Related papers: Interrelationship Between Protein Electrostatics a…
Protein-DNA complexes with loops play a fundamental role in a wide variety of cellular processes, ranging from the regulation of DNA transcription to telomere maintenance. As ubiquitous as they are, their precise in vivo properties and…
Proteins, by virtue of their central role in most biological processes, represent one of the key subjects of the study of molecular evolution. Inherent to the indispensability of proteins for living cells is the fact that a given protein…
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…
Protein-protein interactions are fundamental to many biological processes. Experimental screens have identified tens of thousands of interactions and structural biology has provided detailed functional insight for select 3D protein…
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…
We summarize some aspects of electrostatic interactions in the context of viruses. A simplified but, within well defined limitations, reliable approach is used to derive expressions for electrostatic energies and the corresponding osmotic…
Population dynamics and evolutionary genetics underly the structure of ecosystems, changing on the same timescale for interacting species with rapid turnover, such as virus (e.g. HIV) and immune response. Thus, an important problem in…
Biological diversity has evolved despite the essentially infinite complexity of protein sequence space. We present a hierarchical approach to the efficient searching of this space and quantify the evolutionary potential of our approach with…
We propose a dissipative electro-elastic network model (DENM) to describe the dynamics and statistics of electrostatic fluctuations at active sites of proteins. The model combines the harmonic network of residue beads with overdamped…
Major advances in large-scale yeast two hybrid (Y2H) screening have provided a global view of binary protein-protein interactions across species as dissimilar as human, yeast, and bacteria. Remarkably, these analyses have revealed that all…
Since protein mutations are the main driving force of evolution at the molecular level, a proper analysis of them (and the factors controlling them) will enable us to find a response to several crucial queries in evolutionary biology. Among…
Polymorphism has been observed in viral capsid assembly, demonstrating the ability of identical protein dimers to adopt multiple geometries under the same solution conditions. A well-studied example is the hepatitis B virus (HBV), which…
We review the status of protein-based molecular electronics. First we discuss fundamental concepts of electron transfer and transport in and across proteins and proposed mechanisms for these processes. We then describe the immobilization of…
Homeostasis of protein concentrations in cells is crucial for their proper functioning, and this requires concentrations (at their steady-state levels) to be stable to fluctuations. Since gene expression is regulated by proteins such as…
Hemoglobin exhibits allosteric structural changes upon ligand binding due to the dynamic interactions between the ligand binding sites, the amino acids residues and some other solutes present under physiological conditions. In the present…
Heterochromatin protein 1 (HP1) participates in establishing and maintaining heterochromatin via its histone modification dependent chromatin interactions. In recent papers HP1 binding to nucleosomal arrays was measured in vitro and…
Phase separation is as familiar as watching vinegar separating from oil in vinegrette. The observation that phase separation of proteins and nucleic acids is widespread in living cells has opened an entire field of research into the…
While almost any kind of face mask offers some protection against particles and pathogens of different sizes, the most efficient ones make use of a layered structure where one or more layers are electrically charged. This electret layer is…
Epigenetic histone modifications play an important role in the maintenance of different cell phenotypes. The exact molecular mechanism for inheritance of the modification patterns over cell generations remains elusive. We construct a…
Global coevolutionary models of homologous protein families, as constructed by direct coupling analysis (DCA), have recently gained popularity in particular due to their capacity to accurately predict residue-residue contacts from sequence…