Protein modeling
UCPH and Kresten Lindorff-Larsen
Revealing rare, transiently structured states in disordered proteins through multithermal simulation and experimental reweighting.
- Disordered protein ensembles
- OPES multithermal sampling
- Experimental ensemble validation
Why we partner
Intrinsically disordered proteins are defined by motion, yet the rare states that shape recognition and function are difficult to recover with conventional simulation alone. We partnered with Prof. Kresten Lindorff-Larsen and the University of Copenhagen to address that sampling problem directly. His group combines molecular simulation with structural biology experiments, an approach that aligns with Peptone's ensemble-first modeling. Together, we tested whether multithermal enhanced sampling could broaden conformational exploration while remaining accountable to experimental evidence.
Scientific focus
The study examined On-the-fly Probability Enhanced Sampling in a multithermal ensemble, known as OPES multiT. A single simulation replica samples a range of temperatures and can then be reweighted to a target condition. We applied the method across peptides and disordered proteins from 15 to 71 residues, comparing the resulting ensemble averages with unbiased molecular dynamics and REST2. For ACTR, Bayesian maximum entropy reweighting incorporated NMR data, while independent NMR and SAXS observables tested the ensemble.
What Peptone brings
Peptone brings enhanced sampling, ensemble reweighting, and computational analysis into one evidence-led modeling workflow. These methods help simulations move beyond common conformations and recover rare states that may influence protein behaviour. Experimental measurements are then used to test and refine the resulting ensembles. This keeps each model tied to physical evidence rather than a single predicted structure.
What we did together
The collaboration evaluated OPES multiT across peptides and disordered proteins of increasing size and complexity. We compared the method with conventional molecular dynamics and REST2 to determine whether it could explore a broader conformational landscape without distorting ensemble averages. For ACTR, NMR data refined the ensemble, while independent NMR and SAXS measurements tested the result. This combined approach revealed low-population compact states and showed that they were sampled reversibly.
Why it matters
OPES multiT produced ensemble averages broadly consistent with the comparison methods while exploring more low-population conformations. In ACTR, the reweighted ensemble exposed an approximately 3 percent subset in which two binding helices were largely formed, a third was partly formed, and tertiary contacts created compact states. These states were sampled reversibly and were consistent with the experimental observables considered. The study does not claim exhaustive sampling, a drug, or an experimentally validated druggable pocket. Its value is methodological: a practical route to atomistic ensembles that can expose rare structure and generate testable hypotheses for functional studies, interaction studies, and molecular design.