Highly specific transcriptional regulation depends on the cooperative association of transcription factors into enhanceosomes. Usually, their DNA-binding cooperativity originates from either direct interactions or DNA-mediated allostery. Here, we performed unbiased molecular simulations followed by simulations of protein-DNA unbinding and free energy profiling to study the cooperative DNA recog...

Two-state cooperativity is an important characteristic in protein folding. It is defined by a depletion of states that lie energetically between folded and unfolded conformations. There are different ways to test for two-state cooperativity; however, most of these approaches probe indirect proxies of this depletion. Generalized-ensemble computer simulations allow us to unambiguously identify th...

The aim of this work is to incorporate cooperativity into Huxley-type cross-bridge model in thermodynamically consistent way. While the Huxley-type models assume that cross-bridges act independently from each other, we take into account that each cross-bridge is influenced by its neighbors and cooperativity is induced by tropomyosin movement. For that, we introduce ensembles of cross-bridge gro...

The respective roles of local and nonlocal interactions in the thermodynamic cooperativity of proteins are investigated using continuum (off-lattice) native-centric Gō-like models with a coarse-grained Ca chain representation. We study a series of models in which the (local) bondand torsion-angle terms have different strengths relative to the (nonlocal) pairwise contact energy terms. Conformati...

Circular permutations usually retain the native structure and function of a protein while inevitably perturbing its folding dynamics. By using simulations with a structure-based model and a rigorous methodology to determine free-energy surfaces from trajectories, we evaluate the effect of a circular permutation on the free-energy landscape of the protein T4 lysozyme. We observe changes which, a...

MOTIVATION Transcription factor binding sites are known to co-occur in the same gene owing to cooperativity of the transcription factors (TFs) that bind to them. Genome-wide location data can help us understand how an individual TF regulates its target gene. Nevertheless, how TFs cooperate to regulate their target genes still needs further study. In this study, genome-wide location data and exp...

Ru3(μ-CO)3(CO)5-type clusters bound to the dinucleating PNNP expanded pincer ligand are described. Deprotonation of a methylene linker gives an anionic triruthenium cluster featuring dearomatized ligand. Interestingly, H2 activation by resulting appears not proceed through metal-ligand cooperativity.