Unconstrained peptoid tetramer exhibits a predominant conformation in aqueous solution

Journal Article · 04 March 2019 · Biopolymers

DOI: https://doi.org/10.1002/bip.23267 · OSTI ID:1498163

Roe, Leah T. ^[1]; Pelton, Jeffrey G. ^[2]; Edison, John R. ^[1]; Butterfoss, Glenn L. ^[3]; Tresca, Blakely W. ^[4]; LaFaye, Bridgette A. ^[1]; Whitelam, Stephen ^[1]; Wemmer, David E. ^[5]; Zuckermann, Ronald N.  ^[1]

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1. The Molecular Foundry Lawrence Berkeley National Laboratory Berkeley California
2. QB3 Institute University of California Berkeley California
3. Center for Genomics and Systems Biology New York University Abu Dhabi Abu Dhabi United Arab Emirates
4. The Molecular Foundry Lawrence Berkeley National Laboratory Berkeley California, Department of Chemistry Kalamazoo College Kalamazoo Michigan
5. Department of Chemistry University of California Berkeley California

Abstract Conformational control in peptoids, N ‐substituted glycines, is crucial for the design and synthesis of biologically‐active compounds and atomically‐defined nanomaterials. While there are a growing number of structural studies in solution, most have been performed with conformationally‐constrained short sequences (e.g., sterically‐hindered sidechains or macrocyclization). Thus, the inherent degree of heterogeneity of unconstrained peptoids in solution remains largely unstudied. Here, we explored the folding landscape of a series of simple peptoid tetramers in aqueous solution by NMR spectroscopy. By incorporating specific ¹³ C‐probes into the backbone using bromoacetic acid‐2‐ ¹³ C as a submonomer, we developed a new technique for sequential backbone assignment of peptoids based on the 1, n ‐Adequate pulse sequence. Unexpectedly, two of the tetramers, containing an N ‐(2‐aminoethyl)glycine residue (Nae), had preferred conformations. NMR and molecular dynamics studies on one of the tetramers showed that the preferred conformer (52%) had a trans‐cis‐trans configuration about the three amide bonds. Moreover, >80% of the ensemble contained a cis amide bond at the central amide. The backbone dihedral angles observed fall directly within the expected minima in the peptoid Ramachandran plot. Analysis of this compound against similar peptoid analogs suggests that the commonly used Nae monomer plays a key role in the stabilization of peptoid structure via a side‐chain‐to‐main‐chain interaction. This discovery may offer a simple, synthetically high‐yielding approach to control peptoid structure, and suggests that peptoids have strong intrinsic conformational preferences in solution. These findings should facilitate the predictive design of folded peptoid structures, and accelerate application in areas ranging from drug discovery to biomimetic nanoscience.

• Sponsoring Organization: USDOE
• Grant/Contract Number: AC02-05CH11231
• OSTI ID: 1498163
• Journal Information: Biopolymers, Journal Name: Biopolymers Journal Issue: 6 Vol. 110; ISSN 0006-3525
• Publisher: Wiley Blackwell (John Wiley & Sons)Copyright Statement
• Country of Publication: United States
• Language: English