The importance of the amino terminus of the mitochondrial precursor protein apocytochrome c for translocation across model membranes

Molecular dynamics simulations of cytochrome c unfolding in AOT reverse micelles: The first steps

This paper explores the reduced form of horse cytochrome c confined in reverse micelles (RM) of sodium bis-(2-ethylhexyl) sulfosuccinate (AOT) in isooctane by molecular dynamics simulation. RMs of two sizes were constructed at a water content of W (o) = [ H₂O ]/[AOT] = 5.5 and 9.1. Our results show that the protein secondary structure and the heme conformation both depend on micellar hydration. At low hydration, the protein structure and the heme moiety remain stable, whereas at high water content the protein becomes unstable and starts to unfold. At W (o) = 9.1 , according to the X-ray structure, conformational changes are mainly localized on protein loops and around the heme moiety, where we observe a partial opening of the heme crevice. These findings suggest that within our time window (10ns), the structural changes observed at the heme level are the first steps of the protein denaturation process, previously described experimentally in micellar solutions. In addition, a specific binding of AOT molecules to a few lysine residues of the protein was found only in the small-sized RM.

Stabilization of partially folded states of cytochrome c in aqueous surfactant: effects of ionic and hydrophobic interactions

The interaction of submicellar concentrations of sodium dodecyl sulfate (SDS) with horse heart cytochrome c has been found to stabilize two spectroscopically distinct partially folded intermediates at pH 7. The first intermediate is formed by the interaction of SDS with native cytochrome c, and this intermediate retains the majority of the secondary structure while the tertiary structure of the protein is lost. The unfolding of this intermediate with urea leads to the formation of a second intermediate, which is also formed on refolding of the unfolded protein (unfolded by urea) by SDS. The second intermediate retains about 50% of the native secondary structure with no tertiary structure of the protein. The second intermediate was found to be absent at low pH. While induction of helical structure of a protein by SDS in the native condition has been reported earlier, this is possibly the first report of the refolding of a protein in a strongly denaturing condition (in the presence of 10 M urea). The relative contributions of the hydrophobic and the electrostatic interactions of the surfactants with cytochrome c have been determined from the formation of the molten globule species from the acid-induced unfolded protein in the presence of SDS or lauryl maltoside.

Structural transformation of cytochrome c and apo cytochrome c induced by sulfonated polystyrene

The structural transformation of cytochrome c (cyt c) and its heme-free precursor, apo cyt c, induced by negatively charged sulfonated polystyrene (SPS) with different charge density (degree of sulfonation) and chain length was studied to understand the factors that influence the folding and unfolding of the protein. SPS forms stable transparent nanoparticles in aqueous solution. The hydrophobic association of the backbone chain and phenyl groups is balanced by the electrostatic repulsion of the sulfonate groups on the particle surface. The binding of cyt c to negatively charged SPS particles causes an extensive disruption of the native compact structure of cyt c: the cleavage of Fe-Met80 ligand, about 40% loss of the helical structure, and the disruption of the asymmetry environment of Trp59. On the other hand, SPS particle-bound apo cyt c undergoes a conformational change from the random coil to alpha-helical structure. The folding of apo cyt c in SPS particles was influenced by pH and ionic strength of the solution, SPS concentration, and the degree of sulfonation and chain length of SPS. The folding can reach more than 90% of the alpha-helix content of native cyt c in solution. Poly(sodium 4-styrenesulfonate) (PSS), which is 100% sulfonated polystyrene and cannot form hydrophobic cores in the solution, induces only two-thirds of the alpha-helix content compared with SPS. It appears that the electrostatic interaction between PSS/SPS and apo cyt c induces an early partially folded state of apo cyt c. The hydrophobic interaction between nonpolar residues in apo cyt c and the hydrophobic cores in SPS particles extends the alpha-helical structure of apo cyt c.

Peptide 68-88 of apocytochrome c plays a crucial role in its insertion into membrane and binding to mitochondria

Apocytochrome c (Apocyt. c) is the precursor of cytochrome c. It is synthesized in the cytosol and posttranslationally imported into mitochondria. In order to determine the crucial sequence in apocyt. c translocation, deleted mutant and chemically synthesized peptides with different length were used. Obtained results showed that sequence 68-88 of apocyt. c plays a critical role in its insertion into membrane and binding to mitochondria.

Unfolding and refolding of cytochrome c driven by the interaction with lipid micelles

Binding of native cyt c to L-PG micelles leads to a partially unfolded conformation of cyt c. This micelle-bound state has no stable tertiary structure, but remains as alpha-helical as native cyt c in solution. In contrast, binding of the acid-unfolded cyt c to L-PG micelles induces folding of the polypeptide, resulting in a similar helical state to that originated from the binding of native cyt c to L-PG micelles. Far-ultraviolet (UV) circular dichroism (CD) spectra showed that this common micelle-associated helical state (HL) has a native-like alpha-helix content, but is highly expanded without a tightly packed hydrophobic core, as revealed by tryptophan fluorescence, near-UV, and Soret CD spectroscopy. The kinetics of the interaction of native and acid-unfolded cyt c was investigated by stopped-flow tryptophan fluorescence. Formation of H(L) from the native state requires the disruption of the tightly packed hydrophobic core in the native protein. This micelle-induced unfolding of cyt c occurs at a rate approximately 0.1 s(-1), which is remarkably faster in the lipid environment compared with the expected rate of unfolding in solution. Refolding of acid-unfolded cyt c with L-PG micelles involves an early highly helical collapsed state formed during the burst phase (<3 ms), and the observed main kinetic event reports on the opening of this early compact intermediate prior to insertion into the lipid micelle.

Identification of non-covalent structure in apocytochrome c by hydrogen exchange and mass spectrometry

Apocytochrome c, the in vivo precursor to active cytochrome c, was analyzed by amide hydrogen exchange and mass spectrometry to search for fixed, non-covalent structure. The protein was incubated in H(2)O at pH 3.3 or 6.7 for various times, then exposed to D(2)O to initiate isotope labeling of unfolded regions. Following acid quenching of hydrogen exchange, the labeled apocytochrome c was digested with pepsin into fragments that were analyzed by directly coupled high-performance liquid chromatography/electrospray ionization mass spectrometry. The intermolecular distribution of deuterium and the deuterium levels in structurally distinctive populations were determined from the mass spectra of the peptic fragments. Spectra of peptic fragments derived from apocytochrome c incubated at pH 3.3 had single envelopes of isotope peaks with masses indicating that all of the amide hydrogens had been replaced with deuterium. These results showed that apocytochrome c at pH 3.3 offered little resistance to hydrogen exchange, indicating that it was unfolded with little fixed structure. However, mass spectra of peptic fragments including residues 81-94 of apocytochrome c incubated at pH 6.7 had two envelopes of isotope peaks, indicating that one population was unfolded and the other population was highly structured in this region. Mass spectra of peptic fragments including residues N-terminal to residue 81 indicated that this region of the protein remained unfolded with little fixed structure at pH 6.7.

Structure and dynamics of lipid-associated states of apocytochrome c

Apocytochrome c (apocyt c), which in aqueous solution is largely unstructured, acquires an alpha-helical conformation upon association with lipid membranes. The extent of alpha-helix induced in apocyt c is lipid-dependent and this folding process is driven by both electrostatic and hydrophobic lipid-protein interactions. The structural and dynamic properties of apocyt c in lipid membranes were investigated by attenuated total reflection Fourier transform infrared spectroscopy combined with amide H-D exchange kinetics. Apocyt c acquires a higher content of alpha-helical structure with negatively charged membranes than with zwitterionic ones. For all membranes studied here, the helices of these partially folded states of apocyt c have a preferential orientation perpendicular to the plane of the lipid membrane. The H-D exchange revealed that a small fraction of amide protons of apocyt c, possibly associated with a stable folded domain protected by the lipid, remained protected from exchange over 20 min. However, a large fraction of amide protons exchanged in less than 20 min, indicating that the helical states of apocyt c in lipid membranes are very dynamic.

Folding of apocytochrome c in lipid micelles: formation of alpha-helix precedes membrane insertion

Apocytochrome c, which in aqueous solution is largely unstructured, acquires a highly alpha-helical structure upon interaction with lipid. The alpha-helix content induced in apocytochrome c depends on the lipid system, and this folding process is driven by both electrostatic and hydrophobic lipid-protein interactions. The folding kinetic mechanism of apocytochrome c induced by zwitterionic micelles of lysophosphatidylcholine (L-PC), predominantly driven by hydrophobic lipid-protein interactions, was investigated by fluorescence stopped-flow measurements of Trp 59 and fluorescein-phosphatidylethanolamine-(FPE) labeled micelles, in combination with stopped-flow far-UV circular dichroism. It was found that formation of the alpha-helical structure of apocytochrome c precedes membrane insertion. The unfolded state in solution (U(W)) binds to the micelle surface in a helical conformation (I(S)) and is followed by insertion into the lipid micelle, i.e., formation of the final helical state H(L). Binding of apocytochrome c to the lipid micelle (U(W) --> I(S)) is concurrent with formation of a large fraction (75-100%, depending on lipid concentration) of the alpha-helical structure of the final lipid-inserted state H(L). The highly helical intermediate I(S) is formed on the time scale of 3-12 ms, depending on lipid concentration, and inserts into the lipid micelle (I(S) --> H(L)) in the time range of approximately 200 ms to >1 s, depending on lipid-to-protein ratio. The final lipid-inserted helical state H(L) in L-PC micelles has an alpha-helix content approximately 65% of that of cytochrome c in solution and has no compact stable tertiary structure as revealed by circular dichroism results.

Folding of apocytochrome c induced by the interaction with negatively charged lipid micelles proceeds via a collapsed intermediate state

Unfolded apocytochrome c acquires an alpha-helical conformation upon interaction with lipid. Folding kinetic results below and above the lipid's CMC, together with energy transfer measurements of lipid bound states, and salt-induced compact states in solution, show that the folding transition of apocytochrome c from the unfolded state in solution to a lipid-inserted helical conformation proceeds via a collapsed intermediate state (I(C)). This initial compact state is driven by a hydrophobic collapse of the polypeptide chain in the absence of the heme group and may represent a heme-free analogue of an early compact intermediate detected on the folding pathway of cytochrome c in solution. Insertion into the lipid phase occurs via an unfolding step of I(C) through a more extended state associated with the membrane surface (I(S)). While I(C) appears to be as compact as salt-induced compact states in solution with substantial alpha-helix content, the final lipid-inserted state (Hmic) is as compact as the unfolded state in solution at pH 5 and has an alpha-helix content which resembles that of native cytochrome c.

Electrostatic and hydrophobic contributions to the folding mechanism of apocytochrome c driven by the interaction with lipid

In aqueous solution, while cytochrome c is a stably folded protein with a tightly packed structure at the secondary and tertiary levels, its heme-free precursor, apocytochrome c, shows all features of a structureless random coil. However, upon interaction with phospholipid vesicles or lysophospholipid micelles, apocytochrome c undergoes a conformational transition from its random coil in solution to an alpha-helical structure on association with lipid. The driving forces of this lipid-induced folding process of apocytochrome c were investigated for the interaction with various phospholipids and lysophospholipids. Binding of apocytochrome c to negatively charged phospholipid vesicles induced a partially folded state with approximately 85% of the alpha-helical structure of cytochrome c in solution. In contrast, in the presence of zwitterionic phospholipid vesicles, apocytochrome c remains a random coil, suggesting that negatively charged phospholipid headgroups play an important role in the mechanism of lipid-induced folding of apocytochrome c. However, negatively charged lysophospholipid micelles induce a higher content of alpha-helical structure than equivalent negatively charged diacylphospholipids in bilayers, reaching 100% of the alpha-helix content of cytochrome c in solution. Furthermore, micelles of lysolipids with the same zwitterionic headgroup of phospholipid bilayer vesicles induce approximately 60% of the alpha-helix content of cytochrome c in solution. On the basis of these results, we propose a mechanism for the folding of apocytochrome c induced by the interaction with lipid, which accounts for both electrostatic and hydrophobic contributions. Electrostatic lipid-protein interactions appear to direct the polypeptide to the micelle or vesicle surface and to induce an early partially folded state on the membrane surface. Hydrophobic interactions between nonpolar residues in the protein and the hydrophobic core of the lipid bilayer stabilize and extend the secondary structure upon membrane insertion.

Protein import into mitochondria

Mitochondria import many hundreds of different proteins that are encoded by nuclear genes. These proteins are targeted to the mitochondria, translocated through the mitochondrial membranes, and sorted to the different mitochondrial subcompartments. Separate translocases in the mitochondrial outer membrane (TOM complex) and in the inner membrane (TIM complex) facilitate recognition of preproteins and transport across the two membranes. Factors in the cytosol assist in targeting of preproteins. Protein components in the matrix partake in energetically driving translocation in a reaction that depends on the membrane potential and matrix-ATP. Molecular chaperones in the matrix exert multiple functions in translocation, sorting, folding, and assembly of newly imported proteins.

V92A mutation altered the folding propensity of chicken apocytochrome c and its interaction with phospholipids

Chicken apocytochrome c has been shown to possess a much stronger tendency to fold spontaneously in aqueous solution than the equivalent enzyme from other species. In the present work, the amino acid that determines its folding ability was elucidated by site-directed mutagenesis. Wild-type chicken apocytochrome c and three mutants V92A, S103A, and V92A/S103A were expressed in Escherichia coli. The wild-type apoprotein and S103A exhibited the same folding property during dialysis renaturation processes as that chemically prepared from chicken cytochrome c, while those containing V92A mutation did not. Quantitative studies by 2,2,2-trifluoroethanol (TFE) and sodium perchlorate (NaClO4) titration demonstrated that the V92A mutation decreased the helix content that could be induced and confirmed that valine 92 is the major determinant of the folding propensity of chicken apocytochrome c. Furthermore, CD spectra, turbidity measurements, and a translocation assay on a model membrane system showed that the V92A mutation also drastically altered the conformation of apocytochrome c after being incorporated into lipid bilayer and decreased the aggregation of phospholipid vesicles after association of the apoprotein, thus rendering the molecule more competent for translocation across the membrane. Our results showed that a single amino acid substitution could radically alter the folding propensity of an unfolded polypeptide chain and thus influence the conformation following its insertion into phospholipid bilayer.

Translocation of apocytochrome c across the outer membrane of mitochondria

Apocytochrome c follows a unique pathway into mitochondria. Import does not require the general protein translocation machinery, protease-sensitive components of the outer membrane, or a membrane potential across the inner membrane. We investigated the membrane binding and translocation steps of the import reaction using purified outer membrane vesicles (OMV) from Neurospora crassa mitochondria. OMV specifically bound, but did not import apocytochrome c. If, however, specific antibodies were enclosed inside OMV, apocytochrome c was accumulated in soluble form in the lumen. Import was reversible, since apocytochrome c became accessible to external protease after release from the antibodies. Thus, OMV are competent of translocating apocytochrome c into their lumen, but lack a binding partner which traps the apoprotein. In intact mitochondria, cytochrome c heme lyase (CCHL), a peripheral protein of the inner membrane, serves such a function by stably associating with apocytochrome c in a complex which is detectable by co-immunoprecipitation. We suggest a model for the import mechanism of apocytochrome c in which the apoprotein specifically associates with and reversibly passes across the outer membrane. Translocation is rendered unidirectional by stable association with CCHL which serves as a "trans side receptor." Finally, heme is attached by CCHL and the holoprotein folds into its native structure.

Orientation of the alpha-helices of apocytochrome c and derived fragments at membrane interfaces, as studied by circular dichroism

The orientation of the different helical regions of the mitochondrial precursor protein apocytochrome c has been studied using circular dichroism on isolated fragments of this protein associated with oriented films composed of various phospholipids [de Jongh, H. H. J., Goormaghtigh, E., & Killian, J. A. (1994) Biochemistry (preceding article in this issue)]. Both the N and C terminus adopt helical structures in a membrane environment. The middle region can also be helical, but only in the presence of the N-terminal domain of the protein. In the presence of the unsaturated lipids dioleoylphosphatidylcholine and dioleoylphosphatidylglycerol, all three helices are found to have a preferred orientation perpendicular to the membrane normal, whereas in the presence of the saturated lipids dimyristoylphosphatidylcholine and dimyristoylphosphatidylglycerol, the terminal helices are preferentially oriented parallel to the membrane normal. In films composed of dioleoylphosphatidylserine, it is found that the N-terminal helix is oriented preferentially perpendicular, whereas the C-terminal helix is aligned more parallel to the membrane normal. The differences in preferred orientation between the terminal helices are demonstrated by molecular modeling of the helices at a water-lipid interface. The results are discussed in light of the translocation of apocytochrome c over the outer mitochondrial membrane, an important step in the import process of this protein in mitochondria.

Evaluation of electrostatic and hydrophobic effects on the interaction of mitochondrial signal sequences with phospholipid bilayers

The information that directs a nuclear-coded protein to be imported into mitochondria resides in an N-terminal extension, called a signal sequence. The primary sequences of all known ones differ. The only common feature is their ability to theoretically form an amphiphilic, positively charged, alpha-helix. We previously showed that a short stable helical segment was required for a peptide to be functional in import [Wang, Y., & Weiner, H. (1993) J. Biol. Chem. 268, 4759-4765]. Here we investigate the interaction of three altered signal sequences with phospholipid membranes containing cardiolipin to ascertain the importance of electrostatic and hydrophobic interactions with the membrane. The three already described peptides were derivatives of the signal sequence from aldehyde dehydrogenase, which is composed of three segments, two helices separated by a linker. ANCN had the C-helix replaced by the N-helix of the signal sequence of cytochrome c oxidase subunit IV, ANCC had the C-terminal helix replaced by the C-terminal random coil of cytochrome oxidase subunit IV, and linker deleted had the linker region deleted. ANCC, which functioned poorly as a signal sequence, had a very low affinity for binding to the negatively charged membranes. In contrast, both ANCN and linker deleted showed a relatively high affinity for the membranes and were capable of functioning as a good leader sequence. It appears that linker deleted possessed a stronger hydrophobic effect with membranes while ANCN had a higher electrostatic interaction. On the basic of these studies, a model was proposed to describe the interaction of mitochondrial signal sequences with negatively charged phospholipid membranes involving electrostatic interaction for initial binding and hydrophobic interaction for insertion.(ABSTRACT TRUNCATED AT 250 WORDS)

Anionic phospholipids and protein translocation

Anionic phospholipids determine, in diverse ways, the membrane interaction of proteins involved in or undergoing membrane insertion or translocation. How these lipids modulate protein localization, organization, folding and membrane insertion is herein summarized and generalized, leading to a proposal for the function of anionic lipids in cellular transport of newly synthesized proteins.

The interaction of horse heart cytochrome c with phospholipid bilayers. Structural and dynamic effects

The interaction of cytochrome c with phospholipid bilayers is reviewed. Special emphasis is given to the structural and dynamic perturbations induced, either in the membrane lipid component or protein itself, by the lipid-protein interaction. The lipid-induced perturbations in the structure of cytochrome c involve: i) conformational changes in and around the heme crevice, converting the heme iron to a high-spin state: and ii) a destabilisation/loosening of the overall tertiary and secondary structure. This highly mobile, partially unfolded intermediate of cytochrome c has a remarkable resemblance to partially folded membrane-bound intermediates of the precursor protein. The functional implications of lipid-protein intermediates for (apo) cytochrome c in (protein-translocation) electron-transfer are discussed.

Protein stability regulates the expression of cytochrome c during the developmental cycle of Trypanosoma brucei

The expression of cytochrome c is developmentally regulated during the life cycle of Trypanosoma brucei. The level of regulation appears to be post-transcriptional since cytochrome c mRNA is present in all life stages of the parasite. We have used RNA from each life stage to prime in vitro translation systems and found that the cytochrome c mRNAs are equally translatable. Continuous labeling experiments conducted in vivo indicate that cytochrome c is synthesized at similar rates in both bloodstream and procyclic trypanosomes. Western blots, however, confirm that steady-state levels of cytochrome c are severely depressed in bloodstream forms. In a series of pulse/chase experiments we demonstrate that the half-life of cytochrome c is approximately 1 h in the bloodstream form and no detectable turnover occurred in the procyclic form. We conclude that a major step in the developmental regulation of cytochrome c expression in T. brucei occurs post-translationally due to rapid turnover of the protein in the bloodstream trypanosomes.

Bilayer-penetrating properties enable apocytochrome c to follow a special import pathway into mitochondria

In this study, we have investigated the protein/lipid interactions of two mitochondrial precursor proteins, apocytochrome c and pCOX IV-DHFR, which exhibit mitochondrial import pathways with different characteristics. In-vitro-synthesized apocytochrome c was found to bind efficiently and specifically to liposomes composed of negatively charged phospholipids and showed a (at least partial) translocation across a lipid bilayer, as reported previously for the chemically prepared precursor protein [Rietveld, A. & de Kruijff, B. (1984) J. Biol. Chem. 259, 6704-6707; Dumont, M. E. & Richards, F. M. (1984) J. Biol. Chem. 259, 4147-4156]. Negatively charged liposomes were shown to efficiently compete with mitochondria for import of in-vitro-synthesized apocytochrome c into the organelle, suggesting an important role for negatively charged phospholipids in the initial binding of apocytochrome c to mitochondria. In contrast, the purified and in-vitro-synthesized precursor fusion protein pCOX IV-DHFR, consisting of the presequence of yeast cytochrome oxidase subunit IV fused to mouse dihydrofolate reductase was unable to translocate across a pure lipid bilayer. The data indicate that the ability of apocytochrome c to spontaneously translocate across the bilayer is not shared by all mitochondrial precursor proteins. The implications of the special protein/lipid interaction of apocytochrome c for import into mitochondria will be discussed.

A water-lipid interface induces a highly dynamic folded state in apocytochrome c and cytochrome c, which may represent a common folding intermediate

In this study, we have used CD and NMR techniques to investigate the secondary structure of (apo-) cytochrome c both in solution and when associated with micelles. In aqueous solution, the holoprotein cytochrome c is tightly folded at secondary and tertiary levels and differs strongly from its random-coiled precursor. However, in the presence of 12-PN/12-Pglycol (9:1) micelles, we observed a remarkable resemblance between the CD spectra of these partially helical proteins. The water-lipid interface induces a secondary folding of apocytochrome c, whereas cytochrome c is suggested to partially lose its tertiary structure. The exchange of all amide protons and, using deuterium-labeled proteins, of all amide deuterons with the solvent was monitored by NMR. A rapid exchange rate was observed, indicating that these folding states are highly dynamic. Saturation-transfer NMR of micelle-associated apocytochrome c showed that the exchange takes place at the (sub-) second time scale. The holoprotein in the presence of micelles was found to have two distinct exchange rates: (1) a fast rate, comparable to that found for the micelle-associated precursor and 4.5 times slower than that of the random-coiled apocytochrome c, and (2) a slow rate which is 75 times slower than the precursor in solution. Urea denaturation studies showed the micelle-bound proteins to have a low helix stability, which explains the inability of the lipid-induced secondary structure to prevent its labile protons from rapid exchange. The uniqueness of this lipid-induced highly dynamic folding state of (apo-) cytochrome c is demonstrated by comparison with amphiphilic polypeptides like melittin, and its implications for membrane translocation and functioning are discussed.

Constraints on amino acid substitutions in the N-terminal helix of cytochrome c explored by random mutagenesis

The interaction of the N- and C-terminal helices is a hallmark of the cytochrome c family. Oligodeoxyribonucleotide-directed random mutagenesis within the gene encoding the C102T protein variant of Saccharomyces cerevisiae iso-1-cytochrome c was used to generate a library of mutations at the evolutionary invariant residues Gly-6 and Phe-10 in the N-terminal helix. Transformation of this library (contained on a low-copy-number yeast shuttle phagemid) into a yeast strain lacking a functional cytochrome c, followed by selection for cytochrome c function, reveals that 4-10% of the 400 possible amino acid substitutions are compatible with function. DNA sequence analysis of phagemids isolated from transformants exhibiting the functional phenotype elucidates the requirements for a stable helical interface. Basic residues are not tolerated at position 6 or 10. There is a broad volume constraint for amino acids at position 6. The amino acid substitutions observed to be compatible with function at Phe-10 show that the hydrophobic effect alone is sufficient to promote helical association. There are severe constraints that limit the combinations consistent with function, but the number of functionally consistent combinations observed exemplifies the plasticity of proteins.

Membrane insertion and lateral mobility of synthetic amphiphilic signal peptides in lipid model membranes

Amphiphilic signal sequences with the potential to form alpha-helices with a polar, charged face and an apolar face are common in proteins which are imported into mitochondria, in the PTS permeases of bacteria, and in bacterial rhodopsins. Synthetic peptides of such sequences partition into the surface region of lipid membranes where they can adopt different secondary structures. A finely controlled balance of electrostatic and hydrophobic interactions determines the 'affinity' of amphiphilic signal peptides for lipid membranes, as well as the structure, orientation and depth of penetration of these peptides in lipid bilayer membranes. The ability of an individual peptide to associate with lipid bilayer membranes in several different modes is, most likely, a general feature of amphiphilic signal peptides and is reflected in several common physical properties of their amino acid sequences.

Structural and functional approach toward a classification of the complex cytochrome c system found in sulfate-reducing bacteria

Following the discovery of the tetraheme cytochrome c3 in the strict anaerobic sulfate-reducing bacteria (Postgate, J.R. (1954) Biochem. J. 59, xi; Ishimoto et al. (1954) Bull. Chem. Soc. Japan 27, 564-565), a variety of c-type cytochromes (and others) have been reported, indicating that the array of heme proteins in these bacteria is complex. We are proposing here a tentative classification of sulfate- (and sulfur-) reducing bacteria cytochromes c based on: number of hemes per monomer, heme axial ligation, heme spin state and primary structures (whole or fragmentary). Different and complementary spectroscopic tools have been used to reveal the structural features of the heme sites.

Interaction of apocytochrome c and derived polypeptide fragments with sodium dodecyl sulfate micelles monitored by photochemically induced dynamic nuclear polarization 1H NMR and fluorescence spectroscopy

The topology of apocytochrome c, the heme-free precursor of the mitochondrial protein cytochrome c, was investigated in a lipid-associated form. For this purpose photochemically induced dynamic nuclear polarization 1H nuclear magnetic resonance (CIDNP 1H NMR) spectroscopy and quenching of tryptophan and tyrosine fluorescence by acrylamide were applied to an apocytochrome c-sodium dodecyl sulfate (SDS) micellar system. A pH titration of the chemical shifts of the histidine C2 proton resonances of apocytochrome c, using conventional 1H NMR, yielded pK(a)'s of 5.9 +/- 0.1 and 6.2 +/- 0.1, which were assigned to histidine-18 and -33 and histidine-26, respectively. In the presence of SDS micelles an average pK(a) of 8.1 +/- 0.1 was obtained for all histidine C2 protons. Photo-CIDNP enhancements of the histidine, tryptophan, and tyrosine residues, contained in the intact apocytochrome c and in chemically and enzymatically prepared fragments of the precursor, were reduced in the presence of SDS micelles. Similarly, the quenching of the tryptophan fluorescence of the polypeptides by acrylamide was diminished in the presence of SDS. These results indicate the aromatic residues studied are localized in the interface of the SDS micelle.

The conformational changes of apocytochrome c upon binding to phospholipid vesicles and micelles of phospholipid based detergents: a circular dichroism study

The influence of lipid aggregates on the secondary structure of the mitochondrial precursor protein apocytochrome c was investigated by circular dichroism techniques. A conformational change of the protein from a random coil to partially alpha-helical structures was observed upon binding to negatively charged DOPS SUVs. Also DOPC SUVs showed to induce such a conformational change, but to a lesser extent. The detergents decyl-, lauryl and myristoyl-phosphoglycol or -phosphocholine, were synthesized as micel forming phospholipid analogs and are shown to mimic the phospholipids well in their ability to induce alpha-helices in the protein. A full assignment of the regions where the possible alpha-helices are formed is proposed by making use of derived fragments of apocytochrome c, prediction methods and the known X-ray structure of cytochrome c. Besides a helix at the N-terminus (residues 1-22) and at the C-terminal part (residues 80-101), two regions in the middle section (residues 49-54 and 59-70) are suggested to be helical. It is inferred that the two cysteines in the positions 14 an 17 at the N-terminal part are facing in the same direction, which could facilitate the covalent attachment of the heme group to the precursor in the translocation process.

The mitochondrial precursor protein apocytochrome c strongly influences the order of the headgroup and acyl chains of phosphatidylserine dispersions. A 2H and 31P NMR study

Deuterium and phosphorus nuclear magnetic resonance techniques were used to study the interaction of the mitochondrial precursor protein apocytochrome c with headgroup-deuterated (dioleoylphosphatidyl-L-[2-2H1]serine) and acyl chain deuterated (1,2-[11,11-2H2]dioleoylphosphatidylserine) dispersions. Binding of the protein to dioleoylphosphatidylserine liposomes results in phosphorus nuclear magnetic resonance spectra typical of phospholipids undergoing fast axial rotation in extended liquid-crystalline bilayers with a reduced residual chemical shift anisotropy and an increased line width. 2H NMR spectra on headgroup-deuterated dioleoylphosphatidylserine dispersions showed a decrease in quadrupolar splitting and a broadening of the signal on interaction with apocytochrome c. Addition of increasing amounts of apocytochrome c to the acyl chain deuterated dioleoylphosphatidylserine dispersions results in the gradual appearance of a second component in the spectra with a 44% reduced quadrupolar splitting. Such large reduction of the quadrupolar splitting has never been observed for any protein studied yet. The lipid structures corresponding to these two components could be separated by sucrose gradient centrifugation, demonstrating the existence of two macroscopic phases. In mixtures of phosphatidylserine and phosphatidylcholine similar effects are observed. The induction of a new spectral component with a well-defined reduced quadrupolar splitting seems to be confined to the N-terminus since addition of a small hydrophilic amino-terminal peptide (residues 1-38) also induces a second component with a strongly reduced quadrupolar splitting. A chemically synthesized peptide corresponding to amino acid residues 2-17 of the presequence of the mitochondrial protein cytochrome oxidase subunit IV also has a large perturbing effect on the order of the acyl chains, indicating that the observed effects may be a property shared by many mitochondrial precursor proteins. In contrast, binding of the mature protein, cytochrome c, to acyl chain deuterated phosphatidylserine dispersions has no effect on the deuterium and phosphorus nuclear magnetic resonance spectra, thereby demonstrating precursor-specific perturbation of the phospholipid order. The inability of holocytochrome c to perturb the phospholipid order is due to folding of this protein, since unfolding of cytochrome c by heat or urea treatment results in similar effects on dioleoylphosphatidylserine bilayers, as observed for the unfolded precursor. Implications of these data for the import of apocytochrome c into mitochondria will be discussed.

Apocytochrome c: an exceptional mitochondrial precursor protein using an exceptional import pathway

The cytochrome c import pathway differs markedly from the general route taken by the majority of other imported proteins, which is characterized by the import involvement of namely, surface receptors, the general insertion protein (GIP), contact sites and by the requirement of a membrane potential (delta psi). Unique features of both the cytochrome c precursor (apocytochrome c) and of the mechanism that transports it into mitochondria, have contributed to the evolution of a distinct import pathway that is not shared by any other mitochondrial protein analysed thus far. The cytochrome c pathway is particularly unique because i) apocytochrome c appears to have spontaneous membrane insertion-activity; ii) cytochrome c heme lyase seems to act as a specific binding site in lieu of a surface receptor and; iii) covalent heme addition and the associated refolding of the polypeptide appears to provide the free energy for the translocation of the cytochrome c polypeptide across the outer mitochondrial membrane.

Early steps in mitochondrial protein import: receptor functions can be substituted by the membrane insertion activity of apocytochrome c

The process of insertion of precursor proteins into mitochondrial membranes was investigated using a hybrid protein (pSc1-c) that contains dual targeting information and, at the same time, membrane insertion activity. pSc1-c is composed of the matrix-targeting domain of the cytochrome c1 presequence joined to the amino terminus of apocytochrome c. It can be selectively imported along either a cytochrome c1 route into the mitochondrial matrix or via the cytochrome c route into the intermembrane space. In contrast to cytochrome c1, pSc1-c does not require the receptor system/GIP for entry into the matrix. The apocytochrome c in the pSc1-c fusion protein appears to exert its membrane insertion activity in such a manner that the matrix-targeting sequence gains direct access to the membrane potential-dependent step. These results attribute an essential function to the receptor system in facilitating the initial insertion of precursors into the mitochondrial membranes.

Inhibition of PhoE translocation across Escherichia coli inner-membrane vesicles by synthetic signal peptides suggests an important role of acidic phospholipids in protein translocation

To obtain insight into the mechanism of precursor protein translocation across membranes, the effect of synthetic signal peptides and other relevant (poly)peptides on in vitro PhoE translocation was studied. The PhoE signal peptide, associated with inner membrane vesicles, caused a concentration-dependent inhibition of PhoE translocation, as a result of a specific interaction with the membrane. Using a PhoE signal peptide analog and PhoE signal peptide fragments, it was demonstrated that the hydrophobic part of the peptide caused the inhibitory effect, while the basic amino terminus is most likely important for an optimal interaction with the membrane. A quantitative analysis of our data and the known preferential interaction of synthetic signal peptides with acidic phospholipids in model membranes strongly suggest the involvement of negatively charged phospholipids in the inhibitory interaction of the synthetic PhoE signal peptide with the inner membrane. The important role of acidic phospholipids in protein translocation was further confirmed by the observation that other (poly)peptides, known to have both a high affinity for acidic lipids and hydrophobic interactions with model membranes, also caused strong inhibition of PhoE translocation. The implication of these results with respect to the role of signal peptides in protein translocation is indicated.