Valerio Rizzi
valeriorizzi.bsky.social
Valerio Rizzi
@valeriorizzi.bsky.social
Maître-assistant @gervasiolab.bsky.social UniGe | PostDoc
@GroupParrinello IIT ETHZ | PhD @QUBelfast.
Computational physicist, #MolecularDynamics #Biophysics
Reposted by Valerio Rizzi
How do proteins really fold? Our latest @pubs.acs.org JPCL paper with @saureli.bsky.social @valeriorizzi.bsky.social @mheritier.bsky.social unveils a new MD strategy to investigate it in atomistic resolution by focusing on water and side-chain interactions. check it out pubs.acs.org/doi/10.1021/...
The Arch from the Stones: Understanding Protein Folding Energy Landscapes via Bioinspired Collective Variables
Protein folding remains a formidable challenge despite significant advances, particularly in sequence-to-structure prediction. Accurately capturing thermodynamics and intermediates via simulations dem...
pubs.acs.org
September 8, 2025 at 1:13 PM
Reposted by Valerio Rizzi
New in @pubs.acs.org JCTC: We've mapped the complete activation pathway of the β1-adrenergic receptor using our OneOPES enhanced sampling method and tailored CVs. Our approach reveals how sodium ions, water networks & protein microswitches work together. pubs.acs.org/doi/full/10.... #GPCR
Enhanced Sampling and Tailored Collective Variables Yield Reproducible Free Energy Landscapes of Beta-1 Adrenergic Receptor Activation
The beta-1 adrenergic receptor (ADRB1) is a critical target for cardiovascular drugs, yet our understanding of how it is activated remains incomplete. Capturing the concerted interplay of agonists, solvent, ions, and protein microswitches is a significant challenge for conventional simulation methods and is essential for unraveling this process. Here, we address this challenge by implementing a powerful enhanced sampling framework that integrates the OneOPES enhanced sampling algorithm with a set of biologically motivated collective variables (CVs). These CVs are designed to track several key features of the activation process simultaneously, including rearrangement of conserved microswitches, the state of the sodium ion binding pocket, and dynamics of critical water molecules. Using this framework, we mapped the multidimensional free energy landscapes of the ADRB1 receptor in both its apo- and adrenaline-bound holo states. Our analysis reveals a detailed, stepwise activation pathway that quantifies the known modulatory roles of sodium ions and protonation states and identifies essential water-mediated networks that stabilize the active conformation. This work provides a detailed overview of ADRB1 activation and establishes the robustness of our OneOPES approach for investigating complex activation mechanisms with the potential for application to other Class A GPCRs.
pubs.acs.org
August 1, 2025 at 11:59 AM
Reposted by Valerio Rizzi
Very proud of our new review article on the Beta 1-Adrenergic GPCR now available on bioRxiv: www.biorxiv.org/content/10.1....
With @saureli.bsky.social @valeriorizzi.bsky.social and Nicola we used OneOPES to fully converge the free energy landscapes associated with B1AR apo/holo activation.
March 12, 2025 at 1:27 PM