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Journal of the American Chemical Society
Volumn 130, Issue 44, 2008, Pages 14675-14683
Probing the lower size limit for protein-like fold stability: Ten-residue microproteins with specific, rigid structures in water
Author keywords

[No Author keywords available]
Indexed keywords

FLOW INTERACTIONS; MELTING POINT; NUCLEAR MAGNETIC RESONANCE; OPTIMIZATION; PORT TERMINALS;
EID: 55549093135     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja804656h     Document Type: Article
Times cited : (38)
References (72)
  • 10
    • 55549105220 scopus 로고    scopus 로고
    • The term miniprotein has typically been applied to 20-45 residue polypeptides that form a stable fold; it has mostly been used for designed systems rather than naturally occurring ones. This term dates back to at least 1996 (Drug Design & Discovery, with a PNAS citation in 1998, and was in common usage prior to our application of it to the Trp-cage fold.4 Microprotein appears to have two uses in the literature; an older one for specific urinary excretion products and, starting in 2004 Current Opinions in Biotechnology, as a term for small natural cystine-knot proteins in the plant-cyclotide and conotoxin areas. Herein, following the usual view that micro is smaller then mini, we use microprotein to designated folds with protein-like stability that are much smaller than typical miniproteins
    • 4 "Microprotein" appears to have two uses in the literature; an older one for specific urinary excretion products and, starting in 2004 (Current Opinions in Biotechnology), as a term for small natural cystine-knot proteins in the plant-cyclotide and conotoxin areas. Herein, following the usual view that "micro" is smaller then "mini", we use "microprotein" to designated folds with protein-like stability that are much smaller than typical miniproteins.
  • 22
    • 55549093231 scopus 로고    scopus 로고
    • Aryl/aryl ring interactions are classified as parallel stacking or T geometry interactions which are designated as edge-to-face (EtF) interactions. EtF aromatic/aromatic interactions have been recognized as contributors to the CD spectra of proteins since at least 1994.12 Although less common as specific cross-strand interactions in β sheets, this interaction has been seen in hairpin models9,10 and has become a strategy for hairpin stabilization.10c In the case of Trp/Trp interactions, quantum mechanical calculations13 indicate a strong preference for the EtF geometry and that the interaction is a multipole interaction rather than a classic hydrophobic interaction. For aryl/aryl interactions in hairpins, we make a further distinction based on the location, at the N-terminus versus C-terminus of the turn, of the aromatic ring that presents its edge to the face of the cross-strand aromatic. The interaction is EfF wh
    • 13 indicate a strong preference for the EtF geometry and that the interaction is a multipole interaction rather than a classic hydrophobic interaction. For aryl/aryl interactions in hairpins, we make a further distinction based on the location, at the N-terminus versus C-terminus of the turn, of the aromatic ring that presents its edge to the face of the cross-strand aromatic. The interaction is "EfF" when the edge aromatic is located in the N-terminal strand and as "FtE" when the edge aromatic is in the C-terminal strand.
  • 36
    • 55549124342 scopus 로고    scopus 로고
    • Andersen, N. H.; Barua, B.; Fesinmeyer, R. M.; Hudson, F. M.; Lin, J.; Euser, A.; White, G. Chemical shifts, the ultimate test of polypeptide folding cooperativity. In Peptides 2002: Proceedings of the 27th European Peptide Symposium, Sorrento, Italy; Edizioni Ziino: Napoli, Italy, 2002; pp 824-825.
    • (a) Andersen, N. H.; Barua, B.; Fesinmeyer, R. M.; Hudson, F. M.; Lin, J.; Euser, A.; White, G. Chemical shifts, the ultimate test of polypeptide folding cooperativity. In Peptides 2002: Proceedings of the 27th European Peptide Symposium, Sorrento, Italy; Edizioni Ziino: Napoli, Italy, 2002; pp 824-825.
  • 52
    • 0035544152 scopus 로고    scopus 로고
    • Chemical shift calculations were made using the SHIFTS program of David Case, version 4.1: Xu, X. P, Case, D. A. J. Biomol. NMR 2001, 21, 321-333
    • (a) Chemical shift calculations were made using the SHIFTS program of David Case, version 4.1: Xu, X. P.; Case, D. A. J. Biomol. NMR 2001, 21, 321-333.
  • 53
    • 0029881007 scopus 로고    scopus 로고
    • In the case of ring current shifts, these calculations were supplemented by results obtained using the CalShift function, using both Johnson-Bovey and Heigh-Mallion models, within MolMol: Koradi, R, Billeter, M, Wüthrich, K. J. Mol. Graphics 1996, 14, 51-55
    • (b) In the case of ring current shifts, these calculations were supplemented by results obtained using the CalShift function, using both Johnson-Bovey and Heigh-Mallion models, within MolMol: Koradi, R.; Billeter, M.; Wüthrich, K. J. Mol. Graphics 1996, 14, 51-55.
  • 54
    • 0034010423 scopus 로고    scopus 로고
    • 15,22 The statistical observation of increased β-strand propensity after an N-terminal ammonium ion (Pal, D.; Chakrabarti, P. Biopolymers 2000, 53, 467-475. ) is also contrary to the observation of increased β-hairpin formation upon acetylation (Table 1, entry #7 versus #9).
    • 15,22 The statistical observation of increased β-strand propensity after an N-terminal ammonium ion (Pal, D.; Chakrabarti, P. Biopolymers 2000, 53, 467-475. ) is also contrary to the observation of increased β-hairpin formation upon acetylation (Table 1, entry #7 versus #9).
  • 56
    • 55549129412 scopus 로고    scopus 로고
    • Other N-terminal comparisons included TWINGKWTG and Ac-TWINGKWTG-NH 2 vs AC-WINGKWTG-NH2 (similar stability, but with less specificity in the W/W interactions, and a greatly reduced C-terminal Gly H N CSD) and (Ac-)PWIpGLWTGPS vs Ac-WINGKWTG-NH2, The Ac-P version appeared to be a somewhat less stable hairpin, though the WTG interaction at the opposite terminus remained, Curiously, the Ac-P amide bond was ∼50% cis. The fact that proline is even remotely tolerated at this position is remarkable, considering that it is, in principle, at an H-bonding position in a β sheet. The N-terminal Pro species without the acetyl cap was a more stable hairpin based on the magnitude of the CSDs for protons that are directed inward toward the aligned strand especially I2H N, However, as was also the case for the Glyl analog with a free N-terminal amine, it lacked the large upheld shift at the G8 HN
    • N.
  • 57
    • 55549103487 scopus 로고    scopus 로고
    • The φ/Ψ values observed for T7 in the ensemble shown in Figure 6 are-132 ± 5° and +23 ± 7°, which still place the Ψ value in a range that is less favorable for β-branched residues.
    • The φ/Ψ values observed for T7 in the ensemble shown in Figure 6 are-132 ± 5° and +23 ± 7°, which still place the Ψ value in a range that is less favorable for β-branched residues.
  • 58
    • 0028503363 scopus 로고    scopus 로고
    • Hydroxyl protons of Ser and Thr sidechains in peptides and proteins dissolved in water can only be seen by NMR with special experiments for water suppression29 see also Jahnke, W, Kessler, H. J. Biomol. NMR 1994, 4, 735-740, or when well buried in the hydrophobic core of a proteins.5,33 On the basis of the intrinsic exchange rates for OH groups, fold-populations in excess of ∼0.90 are required for the observation of an H-bonded Thr OH by NMR under typical aqueous solvent conditions using standard water suppression techniques. The intrinsic OH exchange rate, and thus the required fold population required for observation of the OH signal, increases with temperature. We have not observed this resonance in peptides less than ∼85-90% folded based on CSD-measure of folding
    • 5,33 On the basis of the intrinsic exchange rates for OH groups, fold-populations in excess of ∼0.90 are required for the observation of an H-bonded Thr OH by NMR under typical aqueous solvent conditions using standard water suppression techniques. The intrinsic OH exchange rate, and thus the required fold population required for observation of the OH signal, increases with temperature. We have not observed this resonance in peptides less than ∼85-90% folded based on CSD-measure of folding.
  • 59
    • 0028988431 scopus 로고
    • A search of the BMRB assignment data for proteins
    • (a) A search of the BMRB assignment data for proteins: Hammen, P. K.; Scholtz, J. M.; Anderson, J. W.; Waygood, E. B.; Klevit, R. E. Protein Sci. 1995, 4, 936-944; http://www.bmrb.wisc.edu/ref_info/ statsel.htm.
    • (1995) Protein Sci , vol.4 , pp. 936-944
    • Hammen, P.K.1    Scholtz, J.M.2    Anderson, J.W.3    Waygood, E.B.4    Klevit, R.E.5
  • 65
    • 55549114492 scopus 로고    scopus 로고
    • N) with a protection factor above 20 at 277 K.
    • N) with a protection factor above 20 at 277 K.
  • 68
    • 34848842845 scopus 로고    scopus 로고
    • For proteins, a recent survey of aryl/Trp interactions (Chakrabarti, P.; Bhattacharyya, R. Prog. Biophys. Mol. Biol. 2007, 95, 83-137.) confirmed the high propensity of Trp/Trp, Tyr/Tyr, and Tyr/Trp interaction to be EtF and indicates that Tyr is somewhat more likely to be the face residue in the latter interactions.
    • (b) For proteins, a recent survey of aryl/Trp interactions (Chakrabarti, P.; Bhattacharyya, R. Prog. Biophys. Mol. Biol. 2007, 95, 83-137.) confirmed the high propensity of Trp/Trp, Tyr/Tyr, and Tyr/Trp interaction to be EtF and indicates that Tyr is somewhat more likely to be the face residue in the latter interactions.

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