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Though the problem of sequence-reversed protein folding is largely unexplored, one might speculate that reversed native protein sequences should be significantly more foldable than purely random heteropolymer sequences. In this article, we…
We investigate protein-protein interactions in solution by small-angle X-ray scattering (SAXS) and theoretical modeling. The structure factor for solutions of bovine pancreatic trypsin inhibitor (BPTI), myoglobin (Mb), and intestinal fatty…
The intricate three-dimensional geometries of protein tertiary structures underlie protein function and emerge through a folding process from one-dimensional chains of amino acids. The exact spatial sequence and configuration of amino…
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…
Protein structure is generally conceptualized as the global arrangement or of smaller, local motifs of helices, sheets, and loops. These regular, recurring secondary structural elements have well-understood and standardized definitions in…
Antiagglomerants (AAs) are surface active molecules widely used in the rubber and petroleum industry, among others. In the petroleum industry, it is believed that AAs strongly adsorb to the surface of hydrate particles to prevent the growth…
A goal of computational studies of protein-protein interfaces (PPIs) is to predict the binding site between two monomers that form a heterodimer. The simplest version of this problem is to rigidly re-dock the bound forms of the monomers,…
The aggregate glue of spider orb web is an excellent natural adhesive. Orb-weaver spiders use micron-scale aggregate glue droplets to retain prey in the capture spiral silks of their orb web. In aggregate glue droplets, highly glycosylated…
A theoretical approach is developed to quantify hydrophobic hydration and interactions on a molecular scale, with the goal of gaining insight into the molecular origins of hydrophobic effects. The model is based on the fundamental relation…
We synthesize thermoresponsive poly(N-isopropylacrylamide) (PNIPAM) colloidal microgel particles of different stiffnesses by controlling the concentration of crosslinker in a one-pot synthesis method. We employ oscillatory rheology and…
We fit the Fourier transforms of solvent accessibility and hydrophobicity profiles of a representative set of proteins to a joint multi-variable Gaussian. This allows us to separate the intrinsic tendencies of sequence and structure…
Most properties of liquid water are determined by its hydrogen-bond network. Because forming an aqueous interface requires termination of this network, one might expect the molecular level properties of interfacial water to markedly differ…
The control of biopolymer length is mediated by proteins that localize to polymer ends and regulate polymerization dynamics. Several mechanisms have been proposed to achieve end localization. Here, we propose a novel mechanism by which a…
We have employed molecular dynamics simulations based on the TIP4P/2005 water model to investigate the local structural, dynamical, and dielectric properties of the two recently reported body-centered-cubic and face-centered-cubic plastic…
To manipulate the protein population at certain functional state through chemical stabilizers is crucial for protein-related studies. It not only plays a key role in protein structure analysis and protein folding kinetics, but also affects…
Proteins are commonly used by biochemical industry for numerous processes. Refining these proteins' properties via mutations causes stability effects as well. Accurate computational method to predict how mutations affect protein stability…
Biocompatible and functionalizable hydrogels have a wide range of (potential) medicinal applications. In contrast to conventional hydrogels formed by interconnected or interlocked polymer chains, self-assembled hydrogels form from small…
In order to inquire the microscopic origin of observed multiple time scales in solvation dynamics we carry out several computer experiments. We perform atomistic molecular dynamics simulations on three protein-water systems namely,…
The use of colloidal supported lipid bilayers (CSLBs) has recently been extended to create colloidal joints, that - in analogy to their macroscopic counterparts - can flexibly connect colloidal particles. These novel elements enable the…
Using molecular dynamics simulations, we investigated an integrated bio-nano interface consisting of a \b{eta}-sheet protein stacked onto graphene. We found that the stacking assembly of the model protein on graphene could be controlled by…