Co-evolution Research Of Protein Secondary Structure Elements At Bacteria Level

At the molecular level, the change of one gene (protein) can lead to the changes of the other potentially related genes (protein), which is called co-evolution. These co-evolution phenomenon maybe embodied in several levels, such as inside a single gene locus(intra-molecular co-evolution), between different genes (inter-molecular co-evolution),and even between different structural elements of gene or protein. Nowadays, there are many co-evolution studies focused on the site level and gene or protein level, for gene or protein level, such as co-evolution of protein secondary structure is still relatively rare. With the development of systems biology, co-evolution analysis of protein secondary structural elements at genomic level can be used to explore the protein co-evolution and interaction relationship, which has great significance.In this article, we use respectively two protein co-evolution analysis models, which is based on multi-sequence of668bacterial protein orthologous families, initially explored the co-evolution strength of the chemical and physical properties of residues of three types of protein secondary structures (α-helix, β-strand, and loop) in bacterial. This enabled us to deduce the influence of physical and chemical properties, such as charge, hydrophobicity and polarity, on the protein secondary structure element interaction in the bacteria.Through the analysis of this thesis, we have come to the following meaningful conclusion:1) In each bacterial combination type of protein secondary structure elements, co-evolution scores of the real model are higher than the null model, and co-evolution scores of null model are close to zero. This shows the real model is reliable in bacteria.2)At a bacteria level the different combination of secondary structure element, the chemical and physical properties of different residues has different intensity of co-evolution, and co-evolution signal of interaction with the physical and chemical properties is much stronger than without interactions. This shows that the interaction with the physical and chemical properties of the protein secondary structure elements may be generated co-evolution phenomenon due to a binding interaction during bacteria co-evolution. Bacteria co-evolution of structure reflects functional constraints on the structure evolution.3)In bacteria, the two combination types, greater co-evolution signal was detected. Charge show common change in the opposite direction.