Dutta, Pallab Kshirsagar, Abhay Bibekar, Parth Sengupta, Neelanjana
Published in
Biophysical journal
The nonstructural protein-1 (NSP1) of the severe acute respiratory syndrome-associated coronavirus 2 plays a crucial role in the translational shutdown and immune evasion inside host cells. Despite its known intrinsic disorder, the C-terminal domain (CTD) of NSP1 has been reported to form a double α-helical structure and block the 40S-ribosomal cha...
Dokainish, Hisham M Sugita, Yuji
Published in
Biophysical journal
A single mutation from aspartate to glycine at position 614 has dominated all circulating variants of the severe acute respiratory syndrome coronavirus 2. D614G mutation induces structural changes in the spike (S) protein that strengthen the virus infectivity. Here, we use molecular dynamics simulations to dissect the effects of mutation and 630-lo...
Mugnai, Mauro L. Shin, Sucheol Thirumalai, D.
Published in
Biophysical Journal
The spike protein of the SARS-CoV-2 virus (the causative agent of COVID-19) recognizes the host cell by binding to the peptidase domain (PD) of the extracellular receptor angiotensin-converting enzyme 2 (ACE2). A variety of carbohydrates could be attached to the six asparagines in the PD, resulting in a heterogeneous population of ACE2 glycoforms. ...
Song, Kaiyuan Xu, Honglin Da, Lin-Tai
Published in
Biophysical journal
Major histocompatibility complex class II (MHC-II) plays an indispensable role in activating CD4+ T cell immune responses by presenting antigenic peptides on the cell surface for recognition by T cell receptors. The assembly of MHC-II and antigenic peptide is therefore a prerequisite for the antigen presentation. To date, however, the atomic-level ...
Robertson, Gail A Clemons, William M Jr Griffith, Theanne N
Published in
Biophysical journal
Eyckmans, Jeroen
Published in
Biophysical journal
Han, Keqin Ma, Shuhao Sun, Jiehui Xu, Miao Qi, Xiaojing Wang, Shuo Li, Li Li, Xuejin
Published in
Biophysical journal
Increased blood viscosity in type 2 diabetes mellitus (T2DM) is a risk factor for the development of insulin resistance and diabetes-related vascular complications; however, individuals with T2DM exhibit heterogeneous hemorheological properties, including cell deformation and aggregation. Using a multiscale red blood cell (RBC) model with key param...
Chalopin, Yann Cramer, Stephen P Arragain, Simon
Published in
Biophysical journal
[FeFe] hydrogenases are enzymes that have acquired a unique capacity to synthesize or consume molecular hydrogen (H2). This function relies on a complex catalytic mechanism involving the active site and two distinct electron and proton transfer networks working in concert. By an analysis based on terahertz vibrations of [FeFe] hydrogenase structure...
Wang, Xunxun Tan, Ya-Lan Yu, Shixiong Shi, Ya-Zhou Tan, Zhi-Jie
Published in
Biophysical journal
RNA pseudoknots are a kind of important tertiary motif, and the structures and stabilities of pseudoknots are generally critical to the biological functions of RNAs with the motifs. In this work, we have carefully refined our previously developed coarse-grained model with salt effect through involving a new coarse-grained force field and a replica-...
Kurz, Felix T Aon, Miguel A Schlemmer, Heinz-Peter Jende, Johann M E O'Rourke, Brian Armoundas, Antonis A
Published in
Biophysical journal
Mitochondrial inner membrane potentials in cardiomyocytes may oscillate in cycles of depolarization/repolarization when the mitochondrial network is exposed to metabolic or oxidative stress. The frequencies of such oscillations are dynamically changing while clusters of weakly coupled mitochondrial oscillators adjust to a common phase and frequency...
