... published by Portland Press Limited on behalf of the Biochemical Society and distributed under the Creative Commons Attribution License 4.0 (CC BY) . cell cycle chromatin epigenetics mass spectrometry molecular dynamics protein-protein interactions Emerging evidence implicates repressive...

... and of their lipid-binding domains are typically solved in a soluble form, sometimes with a lipid or lipid headgroup at the binding site. To provide a detailed molecular view of PMP interactions with the membrane, computational methods such as molecular dynamics (MD) simulations can be applied. Here, we outline...

... residues in close proximity to the hemoglobin-binding region and the active site cavity (ASC), respectively. The mutations changed the distribution of hydrogen bonds and the local electrostatic potential. Long-term molecular dynamics (MD) simulations demonstrated the destabilization of the mutant proteins...

... (AChE) was performed by the oxime asoxime (HI-6) at different pH in the presence and absence of lyotropic salts: a neutral salt (NaCl), a strong chaotropic salt (LiSCN) and strong kosmotropic salts (ammonium sulphate and phosphate HPO 4 2− ). At the same time, molecular dynamic (MD) simulations...

...) to the tetratricopeptide repeat (TPR) domain of cyclophilin 40 (Cyp40) allosterically changes the dynamics of the cyclophilin-active site and reduces peptidyl-prolyl isomerase (PPIase) activity. allostery heat-shock protein 90 immunophilin molecular dynamics peptidyl-prolyl isomerase tetratricopeptide (TPR...

...Atushi Suenaga; Yuto Komeiji; Masami Uebayasi; Toshiyuki Meguro; Minoru Saito; Ichiro Yamato The ion permeation process, driven by a membrane potential through an outer membrane protein, OmpF porin of Escherichia coli , was simulated by molecular dynamics. A Na + ion, initially placed...