相关论文: A Novel Mathematical Model of Protein Interactions…
Proteins often regulate their activities via allostery - or action at a distance - in which the binding of a ligand at one binding site influences the affinity for another ligand at a distal site. Although less studied than in proteins,…
Allostery refers to the puzzling phenomenon of long-range communication between distant sites in proteins. Despite its importance in biomolecular regulation and signal transduction, the underlying dynamical process is not well understood.…
Proteins need to selectively interact with specific targets among a multitude of similar molecules in the cell. But despite a firm physical understanding of binding interactions, we lack a general theory of how proteins evolve high…
Allostery is a fundamental property of proteins that represents the functional coupling between distantly located sites. In different manifestations, this property underlies signal transduction, gene expression, and regulation -- elementary…
Cooperativity plays an important role in the action of proteins bound to DNA. A simple, mechanical mechanism for cooperativity, in the form of a tension-mediated interaction between proteins bound to DNA at two different locations is…
Many signalling functions in molecular biology require proteins bind to substrates such as DNA in response to environmental signals such as the simultaneous binding to a small molecule. Examples are repressor proteins which may transmit…
Numerous cellular functions rely on protein$\unicode{x2013}$protein interactions. Efforts to comprehensively characterize them remain challenged however by the diversity of molecular recognition mechanisms employed within the proteome. Deep…
Understanding the link between structure and function in proteins is fundamental in molecular biology and proteomics. A central question in this context is whether allostery - where the binding of a molecule at one site affects the activity…
Cellular function is widely believed to be organized in a modular fashion. On all scales and at all levels of complexity, relatively independent sub-units perform relatively independent sub-tasks of biological function. This functional…
A major issue in biology is the understanding of the interactions between proteins. These interactions can be described by a network, where the proteins are modeled by nodes and the interactions by edges. The origin of these protein…
It has recently been demonstrated that many biological networks exhibit a scale-free topology where the probability of observing a node with a certain number of edges (k) follows a power law: i.e. p(k) ~ k^-g. This observation has been…
How do living cells achieve sufficient abundances of functional protein complexes while minimizing promiscuous non-functional interactions? Here we study this problem using a first-principle model of the cell whose phenotypic traits are…
Allosteric regulation in proteins is often accompanied by conformational changes that facilitate transmission of mechanical signals between distant ligand binding sites. Typically, these deformations are classified in terms of specific…
Protein-DNA interactions are vital for many processes in living cells, especially transcriptional regulation and DNA modification. To further our understanding of these important processes on the microscopic level, it is necessary that…
Allosteric interactions between molecules bound to DNA at distant locations have been known for a long time. The phenomenon has been studied via experiments and numerical simulations, but a comprehensive understanding grounded in a theory…
Cooperativity is a hallmark of proteins, many of which show a modular architecture comprising discrete structural domains. Detecting and describing dynamic couplings between structural regions is difficult in view of the many-body nature of…
Proteins are a matter of dual nature. As a physical object, a protein molecule is a folded chain of amino acids with multifarious biochemistry. But it is also an instantiation along an evolutionary trajectory determined by the function…
Biological functions stem from coordinated interactions among proteins, nucleic acids and small molecules. Mass spectrometry technologies for reliable, high throughput single-cell proteomics will add a new modality to genomics and enable…
Proteins are the common constituents of all living cells. They are molecular machines that interact with each other as well as with other cell products and carry out a dizzying array of functions with distinction. These interactions follow…
Allostery, the intriguing phenomenon of long-range communication between distant sites in proteins, plays a central role in biomolecular regulation and signal transduction. While it is commonly attributed to conformational rearrangements,…