Are membrane proteins “inside‐out” proteins?

One of the central paradigms of structural biology is that membrane proteins are “inside‐out” proteins, in that they have a core of polar residues surrounded by apolar residues. This is the reverse of the characteristics found in water‐soluble proteins. We have decided to test this paradigm, now that sufficient numbers of transmembrane α‐helical structures are accessible to statistical analysis. We have analyzed the correlation between accessibility and hydrophobicity of both individual residues and complete helices. Our analyses reveal that hydrophobicity of residues in a transmembrane helical bundle does not correlate with any preferred location and that the hydrophilic vector of a helix is a poor indicator of the solvent exposed face of a helix. Neither polar nor hydrophobic residues show any bias for the exterior or the interior of a transmembrane domain. As a control, analysis of water‐soluble helical bundles performed in a similar manner has yielded clear correlations between hydrophobicity and accessibility. We therefore conclude that, based on the data set used, membrane proteins as “inside‐out” proteins is an unfounded notion, suggesting that packing of α‐helices in membranes is better understood by maximization of van der Waal's forces, rather than by a general segregation of hydrophobicities driven by lipid exclusion. Proteins 1999;36:135–143. © 1999 Wiley‐Liss, Inc.

[1]  D Eisenberg,et al.  Hydrophobic organization of membrane proteins. , 1989, Science.

[2]  D. Engelman,et al.  Structure-based prediction of the stability of transmembrane helix-helix interactions: the sequence dependence of glycophorin A dimerization. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[3]  Sung-Hou Kim,et al.  Electron transfer by domain movement in cytochrome bc1 , 1998, Nature.

[4]  P. Kraulis.  A program to produce both detailed and schematic plots of protein structures , 1991 .

[5]  D. Engelman,et al.  Membrane protein folding and oligomerization: the two-stage model. , 1990, Biochemistry.

[6]  D A Agard,et al.  Three-dimensional structure of the LDL receptor-binding domain of human apolipoprotein E. , 1991, Science.

[7]  David Eisenberg,et al.  The helical hydrophobic moment: a measure of the amphiphilicity of a helix , 1982, Nature.

[8]  K. Dill,et al.  From Levinthal to pathways to funnels , 1997, Nature Structural Biology.

[9]  Paul D. Adams,et al.  Computational searching and mutagenesis suggest a structure for the pentameric transmembrane domain of phospholamban , 1995, Nature Structural Biology.

[10]  A G Murzin,et al.  Structural classification of proteins: new superfamilies. , 1996, Current opinion in structural biology.

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

[12]  R. Cogdell,et al.  Purple bacterial antenna complexes. , 1996, Current opinion in structural biology.

[13]  R Henderson,et al.  Electron-crystallographic refinement of the structure of bacteriorhodopsin. , 1996, Journal of molecular biology.

[14]  James H. Prestegard,et al.  A Transmembrane Helix Dimer: Structure and Implications , 1997, Science.

[15]  D. Engelman,et al.  Structural organization of the pentameric transmembrane alpha‐helices of phospholamban, a cardiac ion channel. , 1994, The EMBO journal.

[16]  Keng S. Liang,et al.  Stabilization of the membrane protein bacteriorhodopsin to 140 °C in two-dimensional films , 1993, Nature.

[17]  A T Brünger,et al.  A dimerization motif for transmembrane alpha-helices. , 1994, Nature structural biology.

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

[19]  W. V. Shaw,et al.  Solving the structure of human H ferritin by genetically engineering intermolecular crystal contacts , 1991, Nature.

[20]  G. Fritzsch,et al.  Structure of the photosynthetic reaction centre from Rhodobacter sphaeroides at 2.65 A resolution: cofactors and protein-cofactor interactions. , 1994, Structure.

[21]  D. Engelman,et al.  Sequence specificity in the dimerization of transmembrane alpha-helices. , 1992, Biochemistry.

[22]  H. Michel,et al.  Structure at 2.7 A resolution of the Paracoccus denitrificans two-subunit cytochrome c oxidase complexed with an antibody FV fragment. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[23]  G. von Heijne,et al.  A 12-Residue-long Polyleucine Tail Is Sufficient to Anchor Synaptobrevin to the Endoplasmic Reticulum Membrane (*) , 1996, The Journal of Biological Chemistry.

[24]  D. Engelman,et al.  Bacteriorhodopsin is an inside-out protein. , 1980, Proceedings of the National Academy of Sciences of the United States of America.

[25]  A. Brunger,et al.  Statistical analysis of predicted transmembrane alpha-helices. , 1998, Biochimica et biophysica acta.

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

[27]  I. Rayment,et al.  Molecular structure of an apolipoprotein determined at 2.5-A resolution. , 1991, Biochemistry.

[28]  D. Engelman,et al.  A dimerization motif for transmembrane α–helices , 1994, Nature Structural Biology.

[29]  E. Grishin,et al.  Three-dimensional structure of ectatomin from Ectatomma tuberculatum ant venom , 1995, Journal of biomolecular NMR.

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

[31]  C. Sander,et al.  The structure of ColE1 rop in solution , 1991, Journal of biomolecular NMR.

[32]  M. Levitt,et al.  The volume of atoms on the protein surface: calculated from simulation, using Voronoi polyhedra. , 1995, Journal of molecular biology.

[33]  F. Lederer,et al.  Improvement of the 2.5 A resolution model of cytochrome b562 by redetermining the primary structure and using molecular graphics. , 1979, Journal of molecular biology.

[34]  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.

[35]  A T Brünger,et al.  Are there dominant membrane protein families with a given number of helices? , 1997, Proteins.

[36]  D. Engelman,et al.  Refolding of bacteriorhodopsin in lipid bilayers. A thermodynamically controlled two-stage process. , 1987, Journal of molecular biology.

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