Rethinking the protein folding problem from a new perspective

TL;DR

This paper revisits the protein folding problem by proposing a new perspective inspired by Leibnitz and Kant, questioning the effectiveness of force-field-based approaches in predicting protein structures and understanding folding mechanisms.

Contribution

It introduces a novel perspective on protein folding as an analytic whole, challenging traditional force-field methods and aiming to deepen understanding of sequence-structure relationships.

Findings

Force-field approaches have failed to accurately predict protein structures.

The new perspective emphasizes the need for alternative methods beyond traditional force fields.

The paper highlights unresolved questions about how amino acid sequences encode folding information.

Abstract

One of the main concerns of Anfinsen was to reveal the connection between the amino acid sequence and their biologically active conformation. This search gave rise to two crucial questions in structural biology, namely, why the proteins fold and how a sequence encodes its folding. As to the why, he proposes a plausible answer, namely, at a given milieu a protein folds into its functional form -- native state -- because such structure represents the lowest free-energy minimum among all feasible conformations -- the thermodynamic hypothesis or Anfinsen dogma. As to the how, this remains as an unsolved challenge and, hence, this inquiry is examined here from a new perspective of protein folding, namely, as an analytic whole -- a notion proposed by Leibnitz and Kant. This new perspective forces us to discuss in detail why the theoretical force-field-based approaches have failed in both their ability to predict the three-dimensional structure of a protein accurately and in their capacity to answer one of the most critical questions in structural biology: how a sequence encodes its folding.