Biomolecules
We investigate the role of order/disorder transitions in alchemical simulations of protein-ligand absolute binding free energies. We show, in the context of a potential of mean force description, that for a benchmarking system (the complex…
Peptide nucleic acids (PNAs) are artificial nucleic acids with a peptide backbone instead of sugar phosphate backbone of DNA or RNA. Their resistance to degradation, selectivity and greater binding affinity in comparison to usual nucleic…
DNA and RNA quadruplexes are extensively studied for the key roles they are suspected to play in the cellular regulation networks at both genomic and transcriptomic levels. The reliable detection of quadruplexes in cells was and remains a…
RNA interference, particularly siRNA induced gene silencing is becoming an important avenue of modern therapeutics. The siRNA is delivered to the cells as short double helical RNA which becomes single stranded for forming the RISC complex.…
Proteins have evolved to perform diverse cellular functions, from serving as reaction catalysts to coordinating cellular propagation and development. Frequently, proteins do not exert their full potential as monomers but rather undergo…
In the course of evolution, proteins undergo important changes in their amino acid sequences, while their three-dimensional folded structure and their biological function remain remarkably conserved. Thanks to modern sequencing techniques,…
Background: Genotype-phenotype maps provide a meaningful filtration of sequence space and RNA secondary structures are particular such phenotypes. Compatible sequences i.e.~sequences that satisfy the base pairing constraints of a given RNA…
Proteins display generic properties that are challenging to explain by direct selection, notably allostery, the capacity to be regulated through long-range effects, and evolvability, the capacity to adapt to new selective pressures. An…
Filament formation by non-cytoskeletal enzymes has been known for decades, yet only relatively recently has its wide-spread role in enzyme regulation and biology come to be appreciated. This comprehensive review summarizes what is known for…
Use of a combination of statistical thermodynamics and the Gershgorin theorem enable us to guess, in the thermodynamic limit, a plausible value for the upper bound free-energy difference between native-like structures of monomeric globular…
DNA surface-hybridization biosensors utilize the selective hybridization of target sequences in solution to surface-immobilized probes. In this process, the target is usually assumed to be in excess, so that its concentration does not…
Statistical models for families of evolutionary related proteins have recently gained interest: in particular pairwise Potts models, as those inferred by the Direct-Coupling Analysis, have been able to extract information about the…
Chen et al. solved the crystal structure of bovine DHX36 bound to a DNA with a G-quadruplex (G4) and a single-stranded DNA segment. They believed that the mechanism they proposed may represent a general model for describing how a…
In this work it is shown that 20 canonical amino acids (AAs) within genetic code appear to be a whole system with strict distinction in Genetic Code Table (GCT) into some different quantums: 20, 23, 61 amino acid molecules. These molecules…
Levan is a bacterial homopolysaccharide, which consists of beta-2,6 linked beta-D-fructose monomers. Because of its structural properties and its health promoting effects, levan is a promising functional ingredient for the food, cosmetic…
An ideal signature material and method, which can be used to prove the authenticity of a physical item and against forgery, should be immune to the fast developments in digital and engineering technologies. Herein, the design of signature…
Molecular chaperones are ATP-consuming biological machines, which facilitate the folding of proteins and RNA molecules that are kinetically trapped in misfolded states for long times. Unassisted folding occurs by the kinetic partitioning…
Grid diagrams with their relatively simple mathematical formalism provide a convenient way to generate and model projections of various knots. It has been an open question whether these 2D diagrams can be used to model a complex 3D process…
Identifying the secondary structure of an RNA is crucial for understanding its diverse regulatory functions. This paper focuses on how to enhance target identification in a Boltzmann ensemble of structures via chemical probing data. We…
Evidence accumulated over the past decade provides support for liquid-liquid phase separation as the mechanism underlying the formation of biomolecular condensates, which include not only membraneless organelles such as nucleoli and RNA…