Related papers: Resistance proof, folding-inhibitor drugs
The folding of the cholesterol trapping apolipoprotein A1 in aqueous solution at increasing ionic strength is studied using atomically detailed molecular dynamics simulations. We calculate various structural properties to characterize the…
The classical theory of enzymatic inhibition aims to quantitatively describe the effect of certain molecules -- called inhibitors -- on the progression of enzymatic reactions, but growing signs indicate that it must be revised to keep pace…
Novel numerical techniques, validated by an analysis of barnase and chymotrypsin inhibitor, are used to elucidate the paramount role played by the geometry of the protein backbone in steering the folding to the correct native state. It is…
This paper presents a method of reconstruction a primary structure of a protein that folds into a given geometrical shape. This method predicts the primary structure of a protein and restores its linear sequence of amino acids in the…
Most single-molecule studies derive the kinetic rates of native, intermediate, and unfolded states from equilibrium hopping experiments. Here, we apply Kramers kinetic diffusive model to derive the force-dependent kinetic rates of…
Cyclic peptides offer inherent advantages in pharmaceuticals. For example, cyclic peptides are more resistant to enzymatic hydrolysis compared to linear peptides and usually exhibit excellent stability and affinity. Although deep generative…
A pharmacological effect of a drug on cells, organs and systems refers to the specific biochemical interaction produced by a drug substance, which is called its mechanism of action. Drug repositioning (or drug repurposing) is a fundamental…
Understanding protein folding has been one of the great challenges in biochemistry and molecular biophysics. Over the past 50 years, many thermodynamic and kinetic studies have been performed addressing the stability of globular proteins.…
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…
For the vast majority of naturally occurring, small, single domain proteins folding is often described as a two-state process that lacks detectable intermediates. This observation has often been rationalized on the basis of a nucleation…
Natural protein sequences somehow encode the structural forms that these molecules adopt. Recent developments in structure-prediction are agnostic to the mechanisms by which proteins fold and represent them as static objects. However, the…
Proteins with nontrivial topology, containing knots and slipknots, have the ability to fold to their native states without any additional external forces invoked. A mechanism is suggested for folding of these proteins, such as YibK and…
A small amount of polymer dissolved in a droplet suppresses droplet rebound when it impinges on a supersolvophobic surface. This work investigates impacting dynamics of a droplet of dilute polymer solution depending on the molecular weight…
The assumption that similar structures have similar folding probabilities ($p_{fold}$) leads naturally to a procedure to evaluate $p_{fold}$ for every snapshot saved along an equilibrium folding-unfolding trajectory of a structured peptide…
A phenomenological model hamiltonian to describe the folding of a protein with any given sequence is proposed. The protein is thought of as a collection of pieces of helices; as a consequence its configuration space increases with the…
Extensive Monte Carlo folding simulations for four proteins of various structural classes are carried out, using a single atomistic potential. In all cases, collapse occurs at a very early stage, and proteins fold into their native-like…
Cells accomplish diverse functions using the same molecular building blocks, from setting up cytoplasmic flows to generating mechanical forces. In particular, transitions between these non-equilibrium states are triggered by regulating the…
Many native structures of proteins accomodate complex topological motifs such as knots, lassos, and other geometrical entanglements. How proteins can fold quickly even in the presence of such topological obstacles is a debated question in…
The differing ability of polypeptide conformations to act as the native state of proteins has long been rationalized in terms of differing kinetic accessibility or thermodynamic stability. Building on the successful applications of physical…
We find that thin peptide films and coatings doped with metallic nanoparticles are more stable due to the role of electromagnetic fluctuations. It is shown that for the doped freestanding in vacuum peptide film the Casimir attraction…