The Spectrophotometric Determination of the Patchy Surface Potential of Viruses Using pH-Sensitive Molecular Probes

Chemistry experiments involving biological aspects are in high demand. This laboratory exercise blends biochemistry and physical chemistry, illustrates key concepts of the virus capsid surface, and is designed for a chemistry laboratory course for students majoring in biology in college. The experimental part provides a mastery of spectrophotometric and potentiometric methods as well as numerical and graphical analysis of the data obtained. The experimental determination of pKa for neutral red, NR, and p-nitrophenol, NP, attracted to the surface of the MS2 bacteriophage results in an estimation of its local surface potential, Ψ. A distinctive feature of this lab is the twofold result: the positive Ψ value in the NP localization patch and the negative Ψ value in the NR localization patch. Discussions with students are focused on considering the surface (i) as an unstructured continuum that is characterized by physical quantities such as electrophoretic mobility and zeta potential and (ii) as a discontinuum containing certain charged groups that form discrete patches diverse in charge density and in the sign of the charges. The full-atom model of the MS2 capsid recently presented in the scientific literature provides reasonable confirmation of the experimental results obtained.