Ab initio modeling of amide I coupling in antiparallel beta-sheets and the effect of (super 13)C isotopic labeling on infrared spectra

Article Abstract:

The study demonstrates that the (super 13)C coupling across antiparallel beta-sheet strands can be identified in the absorption spectrum. The interaction between labeled amide groups in different strands can be used as an indicator of local beta-structure formation, because coupling between close-lying C=O groups on opposing chains leads to the largest frequency shifts, yet some alternate placements can lead to intensity enhancements.

Proteins, Protein structure, Spectra, Amides, Absorption spectra, Properties

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Vibrational spectral simulation for peptides of mixed secondary structure: Method comparison with the Trpzip Model Hairpin

Article Abstract:

Infrared absorption and vibrational circular dichroism (IR and VCD) spectra of model fragments of TrpZip style beta-hairpin structures are simulated using density functional theory method. This approach significantly reduces computational times and opens up a wider range of systems that can be studied with a DFT-based approach and is compared to other methods based on uniform repeating sequence.

Usage, Peptides, Density functionals, Density functional theory

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Simulations of structure and vibrational spectra of deoxyoctanucleotides

Article Abstract:

Combined molecular dynamics and ab initio computations were applied for analysis of infrared absorption and vibrational circular dichroism spectra of deoxyoctanucleotides. Vibrational spectra for the whole octamers including hydrogen-bonded solvent molecules were simulated on the basis of density -functional calculations on small fragments and subsequent transfer of molecular property tensors.

Biological Product (except Diagnostic) Manufacturing, Nucleic Acid Derivatives, Molecular dynamics, Nucleotides, Structure

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