated myosin worms, indicating a reduced attachment rate constant and possibly increased detachment rate constant of myosin from actin. These effects revert those caused by Twitchin and troponin mutations. Further research involves testing additional myosin mutations to validate our hypothesis that they similarly alter attachment and detachment rates, potentially offering insights into therapeutic interventions for aberrant muscle contractions
Unraveling the role of the RPA winged-helix domain in the yeast cell cycle
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The statistical building blocks of animal movement simulations
No full textAnimal movement plays a key role in many ecological processes and has a direct influence on an individual\u27s fitness at several scales of analysis (i.e., next-step, subdiel, day-by-day, seasonal). This highlights the need to dissect movement behavior at different spatio-temporal scales and develop hierarchical movement tools for generating realistic tracks to supplement existing single-temporal-scale simulators. In reality, animal movement paths are a concatenation of fundamental movement elements (FuMEs: e.g., a step or wing flap), but these are not generally extractable from a relocation time-series track (e.g., sequential GPS fixes) from which step-length (SL, aka velocity) and turning-angle (TA) time series can be extracted. For short, fixed-length segments of track, we generate their SL and TA statistics (e.g., means, standard deviations, correlations) to obtain segment-specific vectors that can be cluster into different types. We use the centroids of these clusters to obtain a set of statistical movement elements (StaMEs; e.g.,directed fast movement versus random slow movement elements) that we use as a basis for analyzing and simulating movement tracks. Our novel concept is that sequences of StaMEs provide a basis for constructing and fitting step-selection kernels at the scale of fixed-length canonical activity modes: short fixed-length sequences of interpretable activity such as dithering, ambling, directed walking, or running. Beyond this, variable length pure or characteristic mixtures of CAMs can be interpreted as behavioral activity modes (BAMs), such as gathering resources (a sequence of dithering and walking StaMEs) or beelining (a sequence of fast directed-walk StaMEs interspersed with vigilance and navigation stops). Here we formulate a multi-modal, step-selection kernel simulation framework, and construct a 2-mode movement simulator (Numerus ANIMOVER_1), using Numerus RAMP technology. These RAMPs run as stand alone applications: they require no coding but only the input of selected parameter values. They can also be used in R programming environments as virtual R packages. We illustrate our methods for extracting StaMEs from both ANIMOVER_1 simulated data and empirical data from two barn owls (Tyto alba) in the Harod Valley, Israel. Overall, our new bottom-up approach to path segmentation allows us to both dissect real movement tracks and generate realistic synthetic ones, thereby providing a general tool for testing hypothesis in movement ecology and simulating animal movement in diverse contexts such as evaluating an individual\u27s response to landscape changes, release of an individual into a novel environment, or identifying when individuals are sick or unusually stressed
Evolution of Cellular Organization Along the First Branches of the Tree of Life
No full textCurrent evidence suggests that some form of cellular organization arose well before the time of the last universal common ancestor (LUCA). Standard phylogenetic analyses have shown that several protein families associated with membrane translocation, membrane transport, and membrane bioenergetics were very likely present in the proteome of the LUCA. Despite these cellular systems emerging prior to the LUCA, extant archaea, bacteria, and eukaryotes have significant differences in cellular infrastructure and the molecular functions that support it, leading some researchers to argue that true cellularity did not evolve until after the LUCA. Here, we use recently reconstructed minimal proteomes of the LUCA as well as the last archaeal common ancestor (LACA) and the last bacterial common ancestor (LBCA) to characterize the evolution of cellular systems along the first branches of the tree of life. We find that a broad set of functions associated with cellular organization were already present by the time of the LUCA. The functional repertoires of the LACA and LBCA related to cellular organization nearly doubled along each branch following the divergence of the LUCA. These evolutionary trends created the foundation for similarities and differences in cellular organization between the taxonomic domains that are still observed today
Waring\u27s Problem for Squares of the Hurwitz Quaternions
No full textThis paper considers sums of squares in quaternion rings with integral or half- integral coefficients and proves global bounds on the minimum number of squares needed to represent any such quaternion as the sum of squares
