1e0q › Citations

Structural characterization of a mutant peptide derived from ubiquitin: implications for protein folding.

Zerella R, Chen PY, Evans PA, Raine A, Williams DH
Protein Sci 9 2142-50 (2000)
Cited: 38 times
EuropePMC logo PMID: 11152124

Abstract

The formation of the N-terminal beta-hairpin of ubiquitin is thought to be an early event in the folding of this small protein. Previously, we have shown that a peptide corresponding to residues 1-17 of ubiquitin folds autonomously and is likely to have a native-like hairpin register. To investigate the causes of the stability of this fold, we have made mutations in the amino acids at the apex of the turn. We find that in a peptide where Thr9 is replaced by Asp, U(1-17)T9D, the native conformation is stabilized with respect to the wild-type sequence, so much so that we are able to characterize the structure of the mutant peptide fully by NMR spectroscopy. The data indicate that U(1-17)T9D peptide does indeed form a hairpin with a native-like register and a type I turn with a G1 beta-bulge, as in the full-length protein. The reason for the greater stability of the U(1-17)T9D mutant remains uncertain, but there are nuclear Overhauser effects between the side chains of Asp9 and Lys 11, which may indicate that a charge-charge interaction between these residues is responsible.

Reviews - 1e0q mentioned but not cited (1)

  1. The Mystery of Homochirality on Earth. Weller MG. Life (Basel) 14 341 (2024)

Articles - 1e0q mentioned but not cited (13)

  1. Tryptophan zippers: stable, monomeric beta -hairpins. Cochran AG, Skelton NJ, Starovasnik MA. Proc Natl Acad Sci U S A 98 5578-5583 (2001)
  2. PEP-FOLD: an online resource for de novo peptide structure prediction. Maupetit J, Derreumaux P, Tuffery P. Nucleic Acids Res 37 W498-503 (2009)
  3. Bhageerath: an energy based web enabled computer software suite for limiting the search space of tertiary structures of small globular proteins. Jayaram B, Bhushan K, Shenoy SR, Narang P, Bose S, Agrawal P, Sahu D, Pandey V. Nucleic Acids Res 34 6195-6204 (2006)
  4. Assessing AMBER force fields for protein folding in an implicit solvent. Shao Q, Zhu W. Phys Chem Chem Phys 20 7206-7216 (2018)
  5. Folding of small proteins using constrained molecular dynamics. Balaraman GS, Park IH, Jain A, Vaidehi N. J Phys Chem B 115 7588-7596 (2011)
  6. A free-energy approach for all-atom protein simulation. Verma A, Wenzel W. Biophys J 96 3483-3494 (2009)
  7. Generalized pattern search algorithm for Peptide structure prediction. Nicosia G, Stracquadanio G. Biophys J 95 4988-4999 (2008)
  8. Direct folding studies of various alpha and beta strands using replica exchange molecular dynamics simulation. Kim E, Jang S, Pak Y. J Chem Phys 128 175104 (2008)
  9. A hybrid, bottom-up, structurally accurate, Go¯-like coarse-grained protein model. Sanyal T, Mittal J, Shell MS. J Chem Phys 151 044111 (2019)
  10. Determining the Secondary Structure of Membrane Proteins and Peptides Via Electron Spin Echo Envelope Modulation (ESEEM) Spectroscopy. Liu L, Mayo DJ, Sahu ID, Zhou A, Zhang R, McCarrick RM, Lorigan GA. Methods Enzymol 564 289-313 (2015)
  11. Parallel implementation of 3D protein structure similarity searches using a GPU and the CUDA. Mrozek D, Brożek M, Małysiak-Mrozek B. J Mol Model 20 2067 (2014)
  12. Multiple Simulated Annealing-Molecular Dynamics (MSA-MD) for Conformational Space Search of Peptide and Miniprotein. Hao GF, Xu WF, Yang SG, Yang GF. Sci Rep 5 15568 (2015)
  13. Folding a protein with equal probability of being helix or hairpin. Lin CY, Chen NY, Mou CY. Biophys J 103 99-108 (2012)


Reviews citing this publication (1)

  1. Ubiquitin: a small protein folding paradigm. Jackson SE. Org Biomol Chem 4 1845-1853 (2006)

Articles citing this publication (23)

  1. Structure-function-folding relationship in a WW domain. Jäger M, Zhang Y, Bieschke J, Nguyen H, Dendle M, Bowman ME, Noel JP, Gruebele M, Kelly JW. Proc Natl Acad Sci U S A 103 10648-10653 (2006)
  2. Discerning the structure and energy of multiple transition states in protein folding using psi-analysis. Krantz BA, Dothager RS, Sosnick TR. J Mol Biol 337 463-475 (2004)
  3. Ubiquitin folds through a highly polarized transition state. Went HM, Jackson SE. Protein Eng Des Sel 18 229-237 (2005)
  4. Yeast display evolution of a kinetically efficient 13-amino acid substrate for lipoic acid ligase. Puthenveetil S, Liu DS, White KA, Thompson S, Ting AY. J Am Chem Soc 131 16430-16438 (2009)
  5. Turn stability in beta-hairpin peptides: Investigation of peptides containing 3:5 type I G1 bulge turns. Blandl T, Cochran AG, Skelton NJ. Protein Sci 12 237-247 (2003)
  6. Exploring peptide energy landscapes: a test of force fields and implicit solvent models. Steinbach PJ. Proteins 57 665-677 (2004)
  7. Effects of turn residues in directing the formation of the beta-sheet and in the stability of the beta-sheet. Chen PY, Lin CK, Lee CT, Jan H, Chan SI. Protein Sci 10 1794-1800 (2001)
  8. Measuring the refolding of beta-sheets with different turn sequences on a nanosecond time scale. Chen RP, Huang JJ, Chen HL, Jan H, Velusamy M, Lee CT, Fann W, Larsen RW, Chan SI. Proc Natl Acad Sci U S A 101 7305-7310 (2004)
  9. Engineering enhanced protein stability through beta-turn optimization: insights for the design of stable peptide beta-hairpin systems. Simpson ER, Meldrum JK, Bofill R, Crespo MD, Holmes E, Searle MS. Angew Chem Int Ed Engl 44 4939-4944 (2005)
  10. Direct folding simulation of alpha-helices and beta-hairpins based on a single all-atom force field with an implicit solvation model. Jang S, Kim E, Pak Y. Proteins 66 53-60 (2007)
  11. A logical OR redundancy within the Asx-Pro-Asx-Gly type I beta-turn motif. Lee J, Dubey VK, Longo LM, Blaber M. J Mol Biol 377 1251-1264 (2008)
  12. Convergent evolution in structural elements of proteins investigated using cross profile analysis. Tomii K, Sawada Y, Honda S. BMC Bioinformatics 13 11 (2012)
  13. Structure and properties of a dimeric N-terminal fragment of human ubiquitin. Bolton D, Evans PA, Stott K, Broadhurst RW. J Mol Biol 314 773-787 (2001)
  14. Determining α-helical and β-sheet secondary structures via pulsed electron spin resonance spectroscopy. Zhou A, Abu-Baker S, Sahu ID, Liu L, McCarrick RM, Dabney-Smith C, Lorigan GA. Biochemistry 51 7417-7419 (2012)
  15. Local structural preferences and dynamics restrictions in the urea-denatured state of SUMO-1: NMR characterization. Kumar A, Srivastava S, Mishra RK, Mittal R, Hosur RV. Biophys J 90 2498-2509 (2006)
  16. Insights into the determinants of beta-sheet stability: 1H and 13C NMR conformational investigation of three-stranded antiparallel beta-sheet-forming peptides. Santiveri CM, Rico M, Jiménez MA, Pastor MT, Pérez-Payá E. J Pept Res 61 177-188 (2003)
  17. Mechanism of formation of the C-terminal beta-hairpin of the B3 domain of the immunoglobulin binding protein G from Streptococcus. II. Interplay of local backbone conformational dynamics and long-range hydrophobic interactions in hairpin formation. Skwierawska A, Zmudzińska W, Ołdziej S, Liwo A, Scheraga HA. Proteins 76 637-654 (2009)
  18. Modeling of protein refolding from inclusion bodies. Zhang T, Xu X, Shen L, Feng Y, Yang Z, Shen Y, Wang J, Jin W, Wang X. Acta Biochim Biophys Sin (Shanghai) 41 1044-1052 (2009)
  19. The role of the unfolded state in hairpin stability. Lei H, Smith PE. Biophys J 85 3513-3520 (2003)
  20. Expected and unexpected results from combined beta-hairpin design elements. Dhanasekaran M, Prakash O, Gong YX, Baures PW. Org Biomol Chem 2 2071-2082 (2004)
  21. Pescador: the PEptides in Solution ConformAtion Database: Online Resource. Pajon A, Vranken WF, Jimenez MA, Rico M, Wodak SJ. J Biomol NMR 23 85-102 (2002)
  22. Hairpin conformation of an 11-mer peptide. Mei CG, Jahr N, Singer D, Berger S. Bioorg Med Chem 19 3497-3501 (2011)
  23. Peptide and Protein Structure Prediction with a Simplified Continuum Solvent Model. Steinbach PJ. J Phys Chem B 122 11355-11362 (2018)


Quick links