Single-stranded DNA-binding proteins (SSBs) play a key role in genome maintenance, binding and organizing single-stranded DNA (ssDNA) intermediates. Multimeric SSBs, such as the human mitochondrial SSB (HmtSSB), present multiple sites to interact with ssDNA, which has been shown in vitro to enable them to bind a variable number of single-stranded nucleotides depending on the salt and protein concentration. It has long been suggested that different binding modes might be used selectively for different functions. To study this possibility, we used optical tweezers to determine and compare the structure and energetics of long, individual HmtSSB–DNA complexes assembled on preformed ssDNA and on ssDNA generated gradually during ‘in situ’ DNA synthesis. We show that HmtSSB binds to preformed ssDNA in two major modes, depending on salt and protein concentration. However, when protein binding was coupled to strand-displacement DNA synthesis, only one of the two binding modes was observed under all experimental conditions. Our results reveal a key role for the gradual generation of ssDNA in modulating the binding mode of a multimeric SSB protein and consequently, in generating the appropriate nucleoprotein structure for DNA synthetic reactions required for genome maintenance.
We study electric and magnetic monopoles in static, spherically symmetric and constant curvature geometries in the context of the inverse electrodynamics model. We prove that this U(1) invariant Lagrangian density is able to support the standard metric of a Reissner-Nordström Black Hole, but with more complex thermodynamical properties than in the standard case. By employing the Euclidean Action approach we perform a complete analysis of its phase space depending on the sign and singularities of the heat capacity and the Helmholtz free energy.
Ligands binding to polymers regulate polymer functions by changing their physical and chemical properties. This ligand regulation plays a key role in many biological processes. We propose here a model to explain the mechanical, thermodynamic, and kinetic properties of the process of binding of small ligands to long biopolymers. These properties can now be measured at the single molecule level using force spectroscopy techniques. Our model performs an effective decomposition of the ligand-polymer system on its covered and uncovered regions, showing that the elastic properties of the ligand-polymer depend explicitly on the ligand coverage of the polymer (i.e., the fraction of the polymer covered by the ligand). The equilibrium coverage that minimizes the free energy of the ligand-polymer system is computed as a function of the applied force. We show how ligands tune the mechanical properties of a polymer, in particular its length and stiffness, in a force dependent manner. In addition, it is shown how ligand binding can be regulated applying mechanical tension on the polymer. Moreover, the binding kinetics study shows that, in the case where the ligand binds and organizes the polymer in different modes, the binding process can present transient shortening or lengthening of the polymer, caused by changes in the relative coverage by the different ligand modes. Our model will be useful to understand ligand-binding regulation of biological processes, such as the metabolism of nucleic acid. In particular, this model allows estimating the coverage fraction and the ligand mode characteristics from the force extension curves of a ligand-polymer system.
Theoretical analyses of single‐species models have revealed that the degree of synchrony in fluctuations of geographically separated populations increases with increasing spatial covariation in environmental fluctuations and increased interchange of individuals, but decreases with local strength of density dependence. Here we extend these results to include interspecific competition between two species as well as harvesting. We show that the effects of interspecific competition on the geographical scale of population synchrony are dependent on the pattern of spatial covariation of environmental variables. If the environmental noise is uncorrelated between the competing species, competition generally increases the spatial scale of population synchrony of both species. Otherwise, if the environmental noises are strongly correlated between species, competition generally increases the spatial scale of population synchrony of at least one, but also often of both species. The magnitude of these spatial scaling effects is, however, strongly influenced by the dispersal capacity of the two competing species. If the species are subject to proportional harvesting, this may synchronise population dynamics over large geographical areas, affecting the vulnerability of harvested species to environmental changes. However, the strength of interspecific competition may strongly modify this effect of harvesting on the spatial scale of population synchrony. For example, harvesting of one species may affect the spatial distribution of competing species that are not subject to harvesting. These analytical results provide an important illustration of the importance of applying an ecosystem rather than a single‐species perspective when developing harvest strategies for a sustainable management of exploited species.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
hi@scite.ai
10624 S. Eastern Ave., Ste. A-614
Henderson, NV 89052, USA
Copyright © 2024 scite LLC. All rights reserved.
Made with 💙 for researchers
Part of the Research Solutions Family.