Biomolecules
Various approaches have explored the covariation of residues in multiple-sequence alignments of homologous proteins to extract functional and structural information. Among those are principal component analysis (PCA), which identifies the…
Specific interactions between cations and proteins have a strong impact on peptide and protein structure. We here shed light on the nature of the underlying interactions, especially regarding the effects on the polyamide backbone structure.…
Studying all non-redundant proteins in 76 most-commonly found structural domains, the present work attempts to decipher latent patterns that characterize acceptable and unacceptable symmetries in residue-residue interactions in functional…
Computational methods are needed to differentiate the small fraction of missense mutations that contribute to disease by disrupting protein function from neutral variants. We describe several complementary methods using large-scale homology…
Quantum mechanical calculations are performed on 116 conformers of the protein ubiquitin (Lange et al., Science 2008, 320, 1471-1475). The results indicate that the heat of formation (HOF), dipole moment, energy of the frontier orbitals…
Quantum mechanical calculations are performed on the proteins that constitute the ubiquitin-Dsk2 complex whose atomic structure has been experimentally determined by NMR spectroscopy (PDB id 1WR1). The results indicate that the dipole…
Protein folding produces characteristic and functional three-dimensional structures from unfolded polypeptides or disordered coils. The emergence of extraordinary complexity in the protein folding process poses astonishing challenges to…
Proteins experience a wide variety of conformational dynamics that can be crucial for facilitating their diverse functions. How is the intrinsic flexibility required for these motions encoded in their three-dimensional structures? Here, the…
The spatial structure of the cell is highly organized at all levels: from small complexes and assemblies, to local nano- and micro-clusters, to global, micrometer scales across and between cells. We suggest that this multiscale spatial cell…
The conformational change of biological macromolecule is investigated from the point of quantum transition. A quantum theory on protein folding is proposed. Compared with other dynamical variables such as mobile electrons, chemical bonds…
Development of the new antimicrobial agents against antibiotic resistance pathogens is the nowadays challenge. Antimicrobial peptides (AMP) occur as important defence agents in many organisms and offer a viable alternative to conventional…
RNA/protein interactions play crucial roles in controlling gene expression. They are becoming important targets for pharmaceutical applications. Due to RNA flexibility and to the strength of electrostatic interactions, standard docking…
Clathrin mediated endocytosis (CME) is an ubiquitous cellular pathway that regulates central aspects of cell physiology such as nutrient uptake, modulation of signal transduction, synaptic transmission and membrane turn-over. Endocytic…
A mechanism of the translation in oligomer world is proposed. The translation is carried out by a minimum cycle, which is sustained by adaptors and helicases, and the first information processing in oligomer world. We expect that such a…
Plasmodium falciparum 70 kDa heat shock proteins (PfHsp70s) are expressed at all stages of the pathogenic erythrocytic phase of the malaria parasite lifecycle. There are six PfHsp70s, all of which have orthologues in other plasmodial…
In the present work we study and compare unfolding of a small protein, chicken villin headpiece (HP-36) in two different aqueous binary mixtures, namely water-ethanol (EtOH) and water-dimethyl sulphoxide (DMSO). In both the binary mixtures,…
It has been well accepted that the RNA secondary structures of most functional non-coding RNAs (ncRNAs) are closely related to their functions and are conserved during evolution. Hence, prediction of conserved secondary structures from…
RNA duplex stability depends strongly on ionic conditions, and inside cells RNAs are exposed to both monovalent and multivalent ions. Despite recent advances, we do not have general methods to quantitatively account for the effects of…
Chemistry is about chemical reactions. Chemistry is about electrons changing their configurations as atoms and molecules react. Chemistry studies reactions as if they occurred in ideal infinitely dilute solutions. But most reactions occur…
The entire T7 bacteriophage genome contains 39937 base pairs (Database NCBI RefSeq N1001604). Here, electrostatic potential distribution around double helical T7 DNA was calculated by Coulomb method using the computer program of Sorokin…