Conformations And Dynamics Of Protein-like Chains

Protein is the basic part of the life. It is a whole of its composition, interior interaction, structure and dynamics. Therefore, it is an important topic to study the composition,structure and dynamic behaviors. In this paper, we will discuss the conformations of the proteins. And folding behavior and elastic behavior are also investigated. Besides, dynamic behaviors are presented. In the meantime, the study of DNA molecular is also done. Through these studies, it helps us to enhance the understanding of the structure and function of biopolymers.In Chapter 2, we have investigated the different structural properties of proteases and nonproteases. By the computation of contact, it is found that proteases are more compact than nonproteases. The probability P(n) of amino acid residues having n pairs of contacts fits a good Gaussian distribution. However, we also establish a modified ODI (Orientation-Dependent Monomer-Monomer Interaction) model to simulate protein-like chain. Monte Carlo method is used to study the conformations of protein-like chain. It is concluded that< S2>-N2vR. vR is smaller than that of SAW chain. The results of shape parameters show the protein-like chain is globular. For the case of protein-like chain which is adsorbed on a surface, the stronger adsorbed energy is, the flatter the protein-like chain is. The last part of this chapter is to find the change of conformations of compact polymer during the process of tensile elongation. HP model on a two-dimensional square lattice and enumeration calculation method are used. In the meantime, effect of temperature on the conformations is also considered.In Chapter 3, we first present a new parameter nOCD to predict folding rate of proteins. A good linear correlation between the folding rate logarithm lnkf and nOCD with n= 1.2,α= 0.6 is found for two-state folders and n= 2.8,α= 1.5 for three-state folders. Three-state folders are more compact than two-state folders. The folding problem is investigated by the topological structure of proteins. Using enumeration calculation method and HP lattice model, we study the energy, free energy and force of compact polymers. The elastic force f /N increases with elongation ratio, and the energy contribution to the elastic force fu/N increases first and then drops.Chapter 4 shows the dynamics of protein-like chain. First, we use modified ODI model and Monte Carlo method to discuss the diffusion coefficients of protein-like chain. It is shown D-N-a. And the value of ofαis 4.75 for protein-like chain without restriction, while the value for SAW chains is 1.02. Dynamics of adsorbed protein-like chains are investigated by calculation of their diffusion coefficients. Under the same model, we investigate the translocation of protein-like chain through a finite channel by PERM (Pruned-Enriched-Rosenbluth Method) algorithm. No free energy barrier is found in our calculation. However, an energy barrier is shown. The position of the maximum of energy depends on the secondary structures and the channel radius. A study of the peptide sequence prediction based on the steered molecular dynamics (SMD) method is presented. For different adsorbed surface, there are different force-extension curves. From the curves, we can obtain the sequence of peptide. The method may provide some insights into the DNA sequencing.The last chapter is the statistical study of DNA molecules. First, we compare the coding sequence and noncoding sequence. The cluster-size distribution P(S1+S2) with the total size of sequential Pu-cluster and Py-cluster S1+S2 is studied. We observe that it follows an exponential decay. The correlation of fluctuation F(l) with nucleotide cluster distance l is F(l)-lH. The value of H for noncoding sequence is smaller than coding sequence. The power spectrums of nucleotide clusters are also discussed. From the study of human chromosomes 21 and 22, P(S1+S2) has no exponential decay. The distance distributions P0(S) between two nucleotides shows a two-order polynomial fit:log Po (S)= a+bS+cS2. The normalized number of repeats N0(l) can be described by a power law:N0(l)-l-μThe n-tuple Zipf analysis is used in our investigation. All these studies are benefical to understanding of structure and function of biomoleculars.