Related papers: Finding a unifying motif of intermolecular coopera…

Most biological processes are described as a series of interactions between proteins and other molecules, and interactions are in turn described in terms of atomic structures. To annotate protein functions as sets of interaction states at…

We propose a protein model based on a hierarchy of constraints that force the protein to follow certain pathways when changing conformation. The model exhibits a first order phase transition, cooperativity and is exactly solvable. It also…

Active centres and hot spots of proteins have a paramount importance in enzyme action, protein complex formation and drug design. Recently a number of publications successfully applied the analysis of residue networks to predict active…

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…

Proteins play crucial roles in every cellular process by interacting with each other, with nucleic acids, metabolites, and other molecules. The resulting assemblies can be very large and intricate and pose challenges to experimental…

Protein folding, peptide aggregation and crystallization, as well as adsorption of molecules on soft or solid substrates have an essential feature in common: In all these processes, structure formation is guided by a collective, cooperative…

In this study, we intend to solve a mutual information problem in interacting molecules of any type, such as proteins, nucleic acids, and small molecules. Using machine learning techniques, we accurately predict pairwise interactions, which…

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…

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…

These lectures will address two questions. Is there a simple variational principle underlying the existence of secondary motifs in the native state of proteins? Is there a general approach which can qualitatively capture the salient…

To confer high specificity and affinity in binding, contacts at interfaces between two interacting macromolecules are expected to exhibit pair preferences for types of atoms or residues. Here we quantify these preferences by measuring the…

The behavior of proteins near interfaces is relevant for biological and medical purposes. Previous results in bulk show that, when the protein concentration increases, the proteins unfold and, at higher concentrations, aggregate. Here, we…

Using a structure-based coarse-grained model of proteins, we study the mechanism of unfolding of knotted proteins through heating. We find that the dominant mechanisms of unfolding depend on the temperature applied and are generally…

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…

The spatio-temporal organization of proteins and the associated morphological changes in membranes are of importance in cell signaling. Several mechanisms that promote the aggregation of proteins at low cell surface concentrations have been…

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…

We construct a Hamiltonian for a single domain protein where the contact enthalpy and the chain entropy decrease linearly with the number of native contacts. The hydration effect upon protein unfolding is included by modeling water as ideal…

Most proteins perform their biological function by interacting with one or more molecular partners. In this respect, characterizing the features of the molecular surface, especially in the portions where the interaction takes place, turned…

Protein folding cooperativity is defined by the nature of the finite-size thermodynamic transition exhibited upon folding: two-state transitions show a free energy barrier between the folded and unfolded ensembles, while downhill folding is…

Current experimental and theoretical studies on the effect of intermolecular interactions on molecular conduction appear to be in conflict with each other. In particular, some experimental results, e.g., the observation of 2-dimensional…