Searching, Three Dimensional Proteins

SEARCHING FILES OF THREE-DIMENSIONAL PROTEIN STRUCTURES... 

O. V. Galzitskaya and A. V. Einkelstein, A theoretical search for folding/unfolding nuclei in three-dimensional protein structures. Proc. Natl. Acad. Set USA 96, 11299-11304 (1999). 

Scientists carry out searches on databases. Each EST of interest can be compared with sequences in proteins, and the degree of match can be determined. A technique called threading is used. This involves using data on three-dimensional (3D) protein structure, coupled with knowledge of the physicochemical properties of amino acids, to determine if the amino acid sequence is likely to fold in the same way as a sequence for which the structure is known. In this way, more information about the putative target protein can be assessed. 

Kaminski, J.J., Rane, D.F., Snow, M.E., Weber, L, and Rothofsky, M.L Identification of novel farnesyl protein transferase inhibitors using three-dimensional database searching methods./. Med. Chem. 1997, 40, 4103-4112. 

Peters KP, Fauck J, Frommel C (1996) The automatic search for ligand binding sites in proteins of known three-dimensional structure using only geometric criteria. J Mol Biol 256 201-213... 

Bohm HJ. On the use of LUDI to search the fine chemicals directory for ligands of proteins of known three-dimensional stmcture. J Comput-Aided Mol Design 1994 8 623-632. 

Unit-cell symmetry can also simplify the search for peaks in a three-dimensional Patterson map. For instance, in a unit cell with a 2X axis (twofold screw) on edge c, recall (equivalent positions, Chapter 4, Section II.H) that each atom at (x,y,z) has an identical counterpart atom at (-x,-y,V2 + z). The vectors connecting such symmetry-related atoms will all lie at (u,v,w) = (2x,2y,V2) in the Patterson map (just subtract one set of coordinates from the other), which means they all lie in the plane that cuts the Patterson unit cell at w = l/2. Such planes, which contain the Patterson vectors for symmetry-related atoms, are called Harker sections or Harker planes. If heavy atoms bind to the protein at... 

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