Biophysical Journal

Dynamic gating by ϕ-clamp loop controls peptide translocation through the anthrax toxin nanopore The ϕ clamp, a key active site in the anthrax toxin protective antigen (PA) nanopore, governs the complex process of peptide translocation, yet its precise mechanism remains debated. A key question…

#OPENACCESS: Dynamic gating by ϕ-clamp loop controls peptide translocation through the anthrax toxin nanopore. Jennifer M. Colby and Bryan A. Krantz.

Molecular dynamics in the stratum corneum of plantar heels in atopic dermatitis patients The skin acts as an effective barrier against the uptake of hazardous chemicals and microorganisms as well as prevention of extensive water loss. These barrier functions are mainly assured by the…

#OPENACCESS: Molecular dynamics in the stratum corneum of plantar heels in atopic dermatitis patients. Enamul Mojumdar, Andreas Sonesson, Quoc Dat Pham, Daniel Topgaard, and Emma Sparr.

Cold atmospheric plasma promotes migration persistence, through induced H2O2 and electric field Cold atmospheric plasma (CAP) generates various products, including radiation, electrons, ions, an electric field, and reactive oxygen and nitrogen species. CAP promotes wound healing and has been…

#OPENACCESS: Cold atmospheric plasma promotes migration persistence, through induced H2O2 and electric field. Benjamin Labérie, Louis Saugé, Anna Polesskaya, Antoine Rousseau, and Alexis M. Gautreau.

Quantifying activation delay and the Cole-More shift via current derivatives The kinetics of ion channels arise from transitions through multiple closed and open states. An example is the sigmoidal activation kinetics exhibited by voltage-gated potassium channels upon…

#OPENACCESS: Quantifying activation delay and the Cole-More shift via current derivatives. Bernardo I. Pinto-Anwandter and Francisco Bezanilla

Multiscale mechanobiochemical modeling of cell-substrate adhesion dynamics Cell adhesion is a fundamental biological process that governs cell proliferation, differentiation, migration, and tissue development. Cells adhere to the extracellular matrix through specialized…

Cells are like tiny rock climbers! In Huiyan Liang et al., a multiscale mechanobiochemical model shows how integrins are the climbers’ gear—activating, clustering, and getting pulled by actin to grip the “wall” (ECM). Stiffer walls change the grip and migration style!

Special issue call for papers: Viral Biophysics.

Role of electric fields from cold gas plasmas in biomedical applications Plasma medicine investigates the action and therapeutic potential of gas discharges operated at body temperature, so-called cold atmospheric pressure plasmas (CAPs), for biomedical applications such…

In the New and Notable "Role of electric fields from cold gas plasmas in biomedical applications," Sander Bekeschus highlights the paper "Cold atmospheric plasma promotes migration persistence through induced H2O2 and electric field."

Lipid composition effects on the number and size of liposomes formed by the inverted emulsion method Liposomes have been widely employed as membrane scaffolds in the construction of minimal cell models. In 2003, the inverted emulsion method was introduced as a novel technique for generating giant…

#OPENACCESS: Sakata et al. use the inverted emulsion method to map how phospholipid composition controls liposome yield and size distribution, revealing how moderate addition of charged lipids enhances production, while larger headgroups shift size distribution to larger diameters.

Painting the Birth of an Artificial Cell The cover image was inspired by my long-standing hobby of watercolor painting. When traveling, I often carry a small sketchbook and watercolor inks to capture buildings, streets, and landscapes. For t...

Read about the cover art for the newly released issue of Biophysical Journal on the BPS Blog: www.biophysics.org/blog/paintin...

#OPENACCESS: Multiscale simulations of folded and intrinsically disordered region-containing protein condensates. Lyudmyla Dorosh, Holger Wille, and Maria Stepanova.

#OPENACCESS: Coarse-grained Martini 3 model for collagen fibrils. Matthias Brosz, Johanna Buck, Fabian Grünewald, Debora Monego, Jaewoon Jung, Yuji Sugita, Camilo Aponte-Santamaría, and Frauke Gräter.

#OPENACCESS: Structural basis for efficient Fo motor rotation revealed by MCMD simulation and structural analysis. Shintaroh Kubo and Hiroyuki Noji.

Capturing the dance of the exit tunnel of the ribosome using course-grain simulations illustrates the ballet of newly formed polypeptide.

Special issue call for papers: Viral Biophysics.

#OPENACCESS: Dynamics and lipid membrane coupling of the RAS-RAF complex revealed via multiscale simulations. Timothy S. Carpenter and Fikret Aydin, et al.

A meta-analysis dissects the effect of protein primary-sequence variations on the conformational ensembles populated by protein kinases.

#OPENACCESS: On the curvature and relaxation of microtubule plus-end tips.
Tomasz Skóra, Jiangbo Wu, Daniel Beckett, Weizhi Xue, Gregory A. Voth, and Tamara C. Bidone.

New study using coarse-grained simulations shows how amphiphilic polypeptide-based polymers self-assemble and disassemble in response to binding of a specific protein, paving the way for responsive drug delivery systems and biosensors.

#OPENACCESS: Using coarse-grained molecular dynamics simulations, Brown et al. compare three computational techniques to calculate lipid bilayer bending modulus, revealing method-dependent variations and the complexity of quantifying membrane mechanics.

#OPENACCESS: Asymmetry and heterogeneity in the plasma membrane. Teppei Yamada and Wataru Shinoda.

Artificial intelligence and machine learning are talks of the town today and are making strides in all aspects of science. This review highlights recent advances in machine-learning-driven biomolecular simulations to enhance accuracy and extend the simulation timescales.
Link:

#OPENACCESS: Estimating physical conditions supporting gradients of ATP concentration in the eukaryotic cell. Rajneesh Kumar and Iain G. Johnston.

Sharma and colleagues combine all-atom and coarse-grained molecular dynamics simulations with protein design and machine learning to uncover how sotrovimab resistance emerges in SARS-CoV-2, revealing key resistance mutations.

Check out the newly-released issue of Biophysical Journal: www.cell.com/biophysj/cur...

#OPENACCESS: How protein hydration depends on amino acid composition, peptide conformation, and force fields. Johanna-Barbara Linse, Tobias M. Fischbach, and Jochen S. Hub.

#OPENACCESS: Dynamics of excitability in axonal trees. Laurie D. Cohen, Tamar Galateanu, and Shimon Marom.

#OPENACCESS: The influence of intercalated disk nanostructure on local ionic currents and cardiac conduction. Ruichen Sui, Nicolae Moise, and Seth H. Weinberg.

Special issue call for papers: Viral Biophysics.

In the New and Notable "Deciphering the mechanics of spindle positioning,"
Dechang Li highlights the paper "A Constitutive Model Deciphers the Viscoelastic Mechanics of Metaphase Spindle Positioning."

Like tiny “energy carts” in a factory shifting to busy assembly lines when orders (glucose) flood in, mitochondria in beta cells move toward the edge on glucose cues to power insulin release!