Showing papers by "James U. Bowie published in 1996"

Screening method for identifying ligands for target proteins

Abstract: A novel method for screening chemical compounds, test ligands, for potential pharmaceutical effectiveness. The disclosed method identifies possible therapeutic test ligands by placing them in the presence of target proteins and determining the ability of test ligands to increase the ratio of folded target protein to unfolded target protein. This differs significantly from known methods of novel pharmaceutical testing in that the biochemical function of the target protein need not be known and, except for one of the five embodiments of the method, the existence of any known ligands of the target protein is unnecessary.

Assigning amino acid sequences to 3-dimensional protein folds.

Abstract: With the advent of genome sequencing projects, the amino acid sequences of thousands of proteins are determined every year. Each of these protein sequences must be identified with its function and its 3-dimensional structure for us to gain a full understanding of the molecular biology of organisms. To meet this challenge, new methods are being developed for fold recognition, the computational assignment of newly determined amino acid sequences to 3-dimensional protein structures. These methods start with a library of known 3-dimensional target protein structures. The new probe sequence is then aligned to each target protein structure in the library and the compatibility of the sequence for that structure is scored. If a target structure is found to have a significantly high compatibility score, it is assumed that the probe sequence folds in much the same way as the target structure. The fundamental assumptions of this approach are that many different sequences fold in similar ways and there is a relativel...

Assigning amino acid sequences to 3-dimensional protein folds

Abstract: With the advent of genome sequencing projects, the amino acid sequences of thousands of proteins are determined every year. Each of these protein sequences must be identified with its function and its 3-dimensional structure for us to gain a full understanding of the molecular biology of organisms. To meet this challenge, new methods are being developed for fold recognition, the computational assignment of newly determined amino acid sequences to 3-dimensional protein structures. These methods start with a library of known 3-dimensional target protein structures. The new probe sequence is then aligned to each target protein structure in the library and the compatibility of the sequence for that structure is scored. If a target structure is found to have a significantly high compatibility score, it is assumed that the probe sequence folds in much the same way as the target structure. The fundamental assumptions of this approach are that many different sequences fold in similar ways and there is a relativel...

Exploring the allowed sequence space of a membrane protein.

Abstract: We present a comprehensive view of the tolerance of a membrane protein to sequence substitution. We find that the protein, diacylglycerol kinase from Escherichia coli, is extremely tolerant to sequence changes with three-quarters of the residues tolerating non-conservative changes. The conserved residues are distributed with approximately the same frequency in the soluble and transmembrane portions of the protein, but the most critical active-site residues appear to reside in the second cytoplasmic domain. It is remarkable that a unique structure of the membrane embedded portion of the protein can be encoded by a sequence that is so tolerant to substitution.

Three-dimensional profiles for measuring compatibility of amino acid sequence with three-dimensional structure.

Abstract: Publisher Summary The three-dimensional (3-D) profile method is a general approach for assessing whether a given sequence is compatible with a particular 3-D structure. The method has been used in structure identification, structure verification, de novo protein folding, and secondary structure prediction. This chapter discusses the approaches to fold identification and verification of the correctness of structures using 3-D profiles, three different methods for generating the 3-D profile, and the application of these methods to fold identification and structure verification. One of the uses of 3-D profiles in structure prediction is to determine whether a sequence of unknown structure is compatible with a known 3-D structure. Another application of 3-D profiles is to verify that a proposed model of a protein structure is correct. This is done by testing whether the sequence is compatible with its own structure.

Developmentally expressed myosin heavy-chain kinase possesses a diacylglycerol kinase domain.

Abstract: In Dictyostelium, an ordered actin and myosin assembly-disassembly process is necessary for proper development, differentiation, and motility (Yumura S, Fukui F, 1985, Nature 314(6007): 194-196; Ravid S, Spudich JA, 1989, J Biol Chem 264(25): 15144-15150), and phosphorylation of myosin heavy chains has been implicated in the myosin assembly-disassembly process (Egelhoff TT, Lee RJ, Spudich JA, 1993, Cell 75(2):363-371). The developmentally expressed 84-kDa myosin heavy-chain kinase (MHCK) from Dictyostelium (Ravid S, Spudich JA, 1992, Proc Natl Acad Sci USA 89(13):5877-5881) is known to be a member of the protein kinase C (PKC) family. We have observed a rather striking homology between the large central domain of MHCK and the catalytic domain of diacylglycerol kinase (DGK), indicating that MHCK is in fact a gene fusion between a DGK and a PKC, possessing two separate kinase domains. The combined diacylglycerol kinase/myosin heavy-chain kinase (DGK/MHCK) may therefore have dual functionality, possessing the ability to phosphorylate both protein and lipid. We present a hypothesis that DGK/MHCK can antagonize both actin and myosin assembly, as well as other cellular processes, by coordinated down regulation of signaling via myosin heavy-chain kinase activity and diacylglycerol kinase activity.