The ruggedness of protein-protein energy landscape and the cutoff for 1/r^n potentials

TL;DR

This study investigates how the artificial ruggedness of protein-protein energy landscapes depends on cutoff distances in 1/r^n potentials, revealing critical cutoff values and their relation to potential power n.

Contribution

It provides a systematic analysis of cutoff effects on energy landscape ruggedness for various power-law potentials, identifying critical cutoff values for different thresholds.

Findings

Artificial ruggedness decreases with increasing cutoff distance.

Critical cutoff values are non-monotonic functions of potential power n.

Cutoffs longer than critical values reduce artificial ruggedness to tolerable levels.

Abstract

The interaction cutoff contribution to the ruggedness of protein-protein energy landscape (the artificial ruggedness) is studied in terms of relative energy fluctuations for 1/r^n potentials based on a simplistic model of a protein complex. Contradicting the principle of minimal frustration, the artificial ruggedness exists for short cutoffs and gradually disappears with the cutoff increase. The critical values of the cutoff were calculated for each of eleven popular power-type potentials with n=0-9, 12 and for two thresholds of 5% and 10%. The artificial ruggedness decreases to tolerable thresholds for cutoffs longer than the critical ones. The results showed that for both thresholds the critical cutoff is a non-monotonic function of the potential power n. The functions reach the maximum at n=3-4 and then decrease with the increase of the potential power. The difference between two cutoffs for 5% and 10% artificial ruggedness becomes negligible for potentials decreasing faster than 1/r^12. The results suggest that cutoffs longer than critical ones can be recommended for protein-protein potentials.