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We propose a model for protein folding in vivo based on a Brownian ratchet mechanism in the multidimensional energy landscape space. The device is able to produce directed transport taking advantage of the assumed intrinsic asymmetric properties of the proteins and employing the consumption of energy provided by an external source. Through such a directed transport phenomenon, the polypeptide finds the native state starting from any initial state in the energy landscape with great efficacy and robustness, even in the presence of different types of obstacles. This model solves Levinthal's paradox without requiring biased transition probabilities but at the expense of opening the system to an external field.

Brownian ratchets have recently been considered as models to describe the ability of certain systems to locate very specific states in multidimensional configuration spaces. This directional process has particularly been proposed as an alternative explanation for the protein folding problem, in which the polypeptide is driven toward the native state by a multidimensional Brownian ratchet. Recognizing the relevance of robustness in biological systems, in this work we analyze such a property of Brownian ratchets by pushing to the limits all the properties considered essential to produce directed transport. Based on the results presented here, we can state that Brownian ratchets are able to deliver current and locate funnel structures under a wide range of conditions. As a result, they represent a simple model that solves the Levinthal's paradox with great robustness and flexibility and without requiring any ad hoc biased transition probability. The behavior of Brownian ratchets shown in this article considerably enhances the plausibility of the model for at least part of the structural mechanism behind protein folding process. [ABSTRACT FROM AUTHOR]

Abstract: The overdamped thermal ratchet driven by an external (Orstein–Uhlenbeck) noise is revisited. The ratchet we consider is unbounded in space and not necessarily periodic. We briefly discuss the conditions under which current is obtained by analyzing the corresponding Fokker–Planck equation and its lack of stationary states. Next, two examples in more than one dimension and related to biological systems are presented. First, a two-dimensional model of a “kinesin protein” on a “microtubule” is analyzed and, second, we suggest that a ratchet mechanism may be behind the folding of proteins; the latter is elaborated with a multidimensional ratchet model. [Copyright &y& Elsevier]