Certain peptide sequences, some of them as short as amino acid triplets, are significantly overpopulated in specific secondary structure motifs in folded protein structures. For example, 74% of the EAM triplet is found in α-helices, and only 3% occurs in the extended parts of proteins (typically β-sheets). In contrast, other triplets (such as VIV and IYI) appear almost exclusively in extended parts (79% and 69%, respectively). In order to determine whether such preferences are structurally encoded in a particular peptide fragment or appear only at the level of a complex protein structure, NMR, VCD, and ECD experiments were carried out on selected tripeptides: EAM (denoted as pro-'α-helical' in proteins), KAM(α), ALA(α), DIC(α), EKF(α), IYI(pro-β-sheet or more generally, pro-extended), and VIV(β), and the reference α-helical CATWEAMEKCK undecapeptide. The experimental data were in very good agreement with extensive quantum mechanical conformational sampling. Altogether, we clearly showed that the pro-helical vs. pro-extended propensities start to emerge already at the level of tripeptides and can be fully developed at longer sequences. We postulate that certain short peptide sequences can be considered minimal "folding seeds". Admittedly, the inherent secondary structure propensity can be overruled by the large intramolecular interaction energies within the folded and compact protein structures. Still, the correlation of experimental and computational data presented herein suggests that the secondary structure propensity should be considered as one of the key factors that may lead to understanding the underlying physico-chemical principles of protein structure and folding from the first principles.

• Publication type
• Journal Article MeSH

Raman optical activity (ROA) is commonly measured with green light (532 nm) excitation. At this wavelength, however, Raman scattering of europium complexes is masked by circularly polarized luminescence (CPL). This can be avoided using near-infrared (near-IR, 785 nm) laser excitation, as demonstrated here by Raman and ROA spectra of three chiral europium complexes derived from camphor. Since luminescence is strongly suppressed, many vibrational bands can be detected. They carry a wealth of structural information about the ligand and the metal core, and can be interpreted based on density functional theory (DFT) simulations of the spectra. For example, jointly with ROA experimental data, the simulations make it possible to determine absolute configuration of chiral lanthanide compounds in solution.

• Keywords
• Raman optical activity, chiral lanthanide complexes, circularly polarized luminescence, density functional theory, spectra simulations,
• Publication type
• Journal Article MeSH

The article reviews the application of biomolecular simulation methods to understand the structure, dynamics and interactions of nucleic acids with a focus on explicit solvent molecular dynamics simulations of guanine quadruplex (G-DNA and G-RNA) molecules. While primarily dealing with these exciting and highly relevant four-stranded systems, where recent and past simulations have provided several interesting results and novel insight into G-DNA structure, the review provides some general perspectives on the applicability of the simulation techniques to nucleic acids.

• MeSH
• DNA chemistry   MeSH
• G-Quadruplexes * MeSH
• Guanine chemistry   MeSH
• Nucleic Acid Conformation MeSH
• Ligands MeSH
• RNA chemistry   MeSH
• Solvents chemistry   MeSH
• Molecular Dynamics Simulation * MeSH
• Telomere chemistry   MeSH
• Hydrogen Bonding MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Review MeSH
• Research Support, N.I.H., Extramural MeSH
• Research Support, U.S. Gov't, Non-P.H.S. MeSH
• Names of Substances
• DNA MeSH
• Guanine MeSH
• Ligands MeSH
• RNA MeSH
• Solvents MeSH