Biomolecules
We propose an experiment to demonstrate spontaneous ordering and symmetry breaking of kinesin-driven microtubules confined to an optical trap. Calculations involving the feasibility of such an experiment are first performed which analyze…
In view of recent intense experimental and theoretical interests in the biophysics of liquid-liquid phase separation (LLPS) of intrinsically disordered proteins (IDPs), heteropolymer models with chain molecules configured as self-avoiding…
Cells are complex structures which require considerable amounts of organization via transport of large intracellular cargo. While passive diffusion is often sufficiently fast for the transport of smaller cargo, active transport is necessary…
We present a new method that combines alchemical transformation with physical pathway to accurately and efficiently compute the absolute binding free energy of receptor-ligand complex. Currently, the double decoupling method (DDM) and the…
The field of structural bioinformatics has seen significant advances with the use of Molecular Dynamics (MD) simulations of biological systems. The MD methodology has allowed to explain and discover molecular mechanisms in a wide range of…
Auxin is considered one of the cardinal hormones in plant growth and development. It regulates a wide range of processes throughout the plant. Synthetic auxins exploit the auxin-signalling pathway and are valuable as herbicidal…
Peroxisome proliferator-activated receptors gamma (PPAR{\gamma}) are ligand-activated controllers of various metabolic actions and insulin sensitivity. PPAR{\gamma} is thus considered as an important target to treat type 2 diabetes.…
Photosynthetic eukaryotes show a remarkable variability in photosynthesis, including large differences in light harvesting proteins and pigment composition. In vivo circular spectropolarimetry enables us to probe the molecular architecture…
To obtain an electron-density map from a macromolecular crystal the phase-problem needs to be solved, which often involves the use of heavy-atom derivative crystals and concomitantly the determination of the heavy atom substructure. This is…
Beta-turn prediction is useful in protein function studies and experimental design. Although recent approaches using machine-learning techniques such as SVM, neural networks, and K-NN have achieved good results for beta-turn pre-diction,…
The ability to precisely visualize the atomic geometry of the interactions between a drug and its protein target in structural models is critical in predicting the correct modifications in previously identified inhibitors to create more…
Protein-peptide interactions play essential roles in many cellular processes and their structural characterization is the major focus of current experimental and theoretical research. Two decades ago, it was proposed to employ the steered…
A central goal of protein-folding theory is to predict the stochastic dynamics of transition paths --- the rare trajectories that transit between the folded and unfolded ensembles --- using only thermodynamic information, such as a…
We develop a robust coarse-grained model for single and double stranded DNA by representing each nucleotide by three interaction sites (TIS) located at the centers of mass of sugar, phosphate, and base. The resulting TIS model includes…
All known terrestrial proteins are coded as continuous strings of ~20 amino acids. The patterns formed by the repetitions of elements in groups of finite sequences describes the natural architectures of protein families. We present a method…
How fast a post-translational nascent protein escapes from the ribosomal exit tunnel is relevant to its folding and protection against aggregation. Here, by using Langevin molecular dynamics, we show that non-local native interactions help…
We construct a one-bead-per-residue coarse-grained dynamical model to describe intrinsically disordered proteins at significantly longer timescales than in the all-atom models. In this model, inter-residue contacts form and disappear during…
Computational procedures to foresee the 3D structure of aptamers are in continuous progress. They constitute a crucial input to research, mainly when the crystallographic counterpart of the structures in silico produced is not present. At…
We classify research fields in biology into those on flows of materials, energy, and information. As a representative energy transducing machinery in biology, our research target, V1-ATPase from a bacterium Enterococcus hirae, a typical…
In this conceptual paper we propose to explore the analogy between ontic/epistemic description of quantum phenomena and interrelation between dynamics of conformational and functional states of proteins. Another new idea is to apply theory…