Abstract
A fully quantitative theory connecting protein conformation and optical spectroscopy would facilitate deeper insights into biophysical and simulation studies of protein dynamics and folding. The web server DichroCalc (http://comp.chem.nottingham.ac.uk/dichrocalc) allows one to compute from first principles the electronic circular dichroism spectrum of a (modeled or experimental) protein structure or ensemble of structures. The regular, repeating, chiral nature of secondary structure elements leads to intense bands in the far-ultraviolet (UV). The near-UV bands are much weaker and have been challenging to compute theoretically. We report some advances in the accuracy of calculations in the near-UV, realized through the consideration of the vibrational structure of the electronic transitions of aromatic side chains. The improvements have been assessed over a set of diverse proteins. We illustrate them using bovine pancreatic trypsin inhibitor and present a new, detailed analysis of the interactions which are most important in determining the near-UV circular dichroism spectrum.
Highlights
Circular dichroism (CD) in the near-ultraviolet is widely used to study structural changes in proteins, because of its sensitivity [1,2] to, for example, ligand binding, changes of the environment and catalysis [3]
Aromatic side chains are often found in enzyme active sites, where they play an important role in molecular recognition and biological function
Computing Protein Circular Dichroism Spectroscopy calculations, in the vacuum-UV [8], where bands arise due to charge-transfer transitions, in the far-UV [9], where the backbone nπ* and ππ* transitions appear, and in the near-UV [10,11], where the main contribution is from the aromatic La and Lb ππ* transitions
Summary
Circular dichroism (CD) in the near-ultraviolet (near-UV) is widely used to study structural changes in proteins, because of its sensitivity [1,2] to, for example, ligand binding, changes of the environment and catalysis [3]. Computing Protein Circular Dichroism Spectroscopy calculations, in the vacuum-UV [8], where bands arise due to charge-transfer transitions, in the far-UV [9], where the backbone nπ* and ππ* transitions appear, and in the near-UV [10,11], where the main contribution is from the aromatic La and Lb ππ* transitions.
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