Biomolecules
Protein function and activity are a consequence of its three-dimensional structure. Single particle analysis of cryogenic electron micrographs has radically changed structural biology allowing atomic reconstruction of almost any type of…
The nicotinic acetylcholine receptor (nAChR) is the prototypic member of the `Cys-loop' superfamily of ligand-gated ion channels which mediate synaptic neurotransmission, and whose other members include receptors for glycine,…
The current state of cancer therapeutics has been moving away from one-size-fits-all cytotoxic chemotherapy, and towards a more individualized and specific approach involving the targeting of each tumor's genetic vulnerabilities. Different…
The effects of purification methods and its hypolipidemic function on the total flavonoids of Aurea Helianthus flower were investigated. Liquid-liquid extraction of ethanol extract from Aurea Helianthus flower was carried out by using…
The total phenols and flavonoids content of different polar solvent extracts from Aurea Helianthus flowers, and their antioxidant activity were determined. The ethanol extract of Aurea Helianthus flowers were suspended in water and…
Dynorphin is a neuropeptide involved in pain, addiction and mood regulation. It exerts its activity by binding to the kappa opioid receptor (KOP) which belongs to the large family of G-protein coupled receptors. The dynorphin peptide was…
Sequence set is a widely-used type of data source in a large variety of fields. A typical example is protein structure prediction, which takes an multiple sequence alignment (MSA) as input and aims to infer structural information from it.…
The strength or weakness of an algorithm is ultimately governed by the confidence of its result. When the domain of the problem is large (e.g. traversal of a high-dimensional space), a perfect solution cannot be obtained, so approximations…
We consider a measure of cooperativity based on the minimal absolute interaction required to generate an observed titration behavior. We describe the corresponding algebraic optimization problem and show how it can be solved using the…
Interacting proteins coevolve at multiple but interconnected scales, from the residue-residue over the protein-protein up to the family-family level. The recent accumulation of enormous amounts of sequence data allows for the development of…
A small fraction of all protein structures characterized so far are entangled. The challenge of understanding the properties of these knotted proteins, and the why and the how of their natural folding process, has been taken up in the past…
Monolayer-protected gold nanoparticles (Au NPs) are promising biomedical tools with applications to diagnosis and therapy, thanks to their biocompatibility and versatility. Here we show how the NP surface functionalization can drive the…
Proteins must fold quickly to acquire their biologically functional three-dimensional native structures. Hence, these are mainly stabilized by local contacts, while intricate topologies such as knots are rare. Here, we reveal the existence…
Given native 2D contact map, protein 3D structure could be reconstructed with accuracy of 2A or better, and such reconstruction is a feasible computational approach for protein folding problem. The prediction accuracy from traditional…
Principal component analysis (PCA) represents a standard approach to identify collective variables $\{x_i\}\!=\!\boldsymbol{x}$, which can be used to construct the free energy landscape $\Delta G(\boldsymbol{x})$ of a molecular system.…
Native contacts between residues could be predicted from the amino acid sequence of proteins, and the predicted contact information could assist the de novo protein structure prediction. Here, we present a novel pipeline of a residue…
Comprehensive and unambiguous identification of small molecules in complex samples will revolutionize our understanding of the role of metabolites in biological systems. Existing and emerging technologies have enabled measurement of…
Motivation: Due to the central role of protein structure in molecular recognition, great computational efforts are devoted to modeling protein structures and motions that mediate structural rearrangements. The size, dimensionality, and…
Hydrogen bonding between nucleobases produces diverse DNA structural motifs, including canonical duplexes, guanine (G) quadruplexes and cytosine (C) i-motifs. Incorporating metal-mediated base pairs into nucleic acid structures can…
Artificial RNA molecules with novel functionality have many applications in synthetic biology, pharmacy and white biotechnology. The de novo design of such devices using computational methods and prediction tools is a resource-efficient…