Structural and ultrametric properties of twenty(L-alanine)

TL;DR

This study investigates the energy landscape of twenty(L-alanine), revealing that low-energy configurations are predominantly alpha-helices and exhibit ultrametric properties, indicating a complex, hierarchical structure among minima.

Contribution

It provides the first detailed analysis of ultrametricity in amino acid energy minima, highlighting the fine structure and persistence phenomena in the conformational space.

Findings

Lower-energy configurations are mainly alpha-helices across dielectric constants.

Ultrametricity is observed among low-energy minima, indicating hierarchical organization.

Persistence of alpha-helical segments aligns with previous critical length studies.

Abstract

We study local energy minima of twenty(L-alanine). The minima are generated using high-temperature Molecular Dynamics and Chain-Growth Monte Carlo simulations, with subsequent minimization. We find that the lower-energy configurations are $ \alpha $-helices for a wide range of dielectric constant values $ (\epsilon = 1,10,80), $ and that there is no noticeable difference between the distribution of energy minima in $ \phi \psi $ space for different values of $ \epsilon . $ Ultrametricity tests show that lower-energy $ (\alpha $ -helical) $ \epsilon =1 $ configurations form a set which is ultrametric to a certain degree, providing evidence for the presence of fine structure among those minima. We put forward a heuristic argument for this fine structure. We also find evidence for ultrametricity of a different kind among $ \epsilon =10 $ and $ \epsilon =80 $ energy minima. We analyze the distribution of lengths of $ \alpha $-helical portions among the minimized configurations and find a persistence phenomenon for the $ \epsilon =1 $ ones, in qualitative agreement with previous studies of critical lengths. Email contact: bascle@amoco.saclay.cea.fr