Literature DB >> 19263490

Terminal sidechain packing of a designed beta-hairpin influences conformation and stability.

Lisa Eidenschink1, Edward Crabbe, Niels H Andersen.   

Abstract

While end capping in alpha-helices is well understood, the concept of capping a beta-hairpin is a relatively recent development; to date, favorable Coulombic interactions are the only example of sidechains at the termini influencing the overall stability of a beta-hairpin. While cross-strand hydrophobic residues generally provide hairpin stabilization, particular when flanking the turn region, those remote from this location appear to provide little stabilization. While probing for an optimal residue at a hydrogen bond position near the terminus of a designed beta-hairpin a conservative, hydrophobic, V --> I mutation was observed to not only result in a significant change in fold population but also effected major changes in the structuring shifts at numerous sites in the peptide. Mutational studies reveal that there is an interaction between the sidechain at this H-bonded site and the sidechain at the C-terminal non-H-bonded site of the hairpin. This interaction, which appears to be hydrophobic in character, requires a highly twisted hairpin structure. Modifications at the C-terminal site, for example an E --> A mutation (DeltaDeltaG(U) = 6 kJ/mol), have profound affects on fold structure and stability. The data suggests that this may be a case of hairpin end capping by the formation of a hydrophobic cluster. (c) 2009 Wiley Periodicals, Inc.

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Year:  2009        PMID: 19263490      PMCID: PMC3159043          DOI: 10.1002/bip.21177

Source DB:  PubMed          Journal:  Biopolymers        ISSN: 0006-3525            Impact factor:   2.505


  37 in total

1.  Dissecting the stability of a beta-hairpin peptide that folds in water: NMR and molecular dynamics analysis of the beta-turn and beta-strand contributions to folding.

Authors:  S R Griffiths-Jones; A J Maynard; M S Searle
Journal:  J Mol Biol       Date:  1999-10-08       Impact factor: 5.469

2.  C-terminal capping motifs in model helical peptides.

Authors:  N R Kallenbach; Y Gong
Journal:  Bioorg Med Chem       Date:  1999-01       Impact factor: 3.641

3.  A Designed beta-Hairpin Containing a Natural Hydrophobic Cluster This research was supported by the National Science Foundation (CHE-9820952). J.F.E. was supported by a fellowship from the Ministerio de Educacion y Cultura (Spain) and the Fulbright Commission. The mass spectrometer was purchased in part with a National Science Foundation grant (CHE-9520868), and the NMR spectrometers were purchased in part with a National Institute Of Health grant (1 S10 RR04981). The CD spectrometer and analytical ultracentrifuge are part of the UW Biophysics Instrumentation Facility (NSF BIR-9512577).

Authors: 
Journal:  Angew Chem Int Ed Engl       Date:  2000-07-03       Impact factor: 15.336

4.  Enhanced hairpin stability through loop design: the case of the protein G B1 domain hairpin.

Authors:  R Matthew Fesinmeyer; F Michael Hudson; Niels H Andersen
Journal:  J Am Chem Soc       Date:  2004-06-16       Impact factor: 15.419

5.  Chemical shifts provide fold populations and register of beta hairpins and beta sheets.

Authors:  R Matthew Fesinmeyer; F Michael Hudson; Katherine A Olsen; George W N White; Anna Euser; Niels H Andersen
Journal:  J Biomol NMR       Date:  2005-12       Impact factor: 2.835

6.  Beta-sheet capping: signals that initiate and terminate beta-sheet formation.

Authors:  Fahim Farzadfard; Nava Gharaei; Hamid Pezeshk; Sayed-Amir Marashi
Journal:  J Struct Biol       Date:  2007-10-11       Impact factor: 2.867

7.  Empirical parameterization of a model for predicting peptide helix/coil equilibrium populations.

Authors:  N H Andersen; H Tong
Journal:  Protein Sci       Date:  1997-09       Impact factor: 6.725

8.  A short linear peptide derived from the N-terminal sequence of ubiquitin folds into a water-stable non-native beta-hairpin.

Authors:  M S Searle; D H Williams; L C Packman
Journal:  Nat Struct Biol       Date:  1995-11

9.  Helix capping propensities in peptides parallel those in proteins.

Authors:  A Chakrabartty; A J Doig; R L Baldwin
Journal:  Proc Natl Acad Sci U S A       Date:  1993-12-01       Impact factor: 11.205

10.  Interstrand side chain--side chain interactions in a designed beta-hairpin: significance of both lateral and diagonal pairings.

Authors:  F A Syud; H E Stanger; S H Gellman
Journal:  J Am Chem Soc       Date:  2001-09-12       Impact factor: 15.419

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  5 in total

1.  Parallel β-sheet secondary structure is stabilized and terminated by interstrand disulfide cross-linking.

Authors:  Aaron M Almeida; Rebecca Li; Samuel H Gellman
Journal:  J Am Chem Soc       Date:  2011-12-13       Impact factor: 15.419

2.  Stabilizing capping motif for beta-hairpins and sheets.

Authors:  Brandon L Kier; Irene Shu; Lisa A Eidenschink; Niels H Andersen
Journal:  Proc Natl Acad Sci U S A       Date:  2010-05-19       Impact factor: 11.205

3.  13C structuring shifts for the analysis of model β-hairpins and β-sheets in proteins: diagnostic shifts appear only at the cross-strand H-bonded residues.

Authors:  Irene Shu; Michele Scian; James M Stewart; Brandon L Kier; Niels H Andersen
Journal:  J Biomol NMR       Date:  2013-07-14       Impact factor: 2.835

4.  Crystal and NMR structures of a Trp-cage mini-protein benchmark for computational fold prediction.

Authors:  Michele Scian; Jasper C Lin; Isolde Le Trong; George I Makhatadze; Ronald E Stenkamp; Niels H Andersen
Journal:  Proc Natl Acad Sci U S A       Date:  2012-07-16       Impact factor: 11.205

5.  Aryl-aryl interactions in designed peptide folds: Spectroscopic characteristics and optimal placement for structure stabilization.

Authors:  Jordan M Anderson; Brandon L Kier; Brice Jurban; Aimee Byrne; Irene Shu; Lisa A Eidenschink; Alexander A Shcherbakov; Mike Hudson; R M Fesinmeyer; Niels H Andersen
Journal:  Biopolymers       Date:  2016-06       Impact factor: 2.505

  5 in total

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