Author: Irena Roterman

Publisher:

Published: 2009-01-01

Total Pages: 148

ISBN-13: 9788178954097

The protein structure seems to be the materialization of the secret of Nature. The structures of proteins seem to be at the first glance the completely random arrangements of the ribbon-like polypeptide chain. The short visual analysis reveals the existence of some ordered fragments called helices or beta-forms. The order may be of two categories: local short range arrangement and multi-units system engaging few ordered fragments into the non-random structural form generation. Majority of the structures are of random form. The question can be asked How random structures are able to participate in quite complicated processes. The search for the method allowing prediction the structure on the basis of amino acid sequence has longer than 40 years history. The progress in this discipline is measured every second year in CASP (Critical Assessment of Structure Prediction) and CAPRI (Critical Assessment of Protein Interaction). This progress is difficult to be recognized as significant. The methods applied for structure prediction treat the structure as the main goal to be reached. Another interpretation is presented in this volume of Recent Advances in Structural Bioinformatics. The different point of view shall be defined before this new strategy may be discussed. The assumption is that the Nature is interested in making the organism to be active. The organism requires many processes to be run properly, in the correct moment, with the appropriate speed and in the correct place. This large set of conditions may be achieved only when all elements participating in the processes called life are precisely well defined in respect to their duties (understood as biological function). The assumption is that the proteins are tools to perform particular jobs. The job of high specificity (the participation in particular process) performed with high precision makes the proteins unique and highly specialized. The search for protein structure shall be changed into the search for the biological function. Assume that the particular biological function is necessary. Particular structure making possible the expected process is the research object for bioinformatics. The protein structure problem can be expressed as follows: Let me know the expected function construction of the tool ensuring the expected function will be the output. The papers presented in this volume undertake attempt to solve the protein structure problem taking the biological function as the main point characteristic for proteins in respect to all other (organic and inorganic molecules) chemical compounds. This is why the review of the methods oriented on protein-protein interaction is presented in the Chapter 1 (In-silico docking: predicting protein-protein interactions - Marcin Król, Alexander L. Tournier, Paul A. Bates). The static and dynamic models have been described there to search for structural elements making the proteins able to generate the protein-protein complexes which are also of high specificity. This is why the method enabling the recognition of biological function of protein is presented in Chapter 2 (Proteins functional sites recognition based on geometric hashing methods - Maurizio Di Stefano, Giovanni Minervini, Fabio Polticelli). The critical elements of proteins responsible for interaction with ligands (also of high specificity) are described as the discrimination criteria for proteins similarities ensuring their biological activity. This is why the influence of ligands on the biological function and protein structure is described in Chapter 3 (Self-assembled organic molecules as non-standard protein ligands experimental and computational studies - Barbara Stopa, Pawel Spólnik, Leszek Konieczny, Barbara Piekarska, Janina Rybarska, Anna Jagusiak, Marcin Król, Irena Roterman). The nice collaboration of experimentalists in immunochemistry with specialists in bioinformatics is described. The modification of the immunoglobulin activity (immunological signal) as dependent on the ligand form is discussed to reveal the structure-to-function relation. This is why the protein structure prediction technique of heuristic character is presented in Chapter 4 (Late stage folding intermediate in silico Irena Roterman, Leszek Konieczny, Michal Brylinski). The model applied attempts to be as close as possible to the experimental observation introducing the protein structure prediction rather as the protein folding simulation implementing the multi-step character of this process. This is why the biological function definition is introduced in Chapter 5 treating the irregularity of hydrophobicity density in protein molecule as the criterion for aim-oriented structural motif (Biological function recognition in silico Irena Roterman, Leszek Konieczny, Michal Brylinski). This is why the active ligand participation in protein folding process is described in the Chapter 6 (Folding process simulated in the presence of specific ligand - Irena Roterman, Leszek Konieczny, Michal Brylinski). The irregularity of hydrophobicity density distribution in protein molecule is assumed to the result of mutual influencing of ligand and folding polypeptide. This ensures also the generation of binding cavity of high specificity. The subject of each paper presented in this volume undertakes the attempt to link the biological function with the structure of protein, which is responsible for particular biological function.