Three protein structures

Oschkinat H, Muller T and Dieckmann T 1994 Protein structure determination with three- and four-dimensional spectroscopy Angew. Chem. Int. Ed. Engl. 33 277-93... 

Bdhm H-J 1994 The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure J. Comp.-Aided Mol. Design 8 243-56... 

The catalytic subunit of cAPK contains two domains connected by a peptide linker. ATP binds in a deep cleft between the two domains. Presently, crystal structures showed cAPK in three different conformations, (1) in a closed conformation in the ternary complex with ATP or other tight-binding ligands and a peptide inhibitor PKI(5-24), (2) in an intermediate conformation in the binary complex with adenosine, and (3) in an open conformation in the binary complex of mammalian cAPK with PKI(5-24). Fig.l shows a superposition of the three protein kinase configurations to visualize the type of conformational movement. 

Fig. 1. Superposition of three crystal structures of cAMP-dependent protein kinase that show the protein in a closed conformation (straight line), in an intermediate conformation (dashed line), and in an open conformation (broken line). The structures were superimposed on the large lobe. In three locations, arrows identify corresponding amino acid positions in the small lobe.

Fig. 2. Conformational free energy of closed, intermediate and open protein kinase conformations. cAPK indicates the unbound form of cAMP-dependent protein kinase, cAPKiATP the binary complex of cAPK with ATP, cAPKiPKP the binary complex of cAPK with the peptide inhibitor PKI(5-24), and cAPK PKI ATP the ternary complex of cAPK with ATP and PKI(5-24). Shown are averaged values for the three crystal structures lATP.pdb, ICDKA.pdb, and ICDKB.pdb. All values have been normalized with respect to the free energy of the closed conformations.

A particularly important application of molecular dynamics, often in conjunction with the simulated annealing method, is in the refinement of X-ray and NMR data to determine the three-dimensional structures of large biological molecules such as proteins. The aim of such refinement is to determine the conformation (or conformations) that best explain the experimental data. A modified form of molecular dynamics called restrained moleculai dynarrdcs is usually used in which additional terms, called penalty functions, are added tc the potential energy function. These extra terms have the effect of penalising conformations... 

Bioinformatics is a relatively new discipline that is concerned with the collection, organisatic and analysis of biological data. It is beyond our scope to provide a comprehensive overvie of this discipline a few textbooks and reviews that serve this purpose are now available (s the suggestions for further reading). However, we will discuss some of the main rnethoc that are particularly useful when trying to predict the three-dimensional structure and fum tion of a protein. To help with this. Appendix 10.1 contains a limited selection of some of tf common abbreviations and acronyms used in bioinformatics and Appendix 10.2 lists sorr of the most widely used databases and other resources. 

As more protein structures became available it was observed that some contained more that one distinct region, with each region often having a separate function. Each of these region is usually known as a domain, a domain being defined as a polypeptide chain that can folc independently into a stable three-dimensional structure. 

A number of structured databases have been developed to classify proteins according to the three-dimensional structures. Many of these are accessible via the World Wide Web, T1 protein databanlc (PDB [Bernstein d al. 1977]) is the primary source of data about the stru tures of biological macromolecules and contains a large number of structures, but many i these are of identical proteins (complexed with different ligands or determined at differet resolutions) or are of close homologues. 

A sequence alignment establishes the correspondences between the amino adds in th unknown protein and the template protein (or proteins) from wliich it will be built. Th three-dimensional structures of two or more related proteins are conveniently divided int structurally conserved regions (SCRs) and structurally variable regions (SVRs). Ihe structural conserved regions correspond to those stretches of maximum sequence identity or sequenc... 

Fig, 10.25 The six environment categories used by the 3D profiles method. (Figure adapted from Bowie j U, R Liith. and D Eisenberg 1991. A Method to Identify Protein Sequences That Fold into a Known Three-Dunensinnal Structure. Science 253 164-170.)... 

Noble M E M, R K Wierenga, A-M Lambeir, F R Opperdoes, W H Thunnissen, K H Kalk, H Groendijk and W G J Hoi 1991. The Adaptability of the Active Site of Trypanosomal Triosephosphate Isomerase as Observed in the Crystal Structures of Three Different Complexes. Proteins Structure, Function and Genetics 10 50-69. 

I-J 1994. The Development of a Simple Empirical Scoring Fimction to Estimate the Binding istant for a Protein-ligand Complex of Known Three-Dimensional Structure. Journal of nputer-Aided Molecular Design 8 243-256. 

Charifson P S, J J Corkery, M A Murcko and W P Walters 1999. Consensus Scoring A Method fc Obtaining Improved Hit Rates from Docking Databases of Three-Dimensional Structures int Proteins. Journal of Medicinal Chemistry 42 5100-5109. 

Enzymes are excellent catalysts for two reasons great specificity and high turnover rates. With but few exceptions, all reac tions in biological systems are catalyzed by enzymes, and each enzyme usually catalyzes only one reaction. For most of the important enzymes and other proteins, the amino-acid sequences and three-dimensional structures have been determined. When the molecular struc ture of an enzyme is known, a precise molecular weight could be used to state concentration in molar units. However, the amount is usually expressed in terms of catalytic activity because some of the enzyme may be denatured or otherwise inactive. An international unit (lU) of an enzyme is defined as the amount capable of producing one micromole of its reaction product in one minute under its optimal (or some defined) reaction conditions. Specific activity, the activity per unit mass, is an index of enzyme purity. 

JU Bowie, R Liithy, D Eisenberg. A method to identify protein sequences that fold into a known three-dimensional structure. Science 253 164-170, 1991. 

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