Directed transport as a mechanism for protein foldingin vivo

Abstract

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 type 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.

Reconstructing the free-energy landscape associated to molecular motors processivity

“…In the following sections, we will show that the present scheme for the catalytic reaction can be generalized by considering competitive inhibition by the final products of the sequence of reactions (the production of ADP and P i ) and how this leads to invert the above situation, that is, when due to the presence of inhibitors the M KT state becomes energetically more favorable than the M KT one, which results in the end of the catalytic reaction. In physical terms, these asymmetries shown by the potential imply that the catalytic free-energy landscape we deduced from the biochemical reaction scheme is a type of potential called "tilted ratchet"potential [15][16][17]19,21 . Thus, the biochemical model proposed here gives an experimental basis to these type of potentials heuristically proposed in the literature.…”

“…Often, these models follow two different approaches, one describing the collective behavior and properties by viewing the motors as catalytic agents of a chemical reaction 6,14 whereas the second one focuses on the individual description that analyzes the specific conformational changes occurring during motility [9][10][11][12] . From a more physical point of view, several models taking into account the stochastic and thermodynamic nature of the translational dynamics of a) Electronic mail: isholek@gmail.com molecular motors were proposed and used to describe some general features of molecular motor activity [15][16][17][18][19][20][21] . The essential ingredient to perform the description in these approaches is to provide a model for the energy landscape of the cyclic operation of motors [15][16][17]20,21 , however these models are barely related to the chemical reactions that drive the process.…”

“…From a more physical point of view, several models taking into account the stochastic and thermodynamic nature of the translational dynamics of a) Electronic mail: isholek@gmail.com molecular motors were proposed and used to describe some general features of molecular motor activity [15][16][17][18][19][20][21] . The essential ingredient to perform the description in these approaches is to provide a model for the energy landscape of the cyclic operation of motors [15][16][17]20,21 , however these models are barely related to the chemical reactions that drive the process.…”

Similarity analysis and phylogenetic trees from cellular automata imaging of lysozyme proteins

“…The last 20 years have been of fundamental relevance for molecular biology and bioinformatics with the emergence of different computational approaches designed to study protein folding and classification (see for instance [1][2][3][4] and references therein). With the improvement of protein sequencing techniques, available data in different databases such as GenBank 5 and UniProt 6 grew significantly.…”