An unusual interstrand h-bond stabilizes the heteroassembly of helical αβγ-chimeras with natural peptides

ACS Chemical Biology

Volumn 9, Issue 3, 2014, Pages 613-616

  Nyakatura, Elisabeth K ^a   Rezaei Araghi, Raheleh ^a   Mortier, Jérémie ^a   Wieczorek, Sebastian ^a   Baldauf, Carsten ^b   Wolber, Gerhard ^a   Koksch, Beate ^a  

^a FREIE UNIVERSITÄT BERLIN   (Germany)

^b FRITZ HABER INSTITUT DER MAX PLANCK GESELLSCHAFT   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

4 AMINOBUTYRIC ACID; ALPHA AMINO ACID; AMINO ACID DERIVATIVE; BETA AMINO ACID; CARBONYL DERIVATIVE; CYSTEINE; GAMMA AMINO ACID; PROTEIN VARIANT; UNCLASSIFIED DRUG; AMINO ACID; PEPTIDE; PEPTIDE LIBRARY;

ALPHA HELIX; AMINO ACID SEQUENCE; ARTICLE; BACTERIOPHAGE M13; CHIMERA; HYDROGEN BOND; MUTATIONAL ANALYSIS; PEPTIDE LIBRARY; PEPTIDE SYNTHESIS; PHAGE DISPLAY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN ASSEMBLY; PROTEIN PROTEIN INTERACTION; THERMOSTABILITY; CHEMISTRY; CIRCULAR DICHROISM; MOLECULAR DYNAMICS; MOLECULAR GENETICS; PROTEIN CONFORMATION; THERMODYNAMICS;

AMINO ACID SEQUENCE; AMINO ACIDS; CIRCULAR DICHROISM; HYDROGEN BONDING; MOLECULAR DYNAMICS SIMULATION; MOLECULAR SEQUENCE DATA; PEPTIDE LIBRARY; PEPTIDES; PROTEIN CONFORMATION; THERMODYNAMICS;

EID: 84897013072     PISSN: 15548929     EISSN: 15548937     Source Type: Journal    
DOI: 10.1021/cb4007979     Document Type: Article

References (32)

1. Seebach, D., Overhand, M., Kühnle, F. N., Martinoni, B., Oberer, L., Hommel, U., and Widmer, H. (1996) β-Peptides: Synthesis by Arndt-Eistert homologation with concomitant peptide coupling. Structure determination by NMR and CD spectroscopy and by X-ray crystallography. Helical secondary structure of a β-hexapeptide in solution and its stability towards pepsin Helv. Chim. Acta 79, 913-941
2. Gellman, S. H. (1998) Foldamers: A Manifesto Acc. Chem. Res. 31, 173-180
3. Cheng, R. P., Gellman, S. H., and DeGrado, W. F. (2001) Beta-peptides: from structure to function Chem. Rev. 101, 3219-3232
4. Hill, D. J., Mio, M. J., Prince, R. B., Hughes, T. S., and Moore, J. S. (2001) A field guide to foldamers Chem. Rev. 101, 3893-4012
5. Vasudev, P. G., Chatterjee, S., Shamala, N., and Balaram, P. (2011) Structural chemistry of peptides containing backbone expanded amino acid residues: Conformational features of beta, gamma, and hybrid peptides Chem. Rev. 111, 657-687
6. Stigers, K. D., Soth, M. J., and Nowick, J. S. (1999) Designed molecules that fold to mimic protein secondary structures Curr. Opin. Chem. Biol. 3, 714-723
7. Goodman, C. M., Choi, S., Shandler, S., and DeGrado, W. F. (2007) Foldamers as versatile frameworks for the design and evolution of function Nat. Chem. Biol. 3, 252-262
8. Horne, W. S. and Gellman, S. H. (2008) Foldamers with heterogeneous backbones Acc. Chem. Res. 41, 1399-1408
9. Jochim, A. L., Miller, S. E., Angelo, N. G., and Arora, P. S. (2009) Evaluation of triazolamers as active site inhibitors of HIV-1 protease Bioorg. Med. Chem. Lett. 19, 6023-6026
10. Seebach, D., Beck, A. K., and Bierbaum, D. J. (2004) The world of β- and γ-peptides comprised of homologated proteinogenic amino acids and other components Chem. Biodiversity 1, 1111-1239
11. Baldauf, C., Günther, R., and Hofmann, H.-J. (2006) Helix formation in α,γ- and β,γ-hybrid peptides: Theoretical insights into mimicry of α- and β-peptides J. Org. Chem. 71, 1200-1208
12. Karle, I., Pramanik, A., Banerjee, A., Bhattacharjya, S., and Balaram, P. (1997) '-Amino acids in peptide design. Crystal structures and solution conformations of peptide helices containing a β-alanyl-γ-aminobutyryl segment J. Am. Chem. Soc. 119, 9087-9095
13. Sawada, T. and Gellman, S. H. (2011) Structural mimicry of the α-helix in aqueous solution with an isoatomic α/β/γ- peptide backbone J. Am. Chem. Soc. 133, 7336-7339
14. Vasudev, P. G., Ananda, K., Chatterjee, S., Aravinda, S., Shamala, N., and Balaram, P. (2007) Hybrid peptide design. Hydrogen bonded conformations in peptides containing the stereochemically constrained γ-amino acid residue, gabapentin J. Am. Chem. Soc. 129, 4039-4048
15. Rezaei Araghi, R., Jäckel, C., Cölfen, H., Salwiczek, M., Völkel, A., Wagner, S. C., Wieczorek, S., Baldauf, C., and Koksch, B. (2010) A β/γ motif to mimic α-helical turns in proteins ChemBioChem 11, 335-339
16. Rezaei Araghi, R. and Koksch, B. (2011) A helix-forming αβγ-chimeric peptide with catalytic activity: a hybrid peptide ligase Chem. Commun. 47, 3544-3546
17. Rezaei Araghi, R., Baldauf, C., Gerling, U. I., Cadicamo, C. D., and Koksch, B. (2011) A systematic study of fundamentals in α-helical coiled coil mimicry by alternating sequences of β-and γ-amino acids Amino Acids 41, 733-742
18. Barbas, C. F., III (1993) Recent advances in phage display Curr. Opin. Biotechnol. 4, 526-530
19. Hagemann, U. B., Mason, J. M., Müller, K. M., and Arndt, K. M. (2008) Selectional and mutational scope of peptides sequestering the Jun/Fos coiled-coil domain J. Mol. Biol. 381, 73-88
20. Lai, J. R., Fisk, J. D., Weisblum, B., and Gellman, S. H. (2004) Hydrophobic core repacking in a coiled-coil dimer via phage display: Insights into plasticity and specificity at a protein-protein interface J. Am. Chem. Soc. 126, 10514-10515
21. Nyakatura, E. K., Reimann, O., Vagt, T., Salwiczek, M., and Koksch, B. (2013) Accommodating fluorinated amino acids in helical peptide environments RSC Adv. 3, 6319-6322
22. Vagt, T., Jäckel, C., Samsonov, S., Teresa Pisabarro, M., and Koksch, B. (2009) Selection of a buried salt bridge by phage display Bioorg. Med. Chem. Lett. 19, 3924-3927
23. Vagt, T., Nyakatura, E., Salwiczek, M., Jäckel, C., and Koksch, B. (2010) Towards identifying preferred interaction partners of fluorinated amino acids within the hydrophobic environment of a dimeric coiled coil peptide Org. Biomol. Chem. 8, 1382-1386
24. Duus, J. Ø., Meldal, M., and Winkler, J. R. (1998) Fluorescence energy-transfer probes of conformation in peptides: the 2-aminobenzamide/ nitrotyrosine pair J. Phys. Chem. B 102, 6413-6418
25. Salwiczek, M., Samsonov, S., Vagt, T., Nyakatura, E., Fleige, E., Numata, J., Cölfen, H., Pisabarro, M. T., and Koksch, B. (2009) Position-dependent effects of fluorinated amino acids on the hydrophobic core formation of a heterodimeric coiled coil Chem.' - 'Eur. J. 15, 7628-7636
26. Hess, B., Kutzner, C., Van Der Spoel, D., and Lindahl, E. (2008) GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation J. Chem. Theory Comput. 4, 435-447
27. Oostenbrink, C., Villa, A., Mark, A. E., and Van Gunsteren, W. F. (2004) A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6 J. Comput. Chem. 25, 1656-1676
28. Van Der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E., and Berendsen, H. J. (2005) GROMACS: fast, flexible, and free J. Comput. Chem. 26, 1701-1718
29. Gray, T. and Matthews, B. (1984) Intrahelical hydrogen bonding of serine, threonine and cysteine residues within α-helices and its relevance to membrane-bound proteins J. Mol. Biol. 175, 75-81
30. Gregoret, L. M., Rader, S. D., Fletterick, R. J., and Cohen, F. E. (1991) Hydrogen bonds involving sulfur atoms in proteins Proteins: Struct., Funct., Bioinf. 9, 99-107
31. Kyte, J. and Doolittle, R. F. (1982) A simple method for displaying the hydropathic character of a protein J. Mol. Biol. 157, 105-132
32. Burton, A. J., Thomas, F., Agnew, C., Hudson, K. L., Halford, S. E., Brady, R. L., and Woolfson, D. N. (2013) Accessibility, reactivity, and selectivity of side chains within a channel of de novo peptide assembly J. Am. Chem. Soc. 135, 12524-12527