相关论文: Probing protein orientation near charged nanosurfa…
Protein flexibility is crucial for understanding protein structures, functions, and dynamics, and it can be measured through experimental methods such as X-ray crystallography. Theoretical approaches have also been developed to predict…
Electrostatic interactions involving proteins depend not just on the ionic charges involved but also on their chemical identities. Here we examine the origins of incompletely understood differences in the strength of association of…
Protein-protein binding enables orderly and lawful biological self-organization, and is therefore considered a miracle of nature. Protein-protein binding is steered by electrostatic forces, hydrogen bonding, van der Waals force, and…
Biological macromolecules including nucleic acids, proteins, and glycosaminoglycans are typically anionic and can span domains of up to hundreds of nanometers and even micron length scales. The structures exist in crowded environments that…
The results of minimal model calculations suggest that the stability and the kinetic accessibility of the native state of small globular proteins are controlled by few "hot" sites. By mean of molecular dynamics simulations around the native…
Recent molecular dynamics simulations show that thermal gradients can induce electric fields in water that are comparable in magnitude to electric fields seen in ionic thin films and biomembranes. This surprising non-equilibrium phenomenon…
We study the dynamics of hydration water/protein association in folded proteins, using lysozyme and myoglobin as examples. Extensive molecular dynamics simulations are performed to identify underlying mechanisms of the dynamical transition…
The discharge structure of inductively coupled plasma is studied via fluid simulation and analytic theory collaboration. At low pressure, the discharge is stratified by the double layer, which is modelled as dipole moment. The parabolic…
Predicting accurate protein-ligand binding affinity is important in drug discovery but remains a challenge even with computationally expensive biophysics-based energy scoring methods and state-of-the-art deep learning approaches. Despite…
We report a novel simulation strategy that enables us to identify key parameters controlling the experimentally measurable characteristics of structural protein tags on dsDNA construct translocating through a double nanopore setup. First,…
Metal-oxide sensors are widely used due to their sensitivities to different types of gaseous, and these sensors are suitable for long-term applications, even in the presence of corrosive environments. However, the microscopic mechanisms…
We study charged nanoparticles adsorbed onto surfactant bilayers using small-angle scattering of synchrotron radiation. The in-plane interaction of the particles is well described by a DLVO component (measured independently in solution) and…
We propose and justify a new approach for fast calculation of the electrostatic interaction energy of clusters of charged particles in constrained energy minimization in the framework of rigid protein-ligand docking. Our ``blind search''…
Multivalent particles competing for binding on the same surface can exhibit switch-like behaviour, depending on the concentration of receptors on the surface. When the receptor concentration is low, energy dominates the free energy of…
Deep learning approaches achieved significant progress in predicting protein structures. These methods are often applied to protein-protein interactions (PPIs) yet require Multiple Sequence Alignment (MSA) which is unavailable for various…
Many biologically important ligands of proteins are large, flexible, and often charged molecules that bind to extended regions on the protein surface. It is infeasible or expensive to locate such ligands on proteins with standard methods…
The motion involved in barrier crossing for protein folding are investigated in terms of the chain dynamics of the polymer backbone, completing the microscopic description of protein folding presented in the previous paper. Local reaction…
Understanding polymer adsorption at interfaces is essential for designing advanced polymer-based nanomaterials with tailored interfacial properties. Although adsorption significantly influences the macroscopic properties of polymer…
Despite recent advances in protein-ligand structure prediction, deep learning methods remain limited in their ability to accurately predict binding affinities, particularly for novel protein targets dissimilar from the training set. In…
Refractive index sensing is a highly sensitive and label-free detection method for molecular binding events. Commercial implementations of biosensing concepts based on plasmon resonances typically require significant external…