A novel main-chain anion-binding site in proteins: the nest. A particular combination of φ,ψ values in successive residues gives rise to anion-binding sites that occur commonly and are found often at functionally important regions 1 1Edited by J. Thornton

Watson, James D.; Milner‐White, E. James

doi:10.1006/jmbi.2001.5227

Cited by 161 publications

(167 citation statements)

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“…In asx and ST-turns the most common is type II', whereas the next most common is type I. The structures of type II asx-and ST-turns are the same as those previously identified as asx-nest or ST-nest motifs (Watson and Milner-White 2002a). The tight clustering of e and e angles in type II asx-and ST-turns, seen in Figure 1, D and F, may result from the constrained nest The total numbers of aspartate, asparagine, serine, and threonine residues in the dataset of 500 proteins are given, along with the numbers and percentages of each of that form of asx-and ST-turns (i.e., occupy position i of an asx-or ST-turn).…”

Section: Resultssupporting

confidence: 75%

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Mimicry by asx‐ and ST‐turns of the four main types of β‐turn in proteins

et al. 2004

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Hydrogen-bonded ␤-turns in proteins occur in four categories: type I (the most common), type II, type II', and type I'. Asx-turns resemble ␤-turns, in that both have an NH . . . OC hydrogen bond forming a ring of 10 atoms. Serine and threonine side chains also commonly form hydrogen-bonded turns, here called ST-turns. Asx-turns and ST-turns can be categorized into four classes, based on side chain rotamers and the conformation of the central turn residue, which are geometrically equivalent to the four types of ␤-turns. We propose asx-and ST-turns be named using the type I, II, I', and II' ␤-turn nomenclature. Using this, the frequency of occurrence of both asx-and ST-turns is: type II' > type I > type II > type I', whereas for ␤-turns it is type I > type II > type I' > type II'. Almost all type II asx-turns occur as a recently described three residue feature named an asx-nest.

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Section: Resultssupporting

confidence: 75%

“…This is a recently identified, yet by no means uncommon, protein motif (Watson and Milner-White 2002a). The observation that almost all type II asx-and ST-turns occur as asx-or ST-nest motifs is an unexpected finding of the present work.…”

Section: Discussionsupporting

confidence: 63%

Mimicry by asx‐ and ST‐turns of the four main types of β‐turn in proteins

et al. 2004

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“…Another important finding for anion‐binding proteins was the identification by Watson and Milner‐White of a particular fold, named the “nest”, which can occur with a minimum of just two residues (Figure 11 a) 54. The nest is described by residues with alternating main‐chain dihedral angles of φ , ψ ≈−90,0° and φ , ψ ≈70,40° (or their negative).…”

Section: Macromolecular Recognition Of Anions In Watermentioning

confidence: 99%

Anion Recognition in Water: Recent Advances from a Supramolecular and Macromolecular Perspective

2015

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The recognition of anions in water remains a key challenge in modern supramolecular chemistry, and is essential if proposed applications in biological, medical, and environmental arenas that typically require aqueous conditions are to be achieved. However, synthetic anion receptors that operate in water have, in general, been the exception rather than the norm to date. Nevertheless, a significant step change towards routinely conducting anion recognition in water has been achieved in the past few years, and this Review highlights these approaches, with particular focus on controlling and using the hydrophobic effect, as well as more exotic interactions such as C−H hydrogen bonding and halogen bonding. We also look beyond the field of small‐molecule recognition into the macromolecular domain, covering recent advances in anion recognition based on biomolecules, polymers, and nanoparticles.

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“…35 Such studies may address the open question of the role of non-polar binding sites in protein stabilization and solubilization relative to HB donor Nest and C α NN binding sites. 87,88 There are many open questions here, and new hosts are required for this still developing field. 89 …”

Section: Ion Binding and The Hofmeister Effectmentioning

confidence: 99%

Collaborative routes to clarifying the murky waters of aqueous supramolecular chemistry

et al. 2017

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Collaborative routes to clarifying the murky waters of aqueous supramolecular chemistry. AbstractOn planet Earth, water is everywhere: the majority of the surface is covered with it; it is a key component of all life; its vapor and droplets fill the lower atmosphere; even rocks contain it and undergo geomorphological changes because of it. A community of physical scientists largely drives studies of the chemistry of water and aqueous solutions, with expertise in biochemistry, spectroscopy, and computer modeling. More recently however, supramolecular chemistry -with its expertise in macrocyclic synthesis and measuring supramolecular interactions -have renewed their interest in water-mediated non-covalent interactions. These two groups offer complementary expertise that, if harnessed, offers to accelerate our understanding of aqueous supramolecular chemistry and water writ large. This review summarizes the state-of-the-art of the two fields, and highlights where there is latent chemical space for collaborative exploration by the two groups. 4Water is ubiquitous and essential to life on planet Earth. A full understanding of aqueous solutions is therefore of significance to a wide range of fields within the atmospheric, environmental, biological and geological sciences. Within the chemical sciences, a deeper appreciation of how non-covalent interactions and chemical transformations are influenced by water would benefit a variety of fields. However, as we highlight here, there are many open questions regarding the chemical and physical properties of aqueous solutions.The aqueous realm is frequently bifurcated into the Hofmeister and hydrophobic effects, phenomena that respectively deal with the properties of solutions of salts and relatively nonpolar molecules. However, it is becoming increasingly evident that these areas do in fact frequently overlap; two prime examples being the accumulation of large polarizable anions at the air-water interface, 1-5 and the favorable interactions of polarizable anions with non-polar surfaces. [6][7][8][9][10][11][12][13][14][15] Thus the hydrophobic and Hofmeister effects are but part of a greater continuum of aqueous supramolecular chemistry, with many important and outstanding questions regarding the influence of the different kinds of non-covalent interactions involved.Studies of water and aqueous solutions have mostly been driven by the physical sciences community, a broad range of scientists whose expertise in spectroscopy, computer modeling, and biochemistry (to name just three areas) has generally not involved macrocycles or host molecules in general. However, for some time now, supramolecular chemists -with their expertise in macrocyclic synthesis and measuring weak non-covalent interactions -have been travelling a parallel course of exploration. This Review, inspired by discussions between sixteen members of each community at a recent workshop, 16 is an attempt to summarize what we know about aqueous solutions, what we do not know about them, and where the two communit...

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A novel main-chain anion-binding site in proteins: the nest. A particular combination of φ,ψ values in successive residues gives rise to anion-binding sites that occur commonly and are found often at functionally important regions 1 1Edited by J. Thornton

Cited by 161 publications

References 53 publications

Mimicry by asx‐ and ST‐turns of the four main types of β‐turn in proteins

Mimicry by asx‐ and ST‐turns of the four main types of β‐turn in proteins

Anion Recognition in Water: Recent Advances from a Supramolecular and Macromolecular Perspective

Collaborative routes to clarifying the murky waters of aqueous supramolecular chemistry

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