Membrane protein structure prediction: cytochrome b.
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Cytochrome b Group↗
Biomedical subjects
W A Cramer
Publications and source records attributed to W A Cramer.
Fourier transform infrared evidence for a predominantly alpha-helical structure of the membrane bound channel forming COOH-terminal peptide of colicin E1.
The structure of the membrane bound state of the 178-residue thermolytic COOH-terminal channel forming peptide of colicin E1 was studied by polarized Fourier transform infrared (FTIR) spectroscopy. This fragment was reconstituted into DMPC liposomes at varying peptide/lipid ratios ranging from 1/25-1/500. The amide I band frequency of the protein indicated a dominant alpha-helical secondary structure with limited beta- and random structures. The amide I and II frequencies are at 1,656 and 1,546 cm-1, close to the frequency of the amide I and II bands of rhodopsin, bacteriorhodopsin and other alpha-helical proteins. Polarized FTIR of oriented membranes revealed that the alpha-helices have an average orientation less than the magic angle, 54.6 degrees, relative to the membrane normal. Almost all of the peptide groups in the membrane-bound channel protein undergo rapid hydrogen/deuterium (H/D) exchange. These results are contrasted to the alpha-helical membrane proteins, bacteriorhodopsin, and rhodopsin.
Biophysical Phenomena↗
Membrane topography of ColE1 gene products: the hydrophobic anchor of the colicin E1 channel is a helical hairpin.
The paucity of crystallographic data on the structure of intrinsic membrane proteins necessitates the development of additional techniques to probe their structures. The colicin E1 ion channel domain contains one prominent hydrophobic region near its COOH terminus that has been proposed to be an anchor for the assembly of the channel. Saturation site-directed mutagenesis of the hydrophobic anchor region of the colicin E1 ion channel was used to probe whether it spanned the bilayer once or twice. A nonpolar amino acid was replaced by a charged residue in 29 mutations made at 26 positions in the channel domain. Substitution of the charged amino acid at all positions except those in the center of the hydrophobic region and the periphery of the hydrophobic region caused a large decrease in the cytotoxicity of the purified mutant colicin E1 protein. This result implies that the hydrophobic domain spans the membrane bilayer twice in a helical hairpin loop, with the center of this domain residing in an aqueous or polar phase. The lengths of the trans-membrane helices appear to be approximately 18 and 16 residues. The absence of significant changes in ion selectivity in five of nine mutants indicated that these mutations did not cause a large change in the channel structure. The ion selectivity changes in four mutants and those previously documented for the flanking Lys residues imply that the hydrophobic hairpin is part of the channel lumen. Water may "abhor" the hydrophobic side of the channel, explaining the small effects of residue charge changes on ion selectivity.
Amino Acid Sequence↗
Membrane topography of ColE1 gene products: the immunity protein.
The topography of the colicin E1 immunity (Imm) protein was determined from the positions of TnphoA and complementary lacZ fusions relative to the three long hydrophobic segments of the protein and site-directed substitution of charged for nonpolar residues in the proposed membrane-spanning segments. Inactivation of the Imm protein function required substitution and insertion of two such charges. It was concluded that the 113-residue colicin E1 Imm protein folds in the membrane as three trans-membrane alpha-helices, with the NH2 and COOH termini on the cytoplasmic and periplasmic sides of the membrane, respectively. The approximate spans of the three helices are Asn-9 to Ser-28, Ile-43 to Phe-62, and Leu-84 to Leu-104. An extrinsic highly charged segment, Lys-66 to Lys-74, containing seven charges in nine residues, extends into the cytoplasmic domain. The specificity of the colicin E1 Imm protein for interaction with the translocation apparatus and the colicin E1 ion channel is proposed to reside in its peripheral segments exposed on the surface of the inner membrane. These regions include the highly charged segment Lys-66 to Lys-83 (loop 2) and the short (approximately eight-residue) NH2 terminus on the cytoplasmic side, and Glu-29 to Val-44 (loop 1) and the COOH-terminal segment Gly-105 to Asn-113 on the periplasmic side.
Alkaline Phosphatase↗
Thylakoid membrane protein topography. Location of the termini of the chloroplast cytochrome b6 on the stromal side of the membrane.
The orientation of cytochrome b6 in the thylakoid membrane and the question of whether the number of membrane spanning helices is an even or odd number was tested through the relative trypsin susceptibility of epitopes (Asp-5 to Gln-14) and (Ile-205 to Leu-214) at the NH2 and COOH termini, respectively, of the 214-residue cytochrome b6 polypeptide. A structure of the cytochrome with an even number of helices and the NH2 and COOH termini on the stromal side of the membrane was inferred from the following: 1) cleavage of cytochrome b6 by trypsin added to thylakoids occurs by removal of both of the exposed NH2- and COOH-terminal epitopes. The epitopes at the termini were more sensitive to trypsin after prior treatment of thylakoids with carboxypeptidase A, indicating that these epitopes are shielded on the stromal side of the membrane by the COOH termini of other proteins. 2) Both epitopes were more trypsin-sensitive in thylakoid membranes than was cytochrome f that is only sensitive to trypsin acting on the lumen side of the membrane. 3) The NH2- and COOH-terminal epitopes of cytochrome b6 were also more sensitive to trypsin added to thylakoid membranes than were the oxygen-evolving complex 16- and 33-kDa proteins that are completely located on the lumen side. 4) The order of trypsin susceptibility was reversed in inside-out membranes, where the cytochrome NH2- and COOH-terminal epitopes were less sensitive than the 16- and 33-kDa proteins. The decreased relative sensitivity of the cytochrome b6 epitopes occurs in spite of a greater absolute sensitivity of these epitopes to trypsin in inside-out membranes. 5) The greater absolute sensitivity can be explained by a 4-helix model that includes trypsin-sensitive sites on the lumen side.
Amino Acid Sequence↗
Identification of a voltage-responsive segment of the potential-gated colicin E1 ion channel.
The voltage dependence of channel activity of the bactericidal protein colicin E1 was found to be correlated with insertion into the membrane bilayer of a specific segment of the 178-residue COOH-terminal thermolytic colicin channel peptide. The insertion into the bilayer was detected by an increase in labeling by one of two different lipophilic photoaffinity probes or by a decrease in iodination of peptide tyrosines from the external solution. Imposition of a potassium diffusion potential of -100 mV resulted in an increase of 35-60% in the labeling of the peptide by the lipophilic probe in the bilayer and a concomitant decrease in labeling of Tyr residues in the peptide by the iodination reagent in the external solution. The change in labeling decreased upon dissipation of the membrane potential with a half-time of about 1 min. The labeling change was localized to a 36-residue peptide segment bounded by alanine-425 and by tryptophan-460. This segment containing seven positively charged residues at low pH is a voltage-sensitive region that inserts into the membrane bilayer when the channel is turned on by the potential and is extruded from it when the voltage is removed and the channel is turned off.
Affinity Labels↗
Solution NMR studies of colicin E1 C-terminal thermolytic peptide. Structural comparison with colicin A and the effects of pH changes.
The aqueous solution structure of the C-terminal thermolytic peptide of colicin E1 has been investigated using both one- and two-dimensional NMR techniques. The NMR data are consistent with a fold for the peptide very similar to that reported for the colicin A C-terminal peptide in the crystalline state, although some differences have been noted. The one-dimensional NMR spectrum of the peptide has been used to follow changes in both the structure and dynamics of the peptide on changing pH. The in vitro functionally competent form of the peptide (present in solution only below pH 6) does not differ in structure significantly from the higher pH form. However, small local conformational changes are observed together with an increase in mobility in some of the more hydrophilic regions. This suggests that the effect of lower pH is to change the ease with which the major conformational changes during insertion into a membrane can occur.
Amino Acid Sequence↗
On the nature of the structural change of the colicin E1 channel peptide necessary for its translocation-competent state.
Acidic pH conditions required in vitro for membrane binding and activity of the channel-forming colicin E1 resulted in an increased susceptibility to proteases of the 178-residue thermolytic channel peptide, an increased accessibility to acrylamide of a fluorescence probe linked to cysteine-505 of the peptide, and an increased partition into nonionic detergent. The structural change in the peptide sensed by the fluorescence probe caused by a transition from pH 6.0 to 3.5 occurred in less than 1 s. The presence of low concentrations of detergents (0.001% SDS or 0.44% octyl beta-D-glucoside) or urea (0.2 M) at pH 6 or 4 also increased the susceptibility of the channel peptide to proteases. The increase in protease susceptibility and acrylamide accessibility at low pH, as well as partition of the peptide into nonionic detergent, suggested that acidic pH or the detergents might cause peptide unfolding. However, the hydrodynamic radius of the channel peptide at pH 6, 21-23 A, was not changed at pH 3.5 or by detergents or urea under conditions that increased the susceptibility of the peptide to protease. The activity of the channel peptide at pH 6 measured with liposomes and planar bilayers, which was a factor of 10(3)-10(4) smaller than that at pH 4, was increased by 2-4 orders of magnitude by 0.001% SDS or 0.44% octyl beta-D-glucoside, with an additional small increment of activity on planar bilayers caused by 0.01% SDS. A small increase in Stokes radius of the peptide in the presence of SDS could be detected that was approximately correlated with increased activity.
Acrylamides↗
Structure and dynamics of the colicin E1 channel.
The toxin-like and bactericidal colicin E1 molecule is of interest for problems of toxin action, polypeptide translocation across membranes, voltage-gated channels, and receptor function. Colicin E1 binds to a receptor in the outer membrane and is translocated across the cell envelope to the inner membrane. Import of the colicin channel-forming domain into the inner membrane involves a translocation-competent intermediate state and a membrane potential-dependent movement of one third to one half of the channel peptide into the membrane bilayer. The voltage-gated channel has a conductance sufficiently large to depolarize the Escherichia coli cytoplasmic membrane. Amino acid residues that affect the channel ion selectivity have been identified by site-directed mutagenesis. The colicin E1 channel is one of a few membrane proteins whose secondary structures in the membrane, predominantly alpha-helix, have been determined by physico-chemical techniques. Hypothesis for the identity of the trans-membrane helices, and the mechanism of binding to the membrane, are influenced by the solved crystal structure of the soluble colicin A channel peptide. The protective action of immunity protein is a unique aspect of the colicin problem, and information has been obtained, by genetic techniques, about the probable membrane topography of the imm gene product.
Amino Acid Sequence↗
Lumen-side topography of the alpha-subunit of the chloroplast cytochrome b-559.
Removal of the extrinsic 33 kDa polypeptide increased the accessibility to trypsin of a COOH-terminal tridecapeptide epitope of the alpha subunit of cytochrome b-559 (psbE gene product). The sensitivity of the cytochrome epitope to trypsin was not measurably affected by removal of the 16 and 23 kDa extrinsic polypeptides, nor increased by removal of the OEC manganese along with the 33 kDa protein. While protecting alpha-cytochrome b-559 against trypsin, the 33 kDa protein is also proteolyzed, suggesting the possibility of an additional protein component involved in the shielding of the cytochrome. Shielding of the COOH-terminal epitope of alpha-cytochrome b-559 by the OEC 33 kDa protein implies that these COOH-terminal chains of the cytochrome are part of a protein network in the lumen space near the photosystem II reaction center. This network may contain residues that are involved in the binding of essential OEC metal ions.
Chlorophyll↗
On the question of interheme electron transfer in the chloroplast cytochrome b6 in situ.
The redox properties, the site of action of the inhibitor NQNO, and the question of interheme transfer in the chloroplast cytochrome b6 have been examined with regard to the role of the b6-f complex in quinol oxidation and H+ translocation. (i) The two hemes of the cytochrome ba and bp, have similar (delta Em less than or equal to 50 mV) oxidation-reduction midpoint potentials that are pH-independent in the range pH 6.5-8.0 (Em7 = -40 mV) but are pH dependent below this range with an estimated pK = 6.7. (ii) Only half of cytochrome b6, the stromal-side heme, ba, was reducible by NADPH and ferredoxin. (iii) The 2-3-fold increase (to 0.60 +/- 0.09 heme/600 Chl) in the amplitude of flash-induced cytochrome reduction caused by NQNO was not affected when heme ba was initially reduced, implying that NQNO affects flash reduction at the site of heme bp. (iv) Multiple light flashes did not increase the amplitude of b6 reduction in the presence or absence of NQNO or show binary oscillations. Together with localization of a site of action of NQNO near heme bp, these data provide no evidence for efficient electron transfer from heme bp to heme ba as specified by the Q cycle model. (v) NQNO interaction with heme bp does not block its oxidation, since reoxidation of the flash-reduced cytochrome in its presence or absence was 4-5 times faster (t1/2 approximately 30 ms) when heme ba was reduced. The faster oxidation of the photoreduced cytochrome after NADPH-Fd reduction of heme ba indicates that the oxidation of ba and bp may be cooperative.
Antimycin A↗
Visualization of antibody binding to the photosynthetic membrane: the transmembrane orientation of cytochrome b-559.
We have used immuno-gold labeling and electron microscopy to study the topography of thylakoid membrane polypeptides. Thylakoid vesicles formed by passage through a French press were adsorbed onto a plastic film supported by an electron microscope grid and processed for single or double immuno-gold labeling. After shadowing with platinum, the inside-out and right-side-out vesicles were identified by their distinctive morphologies. Right-side-out vesicles were labeled by a monoclonal antibody recognizing an epitope located in the trypsin-cleaved, N-terminal portion of the LHC II apoprotein, and by an antibody to CF1. A monoclonal antibody to the alpha-subunit of cytochrome b-559 reacted with a synthetic tridecapeptide corresponding to the C-terminal portion of the polypeptide. Both this antibody and a polyclonal antibody to the synthetic peptide labeled inside-out vesicles exclusively, indicating that the polypeptide C-terminus was exposed on the lumenal (exoplasmic) surface of the membrane.
Amino Acid Sequence↗
Decrease of anion selectivity caused by mutation of Thr501 and Gly502 to Glu in the hydrophobic domain of the colicin E1 channel.
Structure-function relations of the colicin E1 ion channel were studied through the effects of mutations in the 35-residue hydrophobic region of the channel polypeptide and neighboring residues in the channel domain. Mutation of neutral residues threonine 501 and glycine 502 to a more polar or charged glutamic acid generated a protein whose channel conductance properties in each case had a decreased selectivity for anions. There was no significant effect on ion selectivity caused by mutations that changed residue charge outside the hydrophobic domain at the neighboring aspartic acid 509 or at glycine 439. The Thr501----Glu and Gly502----Glu mutants possessed lower cytotoxic and in vitro activity. An altered thermolysin cleavage pattern and a greater binding to membrane vesicles at pH greater than 4.5 of the Gly502----Glu mutant indicated greater exposure of its COOH-terminal hydrophobic domain in solution. It is concluded that the hydrophobic nature of threonine 501 and glycine 502 is important in the structure of the channel lumen and the soluble colicin. Altering proline 462, a residue conserved in five sequenced channel-forming colicins, had no significant effect on channel properties. These conclusions are discussed in the context of sequence-structure-function concepts for channel proteins.
Amino Acid Sequence↗
Prediction of bilayer spanning domains of hydrophobic and amphipathic membrane proteins: application to the cytochrome b and colicin families.
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Amino Acid Sequence↗
Thylakoid membrane protein topography: transmembrane orientation of the chloroplast cytochrome b-559 psbE gene product.
Protease accessibility and antibody to a COOH-terminal peptide were used as probes for the in situ topography of the Mr 10,000 psbE gene product (alpha subunit) of the chloroplast cytochrome b-559. Exposure of thylakoid membranes to trypsin or Staphylococcus aureus V8 protease cleaved the alpha subunit to a slightly smaller polypeptide (delta Mr approximately -1000) as detected on Western blots, without loss of reactivity to COOH-terminal antibody. The disappearance of the parent Mr 10,000 polypeptide from thylakoids in the presence of trypsin correlated with the appearance of the smaller polypeptide with delta Mr = -750, the conversion having a half-time of approximately 15 min. Exposure of inside-out vesicles to trypsin resulted in almost complete loss of reactivity to the antibody, showing that the COOH terminus is exposed on the lumenal side of the membrane. Removal of the extrinsic polypeptides of the oxygen-evolving complex resulted in an increase of the accessibility of the alpha subunit to trypsin. These data establish that the alpha subunit of cytochrome b-559 crosses the membrane once, as predicted from its single, 26-residue, hydrophobic domain. The NH2 terminus of the alpha polypeptide is on the stromal side of the membrane, where it is accessible, most likely at Arg-7 or Glu-6/Asp-11, to trypsin or V8 protease, respectively. As a consequence of this orientation, the single histidine residue in the alpha subunit is located on the stromal side of the hydrophobic domain.(ABSTRACT TRUNCATED AT 250 WORDS)
Amino Acid Sequence↗
Site-directed mutagenesis of the charged residues near the carboxy terminus of the colicin E1 ion channel.
Colicin E1 was altered by oligonucleotide-directed mutagenesis at the site of three charged residues on the COOH side of the 35-residue hydrophobic segment in the channel-forming domain. Asp-509 is one of five conserved acidic residues in the channel domain of colicins A, B, E1, Ia, and Ib and is the first charged residue following the hydrophobic segment, followed by the basic residues Lys-510 and Lys-512. Asp-509 and Lys-512 were changed to amber and ochre stop codons, respectively, while Lys-510 was mutated to a Met codon. Proteins truncated after residue 508 or 511, and missing the last 14 or 11 residues, were obtained from a nonsuppressing cell strain harboring the mutant plasmid while full-length colicin molecules with single residue changes at Asp-509 to Leu, Ser, and Gln, and Lys-512 to Tyr, were obtained by using appropriate suppressor strains. The truncated colicins displayed (i) a low cytotoxicity, approximately 1% of intact wild-type colicin, (ii) 10-fold less in vitro channel activity with liposomes, and (iii) reduced labeling of the colicin in liposomes by a phospholipid photoaffinity probe, showing that one or more of the residues following Asn-511 is necessary for both in vivo and in vitro activity and insertion into the bilayer. (iv) The truncated mutants also displayed an altered conformation at pH 6 that allowed greater binding and activity with liposomes at this pH relative to wild type. The cytotoxicity of single residue substitutions at Asp-509 showed a range of cytotoxicities, wild type greater than Ser-509 greater than Gln-509 greater than Leu-509, although none of these changes greatly affected the in vitro channel activity or pH dependence.(ABSTRACT TRUNCATED AT 250 WORDS)
Amino Acid Sequence↗
Dynamic properties of membrane proteins: reversible insertion into membrane vesicles of a colicin E1 channel-forming peptide.
The binding of colicin E1 and its COOH-terminal channel-forming peptides to artificial membrane vesicles has an optimum at acidic pH values. The Mr 18,000 thermolytic peptide inserted into membrane vesicles at pH 4.0 has a limited accessibility to exogenous protease. It is converted by trypsin cleavage after Lys-381 and Lys-382 to a lower Mr 14,000 peptide. However, when the pH of a vesicle suspension to which peptide has been bound at pH 4.0 is shifted to 6.0, the accessibility to protease increased greatly. This was shown (i) by the large decrease in the amount of Mr 14,000 or Mr 18,000 peptide after the pH 4----6 shift and treatment with trypsin or Pronase, consistent with (ii) a previously observed decrease in membrane-bound radiolabeled peptide after protease treatment. (iii) When a photoactivable nitrene-generating phospholipid probe was used to label the colicin peptide inserted into the bilayer, the extent of labeling decreased by a factor of 3 when the pH was shifted from 4.0 to 6.5. (iv) Colicin peptide added to vesicles at pH 4.0 can "hop" to other vesicles if the pH and ionic strength of donor vesicles are successively increased. It is proposed that deprotonation of acidic residues in contact with the hydrophobic bilayer or the membrane surface destabilizes the inserted channel and causes it to be extruded from the membrane. The pH-dependent extrusion of the inserted colicin channel provides an example of dynamic properties of an intrinsic membrane protein.
Amino Acid Sequence↗
On the explanation of the acidic pH requirement for in vitro activity of colicin E1. Site-directed mutagenesis at Glu-468.
The in vitro acidic pH dependence of colicin E1 channel activity was investigated by directed mutagenesis of Glu-468 in the colicin E1 channel domain, a residue conserved in the sequences of the four channel-forming colicins examined so far. Mutations were made to the amino acids leucine, serine, glutamine, or lysine, residues of different polarity and charge. All of the mutant polypeptides possessed high cytotoxic activity in vivo, although in vitro activity, especially with planar membranes, was lower than that of the wild type protein. A change in the in vitro acidic pH dependence of activity could be readily detected in the mutation to the hydrophobic leucine residue. The dependence of mutant activity on pH in the interval 3.5-5.0 was markedly smaller than that of the wild type, whether assayed on membrane vesicles or membrane bilayers. Differences in pH dependence between the wild type and the polar serine and glutamine mutants were small or of marginal statistical significance. No change in pH dependence could be detected with the charged lysine mutant. The residual pH dependence in all cases indicated that more than one carboxylic residue must be protonated to account for the increased activity at acidic pH values. A role of Glu-468 in the mechanism of channel formation or function was implied by the changes determined in vitro of channel parameters relative to the wild type: (i) the relatively small rates of current increase measured for colicin COOH-terminal peptide derived from the mutants, (ii) the small values of steady-state conductance of mutant peptide at pH 3.5, and (iii) the reduced anion selectivity of peptide from the serine mutant.
Amino Acid Sequence↗