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The principles underlying protein folding remains one of Nature's puzzles with important practical consequences for Life. An approach that has gathered momentum since the late 1990's, looks at protein hetero-polymers and their folding…
Protein-ligand binding is the process by which a small molecule (drug or inhibitor) attaches to a target protein. Binding affinity, which characterizes the strength of biomolecular interactions, is essential for tackling diverse challenges…
The adhesion of biological membranes is mediated by the binding of membrane-anchored receptor and ligand proteins. Central questions are how the binding kinetics of these proteins is affected by the membranes and by the membrane anchoring…
Recent demonstrations of extraordinary stabilization of proteins in mobile protic [1] and aprotic [2] ionic liquid solutions at ambient temperatures have raised hopes of new biopreservation and drug transportation technologies. Here we…
The dynamical characterization of proteins is crucial to understand protein function. From a microscopic point of view, protein dynamics is governed by the local atomic interactions that, in turn, trigger the functional conformational…
We describe Structured Random Binding (SRB), a minimal model of protein-protein interactions rooted in the statistical physics of disordered systems. In this model, nonspecific binding is a generic consequence of the interaction between…
Central to understanding membrane bound cell signaling is to quantify how the membrane ultra-structure consisting of transient spatial domains modulates signaling and how the signaling influences this ultra-structure. Yet, measuring the…
The folding of a peptide chain into a three dimensional structure is a thermodynamically driven process such that the chain naturally evolves to form domains of similar amino acids. The formation of this domain occurs by curling the one…
Intracellular protein patterns regulate many vital cellular functions, such as the processing of spatiotemporal information or the control of shape deformations. To do so, pattern-forming systems can be sensitive to the cell geometry by…
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.…
Domain dynamics in the Piezoresponse Force Spectroscopy (PFS) experiment is studied using the combination of local hysteresis loop acquisition with simultaneous domain imaging. The analytical theory for PFS signal from domain of arbitrary…
Protein dynamics is a fundamental element to comprehend their biological functions. However, a theoretical picture providing microscopic-detail explanation of its relevant features is still missing. One of the outmost relevant properties…
Although DNA is often bent in vivo, it is unclear how DNA-bending forces modulate DNA-protein binding affinity. Here, we report how a range of DNA-bending forces modulates the binding of the Integration Host Factor (IHF) protein to various…
Understanding the molecular mechanisms driving the binding between bio-molecules is a crucial challenge in molecular biology. In this respect, characteristics like the preferentially hydrophobic composition of the binding interfaces, the…
We study two designed and one natural zinc-finger peptide each with the Cys2His2 (CCHH) type of metal binding motif. In the approach we have developed, we describe the role of the protein and solvent outside the Zn(II)-CCHH metal-residue…
We report a 3D structure-based method of predicting protein-protein interaction partners. It involves screening for pairs of tetrahedra representing interacting amino acids at the interface of the protein-protein complex, with one…
The zinc finger structure where a Zn2+ ion binds to 4 cysteine or histidine amino acids in a tetrahedral structure is very common motif of nucleic acid binding proteins. The corresponding interaction model is present in 3% of the genes of…
The eukaryotic Cys2His2 zinc finger proteins bind to DNA ubiquitously at highly conserved domains, responsible for gene regulation and the spatial organization of DNA. To study and understand the zinc finger DNA-protein interaction, we use…
The time evolution of the formation probability of native bonds has been studied for designed sequences which fold fast into the native conformation. From this analysis a clear hierarchy of bonds emerge a) local, fast forming highly stable…
Correlated motions of proteins underpin many physiological mechanisms, such as substrate binding, signal transduction, enzymatic activity and allostery. These motions arise from low frequency collective movements of biomolecules and have…