Motion And Function Of Proteins

The recent rapid increase in the number of available protein three-dimensional (3D) structures has further highlighted the necessity to understand the relationship between biological function and structure. Given the structure of a protein, how can its evolution source and biological function be determined? This is a problem vitally important to both molecular biologists and bioinformatists today. We herein become interests in comparing (-sheet topologies of protein main-chain, identifying combination of the side-chain, introducing structural mobility into secondary structure and conformation, and simulating enzyme active site fluctuation by intelligent polymer catalysts. An understanding of the similarities and differences between protein structures is very important for the relationship between structure and function, and for the analysis of possible evolutionary relationships. A main-chain topology is a representation of a protein 3D structural framework. The topological description of (-sheet has the advantage of simplicity, which makes it possible to implement very fast search and comparison algorithms. Here, we present a general approach for aligning a pair of protein (-topologies represented by two-dimensional matrices. The concise view leads to reclassification of protein structures. We observe that the major (-topological classes have different propensities to carry out certain broad categories of functions.They may be highly specific 3D arrangements of amino acid side-chains in proteins sharing the same catalytic mechanism, but having completely different folds. The classic examples are the proteases, which not only perform the same function despite having totally different structures, but have evolved the same Asp-His-Ser catalytic-triad mechanism. In order to recognize presumptive sidechain interactions, the purpose of the statistical analysis is to find frequently occurring common parts of amino acid polyads, including diads, triads, tetrads andpentads. At the conclusion of the analysis we are able to construct equation and maps giving the chance that side-chain contacts of the diads and histidine-based triads can be approximately predicted at different degrees of amino acid polarity and abundance. At present, accuracies for a variety of the secondary structural predictions scarcely go beyond 75.% in general. Which causes, methods of the theoretic prediction have a flaw, or not all the secondary structures are determined by amino acid sequence? There is considerable redundancy in the protein structural databases, as many protein pairs are identical or very similar in sequence. However, we find that 15.9-38.1.% of the secondary structures are in the state of wobble, and only average 73.18.% of the secondary structure can determined by amino acid sequence. The wobble comprises (-helix/loop and (-strand/loop transitions and play an important role in conformational flexibility.Given the secondary structural wobble, the next question to ask is how the wobble might be translated into a conformational fluctuation. Structure determination is clearly a critical step toward understanding biological function, but protein function requires motion. The conformational fluctuation analysis is the link between structure and function. X-ray diffraction analyses yield accurate static structures of crystalline proteins. The stereo superposition of several sequence-identified proteins can illustrate the conformational fluctuation. Crystallization can "freeze" the fluctuating conformations into a static intermediate sub-state. It is impossible for different laboratories to be equal to each other in crystal packing environments. The repeated determinations for one protein are just like shooting many photographs of an "amoeboid" protein entity. Therefore, X-ray diffraction analyses can also yield "solution structure" of proteins like NMR spectroscopy. Protein fluctuation may be intimately related to the way a structures fulfills a particular function. Enzyme simulation has become a powe...