Molecular Recognition as an Information Channel: The Role of Conformational Changes

TL;DR

This paper models molecular recognition as an information transmission process, highlighting how conformational changes and flexibility can optimize detection performance in noisy biological environments.

Contribution

It introduces the concept of conformational proofreading, proposing that molecular deformation enhances recognition accuracy and explores the optimal flexibility of molecular recognizers.

Findings

Conformational changes can improve detection performance.

Flexible recognizers may outperform rigid ones in noisy conditions.

The concept of conformational proofreading as a design principle.

Abstract

Molecular recognition, which is essential in processing information in biological systems, takes place in a crowded noisy biochemical environment and requires the recognition of a specific target within a background of various similar competing molecules. We consider molecular recognition as a transmission of information via a noisy channel and use this analogy to gain insights on the optimal, or fittest, molecular recognizer. We focus on the optimal structural properties of the molecules such as flexibility and conformation. We show that conformational changes upon binding, which often occur during molecular recognition, may optimize the detection performance of the recognizer. We thus suggest a generic design principle termed 'conformational proofreading' in which deformation enhances detection. We evaluate the optimal flexibility of the molecular recognizer, which is analogous to the stochasticity in a decision unit. In some scenarios, a flexible recognizer, i.e., a stochastic decision unit, performs better than a rigid, deterministic one. As a biological example, we discuss conformational changes during homologous recombination, the process of genetic exchange between two DNA strands.