Should Artificial Intelligence Play a Durable Role in Biomedical Research and Practice? DOI Open Access
Pierre Bongrand

International Journal of Molecular Sciences, Journal Year: 2024, Volume and Issue: 25(24), P. 13371 - 13371

Published: Dec. 13, 2024

During the last decade, artificial intelligence (AI) was applied to nearly all domains of human activity, including scientific research. It is thus warranted ask whether AI thinking should be durably involved in biomedical This problem addressed by examining three complementary questions (i) What are major barriers currently met investigators? suggested that during 2 decades there a shift towards growing need elucidate complex systems, and this not sufficiently fulfilled previously successful methods such as theoretical modeling or computer simulation (ii) potential meet aforementioned need? it recent well-suited perform classification prediction tasks on multivariate possibly help data interpretation, provided their efficiency properly validated. (iii) Recent representative results obtained with machine learning suggest may comparable displayed operators. concluded play an important role practice. Also, already other physics, combining conventional might generate further progress new applications, involving heuristic interpretation.

Language: Английский

Theory and Examples of Catch Bonds DOI Creative Commons
Wolfgang Quapp, Josep María Bofill

The Journal of Physical Chemistry B, Journal Year: 2024, Volume and Issue: 128(17), P. 4097 - 4110

Published: April 18, 2024

We discuss slip bonds, catch and the tug-of-war mechanism using mathematical arguments. The aim is to explain theoretical tool of molecular potential energy surfaces (PESs). For this, we propose simple 2-dimensional surface models demonstrate how a molecule under an external force behaves. Examples are selectins. Catch in particular, explained more detail, they contrasted bonds. can support special two-dimensional PESs for E- L-selectin which allow bond property. that Newton trajectories (NT) powerful tools describe these phenomena. NTs form background mechanochemistry.

Language: Английский

Citations

5
To a mechanical model of synthetic catch-bonds DOI Creative Commons
Wolfgang Quapp, Josep María Bofill, Kerim C. Dansuk

et al.

Journal of Mathematical Chemistry, Journal Year: 2025, Volume and Issue: unknown

Published: May 8, 2025

Language: Английский

Citations

0
Engineering tunable catch bonds with DNA DOI Creative Commons
Micah Yang, David Bakker, Isaac T. S. Li

et al.

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: Oct. 12, 2024

Unlike most adhesive bonds, biological catch bonds strengthen with increased tension. This characteristic is essential to specific receptor-ligand interactions, underpinning adhesion dynamics, cell communication, and mechanosensing. While artificial have been conceived, the tunability of their behaviour limited. Here, we present fish-hook, a rationally designed DNA bond that can be finely adjusted wide range behaviours. We develop models design these structures experimentally validate different behaviours by single-molecule force spectroscopy. The fish-hook architecture supports vast sequence-dependent space, making it valuable tool for reprogramming interactions engineering force-strengthening materials. Biological counter-intuitively when pulled. authors tuneable made from study biomimetic creation

Language: Английский

Citations

3
Comment to: "Topology of molecular deformations induces triphasic catch bonding in selectin-ligand bonds" DOI Creative Commons
Wolfgang Quapp, Josep María Bofill

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Aug. 23, 2024

We contradict diverse mathematical claims of a paper by Casey O. Barkan and Robijn F. Bruinsma in PNAS 2024, 121, No. 6, e2315866121, former BioRxiv preprint from Sept.12,2023. It deals with the physical mechanisms protein-ligand catch bonding for family selectin proteins. Selectins exhibit slip, catch–slip, slip–catch–slip bonding.

Language: Английский

Citations

0
Comment to: “Topology of molecular deformations induces triphasic catch bonding in selectin–ligand bonds” DOI
Wolfgang Quapp, Josep María Bofill

Published: Sept. 30, 2024

We contradict diverse mathematical claims of a paper by Casey O. Barkan and Robijn F. Bruinsma in PNAS 2024, 121, No. 6, e2315866121, former BioRxiv preprint from Sept.12,2023. It deals with the physical mechanisms protein-ligand catch bonding for family selectin proteins. Selectins exhibit slip, catch–slip, slip–catch–slip bonding.

Language: Английский

Citations

0
Force-dependent Reorganization and Mechanostability of the Izumo1:Juno Complex Involved in Human Fertilization DOI Creative Commons

Sean Boult,

Paulina Pacak, Byeongseon Yang

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 18, 2024

Abstract Izumo1:Juno-mediated adhesion between sperm and egg cells is essential for mammalian sexual reproduction. However, conventional biophysical structural approaches have provided only limited functional insights. Using atomic force microscopy-based single- molecule spectroscopy all-atom steered molecular dynamic simulations, we explored the role of mechanical forces in regulating human Izumo1:Juno complex. Our findings reveal a multi-state catch bond capable withstanding up to 600 pN- mechanostability rarely observed among eukaryotic protein complexes. We further found that this was impaired infertility-associated mutant, JunoH177Q. Detailed dynamics simulations show how force-dependent reorganization complex engages new binding conformations achieve state high mechanostability. Overall, study significantly enhances our understanding underpinnings regulate fertilization.

Language: Английский

Citations

0
Comment on ”Exploring potential energy surfaces to reach saddle points above convex regions” [J. Chem. Phys. 160, 232501 (2024)] by M.Gunde et al. DOI Creative Commons
Wolfgang Quapp, Josep María Bofill

Published: Dec. 12, 2024

We comment on the work convex regions of potential energy surface (PES) a molecule by M. Gunde; A. Jay; Poberžnik; N. Salles; Richard; G. Landa; Mousseau; L. Martin-Samos and Hemeryck[1]. In contrast to activation-relaxation technique nouveau (ARTn), in present we apply theory Newton trajectories (NTs) 2D PES. NTs have no problem traversing or concave The ARTn is compared with NTs.

Language: Английский

Citations

0
Should Artificial Intelligence Play a Durable Role in Biomedical Research and Practice? DOI Open Access
Pierre Bongrand

International Journal of Molecular Sciences, Journal Year: 2024, Volume and Issue: 25(24), P. 13371 - 13371

Published: Dec. 13, 2024

During the last decade, artificial intelligence (AI) was applied to nearly all domains of human activity, including scientific research. It is thus warranted ask whether AI thinking should be durably involved in biomedical This problem addressed by examining three complementary questions (i) What are major barriers currently met investigators? suggested that during 2 decades there a shift towards growing need elucidate complex systems, and this not sufficiently fulfilled previously successful methods such as theoretical modeling or computer simulation (ii) potential meet aforementioned need? it recent well-suited perform classification prediction tasks on multivariate possibly help data interpretation, provided their efficiency properly validated. (iii) Recent representative results obtained with machine learning suggest may comparable displayed operators. concluded play an important role practice. Also, already other physics, combining conventional might generate further progress new applications, involving heuristic interpretation.

Language: Английский

Citations

0