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The emerging field of hybrid DNA - protein nanotechnology brings with it the potential for many novel materials which combine the addressability of DNA nanotechnology with versatility of protein interactions. However, the design and…
Availability of high-resolution crystal structures of ribosomal subunits of different species opens a route to investigate about molecular interactions between its constituents and stabilization strategy. Structural analysis of the small…
In this paper, we study the large-scale protein interaction network of yeast uti lizing a stochastic method based upon percolation of random graphs. In order to find the global features of connectivities in the network, we introduce numeric…
This review is a tutorial for scientists interested in the problem of protein structure prediction, particularly those interested in using coarse-grained molecular dynamics models that are optimized using lessons learned from the energy…
The protein-protein interactions (PPIs) are crucial for understanding the majority of cellular processes. PPIs play important role in gene transcription regulation, cellular signaling, molecular basis of immune response and more. Moreover,…
Protein interaction networks (PIN) are popular means to visualize the proteome. However, PIN datasets are known to be noisy, incomplete and biased by the experimental protocols used to detect protein interactions. This paper aims at…
Gene expression and regulation rely on an apparently finely tuned set of reactions between some proteins and DNA. Such DNA-binding proteins have to find specific sequences on very long DNA molecules and they mostly do so in absence of any…
In this work, protein-surface interactions were probed in terms of adsorption and desorption of a model protein, bovine serum albumin, on a low-fouling surface with single-molecule localization microscopy. Single-molecule experiments enable…
Direct observation of single-molecule interactions and dynamic configurations in situ is a demanding challenge but crucial for both chemical and biological systems. However, optical microscopy that relies on bulk measurements cannot meet…
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…
Protein-protein interactions (PPIs) are governed by surface complementarity and hydrophobic interactions at protein interfaces. However, designing diverse and physically realistic protein structure and surfaces that precisely complement…
The interaction between the bacterial S-protein SbpA on different types of lipid membranes has been studied using atomic force microscopy, transmission electron microscopy, and quartz crystal microbalance with dissipation. On one hand, It…
Proteins participating in a protein-protein interaction network can be grouped into homology classes following their common ancestry. Proteins added to the network correspond to genes added to the classes, so that the dynamics of the two…
Deep Learning (DL) algorithms hold great promise for applications in the field of computational biophysics. In fact, the vast amount of available molecular structures, as well as their notable complexity, constitutes an ideal context in…
The interaction of a protein with its environment can be understood and controlled via its 3D structure. Experimental methods for protein structure determination, such as X-ray crystallography or cryogenic electron microscopy, shed light on…
We present a thermodynamically consistent mesoscopic model of protein adsorption at liquid-solid interfaces. First describing the equilibrium state under varying protein concentration of the solution and binding conditions, we predict a…
We investigate diffusion-limited reactions between a diffusing particle and a target site on a semiflexible polymer, a key factor determining the kinetics of DNA-protein binding and polymerization of cytoskeletal filaments. Our theory…
Glycans are structurally diverse and flexible biomolecules that play key roles in many biological processes. Their conformational variability makes the modeling of their interactions with proteins particularly challenging. This chapter…
The enormous size and complexity of genotypic sequence space frequently requires consideration of coarse-grained sequences in empirical models. We develop scaling relations to quantify the effect of this coarse-graining on properties of…
Computational drug discovery provides an efficient tool helping large scale lead molecules screening. One of the major tasks of lead discovery is identifying molecules with promising binding affinities towards a target, a protein in…