1. Stereostructure Dependence Phenomenon on the Self-Assembly of Ala-Ala-Ala Lipotripeptides
He Wei, Shuwei Lin, Wei Liu, Yi Li, Baozong Li, Yonggang Yang Langmuir. 2022 Feb 22;38(7):2248-2256. doi: 10.1021/acs.langmuir.1c02813. Epub 2022 Feb 8.
A series of lipotripeptide stereoisomers based on alanine were synthesized, and their self-assembling behaviors were studied by means of circular dichroism spectra, ATR-IR, temperature-dependent 1H NMR, and X-ray diffraction patterns. In the mixed solvent of hexafluoroisopropanol/H2O (1/9, v/v), eight lipotripeptides were able to self-assembled into nanoflakes or nanoribbons driven by the hydrophobic association of alkyl chains, intermolecular hydrogen bonding among carboxyl groups at C-terminal and amide groups of alanine moieties in the peptide segment. It was found that the stacking chirality of carbonyl groups was determined by the chirality of alanine residue at C-terminal (i.e., "C-terminal determination" rule). Moreover, our research also highlighted the intermolecular hydrogen bonding on amide groups of each alanine residue, terminal carboxyl as well as the molecular packing structures can be subtly manipulated by changing the stereochemical sequence of peptide segment.
2. Refinement of Peptide Conformational Ensembles by 2D IR Spectroscopy: Application to Ala‒Ala‒Ala
Chi-Jui Feng, Balamurugan Dhayalan, Andrei Tokmakoff Biophys J. 2018 Jun 19;114(12):2820-2832. doi: 10.1016/j.bpj.2018.05.003.
Characterizing ensembles of intrinsically disordered proteins is experimentally challenging because of the ill-conditioned nature of ensemble determination with limited data and the intrinsic fast dynamics of the conformational ensemble. Amide I two-dimensional infrared (2D IR) spectroscopy has picosecond time resolution to freeze structural ensembles as needed for probing disordered-protein ensembles and conformational dynamics. Also, developments in amide I computational spectroscopy now allow a quantitative and direct prediction of amide I spectra based on conformational distributions drawn from molecular dynamics simulations, providing a route to ensemble refinement against experimental spectra. We performed a Bayesian ensemble refinement method on Ala-Ala-Ala against isotope-edited Fourier-transform infrared spectroscopy and 2D IR spectroscopy and tested potential factors affecting the quality of ensemble refinements. We found that isotope-edited 2D IR spectroscopy provides a stringent constraint on Ala-Ala-Ala conformations and returns consistent conformational ensembles with the dominant ppII conformer across varying prior distributions from many molecular dynamics force fields and water models. The dominant factor influencing ensemble refinements is the systematic frequency uncertainty from spectroscopic maps. However, the uncertainty of conformer populations can be significantly reduced by incorporating 2D IR spectra in addition to traditional Fourier-transform infrared spectra. Bayesian ensemble refinement against isotope-edited 2D IR spectroscopy thus provides a route to probe equilibrium-complex protein ensembles and potentially nonequilibrium conformational dynamics.
3. Folding of an Ala-Ala-Ala tripeptide into a beta-turn via hydrophobic encapsulation
Shohei Tashiro, Masahide Kobayashi, Makoto Fujita J Am Chem Soc. 2006 Jul 26;128(29):9280-1. doi: 10.1021/ja061722e.
An Ac-Ala-Ala-Ala-NH2 tripeptide was folded into a beta-turn structure even in water through hydrophobic binding by a self-assembled porphyrin cage. The turn conformation of the bound peptide was fully assigned from NOESY measurements and was strongly supported by molecular dynamics simulation. Single mutation experiments and molecular modeling also suggested that CH-pi interactions between methyl groups of Ala residues and porphyrin ligands were important for the stabilization of the turn conformation. Furthermore, we observed the induction of a beta-hairpin structure by encapsulation of a heptapeptide, Ac-Gly-Gly-Ala-Ala-Ala-Gly-Gly-NH2, possessing Ala-Ala-Ala sequence at the middle.
