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Artificial Enzymes
Published in Yubing Xie, The Nanobiotechnology Handbook, 2012
James A. Stapleton, Agustina Rodriguez-Granillo, Vikas Nanda
Peptoids, or N-substituted glycines, are achiral, protease-resistant peptide analogs. A key advantage of peptoids is that they can be polymerized by a convenient and economical submonomer synthetic method (Burkoth et al. 2003) that allows incorporation of any of thousands of commercially available primary amines. An engineered ribosomal system (Kawakami et al. 2008b) has also been developed that could enable selections for enzymatic peptoids via isolation and amplification of encoding mRNA. Programming of polymer function by sequence-level design has been demonstrated with designed peptoids. In one example, a two-helix bundle was designed that selectively bound zinc with nanomolar affinity (Lee et al. 2008). Thiol and imidazole side chains (inspired by the cysteines and histidines used to bind zinc in proteins) were positioned to bind zinc only of the peptoid assumed the target structure. In another study, two peptoid polymers were reported to form two-dimensional crystalline sheets in aqueous solution (Nam et al. 2010). When mixed at a 1:1 ratio, the two 36-mers spontaneously formed a 2.7 nm-thick bilayer. Assembly was driven by the burial of hydrophobic side chains and pairing of positively and negatively charged side chains and did not require a phase interface as a template. Fusing an achiral small molecule catalyst to a structured peptoid resulted in enantioselective catalysis, which depended on the handedness of the peptoid used (Maayan et al. 2009).
Machine learning for collective variable discovery and enhanced sampling in biomolecular simulation
Published in Molecular Physics, 2020
Hythem Sidky, Wei Chen, Andrew L. Ferguson
Second, applications of these approaches tend to focus on single protein molecules (e.g. peptide folding, membrane protein activation). There are very good reasons for this privileging of protein folding from historical – the protein folding problem is a long-standing and alluring challenge [192,193] – biological – there are unquestionably critical problems in protein folding of great biological, biotechnological, and therapeutic value [194,195] – and practical – the best-validated computational force fields and experimental crystal structures are available for proteins – perspectives, but there are also compelling and important problems in related areas such as peptide assembly, peptoid engineering, and nucleic acid folding. It is important to develop methods in the context of diverse applications since it is not always the case that methods developed for proteins may be directly transferable and must be adapted to the specific vicissitudes of each system. For example, peptoid amide bonds occupy both cis and trans configurations (in contrast to those of peptides that are almost exclusively trans) but the transitions between them is a notoriously high-free energy barrier rare event [196]. To paraphrase the Persian poet Ibn Yamin (1286–1367), these slow CVs are ‘known unknowns’ and CV discovery and acceleration must explicitly account for these effects to achieve good sampling and enable CV discovery to identify the ‘unknown unknowns’.