Secondary structure inducing potential of beta-amino acids: Torsion angle clustering facilitates comparison and analysis of the conformation during MD trajectories
Guthöhrlein EW, Malesevic M, Majer Z, Sewald N (2007)
Biopolymers 88(6): 829-839.
Zeitschriftenaufsatz
| Veröffentlicht | Englisch
Download
Es wurden keine Dateien hochgeladen. Nur Publikationsnachweis!
Autor*in
Guthöhrlein, E. W.;
Malesevic, M.;
Majer, Z.;
Sewald, NorbertUniBi ![](https://pub.uni-bielefeld.de/images/icon_orcid.png)
![](https://pub.uni-bielefeld.de/images/icon_orcid.png)
Einrichtung
Abstract / Bemerkung
While numerous examples of P-peptides-exclusively composed of (beta-amino acids-have been investigated during the past decade, there are only few reports on the conformational preference of a single (beta-amino acid when incorporated into a cyclopeptide. The conformational bias of (beta-amino acids on the secondary structure of cyclopeptides has been investigated by NMR spectroscopy in combination with distance geometry (DG) and molecular dynamics (MD) calculations using experimental constraints. The atomic coordinate RMSD criterion usually employed for clustering of conformations after DG and MD calculations does not necessarily group similar peptide conformations, as there is an insufficient correlation between atomic coordinates and torsion angles. To improve on this shortcoming and to eliminate any arbitrary decisions during this process, a torsion angle clustering procedure has been implemented. For the cyclic pentapeptides cyclo-(-Val-(beta-Hala-Phe-Leu-Ile-) 1 and cyclo-(-Ser-Pro-Leu-(beta-Hasn-Asp-) 3, the (beta-amino acid is found in the central position of an extended y-turn (pseudo y-turn, psi gamma-turn), while the (beta-Hpro residue in the cyclic hexapeptide cyclo-(-Ser-(beta-HproLeu-Asn-Ile-Asp-) 5 preferentially occupies position i+1 of a pseudo P-turn (T(psi beta-turn). These results furthercorroborate the hypothesis of (beta-amino acids being reliable inducers of secondary structure in cyclic penta- and hexapeptides. They can be employed in the de novo design of biologically active cyclopeptides in pharmaceutical research, since the three-dimensional presentation of pharmacophoric groups in the side chains can be tailored by incorporation of (beta-amino acids in strategic sequential positions. (c) 2007 Wiley Periodicals, Inc.
Stichworte
cyclopeptide;
turn;
conformational analysis;
beta-amino acid;
secondary structure
Erscheinungsjahr
2007
Zeitschriftentitel
Biopolymers
Band
88
Ausgabe
6
Seite(n)
829-839
ISSN
0006-3525
eISSN
1097-0282
Page URI
https://pub.uni-bielefeld.de/record/1631416
Zitieren
Guthöhrlein EW, Malesevic M, Majer Z, Sewald N. Secondary structure inducing potential of beta-amino acids: Torsion angle clustering facilitates comparison and analysis of the conformation during MD trajectories. Biopolymers. 2007;88(6):829-839.
Guthöhrlein, E. W., Malesevic, M., Majer, Z., & Sewald, N. (2007). Secondary structure inducing potential of beta-amino acids: Torsion angle clustering facilitates comparison and analysis of the conformation during MD trajectories. Biopolymers, 88(6), 829-839. https://doi.org/10.1002/bip.20859
Guthöhrlein, E. W., Malesevic, M., Majer, Z., and Sewald, Norbert. 2007. “Secondary structure inducing potential of beta-amino acids: Torsion angle clustering facilitates comparison and analysis of the conformation during MD trajectories”. Biopolymers 88 (6): 829-839.
Guthöhrlein, E. W., Malesevic, M., Majer, Z., and Sewald, N. (2007). Secondary structure inducing potential of beta-amino acids: Torsion angle clustering facilitates comparison and analysis of the conformation during MD trajectories. Biopolymers 88, 829-839.
Guthöhrlein, E.W., et al., 2007. Secondary structure inducing potential of beta-amino acids: Torsion angle clustering facilitates comparison and analysis of the conformation during MD trajectories. Biopolymers, 88(6), p 829-839.
E.W. Guthöhrlein, et al., “Secondary structure inducing potential of beta-amino acids: Torsion angle clustering facilitates comparison and analysis of the conformation during MD trajectories”, Biopolymers, vol. 88, 2007, pp. 829-839.
Guthöhrlein, E.W., Malesevic, M., Majer, Z., Sewald, N.: Secondary structure inducing potential of beta-amino acids: Torsion angle clustering facilitates comparison and analysis of the conformation during MD trajectories. Biopolymers. 88, 829-839 (2007).
Guthöhrlein, E. W., Malesevic, M., Majer, Z., and Sewald, Norbert. “Secondary structure inducing potential of beta-amino acids: Torsion angle clustering facilitates comparison and analysis of the conformation during MD trajectories”. Biopolymers 88.6 (2007): 829-839.
Daten bereitgestellt von European Bioinformatics Institute (EBI)
5 Zitationen in Europe PMC
Daten bereitgestellt von Europe PubMed Central.
A critical assessment of force field accuracy against NMR data for cyclic peptides containing β-amino acids.
Paissoni C, Nardelli F, Zanella S, Curnis F, Belvisi L, Musco G, Ghitti M., Phys Chem Chem Phys 20(23), 2018
PMID: 29845162
Paissoni C, Nardelli F, Zanella S, Curnis F, Belvisi L, Musco G, Ghitti M., Phys Chem Chem Phys 20(23), 2018
PMID: 29845162
Synthesis and analysis of the conformational preferences of 5-aminomethyloxazolidine-2,4-dione scaffolds: first examples of β(2)- and β(2, 2)-homo-Freidinger lactam analogues.
Greco A, Tani S, De Marco R, Gentilucci L., Chemistry 20(41), 2014
PMID: 25182659
Greco A, Tani S, De Marco R, Gentilucci L., Chemistry 20(41), 2014
PMID: 25182659
Cyclic RGD peptides interfere with binding of the Helicobacter pylori protein CagL to integrins αVβ3 and α5β1.
Conradi J, Huber S, Gaus K, Mertink F, Royo Gracia S, Strijowski U, Backert S, Sewald N., Amino Acids 43(1), 2012
PMID: 21915696
Conradi J, Huber S, Gaus K, Mertink F, Royo Gracia S, Strijowski U, Backert S, Sewald N., Amino Acids 43(1), 2012
PMID: 21915696
Design of cyclic peptides featuring proline predominantly in the cis conformation under physiological conditions.
Malešević M, Schumann M, Jahreis G, Fischer G, Lücke C., Chembiochem 13(14), 2012
PMID: 22969011
Malešević M, Schumann M, Jahreis G, Fischer G, Lücke C., Chembiochem 13(14), 2012
PMID: 22969011
VCD studies on cyclic peptides assembled from L-α-amino acids and a trans-2-aminocyclopentane- or trans-2-aminocyclohexane carboxylic acid.
Vass E, Strijowski U, Wollschläger K, Mándity IM, Szilvágyi G, Jewgiński M, Gaus K, Royo S, Majer Z, Sewald N, Hollósi M., J Pept Sci 16(11), 2010
PMID: 20848613
Vass E, Strijowski U, Wollschläger K, Mándity IM, Szilvágyi G, Jewgiński M, Gaus K, Royo S, Majer Z, Sewald N, Hollósi M., J Pept Sci 16(11), 2010
PMID: 20848613
29 References
Daten bereitgestellt von Europe PubMed Central.
Haubner, Angew Chem Int Ed 36(), 1997
Basic conformers in beta-peptides.
Mohle K, Gunther R, Thormann M, Sewald N, Hofmann HJ., Biopolymers 50(2), 1999
PMID: 10380341
Mohle K, Gunther R, Thormann M, Sewald N, Hofmann HJ., Biopolymers 50(2), 1999
PMID: 10380341
The world of beta- and gamma-peptides comprised of homologated proteinogenic amino acids and other components.
Seebach D, Beck AK, Bierbaum DJ., Chem. Biodivers. 1(8), 2004
PMID: 17191902
Seebach D, Beck AK, Bierbaum DJ., Chem. Biodivers. 1(8), 2004
PMID: 17191902
beta-Peptides: from structure to function.
Cheng RP, Gellman SH, DeGrado WF., Chem. Rev. 101(10), 2001
PMID: 11710070
Cheng RP, Gellman SH, DeGrado WF., Chem. Rev. 101(10), 2001
PMID: 11710070
Theoretical prediction of the basic helix types in alpha,beta-hybrid peptides.
Baldauf C, Gunther R, Hofmann HJ., Biopolymers 84(4), 2006
PMID: 16506208
Baldauf C, Gunther R, Hofmann HJ., Biopolymers 84(4), 2006
PMID: 16506208
Rai, Chem Eur J 13(), 2007
Solvent-mediated conformational transition in beta-alanine containing cyclic peptides. VIII.
Lombardi A, Saviano M, Nastri F, Maglio O, Mazzeo M, Isernia C, Paolillo L, Pavone V., Biopolymers 38(6), 1996
PMID: 8652791
Lombardi A, Saviano M, Nastri F, Maglio O, Mazzeo M, Isernia C, Paolillo L, Pavone V., Biopolymers 38(6), 1996
PMID: 8652791
Schumann, J Am Chem Soc 122(), 2000
Malešević, Int J Pept Res Ther 12(), 2006
Structural properties of cyclic peptides containing cis- or trans-2-aminocyclohexane carboxylic acid.
Strijowski U, Sewald N., Org. Biomol. Chem. 2(8), 2004
PMID: 15064783
Strijowski U, Sewald N., Org. Biomol. Chem. 2(8), 2004
PMID: 15064783
The constrained amino acid beta-Acc confers potency and selectivity to integrin ligands.
Urman S, Gaus K, Yang Y, Strijowski U, Sewald N, De Pol S, Reiser O., Angew. Chem. Int. Ed. Engl. 46(21), 2007
PMID: 17394270
Urman S, Gaus K, Yang Y, Strijowski U, Sewald N, De Pol S, Reiser O., Angew. Chem. Int. Ed. Engl. 46(21), 2007
PMID: 17394270
Kessler, Pure Appl Chem 68(), 1996
The GROMOS software for biomolecular simulation: GROMOS05.
Christen M, Hunenberger PH, Bakowies D, Baron R, Burgi R, Geerke DP, Heinz TN, Kastenholz MA, Krautler V, Oostenbrink C, Peter C, Trzesniak D, van Gunsteren WF., J Comput Chem 26(16), 2005
PMID: 16211540
Christen M, Hunenberger PH, Bakowies D, Baron R, Burgi R, Geerke DP, Heinz TN, Kastenholz MA, Krautler V, Oostenbrink C, Peter C, Trzesniak D, van Gunsteren WF., J Comput Chem 26(16), 2005
PMID: 16211540
Beta-alanine containing cyclic peptides with predetermined turned structure. V.
Pavone V, Lombardi A, Saviano M, Di Blasio B, Nastri F, Fattorusso R, Maglio O, Isernia C., Biopolymers 34(11), 1994
PMID: 7827262
Pavone V, Lombardi A, Saviano M, Di Blasio B, Nastri F, Fattorusso R, Maglio O, Isernia C., Biopolymers 34(11), 1994
PMID: 7827262
Beta-alanine containing cyclic peptides with turned structure: the "pseudo type II beta-turn." VI.
Pavone V, Lombardi A, Saviano M, Nastri F, Fattorusso R, Maglio O, Isernia C, Paolillo L, Pedone C., Biopolymers 34(11), 1994
PMID: 7827263
Pavone V, Lombardi A, Saviano M, Nastri F, Fattorusso R, Maglio O, Isernia C, Paolillo L, Pedone C., Biopolymers 34(11), 1994
PMID: 7827263
Müller, Synthesis (), 1998
An improved method for the solution cyclization of peptides under pseudo-high dilution conditions.
Malesevic M, Strijowski U, Bachle D, Sewald N., J. Biotechnol. 112(1-2), 2004
PMID: 15288942
Malesevic M, Strijowski U, Bachle D, Sewald N., J. Biotechnol. 112(1-2), 2004
PMID: 15288942
Stewart, 1984
Improved spectral resolution in cosy 1H NMR spectra of proteins via double quantum filtering.
Rance M, Sorensen OW, Bodenhausen G, Wagner G, Ernst RR, Wuthrich K., Biochem. Biophys. Res. Commun. 117(2), 1983
PMID: 6661238
Rance M, Sorensen OW, Bodenhausen G, Wagner G, Ernst RR, Wuthrich K., Biochem. Biophys. Res. Commun. 117(2), 1983
PMID: 6661238
Bax, J Magn Res 65(), 1985
Shaka, J Magn Res 77(), 1988
Macura, J Magn Res 43(), 1981
Goddard, 0
The Xplor-NIH NMR molecular structure determination package.
Schwieters CD, Kuszewski JJ, Tjandra N, Clore GM., J. Magn. Reson. 160(1), 2003
PMID: 12565051
Schwieters CD, Kuszewski JJ, Tjandra N, Clore GM., J. Magn. Reson. 160(1), 2003
PMID: 12565051
van, Biomolecular Simulation: The GROMOS96 Manual and User Guide; vdf Hochschulverlag AG an der ETH Zürich: Zürich (), 1996
Schuler, J Comput Chem 22(), 2001
Geerke, J Phys Chem B 108(), 2004
Fioroni, J Phys Chem B 104(), 2000
Ryckaert, J Comp Phys 23(), 1977
Export
Markieren/ Markierung löschen
Markierte Publikationen
Web of Science
Dieser Datensatz im Web of Science®Quellen
PMID: 17922495
PubMed | Europe PMC
Suchen in