| Protein is a type of macromolecular in biological system. It is the basic unit for organic function. Special function of a protein is determined by its specific structure. So it is crucial for investigating the structure of various proteins. In this paper, we analyzed different properties of protein structures which are selected from PDB (Protein Data Bank), and used corresponding features to predict (?) structural class of protein sequences and characterized the amino acid interactive network of protein structure. At the same time, we used the random walk model in complex environment under external potential to simulate the process of Cl-/H+ exchanging in CLC-ec1 structure. The main research contents are as follows.1. Predicting the (?) structural class of protein sequences by using tendency of polypeptidesPrediction of protein domain structural classes is an important topic in protein science. In this paper, we proposed a new conception: structural class tendency of polypeptides (SCTP), which is based on the fact that a given amino acid fragment tends to be presented in certain type of proteins. The SCTP is obtained from an available training data set PDB40-B. When using the SCTP to predict protein structural classes by Intimate Sorting predictive method, we got the predictive accuracy (jackknife test) with 93.7%,96.5%, and 78.6% for the testing data set PDB40-j, Chou&Maggiora and CHOU. These results indicate that the SCTP approach is quite encouraging and promising. This new conception provides an effective tool to extract valuable information from protein sequences.2. Analyzing different topological properties of amino acid network under different interaction forceAn increasing attention has been dedicated to the characterization of complex networks within the protein world. Before now most investigations about protein structures were only considered where the interactive cutoff distance Rc= 5 or 7 A. It is noteworthy that the length of peptide bond is about 1.5 A, the length of hydrogen bond is about 3 A, the range of London-van der Waals force is about 5 A and the range of hydrophobic effect can reach to 12 A in protein molecule. Present work reports a study on the topological properties of the amino acid network constructed by different interactions above. The results indicate that the small-world property of amino acid network constructed by the peptide and hydrogen bond, London-van der Waals force and the hydrophobic effect is strong, very strong and relatively week, respectively. Besides, there exists a precise exponential relation C∝k-0.5 at Rc= 12 A. It means that the amino acid network constructed by the hydrophobic effect tend to be hierarchical. Functional modules could be the cause for hierarchical modularity architecture in protein structures. This study on amino acid interactive network for different interactions facilitates the identification of binding sites which is strongly linked with protein function, and furthermore provides reasonable understanding of the underlying laws of evolution in genomics and proteomics.3.Investigating the transport mechanism of CLC-type Cl-/H+exchangerThe CLC-type Cl-/H+ exchanger has been extensively studied in recent years. CLC-ec1, whose crystal structure is known and several experimental hot spots have been identified, but the concrete mechanism for Cl-/H+ exchanging has not been provided. In this paper, we simulated the process of Cl-/H+ exchanging by using the model of random walk in complex environment under an external potential. The ultimate current-voltage curves is confirm to the experimental results very well. It is indicates that this model is very suitable for the transport process of CLC family. The method which is used to describe the CLC-type Cl-/H+ exchanger can give some appropriate theoretical explanations for the microscopic transport mechanism. |
