Towards Quantitative Classification of Folded Proteins in Terms of Elementary Functions

A comparative classification scheme provides a good basis for several approaches to understand proteins, including prediction of relations between their structure and biological function. But it remains a challenge to combine a classification scheme that describes a protein starting from its well organized secondary structures and often involves direct human involvement, with an atomary level Physics based approach where a protein is fundamentally nothing more than an ensemble of mutually interacting carbon, hydrogen, oxygen and nitrogen atoms. In order to bridge these two complementary approaches to proteins, conceptually novel tools need to be introduced. Here we explain how the geometrical shape of entire folded proteins can be described analytically in terms of a single explicit elementary function that is familiar from nonlinear physical systems where it is known as the kink-soliton. Our approach enables the conversion of hierarchical structural information into a quantitative form that allows for a folded protein to be characterized in terms of a small number of global parameters that are in principle computable from atomary level considerations. As an example we describe in detail how the native fold of the myoglobin 1M6C emerges from a combination of kink-solitons with a very high atomary level accuracy. We also verify that our approach describes longer loops and loops connecting $\alpha$-helices with $\beta$-strands, with same overall accuracy.Comment: 3 figure

Research on the transition dynamics and linear (nonlinear) optical properties of mCherry

In this study, we explore the electron transition mechanism and optical properties of the popular red fluorescent protein mCherry. By examining the charge transfer spectrum and combining it with the mCherry hole-electron distribution, we identify that the charge transfer between the phenolate and imidazolinone loops significantly contributes to the absorption spectrum. Quantitative analysis of charge transfer shows that, overall, the electrons are transferred to the C16 atom in the middle of phenolate and the imidazolinone loops during absorption. We speculate that C16 may also absorb protons to enable the photoconversion of mCherry in the excited state, similar to the blinking mechanism of IrisFP. In addition, we further investigated the optical properties of mcherry in the external field by polarizability (hyperpolarizability), showing the anisotropy of the polarization, the first hyperpolarization and the second hyperpolarization by unit spherical representation. Our results suggest that significant polarization and second hyperpolarizability occur when the field direction and electron transfer direction are aligned. We also analyzed the polarizability and first hyperpolarizabilities for different external fields. The polarizability mutated when the external field satisfies the S_0,min-> S_1 transition. Finally, the study of the first hyperpolarizability shows that adjusting the appropriate field can lead to a linear photoelectric effect or second harmonic generation of mCherry. These studies have certain reference values for various red fluorescent protein correlation simulations and experiments because of the similarity of the red fluorescent protein