生物大分子
Autoreactive B cells have a central role in the pathogenesis of rheumatoid arthritis (RA), and recent findings have proposed that anti-citrullinated protein autoantibodies (ACPA) may be directly pathogenic. Herein, we demonstrate the…
Considering all the PDB annotated allosteric proteins (from ASD - AlloSteric Database) belonging to four different classes (kinases, nuclear receptors, peptidases and transcription factors), this work has attempted to decipher certain…
Elastic network models (ENM) and constraint-based, topological rigidity analysis are two distinct, coarse-grained approaches to study conformational flexibility of macromolecules. In the two decades since their introduction, both have…
Electrical forces are the background of all the interactions occurring in biochemical systems. From here and by using a combination of ab-initio and ad-hoc models, we introduce the first description of electric field profiles with intrabond…
Markov state models (MSMs) have been widely used to analyze computer simulations of various biomolecular systems. They can capture conformational transitions much slower than an average or maximal length of a single molecular dynamics (MD)…
FoF1-ATP synthase catalyzes the synthesis of adenosine triphosphate (ATP). The F1 portion can be stripped from the membrane-embedded Fo portion of the enzyme. F1 acts as an ATP hydrolyzing enzyme, and ATP hydrolysis is associated with…
Motivated by the problem of domain formation in chromosomes, we studied a co--polymer model where only a subset of the monomers feel attractive interactions. These monomers are displaced randomly from a regularly-spaced pattern, thus…
Small molecules are often found to exhibit extraordinarily diverse biological activities. Metformin is one of them. It is widely used as anti-diabetic drug for type-two diabetes. In addition to that, metformin hydrochloride shows…
RNA function is intimately related to its structural dynamics. Molecular dynamics simulations are useful for exploring biomolecular flexibility but are severely limited by the accessible timescale. Enhanced sampling methods allow this…
In the protein sequence space, natural proteins form clusters of families which are characterized by their unique native folds whereas the great majority of random polypeptides are neither clustered nor foldable to unique structures. Since…
We propose an optimized parameter set for protein secondary structure prediction using three layer feed forward back propagation neural network. The methodology uses four parameters viz. encoding scheme, window size, number of neurons in…
Signal transmission at the molecular level in many biological complexes occurs through allosteric transitions. They describe the response a complex to binding of ligands at sites that are spatially well separated from the binding region. We…
Different numerical mappings of the DNA sequences have been studied using a new cluster-scaling method and the well known spectral methods. It is shown, in particular, that the nucleotide sequences in DNA molecules have robust…
Neurotensin receptor 1 (NTSR1) is a G protein-coupled receptor that is important for signaling in the brain and the gut. Its agonist ligand neurotensin (NTS), a 13-amino-acid peptide, binds with nanomolar affinity from the extracellular…
DNA and protein microarrays are a high-throughput technology that allow the simultaneous quantification of tens of thousands of different biomolecular species. The mediocre sensitivity and dynamic range of traditional fluorescence…
In cryo-electron microscopy (EM), molecular structures are determined from large numbers of projection images of individual particles. To harness the full power of this single-molecule information, we use the Bayesian inference of EM…
ATP synthases utilize a proton motive force to synthesize ATP. In reverse, these membrane-embedded enzymes can also hydrolyze ATP to pump protons over the membrane. To prevent wasteful ATP hydrolysis, distinct control mechanisms exist for…
We study the behavior of five proteins at the air-water and oil-water interfaces by all-atom molecular dynamics. The proteins are found to get distorted when pinned to the interface. This behavior is consistent with the phenomenological way…
Hyperpolarized 13C-MRI allows real time observation of metabolism in vivo. Imaging sequences have been developed to follow the metabolism of [1-13C] pyruvate and extract reaction kinetics, which can show tumour treatment response. We…
Aptamers are single stranded DNA, RNA or peptide sequences having the ability to bind a variety of specific targets (proteins, molecules as well as ions). Therefore, aptamer production and selection for therapeutic and diagnostic…