Computational insight into protein circular dichroism: detailed analysis of contributions of individual chromophores in TEM-1 β-lactamase

Circular dichroism (CD) is an extremely powerful method in dynamically developed areas such as proteomics and drug design. However, it is characterized with a low signal resolution, and therefore it is difficult to assign the signals to specific chromophores. In this study, we demonstrate a systematic computational strategy for revealing the contributions of all individual chromophores to complex near-UV CD spectra of proteins. The methodology not only reveals the individual chromophores contributions without any structural perturbation, but also makes mechanistic insight into physical mechanisms possible. We have applied our strategy to a TEM-1 β-lactamase from E. coli—an enzyme of crucial importance to bacterial resistance to β-lactam antibiotics. We analyzed the free enzyme structure, two acyl-enzyme structures and the structure of the transition state analog, thus simulating delicate but very important conformational changes that could take place during enzyme catalysis and binding. Such analysis also accounts for the important effects of the electrostatic environment that could be altered during experiments. We revealed in silico (without structural manipulations) that the strongest contribution in the near-UV CD is due to W210. The individual contribution of each aromatic chromophore was very dynamic with respect to structural changes and electrostatic effects. In contrast, the disulfide group contribution is relatively resistant to such structural dynamics but was dramatically influenced by alterations in the electrostatic environment.