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Review
. 2016 Aug 17:12:1863-1869.
doi: 10.3762/bjoc.12.175. eCollection 2016.

From supramolecular chemistry to the nucleosome: studies in biomolecular recognition

Marcey L Waters  1
Affiliations
Review

From supramolecular chemistry to the nucleosome: studies in biomolecular recognition

Marcey L Waters. Beilstein J Org Chem. .

Abstract

This review highlights the author's indirect path to research at the interface of supramolecular chemistry and chemical biology.

Keywords: aromatic interactions; cation–π interactions; dynamic combinatorial chemistry; histone; molecular recognition in water; nucleosome; post-translational modification; supramolecular chemistry; α-helices; β-hairpin peptides; π–π-stacking.

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Figures

Figure 1
Figure 1
(a) Frodo the dog (copyright to MLW). (b) Ron Waters in an A6 in 1961 at the age of 26 (reproduced with permission from RLW). (c) A picture of Steeple Rock, near Duncan, AZ where we spent many mornings collecting geodes when visiting my grandparents (reproduced with permission from RLW). (d) Sue and Ron Waters in front of a painting by Sue Waters in 1983 (reproduced with permission from ASW and RLW). (e) My first successful artwork – the school logo I designed in elementary school (reproduced with permission from Miller Elementary School).
Figure 2
Figure 2
The Wulff–Dötz reaction.
Figure 3
Figure 3
Work by others that inspired my interests. (a) Cyclophane receptors from Dennis Dougherty’s group in the late ‘80’s and early ‘90’s that demonstrated cation–π interactions [2]. (b) Cyclophane receptors from the Diederich group in the late ‘80’s and early ‘90’s that demonstrated the “nonclassical hydrophobic effect” [3]. (c) The Hunter-Sanders Model for π–π stacking from 1990 [4]. (d) Kool’s nonpolar isostere of thymidine from 1995 [5].(e) Gellman’s model for π–π stacking in aqueous solution [6].
Figure 4
Figure 4
(a) Model β-hairpin for investigation of aromatic interactions. (b) Examples of noncovalent interactions studied, from weakest to strongest [–32].
Figure 5
Figure 5
(a) A clay model of our WKWK peptide (aka “Saratide”) made by Jes Park, a former graduate student in the group (reproduced with permission from Jessica Park). (b) Computational model of Saratide bound to ATP. (c) Inspiration from Nature: an OB fold bound to ssDNA.
Figure 6
Figure 6
(a) Binding pocket of the Drosophila HP1 chromodomain (blue) bound to trimethyllysine (orange), PDB code: 1KNE [39]. (b) Computational model of a synthetic receptor, A2N (blue), bound to KMe3 (orange) [40] (c) Binding pocket of the SMN tudor domain (green) bound to asymmetric dimethylarginine (aDMA, cyan). (d) Computational model of a synthetic receptor, A2D (green), bound to aDMA (cyan) [41].
Figure 7
Figure 7
Dynamic combinatorial chemistry [–42].
See this image and copyright information in PMC

References

    1. Waters M L, Wulff W D. The Synthesis of Phenols and Quinones via Fischer Carbene Complexes. In: Denmark S E, editor. Organic Reactions. Vol. 70. Hoboken, NJ, U.S.A.: John Wiley & Sons; 2008.
    1. Ma J C, Dougherty D A. Chem Rev. 1997;97:1303–1324. doi: 10.1021/cr9603744. - DOI - PubMed
    1. Smithrud D B, Wyman T B, Diederich D. J Am Chem Soc. 1991;113:5420–5426. doi: 10.1021/ja00014a038. - DOI
    1. Hunter C A, Sanders J K M. J Am Chem Soc. 1990;112:5525–5534. doi: 10.1021/ja00170a016. - DOI
    1. Schweitzer B A, Kool E T. J Am Chem Soc. 1995;117:1863–1872. doi: 10.1021/ja00112a001. - DOI - PMC - PubMed

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