Computational Study of Interstrand Carbonyl Coupling in AntiParallel Beta-Sheets

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2010-05Author
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Abstract
Proteins are composed of chains of interlinking peptides, and the backbone of each
peptide consists of a carbon-oxygen double-bond (C=O), or a carbonyl group. When a protein is
excited by infrared radiation at the appropriate frequency, the backbone carbonyl groups couple
with one another as they vibrate and the amide I band is formed in the infrared spectrum.
Hydrogen bonding, covalent bonding, and transition dipole coupling (TDC) collectively
influence peptide coupling and consequently affect the shape and location of this band in the
spectrum.
Several methods to computationally model the vibrational patterns of proteins have been
developed. Ab initio calculations utilize Schrodinger’s equation and take into account all of the
electronic interactions within the protein. A simpler model only considers TDC by calculating
the force field interactions between the dipole moments of the backbone carbonyls within the
protein. TDC calculations have become popular amongst experimental and computational
chemists because they can be performed on a small timescale and they have significantly reduced
the computational power necessary to model large proteins. Nevertheless, many have argued that
TDC calculations cannot fully capture the coupling effects between peptide groups and must be
supplemented with information obtained through ab initio calculations in order to yield accurate
results.
In the current study, we confirm that TDC calculations cannot accurately predict the
amide I mode frequencies of model peptides in the anti-parallel beta-sheet conformation, and we
claim that the primary cause of this discrepancy is the inability of TDC to capture interstrand
hydrogen bonding effects. We have quantitatively illustrated this discrepancy by comparing the
ab initio and TDC frequency calculations of dipeptide dimers. To see if this discrepancy is side
Schaikewitz 4
chain specific, we have performed these experiments on dimers with two different side chains.
Our ultimate goal is to increase the accuracy of the TDC method by constructing a new model
which incorporates the effects of interstrand hydrogen bonding.
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