Molecular Recognition in a Lattice Model: An Enumeration Study

Abstract

We investigate the mechanisms underlying selective molecular recognition of single heteropolymers at chemically structured planar surfaces. To this end, we study systems with two-letter (HP) lattice heteropolymers by exact enumeration techniques. Selectivity for a particular surface is defined by an adsorption energy criterion. We analyze the distributions of selective sequences and the role of mutations. A particularly important factor for molecular recognition is the small-scale structure on the polymers.

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.…”

Developing and analyzing idealized models for molecular recognition

“…Therefore, a universal feature that governs molecular recognition within our model is identified as the local, small-scale structure of the modelled biomolecules. This general behaviour is found in both (small) two-dimensional and three-dimensional systems (Bogner et al, 2004). In addition, for some examined systems also the lowest frequency components, shown in figure 3 by the highest indexing number, add a major contribution.…”

“…To accomplish this task statistical features from a set of sequences each selec-tive for a particular surface pattern can be computed (Bogner et al, 2004). In this approach the sequence of residues is treated as a random vector which is then Fourier transformed.…”

“…In this article we review how coarse-grained models for molecular recognition processes can be developed and summarize results we obtained by employing these models for the investigation of the principle mechanisms underlying molecular recognition (Polotsky et al, 2004a,b;Bogner et al, 2004). In the next section we will particularly demonstrate how these models are developed starting from the findings of experimental investigations of recognition processes.…”

Thermodynamics of Protein Folding from Coarse-Grained Models’ Perspectives

“…Similarly, specificity of peptides and binding affinity to selected substrates could be of great importance for future electronic nanoscale circuits and pattern recognition nanosensory devices [55]. The study of hybrid interface models has considerable applications for a broad variety of problems, e.g., understanding the mechanisms of protein-ligand binding [56], prewetting and layering transitions in polymer solutions as well as dewetting of polymer films [57,58], molecular pattern recognition [59], electrophoretic polymer deposition and growth [60]. Recently, the influence of adhesion and steric hindrance for polymers grafted to a flat substrate [61,50,[62][63][64][65], conformational pseudophase transitions for nongrafted polymers and peptides in a cavity with attractive substrate [66][67][68][69], the shape response to pulling forces [70,71] or external fields [72] were subject of computer simulations and analytical approaches of different models.…”