Conformational changes in the side chains are essential for protein-protein binding. Rotameric states and unbound- to-bound conformational changes in the surface residues were systematically studied on a representative set of protein complexes. The side-chain conformations were mapped onto dihedral angles space. The variable threshold algorithm was developed to cluster the dihedral angle distri...

Protein structure and stability rely on the interplay of a large number of weak molecular interactions working in concert to assure a stable and unique native fold. Throughout evolution, different strategies have been devised to modulate protein conformational stability and enhance function and survival of proteins, even under adverse conditions. The increasing number of characterized genomes a...

Rational mutation of proteins based on their structural and dynamic characteristics is a useful strategy for amplifying specific fluctuations in proteins. Here, we show the effects of mutation on the conformational fluctuations and thermodynamic stability of ubiquitin. In particular, we focus on the salt bridge between K11 and E34 and the hydrogen bond between I36 and Q41, which are predicted t...

Immunoglobulins M (IgMs) are gaining increasing attention as biopharmaceuticals since their multivalent mode of binding can give rise to high avidity. Furthermore, IgMs are potent activators of the complement system. However, they are frequently difficult to express recombinantly and can suffer from low conformational stability. Here, the broadly neutralizing anti-HIV-1 antibody 2G12 was class-...

p53 transcriptional activity depends mainly on posttranslational modifications and protein/protein interaction. Another important mechanism that controls p53 function is its conformational stability since p53 is an intrinsically unstable protein. An altered conformational state of p53, independent from point mutations, has been reported in tissues from patients with Alzheimer's disease (AD), le...

DNA ligases are important enzymes required for cellular processes such as DNA replication, recombination, and repair. NAD(+)-dependent DNA ligases are essentially restricted to eubacteria, thus constituting an attractive target in the development of novel antibiotics. Although such a project might involve the systematic testing of a vast number of chemical compounds, it can essentially gain fro...

The conformational behavior and the structural stability of formyl fluoroketene, formyl chloroketene and formyl methylketene were investigated by utilizing quantum mechanical DFT calculations at B3LYP/6-31I + + G** and ab initio calculations at MP2/6-311 + + G** levels. The three molecules were predicted to have a planar s-cis<-->s-trans conformational equilibrium. From the calculations, the di...

Alzheimer's disease is the most fatal neurodegenerative disorder characterized by the aggregation and deposition of Amyloid β (Aβ) oligomers in the brain of patients. Two principal variants of Aβ exist in humans: Aβ1-40 and Aβ1-42. The former is the most abundant in the plaques, while the latter is the most toxic species and forms fibrils more rapidly. Interestingly, fibrils of Aβ1-40 peptides ...

The Cover Feature illustrates models used to provide detailed structural, conformational, and energetics analysis of the alphabets hachimoji nucleic acids using an amalgamation density functional calculations molecular dynamics simulations. aim is explain experimentally observed stability DNA RNA. design by Indu Negi Purshotam Sharma. More information can be found in Research Article Sharma co-...

much less stable in both cases (Wiseman et al., 1975). Reduced forms contain Fe", which is a high-spin-state form, and this may explain the lower stability, although there is a possibility of a conformational difference for the Fel* form associated with its mechanistic role in oxygen binding. This is another possible case, therefore, of a mechanistic advantage and stability being mutually exclu...