Study Of The Algorithms For The Three- Dimensional Reconstruction Of Icosahedral Virus And Its Applications

"Structure determines function," and so is that in biological macromolecule.Virus is a kind of special biological macromolecule,which is widely distributed in nature and is one of the important pathogens causing human,animal and plant infectious diseases,its structural analysis is the basis of its related functional research.Therefore,it is of great significance to study the structure of virus.Cryo-EM technology has its unique advantages in the structure analysis of biological macromolecular,which are mainly reflected in the following aspects: the research sample has a wide range,and the sample is closer to its active state through rapid freezing;low demand for samples;it can analyze the structure of biological macromolecular with different conformations.Since the "resolution revolution" of Cryo-EM in 2013,many biological macromolecular complex structures have been analyzed using the single particle technology of Cryo-EM,which has gradually developed into a powerful tool for the study of biological macromolecular structures.The 2017 Nobel Prize in chemistry was awarded to three scientists,Richard Henderson,Joachim Frank and Jacques Dubochet,for their work on fundamental theory,reconstruction algorithms and experiments in Cryo-EM.Because of their large molecular weight,viral particles are often difficult to crystallize,Cryo-EM is the most powerful,and sometimes the only tool for analyzing their structure.The greatest advantage of Cryo-EM in virus structure analysis is that the capsid of virus generally has high symmetry(such as icosahedral symmetry).In the process of reconstruction,its high symmetry can be fully used to suppress the image noise and improve the structure's resolution by reconstruction.It is this advantage that,before the "resolution revolution",the resolution of virus reconstruction was the benchmark of Cryo-EM structure analysis.However,the large size of virus particles leads to many problems in threedimensional reconstruction,and it also becomes one of the bottlenecks in three-dimensional reconstruction of viruses by Cryo-EM.First of all,the calculation amount of data processing of Cryo-EM has a cubic relationship with the image size.The huge size of the virus particles leads to an unusually large amount of calculation for its three-dimensional reconstruction,which requires very high computing resources.Currently,some common structural analysis software is difficult to deal with very large viral particles.Secondly,the structural deformation of large viral particles inevitably occurs when samples are prepared by freezing,which destroys the high symmetry of capsid.Therefore,it is difficult to improve the resolution of the analytical structure.It is very important to design software specifically for virus structure analysis.This paper aims at the study on the three-dimensional reconstruction algorithm of icosahedral virus.The main work is as follows: 1)Study on three-dimensional reconstruction algorithm of icosahedral virus by CryoEM.The three-dimensional reconstruction algorithm of virus includes global search algorithm,local refinement algorithm and three-dimensional structure reconstruction algorithm.For a given original three-dimensional model of the low resolution virus,the global search algorithm searches all possible orientation and center by exhaustive method,calculates the minimum residual of the interactive common line between each virus particles image with the template to determine the initial orientation and center of the particles,then obtains the new three-dimensional structure by applying the reconstruction based on direct inverse Fourier transform.Based on this structure,the local refinement algorithm uses the interactive common line method to refine the orientation and the center,and then reconstructs a new three-dimensional structure.Iterate repeatedly and improve the resolution of the structure until the algorithm converges or the structure reaches the expected resolution.2)Development and application of the software for three-dimensional reconstruction of icosahedral virus by Cryo-EM.In this paper,the orientation center determination algorithm based on the interactive common line and the three-dimensional reconstruction algorithm based on the direct Fourier inversion are designed and implemented,and a complete software package for the threedimensional reconstruction of icosahedral virus is constructed.The software operation interface is designed with Python language for convenient use.The designed algorithm and software were applied to analyze the particle structure of three types of herpes simplex virus of A?B?C.The structure differences and major proteins of the capsids were analyzed with the analysis of the structures.