An Improved Diabatization Scheme for Computing the Electronic Circular Dichroism of Proteins

Rogers, David M.; Do, Hainam; Hirst, Jonathan D.

Abstract

We advance the quality of first-principles calculations of protein electronic circular dichroism (CD) through an amelioration of a key deficiency of a previous procedure that involved diabatization of electronic states on the amide chromophore (to obtain interamide couplings) in a β-strand conformation of a diamide. This yields substantially improved calculated far-ultraviolet (far-UV) electronic circular dichroism (CD) spectra for β-sheet conformations. The interamide couplings from the diabatization procedure for 13 secondary structural elements (13 diamide structures) are applied to compute the CD spectra for seven example proteins: myoglobin (α helix), jacalin (β strand), concanavalin A (β type I), elastase (β type II), papain (α + β), 310-helix bundle (310-helix) and snow flea antifreeze protein (polyproline). In all cases, except concanavalin A and papain, the CD spectra computed using the interamide couplings from the diabatization procedure yield improved agreement with experiment with respect to previous first-principles calculations.

Citation

Rogers, D. M., Do, H., & Hirst, J. D. (2024). An Improved Diabatization Scheme for Computing the Electronic Circular Dichroism of Proteins. Journal of Physical Chemistry B, 128(30), 7350-7361. https://doi.org/10.1021/acs.jpcb.4c02582

• Journal Article Type: Article
• Acceptance Date: Jul 9, 2024
• Online Publication Date: Jul 22, 2024
• Publication Date: Aug 1, 2024
• Deposit Date: Jul 23, 2024
• Publicly Available Date: Jul 24, 2024
• Journal: Journal of Physical Chemistry B
• Print ISSN: 1520-6106
• Electronic ISSN: 1520-5207
• Publisher: American Chemical Society
• Peer Reviewed: Peer Reviewed
• Volume: 128
• Issue: 30
• Pages: 7350-7361
• DOI: https://doi.org/10.1021/acs.jpcb.4c02582
• Public URL: https://nottingham-repository.worktribe.com/output/37536571
• Publisher URL: https://pubs.acs.org/doi/10.1021/acs.jpcb.4c02582