Related papers: Robust protein-protein interactions in crowded cel…
In the cell, proteins fold and perform complex functions through global structural rearrangements. Function requires a protein to be at the brink of stability to be susceptible to small environmental fluctuations, yet stable enough to…
Understanding of how protein interaction networks (PIN) of living organisms have evolved or are organized can be the first stepping stone in unveiling how life works on a fundamental ground. Here we introduce a hybrid network model composed…
Bacteria possess diverse mechanisms to regulate their motility in response to environmental and physiological signals, enabling them to navigate complex habitats and adapt their behavior. Among these mechanisms, interspecies recognition…
Protein aggregation in cell membrane is vital for the majority of biological functions. Recent experimental results suggest that transmembrane domains of proteins such as $\alpha$-helices and $\beta$-sheets have different structural…
What are the molecular mechanisms that dictate protein-protein binding stability and whether those are related to the ones behind protein fold stability are still largely open questions. Indeed, despite many past efforts, we still lack…
Studying systems where many individual bodies in motion interact with one another is a complex and interesting area. Simple mechanisms that may be determined for biological, chemical, or physical reasons can lead to astonishingly complex…
The interactions of a protein, its phase behavior, and ultimately, its ability to function, are all influenced by the interactions between the protein and its hydration waters. Here we study proteins with a variety of sizes, shapes,…
The interaction lifetimes between condensate-forming biomolecules can dictate both the specificity of the condensate-forming species as well as the fluidity and exchange dynamics of these condensates. Using a heuristic modeling approach, we…
Protein-Protein Interaction Networks aim to model the interactome, providing a powerful tool for understanding the complex relationships governing cellular processes. These networks have numerous applications, including functional…
Specific binding of proteins to DNA is one of the most common ways in which gene expression is controlled. Although general rules for the DNA-protein recognition can be derived, the ambiguous and complex nature of this mechanism precludes a…
Enzymatic molecules that actively support many cellular processes, including transport, cell division and cell motility, are known as motor proteins or molecular motors. Experimental studies indicate that they interact with each other and…
Inherent structure theory is used to discover strong connections between simple characteristics of protein structure and the energy landscape of a Go model. The potential energies and vibrational free energies of inherent structures are…
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…
Biologists and physicists have a rich tradition of modeling living systems with simple models composed of a few interacting components. Despite the remarkable success of this approach, it remains unclear how to use such finely tuned models…
Biological transport is supported by collective dynamics of enzymatic molecules that are called motor proteins or molecular motors. Experiments suggest that motor proteins interact locally via short-range potentials. We investigate the…
Much of the complexity observed in gene regulation originates from cooperative protein-DNA binding. While studies of the target search of proteins for their specific binding sites on the DNA have revealed design principles for the…
We introduce the idea of weakly coherent collisional models, where the elements of an environment interacting with a system of interest are prepared in states that are approximately thermal, but have an amount of coherence proportional to a…
Protein-protein interactions drive many biological processes, including the detection of phytopathogens by plants' R-Proteins and cell surface receptors. Many machine learning studies have attempted to predict protein-protein interactions…
Identifying the entire set of complexes is essential not only to understand complex formations, but also to map the high level organisation of the cell. Computational prediction of protein complexes faces several challenges including the…
Binding interactions between proteins and other molecules mediate numerous cellular processes, including metabolism, signaling, and regulation of gene expression. These interactions evolve in response to changes in the protein's chemical or…