生物大分子
Urea, a polar molecule with a large dipole moment, not only destabilizes the folded RNA structures, but can also enhance the folding rates of large ribozymes. Unlike the mechanism of urea-induced unfolding of proteins, which is well…
Protein folding cooperativity is defined by the nature of the finite-size thermodynamic transition exhibited upon folding: two-state transitions show a free energy barrier between the folded and unfolded ensembles, while downhill folding is…
The prevalent method for RNA secondary structure prediction for a single sequence is free energy minimization based on the nearest neighbor thermodynamic model (NNTM). One of the least well-developed parts of the model is the energy…
Allostery is an intrinsic spatiotemporal property of all proteins, resulting from long range correlations in the order of several nanometers and time scales of nanoseconds. Information is carried asymmetrically from one part to another by…
Artificial intelligence (AI) tools are gaining more and more ground each year in bioinformatics. Learning algorithms can be taught easily by using the existing enormous biological databases, and the resulting models can be used for the…
Due to the asymmetric nature of the nucleotides, the extant informational biomolecule, DNA, is constrained to replicate unidirectionally on a template. As a product of molecular evolution that sought to maximize replicative potential, DNA's…
Protein-protein interactions (PPIs) perform important roles on biological functions. Researches of mutants on protein interactions can further understand PPIs. In the past, many researchers have developed databases that stored mutants on…
The ionic environment of biomolecules strongly influences their structure, conformational stability, and inter-molecular interactions.This paper introduces GIBS, a grand-canonical Monte Carlo (GCMC) simulation program for computing the…
We investigate dynamical coupling between water and amino acid side-chain residues in solvation dynamics by selecting residues often used as natural probes, namely tryptophan, tyrosine and histidine, located at different positions on…
A minimal, one-parameter model of the excitonic Hamiltonian for the light harvesting complex of purple bacteria (LH2) based on ab initio calculation of the excitonic energies is proposed. The set of input parameters contains positions of…
In response to cold stress, Drosophila Melanogaster increase their expression of Frost, a candidate gene involved in cold response. The direct role of Frost in cold tolerance is yet to be determined, and its importance for survival in cold…
A deep neural network based architecture was constructed to predict amino acid side chain conformation with unprecedented accuracy. Amino acid side chain conformation prediction is essential for protein homology modeling and protein design.…
The 70 kDa Heat Shock Proteins Hsp70 have several essential functions in living systems, such as protecting cells against protein aggregation, assisting protein folding, remodeling protein complexes and driving the translocation into…
Although the disease-relevant microtubule-associated protein tau is known to severely inhibit kinesin-based transport in vitro, the potential mechanisms for reversing this detrimental effect to maintain healthy transport in cells remain…
We consider multi-chain protein native structures and propose a criterion that determines whether two chains in the system are entangled or not. The criterion is based on the behavior observed by pulling at both temini of each chain…
RNA secondary structure folding kinetics is known to be important for the biological function of certain processes, such as the hok/sok system in E. coli. Although linear algebra provides an exact computational solution of secondary…
A grand canonical Monte Carlo (MC) algorithm is presented for studying the lattice gas model (LGM) of multiple protein sequence alignment, which coherently combines long-range interactions and variable-length insertions. MC simulations are…
We use a coarse-grained model to study the conformational changes in two barley proteins, LTP1 and its ligand adduct isoform LTP1b, that result from their adsorption to the air-water interface. The model introduces the interface through…
We present a parameterized analytical model of alchemical molecular binding. The model describes accurately the free energy profiles of linear single-decoupling alchemical binding free energy calculations. The parameters of the model, which…
Anomalous non-exponential relaxation in hydrated biomolecules is commonly attributed to the complexity of the free-energy landscapes, similarly to polymers and glasses. It was found recently that the hydrogen-bond breathing of terminal DNA…