The Multiscale Future of RNA Modeling
Published in Biophysical Journal
The Inhibitory Effect of a Coronavirus Spike Protein Fragment with ACE2
Published in Biophysical Journal
In this article, we investigate the binding processes of a fragment of the coronavirus spike protein receptor binding domain (RBD), the hexapeptide YKYRYL on the angiotensin-converting enzyme 2 (ACE2) receptor, and its inhibitory effect on the binding and activation of the coronavirus-2 spike protein CoV-2 RBD at ACE2. In agreement with an experime...
Requirements for DNA-bridging proteins to act as topological barriers of the bacterial genome
Bacterial genomes have been shown to be partitioned into several kilobases long chromosomal domains that are topologically independent from each other, meaning that change of DNA superhelicity in one domain does not propagate to neighbors. Both in vivo and in vitro experiments have been performed to question the nature of the topological barriers a...
Reflections on the Pandemic
Published in Biophysical Journal
Analysis of NMR Spin-Relaxation Data Using an Inverse Gaussian Distribution Function
Published in Biophysical Journal
Biophysical Parameters of GEVIs: Considerations for Imaging Voltage.
Published in Biophysical journal
Genetically encoded voltage indicators (GEVIs) continue to evolve, resulting in many different probes with varying strengths and weaknesses. Developers of new GEVIs tend to highlight their positive features. A recent article from an independent laboratory has compared the signal/noise ratios of a number of GEVIs. Such a comparison can be helpful to...
Observing Protein Degradation by the PAN-20S Proteasome by Time-Resolved Neutron Scattering
...Published in Biophysical Journal
The proteasome is a key player of regulated protein degradation in all kingdoms of life. Although recent atomic structures have provided snapshots on a number of conformations, data on substrate states and populations during the active degradation process in solution remain scarce. Here, we use time-resolved small-angle neutron scattering of a deut...
Connecting Coil-to-Globule Transitions to Full Phase Diagrams for Intrinsically Disordered Proteins
Published in Biophysical Journal
Phase separation is thought to underlie spatial and temporal organization that is required for controlling biochemical reactions in cells. Multivalence of interaction motifs, also known as stickers, is a defining feature of proteins that drive phase separation. Intrinsically disordered proteins with stickers uniformly distributed along the linear s...
In-Lipid Structure of Pressure-Sensitive Domains Hints Mechanosensitive Channel Functional Diversity
Published in Biophysical Journal
The mechanosensitive channel of large conductance (MscL) from Mycobacterium tuberculosis has been used as a structural model for rationalizing functional observations in multiple MscL orthologs. Although these orthologs adopt similar structural architectures, they reportedly present significant functional differences. Subtle structural discrepancie...
Allosteric Communications between Domains Modulate the Activity of Matrix Metalloprotease-1
Published in Biophysical Journal
An understanding of the structure-dynamics relationship is essential for understanding how a protein works. Prior research has shown that the activity of a protein correlates with intradomain dynamics occurring at picosecond to millisecond timescales. However, the correlation between interdomain dynamics and the function of a protein is poorly unde...
