[NMR paper] NMR Analysis of Tuning Cross-Strand Phe/Tyr/Trp - Trp Interactions in Designed ?-Hairpin Peptides: Terminal Switch from L- to D-Amino Acid as a Strategy for ?-Hairpin Capping.
NMR Analysis of Tuning Cross-Strand Phe/Tyr/Trp - Trp Interactions in Designed ?-Hairpin Peptides: Terminal Switch from L- to D-Amino Acid as a Strategy for ?-Hairpin Capping.
Related ArticlesNMR Analysis of Tuning Cross-Strand Phe/Tyr/Trp - Trp Interactions in Designed ?-Hairpin Peptides: Terminal Switch from L- to D-Amino Acid as a Strategy for ?-Hairpin Capping.
J Phys Chem B. 2015 Apr 7;
Authors: Makwana KM, Mahalakshmi R
Abstract
Interaction among the side chains of aromatic amino acids is a well-known mechanism of protein and peptide structure stabilization, particularly in ?-sheets. Using short ?-hairpin models bearing the sequence Ac-Leu-Xxx-Val-(D)Pro-Gly-Leu-Trp-Val-NH2, we report the surprising observation of significant destabilization in aryl-tryptophan interactions, which results in poorly folded peptide populations, accompanied by lowering of stability. We find that such destabilization arises from forced occupancy of the indole ring in the shielded 'Edge' position, in T-shaped aryl geometries. We demonstrate that this destabilizing effect can be efficiently salvaged by replacing the N-terminal (L)Leu to (D)Leu, which causes an increase in the folded hairpin population, whilst retaining Trp in the 'Edge' position. Our observation of unique cross strand NOEs, and data from temperature-dependent NMR and CD measurements, reveals the formation of a locally stabilized aliphatic-aromatic network, leading to an overall increase in ?G(0)F by ~ -0.6 to -1.2 kcal/mol. Our results suggest that a contextual evaluation of stabilization by tryptophan is necessary in ?-hairpins. Furthermore, we report for the first time, that the use of D-isomers of aliphatic amino acids at the terminus is stabilizing, which can serve as a new strategy for increasing ?-hairpin stability.
PMID: 25849307 [PubMed - as supplied by publisher]
[NMR paper] Nature of aryl-tyrosine interactions contribute to ?-hairpin scaffold stability: NMR evidence for alternate ring geometry.
Nature of aryl-tyrosine interactions contribute to ?-hairpin scaffold stability: NMR evidence for alternate ring geometry.
Nature of aryl-tyrosine interactions contribute to ?-hairpin scaffold stability: NMR evidence for alternate ring geometry.
Phys Chem Chem Phys. 2015 Jan 8;
Authors: Makwana KM, Mahalakshmi R
Abstract
The specific contribution of the acidic-aromatic ?-sheet favouring amino acid tyrosine to the stability of short octapeptide ?-hairpin structures is presented here. Solution NMR analysis in near-apolar...
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Paramagnetic relaxation enhancement of membrane proteins by incorporation of the metal-chelating unnatural amino acid 2-amino-3-(8-hydroxyquinolin-3-yl)propanoic acid (HQA)
Paramagnetic relaxation enhancement of membrane proteins by incorporation of the metal-chelating unnatural amino acid 2-amino-3-(8-hydroxyquinolin-3-yl)propanoic acid (HQA)
Abstract
The use of paramagnetic constraints in protein NMR is an active area of research because of the benefits of long-range distance measurements (>10Â*Ã?). One of the main issues in successful execution is the incorporation of a paramagnetic metal ion into diamagnetic proteins. The most common metal ion tags are relatively long aliphatic chains attached to the side chain of a...
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11-28-2014 11:37 AM
[NMR paper] Amino acid conservation and interactions in rhodopsin: Probing receptor activation by NMR spectroscopy.
Amino acid conservation and interactions in rhodopsin: Probing receptor activation by NMR spectroscopy.
Related Articles Amino acid conservation and interactions in rhodopsin: Probing receptor activation by NMR spectroscopy.
Biochim Biophys Acta. 2013 Oct 29;
Authors: Pope A, Eilers M, Reeves PJ, Smith SO
Abstract
Rhodopsin is a classical two-state G protein-coupled receptor (GPCR). In the dark, its 11-cis retinal chromophore serves as an inverse agonist to lock the receptor in an inactive state. Retinal-protein and protein-protein...
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11-05-2013 06:53 PM
[NMR paper] NMR analysis of cross strand aromatic interactions in an 8 residue hairpin and a 14 residue three stranded ?-sheet peptide.
NMR analysis of cross strand aromatic interactions in an 8 residue hairpin and a 14 residue three stranded ?-sheet peptide.
http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-pubmed-acspubs.jpg Related Articles NMR analysis of cross strand aromatic interactions in an 8 residue hairpin and a 14 residue three stranded ?-sheet peptide.
J Phys Chem B. 2012 Dec 13;116(49):14207-15
Authors: Sonti R, Rai R, Ragothama S, Balaram P
Abstract
Cross strand aromatic interactions between a facing pair of...
[NMR paper] An NMR study on the beta-hairpin region of barnase.
An NMR study on the beta-hairpin region of barnase.
Related Articles An NMR study on the beta-hairpin region of barnase.
Fold Des. 1996;1(3):231-41
Authors: Neira JL, Fersht AR
BACKGROUND: The beta-hairpin of barnase (residues Ser92-Leu95) has been proposed in theoretical and protein engineering studies to be an initiation site for folding . There is evidence for residual structure in this region from NMR studies of the denatured protein under different denaturing conditions . A more detailed analysis is possible by NMR studies of isolated...
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08-22-2010 02:27 PM
[NMR paper] Proton NMR and structural features of a 24-nucleotide RNA hairpin.
Proton NMR and structural features of a 24-nucleotide RNA hairpin.
Related Articles Proton NMR and structural features of a 24-nucleotide RNA hairpin.
Biochemistry. 1995 May 16;34(19):6488-503
Authors: Borer PN, Lin Y, Wang S, Roggenbuck MW, Gott JM, Uhlenbeck OC, Pelczer I
The three-dimensional conformation of a 24-nucleotide variant of the RNA binding sequence for the coat protein of bacteriophage R17 has been analyzed using NMR, molecular dynamics, and energy minimization. The imino proton spectrum is consistent with base pairing...
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[NMR paper] An NMR study of the HIV-1 TAR element hairpin.
An NMR study of the HIV-1 TAR element hairpin.
Related Articles An NMR study of the HIV-1 TAR element hairpin.
Biochemistry. 1993 Nov 23;32(46):12522-30
Authors: Jaeger JA, Tinoco I
The TAR hairpin is an important part of the 5' long terminal repeat of HIV-1 and appears to be recognized by a cellular protein. A 14-base model of the native TAR hairpin 5'-GAGC-GCUC-3' (loop bases in square brackets) has been studied by proton, phosphorus, and natural abundance carbon NMR; these results are compared to other published NMR studies of the TAR...
NMR Analysis of Tuning Cross-Strand Phe/Tyr/Trp - Trp Interactions in Designed ?-Hairpin Peptides: Terminal Switch from L- to D-Amino Acid as a Strategy for ?-Hairpin Capping.
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