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General

  • Protein structure prediction is one of the most important goals pursued by bioinformatics and theoretical chemistry. Its aim is the prediction of the three-dimensional structure of proteins from their amino acid sequences, sometimes including additional relevant information such as the structures of related proteins.

  • The complexes of two or more proteins, where the structures of the proteins are known or can be predicted with high accuracy, protein-protein docking methods can be used to predict the structure of the complex.

  • Protein threading scans the amino acid sequence of an unknown structure against a database of solved structures. In each case, a scoring function is used to assess the compatibility of the sequence to the structure, thus yielding possible three-dimensional models. This type of method is also known as 3D-1D fold recognition.

Process

  • Crystallography plays a major role in current efforts towards protein structure determination. Building a protein model from crystallographic data, however, is a complex and time-consuming process, which is somewhat assisted by the use of computer graphics for tracing the polypeptide chains, and for viewing and improving the resulting model.

  • The wire-bender of Rubin and Richardson is a convenient tool for constructing carbon models of proteins. It has been used in laboratories for building protein backbone models which helped us establish the existence of continuous regions of peptide chain in globular proteins.

  • X-ray crystallography is the main method for structure determination of proteins. This can be a time-consuming process, and it will succeed only if it is possible to find suitable conditions for growing crystals.

Application

  • Protein structure prediction is of high importance in medicine and biotechnology.

  • Homology-based rational drug design is a useful tool for the pharmaceutical industry.

  • The application of the techniques of molecular biology, transgenics, knockouts and antisense have led to many advances in our understanding of drug action, and indeed to the development of new drugs.

Report

  • Knowledge of the three-dimensional (3D) structure of protein-protein complexes provides a valuable systems. The rate of protein structure  determination is increasing rapidly. Today there are some 5,000 entries in the Brookhaven Protein Data Bank (PDB).

  • The development of a new drug, or medicine, is a challenge of tremendous complexity and of truly multi-disciplinary character. It is currently also of a dual nature. Typical trialand error processes are carried out simultaneously with the most advanced biochemical synthetic and computational procedures.

  • In recent years two new techniques have received great interest from medicinal chemists: protein crystallography and computer graphics.

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