scholarly journals Prediction of disulfide dihedral angles using chemical shifts

2018 ◽  
Vol 9 (31) ◽  
pp. 6548-6556 ◽  
Author(s):  
David A. Armstrong ◽  
Quentin Kaas ◽  
K. Johan Rosengren
Keyword(s):  
Disulfide Bonds ◽  
Chemical Shifts ◽  
Solution Nmr ◽  
Dihedral Angles ◽  
Nmr Structures

Chemical shifts can be used to predict the conformation of disulfide bonds, greatly improving resolution of solution NMR structures.

scholarly journals Structure and antimicrobial activity of NCR169, a nodule-specific cysteine-rich peptide of Medicago truncatula

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Noriyoshi Isozumi ◽  
Yuya Masubuchi ◽  
Tomohiro Imamura ◽  
Masashi Mori ◽  
Hironori Koga ◽  
...  
Keyword(s):  
Antimicrobial Activity ◽  
Medicago Truncatula ◽  
Mechanism Of Action ◽  
Disulfide Bonds ◽  
Sinorhizobium Meliloti ◽  
Bound State ◽  
Disulfide Linkage ◽  
Model Legume ◽  
Nmr Structures ◽  
And Function

AbstractA model legume, Medicago truncatula, has over 600 nodule-specific cysteine-rich (NCR) peptides required for symbiosis with rhizobia. Among them, NCR169, an essential factor for establishing symbiosis, has four cysteine residues that are indispensable for its function. However, knowledge of NCR169 structure and mechanism of action is still lacking. In this study, we solved two NMR structures of NCR169 caused by different disulfide linkage patterns. We show that both structures have a consensus C-terminal β-sheet attached to an extended N-terminal region with dissimilar features; one moves widely, whereas the other is relatively stapled. We further revealed that the disulfide bonds of NCR169 contribute to its structural stability and solubility. Regarding the function, one of the NCR169 oxidized forms could bind to negatively charged bacterial phospholipids. Furthermore, the positively charged lysine-rich region of NCR169 may be responsible for its antimicrobial activity against Escherichia coli and Sinorhizobium meliloti. This active region was disordered even in the phospholipid bound state, suggesting that the disordered conformation of this region is key to its function. Morphological observations suggested the mechanism of action of NCR169 on bacteria. The present study on NCR169 provides new insights into the structure and function of NCR peptides.

scholarly journals Glutton: a tool for generating structural ensembles of partly disordered proteins from chemical shifts

2018 ◽  
Vol 35 (7) ◽  
pp. 1234-1236
Author(s):  
Yi He ◽  
Suhani Nagpal ◽  
Mourad Sadqi ◽  
Eva de Alba ◽  
Victor Muñoz
Keyword(s):  
Structure Prediction ◽  
Chemical Shifts ◽  
Disordered Proteins ◽  
Supplementary Information ◽  
Dihedral Angles ◽  
Physiological Conditions ◽  
Accessible Information ◽  
Structural Ensembles ◽  
Folded Proteins ◽  
Partially Disordered Proteins

Abstract Motivation Many proteins are partially disordered in physiological conditions and only fold, fully or partially, upon binding. Their structural analysis is challenging because the accessible information, typically chemical shifts (CS) from nuclear magnetic resonance experiments, are averages over broad ensembles of conformations. We aim to develop a database for the analysis of such data in terms of conformational distributions of the protein backbone rather than of individual high-resolution structures. Results Glutton is the largest available database linking CS and protein 3D structures (5270 entries organized in three levels) and is searchable via a python script. It generates statistical distributions of ϕ−ψ dihedral angles based on CS or vice versa. Such ϕ−ψ distributions are used to calculate structural ensembles of partially disordered proteins from their CS. For folded proteins, such ensembles are excellent starting points for further refinement with additional experimental restraints (structure determination) or computational methods (structure prediction). Availability and implementation Glutton is freely available at https://github.com/YeeHo/Glutton. Supplementary information Supplementary data are available at Bioinformatics online.

The Single Disulfide-Directed β-Hairpin Fold: Role of Disulfide Bond in Folding and Effect of an Additional Disulfide Bond on Stability

2020 ◽  
Vol 73 (4) ◽  
pp. 312
Author(s):  
Balasubramanyam Chittoor ◽  
Bankala Krishnarjuna ◽  
Rodrigo A. V. Morales ◽  
Raymond S. Norton
Keyword(s):  
Disulfide Bond ◽  
Disulfide Bonds ◽  
Solution Structure ◽  
Conformational Stability ◽  
Disulfide Bridge ◽  
Solution Nmr ◽  
Peptide Epitope ◽  
The Core ◽  
Native Fold

Disulfide bonds play a key role in the oxidative folding, conformational stability, and functional activity of many peptides. A few disulfide-rich peptides with privileged architecture such as the inhibitor cystine knot motif have garnered attention as templates in drug design. The single disulfide-directed β-hairpin (SDH), a novel fold identified more recently in contryphan-Vc1, has been shown to possess remarkable thermal, conformational, and chemical stability and can accept a short bioactive epitope without compromising the core structure of the peptide. In this study, we demonstrated that the single disulfide bond is critical in maintaining the native fold by replacing both cysteine residues with serine. We also designed an analogue with an additional, non-native disulfide bridge by replacing Gln1 and Tyr9 with Cys. Contryphan-Vc11–22[Q1C, Y9C] was synthesised utilising orthogonal cysteine protection and its solution structure determined using solution NMR spectroscopy. This analogue maintained the overall fold of native contryphan-Vc1. Previous studies had shown that the β-hairpin core of contryphan-Vc1 was resistant to proteolysis by trypsin and α-chymotrypsin but susceptible to cleavage by pepsin. Contryphan-Vc11–22[Q1C, Y9C] proved to be completely resistant to pepsin, thus confirming our design strategy. These results highlight the role of the disulfide bond in maintaining the SDH fold and provide a basis for the design of more stable analogues for peptide epitope grafting.

Solution NMR Structures of IgG Binding Domains with Artificially Evolved High Levels of Sequence Identity but Different Folds†,‡

Biochemistry ◽  
2005 ◽  
Vol 44 (43) ◽  
pp. 14055-14061 ◽  
Author(s):  
Yanan He ◽  
Deok Cheon Yeh ◽  
Patrick Alexander ◽  
Philip N. Bryan ◽  
John Orban
Keyword(s):  
Solution Nmr ◽  
Sequence Identity ◽  
Binding Domains ◽  
Nmr Structures ◽  
Igg Binding

scholarly journals Solution NMR Structures ofPyrenophora tritici-repentisToxB and Its Inactive Homolog Reveal Potential Determinants of Toxin Activity

2014 ◽  
Vol 289 (37) ◽  
pp. 25946-25956 ◽  
Author(s):  
Afua Nyarko ◽  
Kiran K. Singarapu ◽  
Melania Figueroa ◽  
Viola A. Manning ◽  
Iovanna Pandelova ◽  
...  
Keyword(s):  
Solution Nmr ◽  
Nmr Structures
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