Refinement of the Sugar Puckering Torsion Potential in the AMBER DNA Force Field.

The transition from B-DNA to A-DNA occurs in many protein-DNA interactions or in DNA/RNA hybrid duplexes, and thus plays a role in many important biomolecular processes that convey the biological function of DNA. However, the stability of A-DNA is severely underestimated in current AMBER force fields such as OL15, OL21 or bsc1, potentially leading to unstable or deformed protein-DNA complexes. In this study, we refine the deoxyribose dihedral potential to increase the stability of the north (N) puckering present in A-DNA.

Multistate B- to A- transition in protein-DNA Binding - How well is it described by current AMBER force fields?

When DNA interacts with a protein, its structure often undergoes a significant conformational adaptation, usually involving a transition from B-DNA towards the A-DNA form. This is not a two-state, but rather a multistate transition. The A- and B- forms differ mainly in sugar pucker (north/south) and glycosidic torsion χ (/high-).

Dynamic and Nondynamic Electron Correlation Energy Decomposition Based on the Node of the Hartree-Fock Slater Determinant.

Distinguishing between dynamic and nondynamic electron correlation energy is a fundamental concept in quantum chemistry. It can be challenging to make a clear distinction between the two types of correlation energy or to determine their actual contributions in specific cases using wave function theory. This is because both single-reference and multireference methods cover both types of correlation energy to some extent.

New reports on iron related proteins: Molecular characterization of two ferroportin genes in common carp (Cyprinus carpio L.) and its expression pattern.

Iron uptake, transport, and storage require the involvement of several proteins, including ferroportin (fpn), the sole known iron efflux transporter. Due to its critical function fpn has been studied, particularly in humans. Here, we characterized the ferroportin gene in common carp (Cyprinus carpio L.

Assessing the Current State of Amber Force Field Modifications for DNA─2023 Edition.

Advances in molecular dynamics (MD) software alongside enhanced computational power and hardware have allowed for MD simulations to significantly expand our knowledge of biomolecular structure, dynamics, and interactions. Furthermore, it has allowed for the extension of conformational sampling times from nanoseconds to the microsecond level and beyond. This has not only made convergence of conformational ensembles through comprehensive sampling possible but consequently exposed deficiencies and allowed the community to overcome limitations in the available force fields.