Rapid simulation of glycoprotein structures by grafting and steric exclusion of glycan conformer libraries.

Most membrane proteins are modified by covalent addition of complex sugars through N- and O-glycosylation. Unlike proteins, glycans do not typically adopt specific secondary structures and remain very mobile, shielding potentially large fractions of protein surface. High glycan conformational freedom hinders complete structural elucidation of glycoproteins.

Computational epitope map of SARS-CoV-2 spike protein.

The primary immunological target of COVID-19 vaccines is the SARS-CoV-2 spike (S) protein. S is exposed on the viral surface and mediates viral entry into the host cell. To identify possible antibody binding sites, we performed multi-microsecond molecular dynamics simulations of a 4.

MDBenchmark: A toolkit to optimize the performance of molecular dynamics simulations.

Despite the impending flattening of Moore's law, the system size, complexity, and length of molecular dynamics (MD) simulations keep on increasing, thanks to effective code parallelization and optimization combined with algorithmic developments. Going forward, exascale computing poses new challenges to the efficient execution and management of MD simulations. The diversity and rapid developments of hardware architectures, software environments, and MD engines make it necessary that users can easily run benchmarks to optimally set up simulations, both with respect to time-to-solution and overall efficiency.

In situ structural analysis of SARS-CoV-2 spike reveals flexibility mediated by three hinges.

The spike protein (S) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is required for cell entry and is the primary focus for vaccine development. In this study, we combined cryo-electron tomography, subtomogram averaging, and molecular dynamics simulations to structurally analyze S in situ. Compared with the recombinant S, the viral S was more heavily glycosylated and occurred mostly in the closed prefusion conformation.

Osh Proteins Control Nanoscale Lipid Organization Necessary for PI(4,5)P Synthesis.

The plasma membrane (PM) is composed of a complex lipid mixture that forms heterogeneous membrane environments. Yet, how small-scale lipid organization controls physiological events at the PM remains largely unknown. Here, we show that ORP-related Osh lipid exchange proteins are critical for the synthesis of phosphatidylinositol (4,5)-bisphosphate [PI(4,5)P], a key regulator of dynamic events at the PM.

The molecular recognition of phosphatidic acid by an amphipathic helix in Opi1.

A key event in cellular physiology is the decision between membrane biogenesis and fat storage. Phosphatidic acid (PA) is an important intermediate at the branch point of these pathways and is continuously monitored by the transcriptional repressor Opi1 to orchestrate lipid metabolism. In this study, we report on the mechanism of membrane recognition by Opi1 and identify an amphipathic helix (AH) for selective binding of PA over phosphatidylserine (PS).

What happens to patients who teach?

Background: Over the last 35 years, the use of lay people as teaching patients has evolved from novel to routine.

Purpose: Although many studies have examined the effectiveness, reliability, and validity of using trained patients to evaluate medical students and residents, little is known about the effect on patients of being teachers. This study addresses that question.

A method for measuring interrater agreement on checklists.

A method for measuring interrater agreement on checklists is presented. This technique does not assign individual scores to raters, but computes a single agreement score from the concordance of their check mark configurations. An overall coefficient of agreement, called phi, is derived.

A survey of exercise beliefs and exercise habits among people with arthritis.

Objective: To explore a possible explanation for the problem of why few people exercise despite the positive health advantages, by examining the relationship between exercise beliefs and participation in exercise activities.

Methods: Eighty-one respondents aged 27-80 were recruited from 3 Chicago-area health care facilities to complete the study survey; 68 (84%) did so. Participants were asked about their participation in 6 types of exercise activities; they also reported their beliefs concerning their ability to exercise (self-efficacy for exercise), barriers to exercise, benefits of exercise, and the impact of exercise on their arthritis.

Dance-based aerobic exercise for rheumatoid arthritis.

Reported here are the results of the first effort to examine the effects of a dance-based aerobic exercise program for people with rheumatoid arthritis (RA). Forty-three subjects with RA completed a 16-week program that met twice weekly for 2 hours. One hour was devoted to exercise consisting of 15 to 20 minutes of warm-ups, 20 to 30 minutes of dance-based aerobic exercise, and 15 to 20 minutes of mat work for muscle strengthening and flexibility.