The prion folding problem.

Prion diseases are neurodegenerative disorders in which dramatic conformational change in the structure of the prion protein is the fundamental event. This structural transition involves the loss of substantial alpha-helical content and the acquisition of beta-sheet structure. A convergence of recent biological and structural studies argues that the mechanism underlying the prion diseases is truly unprecedented.

Identification of candidate proteins binding to prion protein.

Prion diseases are disorders of protein conformation that produce neurodegeneration in humans and animals. Studies of transgenic (Tg) mice indicate that a factor designated protein X is involved in the conversion of the normal cellular prion protein (PrPC) into the scrapie isoform (PrPSc); protein X appears to interact with PrPC but not with PrPSc. To search for PrPC binding proteins, we fused PrP with alkaline phosphatase (AP) to produce a soluble, secreted probe. PrP-AP was used to screen a lambdagt11 mouse brain cDNA library, and six clones were isolated. Four cDNAs are novel while two clones are fragments of Nrf2 (NF-E2 related factor 2) transcription factor and Aplp1 (amyloid precursor-like protein 1). The observation that PrP binds to a member of the APP (amyloid precursor protein) gene family is intriguing, in light of possible relevance to Alzheimer's disease. Four of the isolated clones are expressed preferentially in the mouse brain and encode a similar motif.

Modeling protein-ligand complexes.

Increasing the rate at which new biologically active compounds are found is a major goal in pharmaceutical chemistry. Recently, several computational methods have been proposed with this intent. For some time, algorithms have been used to direct ligand evolution on the basis of complementarity to the three-dimensional structure of a selected protein. Current research focuses on enhancements to methods for searching chemical databases, proposing sensible modifications to known active compounds, and construction of novel ligands from theoretical principles.

Molecular modeling of the GM-CSF and IL-3 receptor complexes.

A model for the structure of the cytokine interleukin-3 (IL-3) is presented based on the structural homology of the hematopoietic cytokines and utilizing the crystal structures of interleukin-5 and granulocyte macrophage colony stimulating factor (GM-CSF). In addition, models of the receptor complexes of GM-CSF and IL-3 are presented based on the structural homology of the hematopoietic receptors to growth hormone. Several key interactions between the ligands and their receptors are discovered, some in agreement with previous mutagenesis studies and others that have not yet been the subject of mutagenesis studies. The models provide insights into the binding of GM-CSF and IL-3 to their receptors.

The interleukin-2 and interleukin-4 receptors studied by molecular modelling.

BACKGROUND: Interleukin-2 (IL2) and interleukin-4 (IL4) are members of the four-helix bundle family of cytokines, whose receptors show similarity to each other and to the growth hormone receptor fold. These proteins help to control, among other things, the rate of clonal expansion of lymphocytes, and thus play an important role in the regulation of the immune system. They are therefore of interest as transmembrane signalling proteins, as well as potential pharmaceutical targets. RESULTS: We have modelled structures of the extracellular components of the IL2 and IL4 receptors based on the structure of the complex of human growth hormone with its receptor, and incorporating the recently discovered shared gamma c chain. The models provide possible explanations for several experimental observations, including those from site-directed mutagenesis around the binding sites. Receptor residues that may be close to important side chains on IL2 and IL4 are identified and possible effects of their mutation are discussed. A comparison is made between the models and the growth hormone complex, and between the gamma c chain bound to IL2 and to IL4. CONCLUSIONS: The models offer structural explanations for observed behaviour such as the effects of mutation of the A- and D-helices of the cytokines. In addition, they may be of use in the identification of residues which may interact in the ligand-receptor interfaces, and which would therefore be worthy of further investigation.

Predictive modelling of the 3-D structure of interleukin-13.

Several atomic structures are now available for the family of helical cytokines, which includes growth hormone as well as many of the interleukins. Using structural information from five members of this family, two alternative models of interleukin (IL)-13 are proposed. IL-13 has biological properties similar to those of IL-4 and, like the other interleukins, is a potentially important pharmaceutical target. The model of IL-13 is discussed and compared with the known interleukin structures.

A computer model of the interleukin-4/receptor complex.

Interleukin-4 is a member of the cytokine family, a group of related messenger proteins which collectively help to moderate and control the immune response. It is believed that the folding topology of the beta-sheets of the interleukin-4 receptor (IL4R) is the same as that seen in the crystal structure of CD4. Although the sequence identity is low, homology modeling techniques have been used to model the IL4R structure from CD4. Refinement by molecular dynamics leads to a suggested structure which has been docked to interleukin-4 (IL4). Several residues of apparent importance for binding are identified.

Tertiary structure of calcineurin B by homology modeling.

The crystal structure of the calcium-binding protein calmodulin is used to model the immunologically important calcineurin subunit B. The rough structure is produced by computer-aided homology modeling. Refinement of this using molecular dynamics leads to a suggested structure which appears to satisfy reasonable hydrophilicity and hydrogen-bonding criteria. In the absence of a crystal structure, the model may prove useful in modeling of its interactions with the phosphatase catalytic subunit calcineurin A, and help to explain the calcium modulation of this protein.