Related papers: Site-Selective Dynamics of Ligand-Free and Ligand-…
The spectroscopic response of and structural dynamics around all azido-modified alanine residues (AlaN$_3$) in Lysozyme is characterized. It is found that AlaN$_3$ is a positionally sensitive probe for the local dynamics, covering a…
The changes in the local and global dynamics of azide-labelled Lysozyme compared with that of the wild type protein are quantitatively assessed for all alanine residues along the polypeptide chain. Although attaching -N$_3$ to alanine…
The dynamics of lysozyme is probed by attaching -SCN to all alanine-residues. The 1-dimensional infrared spectra exhibit frequency shifts in the position of the maximum absorption by 4 cm$^{-1}$ which is consistent with experiments in…
While allostery is of paramount importance for protein regulation, the underlying dynamical process of ligand (un)binding at one site, resulting time evolution of the protein structure, and change of the binding affinity at a remote site is…
Prediction of protein-ligand binding affinity is a major goal in drug discovery. Generally, free energy gap is calculated between two states (e.g., ligand binding and unbinding). The energy gap implicitly includes the effects of changes in…
In this work we present a detailed Raman scattering investigation of zinc oxide and aluminum-doped zinc oxide (AZO) films characterized by a variety of nanoscale structure and morphology and synthesized by pulsed laser deposition (PLD)…
Isotope labeling is a fundamental staple for the study of cellular metabolism and protein function. The conventional techniques that allow resolution and identification of isotopically-labeled biomarkers, such as mass spectrometry and…
The structural, electronic, optical and vibrational properties of LiN$_3$ under high pressure have been studied using plane wave pseudopotentials within the generalized gradient approximation for the exchange and correlation functional. The…
We analyze free energy estimators from simulation trials mimicking single-molecule pulling experiments on a neck linker of a kinesin motor. For that purpose, we have performed a version of steered molecular dynamics (SMD) calculations. The…
Determining the complete set of ligands' binding/unbinding pathways is important for drug discovery and to rationally interpret mutation data. Here we have developed a metadynamics-based technique that addressed this issue and allows…
We report density functional theory calculations on the crystal structure, elastic, lattice dynamics and electronic properties of iso-structural layered monoclinic alkali azides, LiN3 and NaN3. The effect of van der Waals interactions on…
While much is known about different allosteric regulation mechanisms, the nature of the "allosteric signal", and the timescale on which it propagates, remains elusive. The PDZ3 domain from postsynaptic density-95 protein is a small protein…
Monitoring the kinetics and conformational dynamics of single enzymes is crucial in order to better understand their biological functions as these motions and structural dynamics are usually unsynchronized among the molecules. Detecting the…
Active Domain Adaptation (ADA) queries the labels of a small number of selected target samples to help adapting a model from a source domain to a target domain. The local context of queried data is important, especially when the domain gap…
The protein dynamical transition is investigated as a function of protein structure using terahertz time domain spectroscopy (THz-TDS). Measurements performed for native state and denatured hen egg white lysozyme (HEWL) show that protein…
The electronic structure and the anisotropy of the Al - N {\pi} and {\sigma} chemical bonding of wurtzite AlN has been investigated by bulk-sensitive total fluorescence yield absorption and soft x-ray emission spectroscopies. The measured N…
Prediction of ligand binding sites of proteins is a fundamental and important task for understanding the function of proteins and screening potential drugs. Most existing methods require experimentally determined protein holo-structures as…
Protein-ligand complex structures have been utilised to design benchmark machine learning methods that perform important tasks related to drug design such as receptor binding site detection, small molecule docking and binding affinity…
Allosteric interactions in DNA are crucial for various biological processes. These interactions are quantified by measuring the change in free energy as a function of the distance between the binding sites for two ligands. Here we show that…
The influence of ligands on the low frequency vibration of different thicknesses cadmium selenide colloidal nanoplatelets is investigated using resonant low frequency Raman scattering. The strong vibration frequency shifts induced by ligand…