Related papers: Evolutionary and Structural Constraints Define a M…
ATP synthases utilize a proton motive force to synthesize ATP. In reverse, these membrane-embedded enzymes can also hydrolyze ATP to pump protons over the membrane. To prevent wasteful ATP hydrolysis, distinct control mechanisms exist for…
Microbial electrolysis cells (MECs) employ electroactive bacteria to perform extracellular electron transfer, enabling hydrogen generation from biodegradable substrates. In previous work, we developed and analyzed a differential-algebraic…
Bacteria such as Escherichia coli (E. coli) exhibit biased motion if kept in a spatially non-uniform chemical environment. Here, we bring out unique time-dependent characteristics of bacterial chemotaxis, in response to a diffusing spatial…
Conjugation is the primary mechanism of horizontal gene transfer that spreads antibiotic resistance among bacteria. Although conjugation normally occurs in surface-associated growth (e.g., biofilms), it has been traditionally studied in…
DFT calculations performed on Si_2H_6, Si_2F_6, Si_2Cl_6, and Si_2Br_6 are reported. The evolution of the energy, the chemical potential and the molecular hardness, as a function of torsion angle, is studied. Results at the…
The near-surface swimming patterns of bacteria are strongly determined by the hydrodynamic interactions between bacteria and the surface, which trap bacteria in smooth circular trajectories that lead to inefficient surface exploration.…
Background: The Epithelial-Mesenchymal Transition (EMT) endows epithelial-looking cells with enhanced migratory ability during embryonic development and tissue repair. EMT can also be co-opted by cancer cells to acquire metastatic potential…
Despite recent advances in our ability to detect adaptive evolution involving the cis-regulation of gene expression, our knowledge of the molecular mechanisms underlying these adaptations has lagged far behind. Across all model organisms…
The transcriptional regulation of gene expression is orchestrated by complex networks of interacting genes. Increasing evidence indicates that these transcriptional regulatory networks (TRNs) in bacteria have an inherently hierarchical…
In a letter published in Molecular Biology Evolution [10], Chen and Zhang argue that the variation of the mutation rate along the Escherichia coli genome that we recently reported [3] cannot be evolutionarily optimised. To support this…
Intracellular transport is an essential function in eucaryotic cells, facilitated by motor proteins - proteins converting chemical energy into kinetic energy. It is known that motor proteins work in teams enabling unidirectional and…
A recently experimentally observed biochemical "threshold filtering" mechanism by processes catalyzed by the enzyme malate dehydrogenase is explained in terms of a model that incorporates an unusual mechanism of inhibition of this enzyme…
We study model one-dimensional chemical systems (representative of their three-dimensional counterparts) using the strictly-correlated electrons (SCE) functional, which, by construction, becomes asymptotically exact in the limit of infinite…
Elucidating the architecture and dynamics of large scale genetic regulatory networks of cells is an important goal in systems biology. We study the system level dynamical properties of the genetic network of Escherichia coli that regulates…
S-adenosylhomocysteine hydrolase (SAHH), a cellular enzyme that plays a key role in methylation reactions including those required for maturation of viral mRNA, is an important drug target in the discovery of antiviral agents. While…
Understanding the organization of reaction fluxes in cellular metabolism from the stoichiometry and the topology of the underlying biochemical network is a central issue in systems biology. In this task, it is important to devise reasonable…
The active sites of enzymes consist of residues necessary for catalysis, and structurally important non-catalytic residues that together maintain the architecture and function of the active site. Examples of evolutionary interactions…
Purpose of review: The epithelial-Mesenchymal Transition (EMT) and the generation of Cancer Stem Cells (CSC) are two fundamental aspects contributing to tumor growth, acquisition of resistance to therapy, formation of metastases, and tumor…
Antimicrobial resistance (AMR) poses a significant threat to public health by increasing mortality, extending hospital stays, and increasing healthcare costs. It affects people of all ages and affects health services, veterinary medicine,…
Many proteins undergo conformational changes during their activity. A full understanding of the function of these proteins can only be obtained if different conformations and transitions between them can be monitored in aqueous solution,…