Sequence-Specific Association in Aqueous Media by Integrating Hydrogen Bonding and Dynamic Covalent Interactions

Li, Minfeng; Yamato, Kazuhiro; Ferguson, John C.; Gong, Bing

doi:10.1021/ja064515n

Cited by 54 publications

(42 citation statements)

References 26 publications

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“…Gong et al reported a very stable sextuple-hydrogen-bonding array, 7, with a K a ≈ 10 9 M −1 in CDCl 3 , in which intramolecular hydrogen bonding played a key role in providing a preorganized, planar arrangement of the donor and acceptor groups. 24,25 2.1.2. Hydrogen-Bonded Supramolecular Polymers.…”

Section: Multiple Hydrogen Bondsmentioning

confidence: 99%

Supramolecular Polymers: Historical Development, Preparation, Characterization, and Functions

et al. 2015

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Section: Multiple Hydrogen Bondsmentioning

confidence: 99%

Supramolecular Polymers: Historical Development, Preparation, Characterization, and Functions

et al. 2015

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“…Disulfide-linked HBS helices can be derived from oxidation of the parent bisthiol peptides allowing a facile approach to control the conformation of the peptide (31)(32)(33)(34). We based our initial peptide design on a short segment from the p53 activation domain: XQEG*FSDLWKLLS (1), where X and G* represent the dsHBS-constrained residues (35).…”

Section: Significancementioning

confidence: 99%

Effects of side chains in helix nucleation differ from helix propagation

Miller

Watkins

Kallenbach

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

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Helix-coil transition theory connects observable properties of the α-helix to an ensemble of microstates and provides a foundation for analyzing secondary structure formation in proteins. Classical models account for cooperative helix formation in terms of an energetically demanding nucleation event (described by the σ constant) followed by a more facile propagation reaction, with corresponding s constants that are sequence dependent. Extensive studies of folding and unfolding in model peptides have led to the determination of the propagation constants for amino acids. However, the role of individual side chains in helix nucleation has not been separately accessible, so the σ constant is treated as independent of sequence. We describe here a synthetic model that allows the assessment of the role of individual amino acids in helix nucleation. Studies with this model lead to the surprising conclusion that widely accepted scales of helical propensity are not predictive of helix nucleation. Residues known to be helix stabilizers or breakers in propagation have only a tenuous relationship to residues that favor or disfavor helix nucleation.synthetic helices | helix propensity T he α-helix is the most prevalent secondary structure in proteins and can form extremely rapidly. Helix formation is thus crucial in early steps of protein folding, and a complete description of the kinetics and thermodynamics of α-helix formation is fundamental for understanding protein folding (1). Theoretical models of the helix-coil transition consider helix formation to proceed in two steps: initial nucleation of a helical sequence, denoted by the parameter σ in the Zimm-Bragg notation (2), followed by more favorable helix propagation, denoted by s parameters. This distinction identifies the energetically unfavorable organization of three consecutive amino acid residues to form a helical nucleus as the slow step in helix formation (2-4). Helix propagation, in contrast, refers to the addition of the next hydrogen bond to a preformed helix (Fig. 1A). Zimm-Bragg or equivalent theories posit that formation of short peptide helices in water is unfavorable because the large decrease in entropy required for nucleation is not adequately compensated by the enthalpic gain from forming a small number of hydrogen bonds.The ability of different peptide sequences to adopt helical conformations has been rigorously investigated, and the stability of α-helices can be estimated from widely used scales of helical propensity (5). These scales are important for our understanding of protein structure, folding, and function. The classical studies for determination of helix propensities have used peptides, coiled-coils, and protein models for host-guest studies in which a guest residue is systematically substituted at a site in a host structure (6-12). Helix-coil transition theory then relates changes in the conformational stability to microscopic helix propensities or s constants for individual residues. The results provide a quantitative basis for evaluating t...

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“…Hydrogen‐bonding interactions are commonly used to drive self‐assembly in apolar solvents, because polar solvents, such as water and DMSO, compete strongly with hydrogen‐bonding sites 61. However, when combined with ion‐pairing interactions, the hydrogen bonding may show considerable strength in polar solvents.…”

Section: Synergistic Binding With Multiple Forcesmentioning

confidence: 99%

How to Make Weak Noncovalent Interactions Stronger

Chen

Zhang

2015

Chemistry A European J

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By employing noncovalent interactions, chemists have constructed a variety of molecular aggregates with well-defined structures and fascinating properties. In fabricating stable and large molecular assemblies, noncovalent interactions with high binding strength are needed. This Concept summarizes some strategies to modify and optimize the structures of building blocks for making weak noncovalent interactions stronger. The strategies include: 1) Preorganization of binding sites; 2) spatial confinement effects; 3) multivalent enhancement; 4) synergistic binding with multiple forces. Examples of the fabrication of supramolecular architectures by utilizing these strategies are presented and discussed. Guidance is offered in the construction and fabrication of stable molecular assemblies and supramolecular materials.

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Sequence-Specific Association in Aqueous Media by Integrating Hydrogen Bonding and Dynamic Covalent Interactions

Cited by 54 publications

References 26 publications

Supramolecular Polymers: Historical Development, Preparation, Characterization, and Functions

Supramolecular Polymers: Historical Development, Preparation, Characterization, and Functions

Effects of side chains in helix nucleation differ from helix propagation

How to Make Weak Noncovalent Interactions Stronger

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