The tryptophan zipper (Trpzip) is an iconic folding motif of β-hairpin peptides capitalizing on two pairs of cross-strand tryptophans, each stabilized by an aromatic-aromatic stacking in an edge-to-face (EF) geometry. Yet, the origins and the contribution of this EF packing to the unique Trpzip stability remain poorly understood. To address this question of structure-stability relationship, a library of Trpzip hairpins was developed by incorporating readily accessible nonproteinogenic tryptophans of varying electron densities. We found that each EF geometry was, in fact, stabilized by an intricate combination of XH/π interactions. By tuning the π-electron density of Trp rings, CH/π interactions are strengthened to gain additional stability. On the contrary, our DFT calculations support the notion that Trp modulations are challenging due to their simultaneous paradoxical engagement as H-bond donors in CH/π and acceptors in NH/π interactions.
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http://dx.doi.org/10.1021/acschembio.3c00553 | DOI Listing |
Front Immunol
June 2022
Facultad de Ciencias Agropecualrias, Universidad de Ciencias Aplicadas y Ambientales (UDCA), Bogotá, Colombia.
Fifty ~20-amino acid (aa)-long peptides were selected from functionally relevant SARS-CoV-2 S, M, and E proteins for trial and another 53 common ones, plus some new ones derived from the virus' main genetic variants for complementary trial . Peptide selection was based on tremendous SARS-CoV-2 genetic variability for analysing them concerning vast human immunogenetic polymorphism for developing the first supramutational, Colombian SARS-protection (SM-COLSARSPROT), peptide mixture. Specific physicochemical rules were followed, i.
View Article and Find Full Text PDFInt J Biol Macromol
May 2022
Chemical Engineering Discipline, School of Engineering, Monash University Malaysia, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor, Malaysia; Advanced Engineering Platform, Monash University Malaysia, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor, Malaysia.
Cholinium aminoates [Ch][AA] have gained tremendous interest as a promising ionic liquid medium for the synthesis and storage of proteins. However, high alkalinity of [Ch][AA] limits its usage with pH-sensitive proteins. Here, we probed the structure, stability, and interactions of a highly unstable therapeutic protein, insulin aspart (IA), in a range of buffered [Ch][AA] (b-[Ch][AA]) using a combination of biophysical tools and in silico pipeline including ultraviolet-visible, fluorescence, and circular dichroism spectroscopies, dynamic light scattering measurements and molecular docking.
View Article and Find Full Text PDFPhys Chem Chem Phys
May 2021
Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India.
Cholinium amino acid-based (Ch-AA) biocompatible ionic liquids (bio-ILs) are synthesized from renewable components and are efficiently used for biomass processing. However, their microscopic structural features that lead to their application as biomass solvents remain undetermined. Herein, we use atomistic simulations to investigate the structures of six different Ch-AA bio-ILs up to the nanometer length scale and demonstrate that, depending on the anion side chain structure, the respective IL exhibits structural ordering at different length scales.
View Article and Find Full Text PDFJ Agric Food Chem
March 2021
Shanxi Engineering Research Center of Biorefinery, Institute of Coal Chemistry, Chinese Academy of Sciences, 27 South Taoyuan Road, Taiyuan 030001, China.
Using environment-friendly catalysts to convert biomass into compounds with high values is one of the central topics of green chemistry. In this work, [Ch][Pro] (cholinium as the cation and l-proline as the anion) ionic liquid was synthesized and applied as a model catalyst in the production of deoxyfructosazine (DOF) and fructosazine (FZ) from d-glucosamine (GlcNH). The C NMR chemical shift titration experiments and the diffusion-ordered NMR spectroscopy (DOSY) measurements showed that, when the [Ch][Pro] interacted with GlcNH, the l-proline anion ([Pro]) played a major catalytic role instead of cholinium cation ([Ch]).
View Article and Find Full Text PDFJ Phys Chem B
August 2020
Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India.
Toward the search of sustainable green solvents, choline amino acid ([Ch][AA]) ionic liquids (ILs), mainly derived from renewable feedstocks, have emerged as a promising atoxic alternative to the conventional solvents. Recent studies have shown the remarkably benign nature of cholinium-based ILs against biomimetic phospholipid membranes. However, few of the contemporaneous experimental studies have contradicted the aforesaid ecofriendly nature of these ILs with anions comprising longer alkyl or aromatic tails.
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