Folding-Driven Control of the Functional PP1 Complex via Multiscale Modeling
- 1Altos Labs Inc
Abstract
Understanding how conformational dynamics regulate protein complex assembly remains a central challenge in molecular systems biology. Here, we develop a multiscale modeling framework that integrates all-atom molecular dynamics (MD) simulations with rule-based kinetic modeling to investigate the formation of the PP1-GADD34-eIF2 complex, a critical regulator of the integrated stress response. Using umbrella sampling, we compute the potential of mean force (PMF) for key interactions, revealing strong thermodynamic driving forces for eIF2 binding ({Delta}G = -89.5 kJ/mol, KD {approx} 0.07 fM) and moderate affinity for PP1-GADD34 association ({Delta}G = -40.7 kJ/mol, KD {approx} 0.138 M). These energetics inform a PySB-based model that incorporates GADD34's folding state as a continuous variable ({varphi}), linking conformational transitions to holoenzyme assembly and activity. Simulations show that catalytic efficiency is maximized when GADD34 folding free energy is 20 kJ/mol and {varphi} = 0.9, reflecting a highly ordered state stabilized by actin and PP1 binding. Comparative analysis of energy-constrained and optimized parameter regimes reveals that folding-dependent assembly enhances both eIF2 dephosphorylation and information transmission, with channel capacities increasing from <0.002 bits to >5.5 bits. These results demonstrate how conformational regulation encodes system-level function and underscore the utility of multiscale models in bridging molecular energetics with dynamic biochemical control.
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BibTeX
@misc{fontana2026foldingdriven,
title = {{Folding-Driven Control of the Functional PP1 Complex via Multiscale Modeling}},
author = {F. Fontana and B. Bogin and M. Irvin and M. Ozen and Z. A. Levine and C. F. Lopez},
howpublished = {bioRxiv},
year = {2026},
month = sep,
doi = {10.64898/2026.09.23.753607},
url = {https://www.biorxiv.org/content/10.64898/2026.09.23.753607v1},
note = {CC BY-NC-ND},
}
RIS
TY - UNPB
TI - Folding-Driven Control of the Functional PP1 Complex via Multiscale Modeling
AU - F. Fontana
AU - B. Bogin
AU - M. Irvin
AU - M. Ozen
AU - Z. A. Levine
AU - C. F. Lopez
PY - 2026
DA - 2026/09/23
PB - bioRxiv
DO - 10.64898/2026.09.23.753607
UR - https://www.biorxiv.org/content/10.64898/2026.09.23.753607v1
AB - Understanding how conformational dynamics regulate protein complex assembly remains a central challenge in molecular systems biology. Here, we develop a multiscale modeling framework that integrates all-atom molecular dynamics (MD) simulations with rule-based kinetic modeling to investigate the formation of the PP1-GADD34-eIF2 complex, a critical regulator of the integrated stress response. Using umbrella sampling, we compute the potential of mean force (PMF) for key interactions, revealing strong thermodynamic driving forces for eIF2 binding ({Delta}G = -89.5 kJ/mol, KD {approx} 0.07 fM) and moderate affinity for PP1-GADD34 association ({Delta}G = -40.7 kJ/mol, KD {approx} 0.138 M). These energetics inform a PySB-based model that incorporates GADD34's folding state as a continuous variable ({varphi}), linking conformational transitions to holoenzyme assembly and activity. Simulations show that catalytic efficiency is maximized when GADD34 folding free energy is 20 kJ/mol and {varphi} = 0.9, reflecting a highly ordered state stabilized by actin and PP1 binding. Comparative analysis of energy-constrained and optimized parameter regimes reveals that folding-dependent assembly enhances both eIF2 dephosphorylation and information transmission, with channel capacities increasing from <0.002 bits to >5.5 bits. These results demonstrate how conformational regulation encodes system-level function and underscore the utility of multiscale models in bridging molecular energetics with dynamic biochemical control.
ER -