Model for the structure of bacteriorhodopsin based on high-resolution electron cryo-microscopy

Henderson, Richard A.; Baldwin, Joyce; Ceska, T.A.; Zemlin, F.; Beckmann, E.; Downing, Kenneth H.

doi:10.1016/s0022-2836(05)80271-2

Cited by 2,921 publications

(1,779 citation statements)

References 82 publications

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“…3D structures are determined experimentally for two types of membrane proteins: (1) helical proteins consisting of typically apolar helices of about 20 residues that cross the membrane perpendicular to its surface [photo-reaction center (Deisenhofer et al, 1985); bacteriorhodopsin (Henderson et al, 1990); light harvesting complex 11 (Wang, 1994)1, cytochrome c oxidase (Iwata et al, 1995); and (2) 0 proteins consisting of 16-stranded &barrels [porin (Weiss & Schulz, 1992;Cowan & Rosenbusch, 1994;Kreusch & Schulz, 1994)]. Methods for the prediction o f protein B Fig.…”

Section: Prediction Of Htmsmentioning

confidence: 99%

Topology prediction for helical transmembrane proteins at 86% accuracy–Topology prediction at 86% accuracy

1996

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Previously, we introduced a neural network system predicting locations of transmembrane helices (HTMs) based on evolutionary profiles (PHDhtm, Rost B, Casadio R, Fariselli P, Sander C, 1995, Protein Sci 4:521-533). Here, we describe an improvement and an extension of that system. The improvement is achieved by a dynamic programming-like algorithm that optimizes helices compatible with the neural network output. The extension is the prediction of topology (orientation of first loop region with respect to membrane) by applying to the refined prediction the observation that positively charged residues are more abundant in extra-cytoplasmic regions. Furthermore, we introduce a method to reduce the number of false positives, i.e., proteins falsely predicted with membrane helices. The evaluation of prediction accuracy is based on a cross-validation and a double-blind test set (in total 131 proteins). The final method appears to be more accurate than other methods published: (1) For almost 89% (+.3%) of the test proteins, all HTMs are predicted correctly. (2) For more than 86% (*3%) of the proteins, topology is predicted correctly. (3) We define reliability indices that correlate with prediction accuracy: for one half of the proteins, segment accuracy raises to 98%; and for two-thirds, accuracy of topology prediction is 95%. (4) The rate of proteins for which HTMs are predicted falsely is below 2% (k 1070). Finally, the method is applied to 1,616 sequences of Haemophilus influenzae. We predict 19% of the genome sequences to contain one or moreHTMs. This appears to be lower than what we predicted previously for the yeast VI11 chromosome (about 25%).Keywords: .dynamic programming; genome analysis; Haemophilus influenzae; postprocessing neural network output; secondary structure prediction; structure prediction for integral membrane proteins; topology prediction for helical transmembrane proteins Integral membrane proteins comprise an important class of proteins for which experimental techniques for 3D structure determination are often not applicable. Fortunately, theoretical prediction of structural aspects is simpler for membrane proteins than for globular proteins because the lipid bilayer imposes strong constraints on the degrees of freedom for the 3D struc-

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Section: Prediction Of Htmsmentioning

confidence: 99%

Topology prediction for helical transmembrane proteins at 86% accuracy–Topology prediction at 86% accuracy

1996

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“…However, consideration of highresolution structural data for proteins with multiple membrane-spanning regions (Deisenhofer et al, 1985;Allen et al, 1987;Henderson et al, 1990;De Vos et al, 1992) indicates that these apolar residues are likely to be in close contact in the folded structure. Perhaps the interactions that stabilize their noncovalent association have been disrupted by adhesion of the (Yl[b,!…”

Section: Comparison Of Experimental and Calculated Hydrodynamic Parammentioning

confidence: 99%

Modeling the α_IIbβ₃ integrin solution conformation

1993

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The (~l I b P 3 platelet integrin is the prototypical member of a widely distributed class of transmembrane receptors formed by the noncovalent association of a and fi subunits. Electron microscopic (EM) images of the a[& complex show an asymmetric particle with a globular domain from which two extended regions protrude to contact the lipid bilayer. Distance constraints provided by disulfide bond patterns, epitope mapping, and ligand mimetic cross-linking studies rather suggest a somewhat more compact conformation for the a r [ b & complex.We have studied the shape of detergent-solubilized a l I b & by employing a low-resolution modeling procedure in which each polypeptide has been represented as an array of interconnected, nonoverlapping spheres (beads) of various sizes. The number, size, and three-dimensional relationships among the beads were defined either solely by dimensions obtained from published EM images of integrin receptors (EM models, 21 beads), or solely by interdomain constraints derived from published biochemical data (biochemical model, 37 beads). Interestingly, although no EM data were employed in its construction, the resulting overall shape of the biochemical model was still compatible with the EM data. Both kinds of models were then evaluated for their calculated solution properties. The more elongated EM models have diffusion and sedimentation coefficients that differ, at best, by +2% and -18% from the experimental values, determined, respectively, in octyl glucoside and Triton X-100. On the other hand, the parameters calculated for the more compact biochemical model showed a more consistent agreement with experimental values, differing by -7% (octyl glucoside) to -6% (Triton X-100).Thus, it appears that using the biochemical constraints as a starting point has resulted in not only a more detailed model of the detergent-solubilized ~111bP3 complex, where the relative spatial location of specific domains the size of 5-10 kDa can be tentatively mapped, but in a model that can also reconcile the electron microscopy with the biochemical and the solution data.

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“…2). On building of this model the conformation of the pGlul-Gly 6 residues has been brought into line with the conformation of (1-7)BR in the (1-7)BR-A5 complex (see section 3), while those of Trpl°-Met 32 had been aligned in accordance with the literature data [2,6]. Thereafter the relative position of these fragments was adjusted by changing the values of the torsion angles Arg 7, Pro s and Glu 9.…”

Section: Discussionmentioning

confidence: 61%

“…Using electron microscopy in conjunction with a low dose electron diffraction the polypeptide chain of BR was shown to be arranged as seven transmembrane helices interconnected by relatively short loops on both sides of the membrane. Based on a wealth of biochemical and molecular biological data the three dimensional structure of the membrane embedded part of BR is now brought to 3.5 ~, resolution [2]. However, there is no information available as to the conformation of outer membrane loops and N-and C-terminal parts of BR.…”

Section: Introductionmentioning

confidence: 99%

Conformation of surface exposed N‐terminus part of bacteriorhodopsin studied by transferred NOE technique

et al. 1996

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Interaction of the monoclonal antibody A5 raised against native bacteriorhodopsin (BR) with the synthetic peptide pGlul-Ala-Gln-Ile-Thr-Gly-ArgT-NH2, corresponding to the amino acid sequence 1-7 was studied by transferred nuclear Overhauser effect (TRNOE) spectroscopy. The denaturing reagents and the specially designed pulse sequences which eliminate broad signals from the TRNOE spectra were used to favour evaluation of the TRNOE peaks. On the basis of the data obtained, the conformation of peptide bound with A5 was calculated. A model of the mutual arrangement of bacteriorhodopsin N-terminus and the first transmembrane c~-helical segment 8-32 was proposed.

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Model for the structure of bacteriorhodopsin based on high-resolution electron cryo-microscopy

Cited by 2,921 publications

References 82 publications

Topology prediction for helical transmembrane proteins at 86% accuracy–Topology prediction at 86% accuracy

Topology prediction for helical transmembrane proteins at 86% accuracy–Topology prediction at 86% accuracy

Modeling the α_IIbβ₃ integrin solution conformation

Conformation of surface exposed N‐terminus part of bacteriorhodopsin studied by transferred NOE technique

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Model for the structure of bacteriorhodopsin based on high-resolution electron cryo-microscopy

Cited by 2,921 publications

References 82 publications

Topology prediction for helical transmembrane proteins at 86% accuracy–Topology prediction at 86% accuracy

Topology prediction for helical transmembrane proteins at 86% accuracy–Topology prediction at 86% accuracy

Modeling the αIIbβ3 integrin solution conformation

Conformation of surface exposed N‐terminus part of bacteriorhodopsin studied by transferred NOE technique

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Modeling the α_IIbβ₃ integrin solution conformation