Foldamers of β-peptides: conformational preference of peptides formed by rigid building blocks. The first MI-IR spectra of a triamide nanosystem
- 308 Downloads
To determine local chirality driven conformational preferences of small aminocyclobutane-1-carboxylic acid derivatives, X-(ACBA) n -Y, their matrix-isolation IR spectra were recorded and analyzed. For the very first time model systems of this kind were deposited in a frozen (~10 K) noble gas matrix to reduce line width and thus, the recorded sharp vibrational lines were analyzed in details. For cis-(S,R)-1 monomer two “zigzag” conformers composed of either a six or an eight-membered H-bonded pseudo ring was identified. For trans-(S,S)-2 stereoisomer a zigzag of an eight-membered pseudo ring and a helical building unit were determined. Both findings are fully consistent with our computational results, even though the relative conformational ratios were found to vary with respect to measurements. For the dimers (S,R,S,S)-3 and (S,S,S,R)-4 as many as four different cis,trans and three different trans,cis conformers were localized in their matrix-isolation IR (MI-IR) spectra. These foldamers not only agree with the previous computational and NMR results, but also unambiguously show for the first time the presence of a structure made of a cis,trans conformer which links a “zigzag” and a helical foldamer via a bifurcated H-bond. The present work underlines the importance of MI-IR spectroscopy, applied for the first time for triamides to analyze the conformational pool of small biomolecules. We have shown that the local chirality of a β-amino acid can fully control its backbone folding preferences. Unlike proteogenic α-peptides, β- and especially (ACBA) n type oligopeptides could thus be used to rationally design and influence foldamer’s structural preferences.
Keywordsβ-peptides Peptide folding Matrix-isolation IR spectroscopy Conformational analysis Synthetic biopolymers
This work was funded by the Hungarian Scientific Research Fund (OTKA K75877, K72973, NK101072), the Spanish Ministerio de Ciencia e Innovación (CTQ2010-15408/BQU) and the Generalitat de Catalunya, Spain (2009SGR-733). The European Union and the European Social Fund have provided financial support to the project under the grant no. TAMOP 4.2.1./B-09/KMR-2010-0003 and COST Action CM0803.
Conflict of interest
The authors declare that they have no competing financial interests.
- Baker J, Wolinski K, Malagoli M, Kinghorn D, Wolinski P, Magyarfalvi G, Saebo S, Janowski T, Pulay P (2009) Quantum chemistry in parallel with PQS. J Comput Chem 30(2):317–335Google Scholar
- Bazsó G, Najbauer EE, Magyarfalvi G, Tarczay G (2013) Near-infrared laser induced conformational change of alanine in low-temperature matrixes and the tunneling lifetime of its conformer VI. J Phys Chem A 117(9):1952–1962Google Scholar
- Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Scalmani G, Barone V, Mennucci B, Petersson GA, Nakatsuji H, Caricato M, Li X, Hratchian HP, Izmaylov AF, Bloino J, Zheng G, Sonnenberg JL, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Vreven T, Montgomery Jr. JA, Peralta JE, Ogliaro F, Bearpark M, Heyd JJ, Brothers E, Kudin KN, Staroverov VN, Kobayashi R, Normand J, Raghavachari K, Rendell A, Burant JC, Iyengar SS, Tomasi J, Cossi M, Rega N, Millam JM, Klene M, Knox JE, Cross JB, Bakken V, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski JW, Martin RL, Morokuma K, Zakrzewski VG, Voth GA, Salvador P, Dannenberg JJ, Dapprich S, Daniels AD, Farkas Ö, Foresman JB, Ortiz JV, Cioslowski J, Fox DJ (2009) Gaussian 09, Revision A.1. Gaussian Inc, Wallingford, CTGoogle Scholar
- Ivanov AYu, Sheina G, Blagoi YuP (1999) FTIR spectroscopic study of the UV-induced rotamerization of glycine in the low temperature matrices (Kr, Ar, Ne). Spectrochim Acta Part A 55(1):219–228Google Scholar
- Mohamadi F, Richards NG, Guida WC, Liskamp R, Lipton M, Caufield C, Chang G, Hendrickson T, Still WC, MacroModel 7.0 (1990) Macromodel—an integrated software system for modeling organic and bioorganic molecules using molecular mechanics. J Comput Chem 11(4):440–467Google Scholar
- Pulay P, Fogarasi G, Pongor G, Boggs JE, Vargha A (1983) Combination of theoretical ab initio and experimental information to obtain reliable harmonic force constants. Scaled quantum mechanical (QM) force fields for glyoxal, acrolein, butadiene, formaldehyde, and ethylene. J Am Chem Soc 105(24):7037–7047CrossRefGoogle Scholar
- Reva ID, Plokhotnichenko AM, Stepanian SG, Ivanov AYu, Radchenko ED, Sheina GG, Blagoi YP (1995) The rotamerization of conformers of glycine isolated in inert gas matrices. An infrared spectroscopic study. Chem Phys Lett 232(1–2):141–148 (1995) Erratum. Chem Phys Lett 235(5–6):617–617CrossRefGoogle Scholar
- Rosado MTS, Duarte MLRS, Fausto R (1997) Vibrational spectra (FT-IR, Raman and MI-IR) of α- and β-alanine. J Mol Struct 410–411:343–348Google Scholar
- Sheina GG, Radchenko ED, Ivanov AY, Stepanian SG, Blagoi YP (1988) Oscillating spectra of leucine. Zh Fiz Khim 62:985–990Google Scholar
- Torres E, Gorrea E, Burusco KK, Da Silva E, Nolis P, Rúa F, Boussert S, Díez-Pérez I, Dannenberg S, Izquierdo S, Giralt E, Jaime C, Branchadell V, Ortuño RM (2010) Folding and self-assembling with beta-oligomers based on (1R,2S)-2-aminocyclobutane-1-carboxylic acid. Org Biomol Chem 8(3):564–575PubMedCrossRefGoogle Scholar