Biology subjects

Bzowka, M.

Publications and source records attributed to Bzowka, M..

4 recordsLinked to original sources

bioRxiv2026

Vasopressin V2 receptor phosphopeptide reshapes the conformational landscape of arrestin-2 beyond C-tail detachment

Binding of phosphorylated GPCR tails influences arrestin conformation, but the contribution of this interaction to the interdomain rotation associated with activation remains incompletely characterised. In particular, it remains unclear whether displacement of the arrestin C-tail is sufficient to favor larger interdomain rotations or whether the bound phosphotail exerts an additional effect on the conformational landscape. Here, we used enhanced-sampling simulations to characterise the conformational free-energy landscapes of basal (unbound) and V2Rpp-bound arrestin-2. We find that V2Rpp binding broadened the range of energetically accessible interdomain rotation angles relative to basal arrestin-2. However, the pronounced rotation observed in the experimental structures, while accessible, was not strongly favored. Strikingly, C-tail displacement alone does not reproduce this effect, as arrestin-2 retains a strong preference for small interdomain rotation angles in the absence of V2Rpp. Moreover, the C-tail-detached state is energetically unfavorable in the absence of V2Rpp. Together, these findings quantify the effects of V2Rpp binding on the interdomain rotation of arrestin-2 and disentangle the effects of phosphopeptide binding from those of C-tail detachment.

biochemistry↗

bioRxiv2026

Buprenorphine Restricts the Conformational Landscape of the μ-Opioid Receptor

Biased signaling and partial agonism in GPCRs are considered promising strategies to develop safer and more effective drugs. Various mechanisms have been proposed to explain these phenomena, including the ability of biased and partial ligands to promote specific receptor conformations able to engage distinct intracellular partners. Recent cryo-electron microscopy structures of the {micro}-opioid receptor (MOR) bound to both G-proteins and {beta}-arrestins have shown clear structural differences shedding light into the putative signaling states. However, the accessibility of such conformations in the absence of the intracellular partner and the mechanisms by which ligands modulate their populations remain poorly understood. In the present manuscript, we employ extensive enhanced-sampling simulations to explore the free-energy landscapes of MOR bound to a biased partial agonist (buprenorphine) and a full unbiased agonist (endomorphin-1) showing that the ligands indeed stabilize distinct ensembles of active-like states. In particular, we observe that endomorphin-1, the natural ligand, explores two different ensembles of active-like conformations, including states compatible with either G-protein or {beta}-arrestin1 recruitment, whereas buprenorphine restricts access to these conformations and favors a narrower subset of active states more prone to G-protein binding. Moreover, we analyze the allosteric pathways connecting the ligands to the different active-like states. Together, our findings provide a thermodynamic framework for understanding biased signaling at MOR and confirm that in MOR ligand efficacy and signaling preference emerge from the selective redistribution of receptor conformational populations even in the absence of the effector proteins. This perspective may guide the rational design of opioid therapeutics with improved signaling profiles and reduced adverse effects.

biophysics↗

bioRxiv2021

Evolution of tunnels in alpha/beta-hydrolase fold proteins - what can we learn from studying epoxide hydrolases?

The evolutionary variability of a proteins residues is highly dependent on protein region and function. Solvent-exposed residues, excluding those at interaction interfaces, are more variable than buried residues whereas active site residues are considered to be conserved. The abovementioned rules apply also to /{beta}-hydrolase fold proteins - one of the oldest and the biggest superfamily of enzymes with buried active sites equipped with tunnels linking the reaction site with the exterior. We selected soluble epoxide hydrolases as representative of this family to conduct the first systematic study on the evolution of tunnels. We hypothesised that tunnels are lined by mostly conserved residues, and are equipped with a number of specific variable residues that are able to respond to evolutionary pressure. The hypothesis was confirmed, and we suggested a general and detailed way of the tunnels evolution analysis based on entropy values calculated for tunnels residues. We also found three different cases of entropy distribution among tunnel-lining residues. These observations can be applied for protein reengineering mimicking the natural evolution process. We propose a perforation mechanism for new tunnels design via the merging of internal cavities or protein surface perforation. Based on the literature data, such a strategy of new tunnel design could significantly improve the enzymes performance and can be applied widely for enzymes with buried active sites. Author SummarySo far very little is known about proteins tunnels evolution. The goal of this study is to evaluate the evolution of tunnels in the family of soluble epoxide hydrolases - representatives of numerous /{beta}-hydrolase fold enzymes. As a result two types of tunnels evolution analysis were proposed (a general and a detailed approach), as well as a perforation mechanism which can mimic native evolution in proteins and can be used as an additional strategy for enzymes redesign.

bioinformatics↗

bioRxiv2020

Molecular Dynamics Simulations Indicate the COVID-19 Mpro Is Not a Viable Target for Small-Molecule Inhibitors Design

The novel coronavirus whose outbreak took place in December 2019 continues to spread at a rapid rate worldwide. In the absence of an effective vaccine, inhibitor repurposing or de novo drug design may offer a longer-term strategy to combat this and future infections due to similar viruses. Here, we report on detailed classical and mix-solvent molecular dynamics simulations of the main protease (Mpro) enriched by evolutionary and stability analysis of the protein. The results were compared with those for a highly similar SARS Mpro protein. In spite of a high level of sequence similarity, the active sites in both proteins show major differences in both shape and size indicating that repurposing SARS drugs for COVID-19 may be futile. Furthermore, analysis of the binding sites conformational changes during the simulation time indicates its flexibility and plasticity, which dashes hopes for rapid and reliable drug design. Conversely, structural stability of the protein with respect to flexible loop mutations indicates that the virus mutability will pose a further challenge to the rational design of small-molecule inhibitors. However, few residues contribute significantly to the protein stability and thus can be considered as key anchoring residues for Mpro inhibitor design.

molecular biology↗