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Department of Physiology and Biophysics and the Program in Structural Biology, University of California, Irvine, California 926974560, USA
Reprint requests to: Dr. Stephen H. White, University of California at Irvine, Department of Physiology and Biophysics, Irvine, California 926974560, USA; e-mail: shwhite{at}uci.edu; fax: (949) 824-8540.
(RECEIVED October 10, 2000; FINAL REVISION November 12, 2000; ACCEPTED November 15, 2000)
Article and publication are at www.proteinscience.org/cgi/doi/10.1110/ps.43501
| Abstract |
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Keywords: Protein structure prediction; prediction accuracy; hydropathy plots
| Introduction |
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The assembly of a dependable database of MP topology from literature reports was less straightforward than expected. Even in the case of membrane proteins whose three-dimensional (3D) structures have been determined, TM segment assignments are often not identified in the original publications and often are not readily determinable from the Protein Data Bank coordinate files. Beyond the MPs of known structure, we sought papers in the MP literature that contained keywords, such as gene fusion, suggestive of direct experimental studies of topology. Reported MP topologies were included in the database only after careful evaluation of published experimental results. For example, in the case of gene fusion data (Boyd 1994), the density of fusions had to be sufficient to inspire confidence that the topology had been explored thoroughly, as in the case of lac permease (Calamia and Manoil 1990). MPtopo has now grown to 90 proteins or subunits contributing 534 TM segments, a size we believe sufficient for evaluating existing prediction algorithms and creating new ones.
| Protein selection criteria and database characteristics |
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Some surface-bound, monotopic membrane proteins without TM segments, such as prostaglandin synthase (Picot et al. 1994), were also included in MPtopo to aid the development of algorithms for distinguishing monotopic from TM proteins. These proteins are identified by an asterisk following the protein name in the data record, appropriate comments in the remarks field, and an asterisk on the TM segment alphabetic assignment, indicating surface-lying helices. The recently reported water and glycerol channel proteins (Fu et al. 2000; Murata et al. 2000) are also marked with asterisks because they have TM segments comprised of two end-to-end helices that are distant in the sequence. In addition to comments in the remarks field, each partial helix is recorded as a TM segment with an asterisk on the alphabetic identifier. To identify the segment pairs constituting the full TM segment, the first partial segment in the sequence is identified, for example, as C*, and the second one as *C.
In the absence of 3D structures, TM sequence assignments were obtained from published reports of topology that included experimental confirmation using techniques such as gene fusion (Manoil and Beckwith 1986), Asn-linked glycosylation (Pan et al. 1999), or amino acid deletions (Wolin and Kaback 1999). In some cases, such as rhodopsin (whose 3-D structure was recently reported [Palczewski et al. 2000]), an overwhelming amount of data of all sorts from a large number of publications provided strong, coherent evidence for TM segment assignments. Even when noncrystallographic experimental data are used to validate topology, however, most specific TM sequence assignments in published reports originate from hydropathy plots. In most cases, authors generally provided topology diagrams that assigned the TM segments believed to be located within the membrane bilayer. Such assignments were used for specifying TM segments in MPtopo. In a few cases, topologies of proteins with long interhelix connecting loops were specified without specific assignment of the membrane-buried segments. Under those circumstances, we identified likely membrane-buried segments by seeking long runs of hydrophobic residues bounded by charged residues. Our assignments included only intervening uncharged residues.
Hydropathy plots vary in important details even among closely related proteins (White and Jacobs 1990); seemingly subtle differences in sequences can have big effects on decision thresholds (Edelman and White 1989; Edelman 1993). Because of our interest in prediction tools based strictly on physiochemical criteria (White and Wimley 1999), we did not reject any protein because of high homology or sequence identity with a protein already in MPtopo.
The data fields and structure of each MPtopo entry are summarized in Figure 1B
. We have divided the entries into three subsets: 3D_helix, 1D_helix, and 3D_other.
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| Accuracies of prediction algorithms |
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1000 soluble proteins. One or two potential TM segments were found for
10% of the proteins.
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| Database accessibility and availability |
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| Acknowledgments |
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The publication costs of this article were defrayed in part by payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 USC section 1734 solely to indicate this fact.
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