Model systems for β-hairpins and β-sheets

Hughes, Robert M.; Waters, Marcey L.

doi:10.1016/j.sbi.2006.06.008

Cited by 186 publications

(120 citation statements)

References 74 publications

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“…With respect to understanding and control, the focus has been exclusively on secondary structure. 106,107 Understanding and controlling tertiary and quaternary structure is daunting, but synthetic modules that engender shape-programmable molecules may lead to artificial mimics of these structures, 108 and the potential diversity of such systems is large. 43 In terms of the recognition of open protein surfaces, supramolecular chemists have been inspired by protein-protein recognition sites and the recognition of convex protein surfaces.…”

Section: Recognition Mimicry and Interactions With Biomoleculesmentioning

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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Section: Recognition Mimicry and Interactions With Biomoleculesmentioning

confidence: 99%

Collaborative routes to clarifying the murky waters of aqueous supramolecular chemistry

et al. 2017

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“…Moreover, our model also retains the zipper-like contact energy from the original WSME model. Before examining more complicated protein systems, we first investigate a relatively simple system: β-hairpins, which have been extensively studied for their simple structural topology [64]. Fig.…”

Section: Introductionmentioning

confidence: 99%

Thermodynamics of protein folding using a modified Wako-Saitô-Muñoz-Eaton model

et al. 2012

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Herein, we propose a modified version of the Wako-Saitô-Muñoz-Eaton (WSME) model. The proposed model introduces an empirical temperature parameter for the hypothetical structural units (i.e., foldons) in proteins to include site-dependent thermodynamic behavior. The thermodynamics for both our proposed model and the original WSME model were investigated. For a system with beta-hairpin topology, a mathematical treatment (contact-pair treatment) to facilitate the calculation of its partition function was developed. The results show that the proposed model provides better insight into the site-dependent thermodynamic behavior of the system, compared with the original WSME model. From this site-dependent point of view, the relationship between probe-dependent experimental results and model's thermodynamic predictions can be explained. The model allows for suggesting a general principle to identify foldon behavior. We also find that the backbone hydrogen bonds may play a role of structural constraints in modulating the cooperative system. Thus, our study may contribute to the understanding of the fundamental principles for the thermodynamics of protein folding.Keywords WSME model · Protein · Beta-hairpin · Backbone hydrogen bond · Thermodynamics · Probe-dependent thermodynamic behavior · Site-dependent behavior · Foldon

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“…Hairpins have been proposed to act as nucleation sites for protein folding [1][2][3][4], and, in particular, β-sheet formation is biomedically relevant due to its role in many diseases, especially amyloid-related ones [5][6][7]. As compared to sheet structures, β-hairpins are more easily studied and modeled since only two strands interact in a restricted manner, rather than multiple strands as is the case for aggregate or fibril structures.…”

Section: Introductionmentioning

confidence: 99%

Impact of β‐Turn Sequence on β‐Hairpin Dynamics Studied with Infrared‐Detected Temperature Jump

Popp

Keiderling

et al. 2012

Journal of Spectroscopy

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Abstract. Folding dynamics for β-structure loss and disordered structure gain were studied in a model β-hairpin peptide based on Cochran's tryptophan zipper peptide Trpzip2, but with an altered Thr-Gly (TG) turn sequence, that is, SWTWETGKWTWK, using laser-induced temperature-jump (T-jump) kinetics with IR detection. As has been shown previously, the TG turn sequence reduces the thermodynamic β-hairpin stability as compared to the Asn-Gly sequence used in Trpzip2 (TZ2-NG). In this study, we found that the TG-turn slows down the overall relaxation dynamics as compared to TZ2-NG, which were studied at higher temperatures where the time constants show little difference between relaxation of the β-strand and the disordered conformation. These time constants become equivalent at lower temperatures for TZ2-TG than was seen for TZ2-NG. The correlation of thermodynamic stability and rates of relaxation suggests that the change from NG to TG turn results in a slowing of folding, lower k f , with less change of the unfolding rate, ku, assuming two state behavior at higher temperatures.

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Model systems for β-hairpins and β-sheets

Cited by 186 publications

References 74 publications

Collaborative routes to clarifying the murky waters of aqueous supramolecular chemistry

Collaborative routes to clarifying the murky waters of aqueous supramolecular chemistry

Thermodynamics of protein folding using a modified Wako-Saitô-Muñoz-Eaton model

Impact of β‐Turn Sequence on β‐Hairpin Dynamics Studied with Infrared‐Detected Temperature Jump

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