The Preference Functions Method for Predicting Protein Helical Turns with Membrane Propensity

The prediction of secondary structure conformation of membrane-buried segments of integral membrane proteins is done in this work by using the method of preference functions (Juretic et al. In Theoretical and Computational Chemistry; Parkanyi, C., Ed.; Elsevier Science:  Amsterdam, 1998; Vol 5, Chapter 13, p 405). The method is here extended by predicting sequence location, hydrophobic moments, and transmembrane orientation of helical segments. Independent evaluation of the method with ubiquinol-cytochrome c reductase subunits is performed before some already known details of the crystal structure of that respiratory complex are released. Tests with potassium channels revealed that their characteristic super-secondary structure in the pore region can be recognized by performing the analysis with preference functions and with hydrophobic moment threshold functions.

[1]  P. Predehl,et al.  Detection of soft X-rays from supernova 1993J six days after outburst , 1994, Nature.

[2]  J Edelman,et al.  Quadratic minimization of predictors for protein secondary structure. Application to transmembrane alpha-helices. , 1993, Journal of molecular biology.

[3]  W A Gilbert,et al.  The prediction of transmembrane protein sequences and their conformation: an evaluation. , 1990, Trends in biochemical sciences.

[4]  Michael Litt,et al.  Episodic ataxia/myokymia syndrome is associated with point mutations in the human potassium channel gene, KCNA1 , 1994, Nature Genetics.

[5]  J A McCammon,et al.  Secondary structure prediction of the H5 pore of potassium channels. , 1995, Protein engineering.

[6]  J. Richardson,et al.  Amino acid preferences for specific locations at the ends of alpha helices. , 1988, Science.

[7]  William A. Catterall,et al.  Structure and function of voltage-gated ion channels , 1993, Trends in Neurosciences.

[8]  F. Jähnig,et al.  Structure Prediction for Membrane Proteins , 1989 .

[9]  F. Jähnig,et al.  Structure predictions of membrane proteins are not that bad. , 1990, Trends in biochemical sciences.

[10]  T. Steitz,et al.  Identifying nonpolar transbilayer helices in amino acid sequences of membrane proteins. , 1986, Annual review of biophysics and biophysical chemistry.

[11]  Yoshinori Fujiyoshi,et al.  Atomic model of plant light-harvesting complex by electron crystallography , 1994, Nature.

[12]  G. Schulz,et al.  Structure of porin refined at 1.8 A resolution. , 1992, Journal of molecular biology.

[13]  T Hoshi,et al.  Effect of forskolin on voltage-gated K+ channels is independent of adenylate cyclase activation. , 1988, Science.

[14]  B. Rost,et al.  Redefining the goals of protein secondary structure prediction. , 1994, Journal of molecular biology.

[15]  E. L. Wright,et al.  Observational confirmation of a circumsolar dust ring by the COBE satellite , 1995, Nature.

[16]  R. Doolittle,et al.  A simple method for displaying the hydropathic character of a protein. , 1982, Journal of molecular biology.

[17]  T. A. Link,et al.  Structure of a water soluble fragment of the 'Rieske' iron-sulfur protein of the bovine heart mitochondrial cytochrome bc1 complex determined by MAD phasing at 1.5 A resolution. , 1996, Structure.

[18]  Hartmut Michel,et al.  Structure at 2.8 Å resolution of cytochrome c oxidase from Paracoccus denitrificans , 1995, Nature.

[19]  C. DeLisi,et al.  Hydrophobicity scales and computational techniques for detecting amphipathic structures in proteins. , 1987, Journal of molecular biology.

[20]  S H White,et al.  Global statistics of protein sequences: implications for the origin, evolution, and prediction of structure. , 1994, Annual review of biophysics and biomolecular structure.

[21]  J Deisenhofer,et al.  Crystallographic refinement at 2.3 A resolution and refined model of the photosynthetic reaction centre from Rhodopseudomonas viridis. , 1989, Journal of molecular biology.

[22]  B. Lee,et al.  Conformational preference functions for predicting helices in membrane proteins , 1993, Biopolymers.

[23]  Roderick MacKinnon,et al.  Agitoxin Footprinting the Shaker Potassium Channel Pore , 1996, Neuron.

[24]  R. Reithmeier,et al.  Characterization and modeling of membrane proteins using sequence analysis. , 1995, Current opinion in structural biology.

[25]  P Argos,et al.  Prediction of transmembrane segments in proteins utilising multiple sequence alignments. , 1994, Journal of molecular biology.

[26]  J. Deisenhofer,et al.  Structure of the protein subunits in the photosynthetic reaction centre of Rhodopseudomonas viridis at 3Å resolution , 1985, Nature.

[27]  M. Jennings.  Topography of membrane proteins. , 1989, Annual review of biochemistry.

[28]  R. Clark,et al.  Classical conditioning and brain systems: the role of awareness. , 1998, Science.

[29]  N. W. Isaacs,et al.  Crystal structure of an integral membrane light-harvesting complex from photosynthetic bacteria , 1995, Nature.

[30]  B. Rost,et al.  Topology prediction for helical transmembrane proteins at 86% accuracy–Topology prediction at 86% accuracy , 1996, Protein science : a publication of the Protein Society.

[31]  B. Chait,et al.  The structure of the potassium channel: molecular basis of K+ conduction and selectivity. , 1998, Science.

[32]  B. Rost,et al.  Prediction of protein secondary structure at better than 70% accuracy. , 1993, Journal of molecular biology.

[33]  Ehud Y. Isacoff,et al.  Transmembrane Movement of the Shaker K+ Channel S4 , 1996, Neuron.

[34]  Marc Van Montagu,et al.  Identification of the signal molecules produced by wounded plant cells that activate T-DNA transfer in Agrobacterium tumefaciens , 1985, Nature.

[35]  D. Eisenberg,et al.  Analysis of membrane and surface protein sequences with the hydrophobic moment plot. , 1984, Journal of molecular biology.

[36]  J. Rosenbusch,et al.  Folding pattern diversity of integral membrane proteins. , 1994, Science.

[37]  T. Tomizaki,et al.  The Whole Structure of the 13-Subunit Oxidized Cytochrome c Oxidase at 2.8 Å , 1996, Science.

[38]  G. Heijne.  Membrane protein structure prediction. Hydrophobicity analysis and the positive-inside rule. , 1992, Journal of molecular biology.

[39]  W. Kabsch,et al.  Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features , 1983, Biopolymers.