A method to find low energy paths in macromolecules is described. It can be applied either to determine paths between two given energy minimum conformations, or to explore low energy paths departing from one energy minimized conformation. The principle of the method consists in carrying out energy minimizations or molecular dynamics simulations with root mean square distance constraints with re...

Abbreviations used: NMR, nuclear magnetic resonance; ppm, parts per million; RMSD, root mean square deviation; HSQC, heteronuclear single quantum coherence spectroscopy; NOE, nuclear Overhauser effect; NOESY, nuclear Overhauser and exchange spectroscopy; RDC, residual dipolar coupling; PDB, Protein Data Bank; pol η UBZ, ubiquitin-binding zinc finger domain of the human Y-family DNA polymerase E...

Protein thermostability can be increased by some glycine to proline mutations in a target protein. However, not all glycine to proline mutations can improve protein thermostability, and this method is suitable only at carefully selected mutation sites that can accommodate structural stabilization. In this study, homology modeling and molecular dynamics simulations were used to select appropriat...

Plexin-B1 is a single-pass transmembrane receptor. Its Rho GTPase binding domain (RBD) can associate with small Rho GTPases and can also self-bind to form a dimer. In total, more than 400 ns of NAMD molecular dynamics simulations were performed on RBD monomer and dimer. Different analysis methods, such as root mean squared fluctuation (RMSF), order parameters (S(2)), dihedral angle correlation,...

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections have triggered a recent pandemic of disease and affected almost every country all over the world. A large amount natural bioactive compounds are under clinical investigation for various diseases. In particular, marine gaining more attention in new drug development process. The present study aimed to identify potential marin...

Adaptive cell immunotherapy with the use of chimeric receptors leads to the best and most specific response against tumors. Chimeric receptors consist of a signaling fragment, extracellular spacer, costimulating domain, and an antibody. Antibodies cause immunogenicity; therefore, VHH is a good replacement for ScFv in chimeric receptors. Since peptide sequences have an influence on chimeric rece...

The objective of the present study was to develop an understanding of short single-stranded DNA (ssDNA) to assist the development of new DNA-based biosensors. A ssDNA model containing twelve bases was constructed from the 130-145 codon sequence of the p53 gene. Various thermodynamic macroscopic observables such as temperature, energy distributions, as well as root mean square deviation (RMSD) o...

Human carbonic anhydrase II (HCA II) is a zinc-metalloenzyme that catalyzes the reversible interconversion of CO2 and HCO3-. The rate-limiting step of this catalysis is the transfer of a proton between the Zn-bound solvent molecule and residue His64. In order to fully characterize the active site structural features implicated in the proton transfer mechanism, the refined X-ray crystal structur...

Conformational states and their interconversion pathways of the zwitterionic form of the pentapeptide Met-enkephalin (MetEnk) are identified. An explicit solvent molecular dynamics (MD) trajectory is used to construct a Markov state model (MSM) based on dihedral space clustering of the trajectory, and transition path theory (TPT) is applied to identify pathways between open and closed conformer...