Simulation of biomimetic recognition between polymers and surfaces

Abstract

Many biological processes, such as transmembrane signaling and pathogen-host interactions, are initiated by a protein recognizing a specific pattern of binding sites on part of a membrane or cell surface. By recognition, we imply that the polymer quickly finds and then adsorbs strongly on the pattern-matched region and not on others. The development of synthetic systems that can mimic such recognition between polymers and surfaces could have significant impact on advanced applications such as the development of sensors, molecular-scale separation processes, and synthetic viral inhibition agents. Attempting to affect recognition in synthetic systems by copying the detailed chemistries to which nature has been led over millenia of evolution does not seem practical for most applications. This leads us to the following question: Are there any universal strategies that can affect recognition between polymers and surfaces? Such generic strategies may be easier to implement in abiotic applications. We describe results that suggest that biomimetic recognition between synthetic polymers and surfaces is possible by exploiting certain generic strategies, and we elucidate the kinetic mechanisms by which this occurs. Our results suggest convenient model systems for experimental studies of dynamics in free energy landscapes characteristic of frustrated systems. It is common in biology for a protein to recognize and bind to a specific pattern of binding sites localized in a region of a surface. It is not our purpose to explain how the intricate chemistries resulting from evolution allow such specific recognition to occur. Rather, in this paper, we explore whether there are minimal universal strategies that would allow synthetic polymers to mimic recognition. Such strategies might be profitably exploited in applications (1, 2). To deduce candidates for such strategies, we were inspired by some coarse-grained observations regarding biological systems. Proteins are composed of many types of monomers and have sequences that are not periodically repeating (3-6). Similarly, the pattern of different binding sites on cell surfaces is not periodically repeating. These observations led us to ask whether competing interactions (because of preferential interactions between different types of monomers and surface sites) and disorder are essential ingredients for biomimetic recognition in synthetic systems. [We note that Muthukumar (7,8) has also thought about questions pertinent to pattern recognition between polymers and surfaces, and Khokhlov and coworkers (9) have considered designing polymer sequences for efficient binding to uniform surfaces that do not bear patterns.] Disordered heteropolymers (DHPs) are synthetic macromolecules with chemically different monomer units distributed along the backbone in a disordered sequence that is described statistically. ʈ Like proteins, they are composed of different monomers, with sequences that are aperiodic and quenched (the sequences cannot change in response to the environment). Unlike protei...

Chain entropy: Spoiler or benefactor in pattern recognition?

“…The simulations of Golumbfskie et al (10) beautifully illustrate all of the abovediscussed features of entropic frustration, as originally enunciated (7)(8)(9). The dynamics of a partially pattern-recognized complex consisting of many loops is demonstrated to be highly cooperative leading to stretched exponential correlations in various properties.…”

“…It is therefore necessary to temporally modify the free-energy landscape to guide the pattern recognition to be successful and efficient. By using dynamic Monte Carlo simulations of a two-component heteropolymer bearing statistical patterns of sequences in the proximity of a heterogeneous surface bearing statistical patches of chemistries with short-range interaction toward the polymer, a vivid demonstration of the above-mentioned theme of pattern recognition is reported in this issue of PNAS by Golumbfskie et al (10).…”

Differences in Solution Behavior among Four Semiconductor-Binding Peptides

“…20 The phase structure for chain adsorption to attractive surfaces has been investigated using lattice models for polymers [21][22][23] and peptides. 24 Simplified statistical-mechanical models have also been used to study molecular recognition of patterned surfaces [25][26][27][28][29][30] and conformational changes of proteins adsorbed to a solid surface. 31,32 Model and Methods Peptides Studied.…”

Computer modeling of radical copolymerization under unusual conditions

“…Obviously, these copolymers could have enormous potential in molecular technology and biotechnology. [61][62][63] Indeed, it is well known that selective interactions between macromolecules with specific primary structures and structured surfaces play a central role in many biological systems. In particular, molecular pattern recognition is an essential element of protein-DNA binding, transmembrane signaling, antibody-antigen recognition, and pathogen-host interactions.…”