Modeling the SHG activities of diverse protein crystals

Abstract

A symmetry-additive ab initio model for second-harmonic generation (SHG) activity of protein crystals was applied to assess the likely protein-crystal coverage of SHG microscopy. Calculations were performed for 250 proteins in nine pointgroup symmetries: a total of 2250 crystals. The model suggests that the crystal symmetry and the limit of detection of the instrument are expected to be the strongest predictors of coverage of the factors considered, which also included secondary-structural content and protein size. Much of the diversity in SHG activity is expected to arise primarily from the variability in the intrinsic protein response as well as the orientation within the crystal lattice. Two or more ordersof-magnitude variation in intensity are expected even within protein crystals of the same symmetry. SHG measurements of tetragonal lysozyme crystals confirmed detection, from which a protein coverage of $84% was estimated based on the proportion of proteins calculated to produce SHG responses greater than that of tetragonal lysozyme. Good agreement was observed between the measured and calculated ratios of the SHG intensity from lysozyme in tetragonal and monoclinic lattices.

Imaging the Nonlinear Susceptibility Tensor of Collagen by Nonlinear Optical Stokes Ellipsometry

“…The structural hierarchy of collagen is illustrated in Fig. 2, where a model amide chromophore, N-methylacetamide (NMA) (a), is considered to be the dominant NLO chromophore within the collagen triple helix (b), consistent with previous experimental and computational determinations (35,36). Triple helices tightly pack together to form collagen fibrils (c), and individual collagen fibrils assemble to form a larger collagen fiber (d).…”

“…In the experiments described in this work, the c ð2Þ l of the fiber can be measured, while the molecular tensor b ð2Þ of the triple helix is challenging to unambiguously access experimentally. Previous work has shown good agreement between ab initio predictions of molecular nonlinear susceptibility tensors, b ð2Þ and experimental results (36,42). Consequently, theoretical predictions of b ð2Þ for a single collagen triple helix were combined with experimental methods to determine c ð2Þ l for a fiber, for us to gain insight into helical organization within a fiber.…”

“…Consequently, theoretical predictions of b ð2Þ for a single collagen triple helix were combined with experimental methods to determine c ð2Þ l for a fiber, for us to gain insight into helical organization within a fiber. For a collagen triple helix specifically, the nonlinear polarizability tensor, b ð2Þ was calculated using the symmetry additive model (36,37), in which ab initio calculations are used to first predict the nonlinear polarizability of NMA, which serves as a model system for the amide bonds of a protein. The amide contributions were then coherently summed for a single collagen triple helix.…”

“…The symmetry additive model was then applied, in which the amide contributions from the amino-acid linkages in collagen were coherently summed (35,45). The input geometry of the NMA was optimized using density functional theory (DFT) calculations with the BL3YP functional (46).…”

Characterization of Protein Nanocrystals Based on the Reversibility of Crystallization

“…Most of the salt crystals are not chiral and have a centrosymmetric space group and therefore do not show any SONICC signal. 30,32,33 However, the possibility cannot be ruled out that in these few cases the precipitate dissolves even though they do not contain any crystalline material. The dilution procedure applied to the mGFPsol crystallization trials led to dissolution of the precipitate at 50 conditions, and for all of them a positive SONICC signal was initially detected.…”