Refolding of cytochromeb562 and its structural stabilization by introducing a disulfide bond

The packing mechanism of the secondary structures (4--helices and 3₁₀-helix) of cytochromeb ₅₆₂ is simulated by the island model, where the formation of protein structure is accomplished by the growth-type mechanism with the driving force of packing of the long-range and specific hydrophobic interactions. Packing proceeds through the formation of the structure at the nonhelical part, where a lot of hydrophobic pairs are distributed. Consequently, conformation, nearly similar to the native one, is successfully obtained. With the help of this result, the theoretical prediction of the possibility of forming this disulfide mutant (N22C/G82C) ofb ₅₆₂ can be performed prior to the experiments by our geometrical criterion (lampshade). This criterion is expected to be a significant principle for introducing possible disulfide bonds into a protein to be engineered.     

Packing constraints of hydrophobic side chains in (α/β)8 barrels

An analysis of possible tight packing of hydrophobic groups simultaneously at the both surfaces of β-hyperboloid-8 was conducted. This analysis shows that the disposition of amino acid side chains at the real β-structure's surface is unique. If we sign the mean distance between adjacent β-strands as “a,” and the mean distance along β-strand between C_α atoms, whose side chains are directed to one side of the β-sheet, as “b,” the ratio b/a = √2 very precisely. This ratio ensures the most efficient packing of side hydrophobic groups at the outer surface of β-hyperboloid-8, forming, at the same time, the second by efficiency packing at its inner surface. © 1995 Wiley-Liss, Inc.     

Formation of engineered intersubunit disulfide bond in cytochrome bc1 complex disrupts electron transfer activity in the complex

Protein domain movement of the Rieske iron-sulfur protein has been speculated to play an essential role in the bifurcated oxidation of ubiquinol catalyzed by the cytochrome bc₁ complex. To better understand the electron transfer mechanism of the bifurcated ubiquinol oxidation at Qp site, we fixed the head domain of ISP at the cyt c₁ position by creating an intersubunit disulfide bond between two genetically engineered cysteine residues: one at position 141 of ISP and the other at position 180 of the cyt c₁ [S141C(ISP)/G180C(cyt c₁)]. The formation of a disulfide bond between ISP and cyt c₁ in this mutant complex is confirmed by SDS-PAGE and Western blot. In this mutant complex, the disulfide bond formation is concurrent with the loss of the electron transfer activity of the complex. When the disulfide bond is released by treatment with β-mercaptoethanol, the activity is restored. These results further support the hypothesis that the mobility of the head domain of ISP is functionally important in the cytochrome bc₁ complex. Formation of the disulfide bond between ISP and cyt c₁ shortens the distance between the [2Fe-2S] cluster and heme c₁, hence the rate of intersubunit electron transfer between these two redox prosthetic groups induced by pH change is increased. The intersubunit disulfide bond formation also decreases the rate of stigmatellin induced reduction of ISP in the fully oxidized complex, suggesting that an endogenous electron donor comes from the vicinity of the b position in the cytochrome b.     

An X-ray determination of the molecular interactions in hemoglobin C: a disease characterized by intraerythrocytic crystals.

The X-ray structure of cyanomet human hemoglobin C has been solved and refined, R ～27%. The molecular packing can be represented in two dimensions by two sets of parallel strands, one set in the $\text{b}$ direction and the other in the $\text{c}$ direction. Taken together the two sets of strands interconnect the molecules into square nets or layers where each molecule contacts its four nearest neighbors. Molecules in one layer are displaced in $\text{a}$ and $\text{b}$ so that they fit into the “holes” of the square arrays of the adjacent layers (normal to $\text{a}$) resulting in a pseudo body-centered cubic packing. This packing can account for the hemoglobin crystallization in and fragility of the erythrocytes. The aberrant β6A3 Lys residue is in a position to influence the crystal formation.     

Protein Engineering of the Quaternary Sulfiredoxin��Peroxiredoxin Enzyme��Substrate Complex Reveals the Molecular Basis for Cysteine Sulfinic Acid Phosphorylation

Oxidative stress can damage the active site cysteine of the antioxidant enzyme peroxiredoxin (Prx) to the sulfinic acid form, Prx-SO₂⁻. This modification leads to inactivation. Sulfiredoxin (Srx) utilizes a unique ATP-Mg²⁺-dependent mechanism to repair the Prx molecule. Using selective protein engineering that involves disulfide bond formation and site-directed mutagenesis, a mimic of the enzyme·substrate complex has been trapped. Here, we present the 2.1 Å crystal structure of human Srx in complex with PrxI, ATP, and Mg²⁺. The Cys⁵² sulfinic acid moiety was substituted by mutating this residue to Asp, leading to a replacement of the sulfur atom with a carbon atom. Because the Srx reaction cannot occur, the structural changes in the Prx active site that lead to the attack on ATP may be visualized. The local unfolding of the helix containing C52D resulted in the packing of Phe⁵⁰ in PrxI within a hydrophobic pocket of Srx. Importantly, this structural rearrangement positioned one of the oxygen atoms of Asp⁵² within 4.3 Å of the γ-phosphate of ATP bound to Srx. These observations support a mechanism where phosphorylation of Prx-SO₂⁻ is the first chemical step.     

Mechanisms of bovine liver glutamate dehydrogenase self-association. I. Kinetic evidence for a random association of polymer chains.

We have undertaken a study of the mechanism of bovine liver glutamate dehydrogenase self-association with scattered light temperature-jump and stopped-flow relaxation techniques. Our results indicate a “random association” mechanism in which association-dissociation reactions occur between all polymerized forms of the oligomer according to

where the specific rate-constants k_a and k_d are independent of chain length. At 15 °C we find k_a = 1.5 × 10⁶m⁻¹s⁻¹ and k_d = 5 s⁻¹. Standard thermodynamic functions and activation parameters have been determined from equilibrium and kinetic experiments at different temperatures. Large entropy effects and heat capacities indicate water participation in the self-aggregation process. We suggest that the rate-determining step in the association of glutamate dehydrogenase molecules is the “melting” of a layer of ordered water structure between two hydrophobic contact sites.     

Mode of binding of cytochrome b5 to phospholipid bilayers in lamellar structure

X-ray diffraction studies were made on the multilamellar systems produced by incubation of phospholipid bilayers and the membrane protein, cytochrome b₅, or non-membrane proteins (albumin, ovalbumin and β-lactoglobulin A) at pH 8.1 in aqueous 5 mM CaCl₂ solutions.Detergent-extracted cytochrome b₅ (soluble aggregate) forms two types of lamellar phase with dipalmitoyl phosphatidylcholine bilayers, depending upon the incubation temperature. One type, which has a repeat distance of 114Å, is formed above 34°C, where the binding of cytochrome b₅ to the bilayers is hydrophobic. The other type, with a repeat distance of 153 Å, is formed below 34°C, where the binding is electrostatic. It is also suggested that cytochrome b₅ is monomeric in the former phase but remains aggregated in the latter phase.When dimyristoyl phosphatidylcholine is used, the boundary temperature for the two types shifts to 12°C. These boundary temperatures coincide with the thermal pretransition points of hydrated dipalmitoyl phosphatidylcholine and dimyristoyl phosphatidylcholine, respectively.Trypsin-treated cytochrome b₅ (monomeric) and the three non-membrane proteins exhibit only binding of the electrostatic type to the bilayers, independently of the incubation temperature. The observed repeat distances suggest that in these cases two layers of protein molecules are incorporated between the bilayers.     

POCKET: A computer graphies method for identifying and displaying protein cavities and their surrounding amino acids

A new interactive graphics program is described that provides a quick and simple procedure for identifying, displaying, and manipulating the indentations, cavities, or holes in a known protein structure. These regions are defined as, e.g., the X₀, y₀, Z₀ values at which a test sphere of radius r can be placed without touching the centers of any protein atoms, subject to the condition that there is some x < x₀ and some x > x₀ where the sphere does touch the protein atoms. The surfaces of these pockets are modeled using a modification of the marching cubes algorithm. This modification provides identification of each closed surface so that by “clicking” on any line of the surface, the entire surface can be selected. The surface can be displayed either as a line grid or as a solid surface. After the desired “pocket” has been selected, the amino acid residues and atoms that surround this pocket can be selected and displayed. The protein database that is input can have more than one protein “segment,” allowing identification of the pockets at the interface between proteins. The use of the program is illustrated with several specific examples. The program is written in C and requires Silicon Graphics graphics routines.     

Structure of the cytosolic part of the subunit b-dimer of Escherichia coli F0F1-ATP synthase

The structure of the external stalk and its function in the catalytic mechanism of the F₀F₁-ATP synthase remains one of the important questions in bioenergetics. The external stalk has been proposed to be either a rigid stator that binds F₁ or an elastic structural element that transmits energy from the small rotational steps of subunits c to the F₁ sector during catalysis. We employed proteomics, sequence-based structure prediction, molecular modeling, and electron spin resonance spectroscopy using site-directed spin labeling to understand the structure and interfacial packing of the Escherichia coli b-subunit homodimer external stalk. Comparisons of bacterial, cyanobacterial, and plant b-subunits demonstrated little sequence similarity. Supersecondary structure predictions, however, show that all compared b-sequences have extensive heptad repeats, suggesting that the proteins all are capable of packing as left-handed coiled-coils. Molecular modeling subsequently indicated that b₂ from the E. coli ATP synthase could pack into stable left-handed coiled-coils. Thirty-eight substitutions to cysteine in soluble b-constructs allowed the introduction of spin labels and the determination of intersubunit distances by ESR. These distances correlated well with molecular modeling results and strongly suggest that the E. coli subunit b-dimer can stably exist as a left-handed coiled-coil.     

The α-helical membrane spanning domain of cytochrome b5 interacts with cytochrome P450 via nonspecific interactions

Cytochrome b₅ (cyt b₅) is an amphipathic membrane-bound heme protein found in the endoplasmic reticulum of eukaryotes. It consists of three domains, an N-terminal cytosolic, hydrophilic domain containing the heme, a short flexible linker and an α-helical membrane-spanning domain. This study investigated whether there are specific side chain helix–helix packing interactions between the COOH-terminal membrane anchor of cyt b₅ and cytochrome P450 (cyt P450) 2B4 in a purified reconstituted system. Alanine was inserted at six positions in the membrane anchor of cyt b₅. Insertion of alanine into an α-helix causes all amino acids at its carboxyl terminus to be rotated by 100°. The ability of the alanine insertion mutants of cyt b₅ to bind to cyt P450 2B4 was similar to that of the wild-type protein as was the ability of the mutant cyts b₅ to stimulate the metabolism of the anesthetic, methoxyflurane. These results demonstrate that the C-terminal hydrophobic α-helix of cyt b₅ does not interact with cyt P450 2B4 through a specific stereochemical fit of amino acid side chains, but rather through nonspecific interactions.     

The Q-cycle reviewed: How well does a monomeric mechanism of the bc1 complex account for the function of a dimeric complex?

Recent progress in understanding the Q-cycle mechanism of the bc₁ complex is reviewed. The data strongly support a mechanism in which the Q_o-site operates through a reaction in which the first electron transfer from ubiquinol to the oxidized iron–sulfur protein is the rate-determining step for the overall process. The reaction involves a proton-coupled electron transfer down a hydrogen bond between the ubiquinol and a histidine ligand of the [2Fe–2S] cluster, in which the unfavorable protonic configuration contributes a substantial part of the activation barrier. The reaction is endergonic, and the products are an unstable ubisemiquinone at the Q_o-site, and the reduced iron–sulfur protein, the extrinsic mobile domain of which is now free to dissociate and move away from the site to deliver an electron to cyt c₁ and liberate the H⁺. When oxidation of the semiquinone is prevented, it participates in bypass reactions, including superoxide generation if O₂ is available. When the b-heme chain is available as an acceptor, the semiquinone is oxidized in a process in which the proton is passed to the glutamate of the conserved -PEWY- sequence, and the semiquinone anion passes its electron to heme b_L to form the product ubiquinone. The rate is rapid compared to the limiting reaction, and would require movement of the semiquinone closer to heme b_L to enhance the rate constant. The acceptor reactions at the Q_i-site are still controversial, but likely involve a “two-electron gate” in which a stable semiquinone stores an electron. Possible mechanisms to explain the cyt b₁₅₀ phenomenon are discussed, and the information from pulsed-EPR studies about the structure of the intermediate state is reviewed.The mechanism discussed is applicable to a monomeric bc₁ complex. We discuss evidence in the literature that has been interpreted as shown that the dimeric structure participates in a more complicated mechanism involving electron transfer across the dimer interface. We show from myxothiazol titrations and mutational analysis of Tyr-199, which is at the interface between monomers, that no such inter-monomer electron transfer is detected at the level of the b_L hemes. We show from analysis of strains with mutations at Asn-221 that there are coulombic interactions between the b-hemes in a monomer. The data can also be interpreted as showing similar coulombic interaction across the dimer interface, and we discuss mechanistic implications.     

The Genetic Algorithm and the Conformational Search of Polypeptides and Proteins

Abstract

The genetic algorithm is a technique of function optimization derived from the principles of evolutionary theory. We have adapted it to perform conformational search on polypeptides and proteins. The algorithm was first tested on several small polypeptides and the 46 amino acid protein crambin under the AMBER potential energy function. The probable global minimum conformations of the polypeptides were located 90% of the time and a non-native conformation of crambin was located that was 150kcal/mol lower in potential energy than the minimized crystal structure conformation. Next, we used a knowledge-based potential function to predict the structures of melittin, pancreatic polypeptide, and crambin. A 2.31 Å ΔRMS conformation of melittin and a 5.33 Å ΔRMS conformation of pancreatic polypeptide were located by genetic algorithm-based conformational search under the knowledge-based potential function. Although the ΔRMS of pancreatic polypeptide was somewhat high, most of the secondary structure was correct. The secondary structure of crambin was predicted correctly, but the potential failed to promote packing interactions. Finally, we tested the packing aspects of our potential function by attempting to predict the tertiary structure of cytochrome b ₅₆₂ given correct secondary structure as a constraint. The final predicted conformation of cytochrome b ₅₆₂ was an almost completely extended continuous helix which indicated that the knowledge-based potential was useless for tertiary structure prediction. This work serves as a warning against testing potential functions designed for tertiary structure prediction on small proteins.     

Thermodynamically controlled supramolecular polymerization of cytochrome b562

A hemoprotein‐based supramolecular polymer that has a covalently linked heme moiety on the protein surface has been constructed based on interprotein heme–heme pocket interactions of the chemically modified apocytochrome b₅₆₂ ( 1 ‐H63C). The thermodynamic properties of the polymer have been investigated by means of size exclusion chromatography, UV–vis spectroscopy, and circular dichroism spectroscopy. The results indicate that, as with other synthetic systems reported so far, the 1 ‐H63C hemoprotein assembly is thermodynamically controlled in aqueous solution: the degree of polymerization is dependent on the 1 ‐H63C concentration and is modulated by the addition of the end‐capping units, native heme, and/or apocytochrome b₅₆₂ mutant (apoH63C). These properties suggest a potential use for the hemoprotein self‐assembly in preparation of stimuli‐responsive functional nanobiomaterials. © 2008 Wiley Periodicals, Inc. Biopolymers 91: 194–200, 2009. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com     

Solution structure of β2-microglobulin and insights into fibrillogenesis

The solution structure of human β₂-microglobulin (β₂-m) was determined by ¹H NMR spectroscopy and restrained modeling calculations. Compared to the crystal structure of type I major histocompatibility complex (MHC-I), where the protein is associated to the heavy-chain component, several differences are observed, i.e., increased separation between strands A and B, displacements of strand C′ and loop DE, shortening of strands D and E. These modifications can be considered as the prodromes of the amyloid transition. Even minor charge changes in response to pH, as is the case with H31 imidazole protonation, trigger the transition that starts with unpairing of strand A. The same mechanism accounts for the partial unfolding and fiber formation subsequent to Cu²⁺ binding which is shown to occur primarily at H31. Solvation of the protected regions in MHC-I decreases the tertiary packing by breaking the contiguity of the surface hydrophobic patches via surface charge cluster. Mutants or truncated forms of β₂-m can be designed to remove the instability from H31 titration or to enhance the instability through surface charge suppression. By monitoring the conformational evolution of wild-type protein and variants thereof, either in response or absence of external perturbation, valuable insights into intermediate structure and fibrillogenesis mechanisms are gained.     

The role of cytochrome b 5 structural domains in interaction with cytochromes P450

To understand the role of the structural elements of cytochrome b ₅ in its interaction with cytochrome P450 and the catalysis performed by this heme protein, we carried out comparative structural and functional analysis of the two major mammalian forms of membrane-bound cytochrome b ₅ — microsomal and mitochondrial, designed chimeric forms of the heme proteins in which the hydrophilic domain of one heme protein is replaced by the hydrophilic domain of another one, and investigated the effect of the highly purified native and chimeric heme proteins on the enzymatic activity of recombinant cytochromes P4503A4 and P45017A1 (CYP3A4 and CYP17A1). We show that the presence of a hydrophobic domain in the structure of cytochrome b ₅ is necessary for its effective interaction with its redox partners, while the nature of the hydrophobic domain has no significant effect on the ability of cytochrome b ₅ to stimulate the activity of cytochrome P450-catalyzed reactions. Thus, the functional properties of cytochrome b ₅ are mainly determined by the structure of the hemebinding domain.     

Intermembrane electron transport in the absence of added water-soluble carriers

Electron transport from untreated to mersalyzed microsomal vesicles at the level of NADH-cytochrome b₅ reductase or cytochrome b₅ has been demonstrated in the absence of added water-soluble electron carriers. A similar effect was shown in the systems “intact mitochondria — mersalyzed microsomes” and “mersalyzed mitochondria— untreated microsomes”. No measurable electron transport between intact and mersalyzed particles of inner mitochondrial membrane was found. The obtained data suggest that the capability to carry out intermembrane electron transfer is specific for NADH-cytochrome b₅ reductase and/or cytochrome b₅, localized in microsomal and outer mitochondrial membranes.     

The molecular structure of the receptor-ionophore complex at the neuromuscular junction.

A general theory of the molecular structure of receptors for transmitters based only on protein has been presented elsewhere (Smythies, 1974a,b). The acetylcholine receptor at the neuromuscular junction is postulated in particular to be based on a Kusnetsov-Ghokov grid with four sequencestwo “primary” chains A-x-B-cys-A-x-B where A = arg or lys and B = glu or phosphoser and two “secondary” chains of sequence -gly-x-gly-pro-x-ile-cys-asp-x- forming a symmetrical receptor cup of rectangular form. The present paper extends the model to include the gate over the adjacent ionophore (or “ion conductance modulator”: ICM) and the linking mechanism from receptor to gate. These are postulated to consist of a second Kusnetsov-Ghokov grid generated by a third “primary” chain along the side that covers the orifice to the ion conducting channel. The action of ACh is postulated to be to displace an hydrated Ca⁺⁺ ion from the receptor cup and to disrupt the AB rungs in the receptor grid. The middle primary chain then slides 14 Å and the AB links reform. This replaces a bulky amino acid pair normally blocking the ion channel by a less bulky amino acid pair and so hydrated ions can be transmitted. It is further postulated that snake neurotoxins (ACh blockers) in a specified conformation bind mainly to the ionophore grid and prevent the sliding filament mechanism from opening; whereas the snake “cardiotoxins” (ACh agonists)—in a specified conformation—bind to the same sliding filament mechanism in its “open” ionophore gate and prevent it being closed: and histrionicotoxin binds to the same open “gate” but blocks it physically. The hypothesis may rigorously be tested by experiment as it makes detailed predictions on the X-ray structure of the snake neurotoxins and cardiotoxins.     

Common structural features of cholesterol binding sites in crystallized soluble proteins

Cholesterol-protein interactions are essential for the architectural organization of cell membranes and for lipid metabolism. While cholesterol-sensing motifs in transmembrane proteins have been identified, little is known about cholesterol recognition by soluble proteins. We reviewed the structural characteristics of binding sites for cholesterol and cholesterol sulfate from crystallographic structures available in the Protein Data Bank. This analysis unveiled key features of cholesterol-binding sites that are present in either all or the majority of sites: i) the cholesterol molecule is generally positioned between protein domains that have an organized secondary structure; ii) the cholesterol hydroxyl/sulfo group is often partnered by Asn, Gln, and/or Tyr, while the hydrophobic part of cholesterol interacts with Leu, Ile, Val, and/or Phe; iii) cholesterol hydrogen-bonding partners are often found on α-helices, while amino acids that interact with cholesterol's hydrophobic core have a slight preference for β-strands and secondary structure-lacking protein areas; iv) the steroid's C21 and C26 constitute the “hot spots” most often seen for steroid-protein hydrophobic interactions; v) common “cold spots” are C8–C10, C13, and C17, at which contacts with the proteins were not detected. Several common features we identified for soluble protein-steroid interaction appear evolutionarily conserved.     

The pathway of electrons through QH2:cytochrome c oxidoreductase studied by pre-steady-state kinetics

(1) The kinetic behaviour of the prosthetic groups and the semiquinones in QH₂:cytochrome c oxidoreductase has been studied using a combination of the freeze-quench technique, low-temperature diffuse-reflectance spectroscopy, EPR and stopped flow. (2) In the absence of antimycin, cytochrome b-562 is reduced in two phases separated by a lag time. The initial very rapid reduction phase, that coincides with the formation of the antimycin-sensitive Q^?_in, is ascribed to high-potential cytochrome b-562 and the slow phase to low-potential cytochrome b-562. The two cytochromes are present in a 1:1 molar ratio. The lag time between the two reduction phases decreases with increasing pH. Both the [2 Fe-2 S] clusters and cytochrome c₁ are reduced monophasically under these conditions, but at a rate lower than that of the initial rapid reduction of cytochrome b-562. (3) In the presence of antimycin and absence of oxidant, cytochrome b-562 is still reduced biphasically, but there is no lag between the two phases. No Q^?_in is formed and both the Fe-S clusters and cytochrome c₁ are reduced biphasically, one-half being reduced at the same rate as in the absence of antimycin and the other half 10-times slower. (4) In the presence of antimycin and oxidant, the recently described antimycin-insensitive species of semiquinone anion, Q^?_out (De Vries, S., Albracht, S.P.J., Berden, J.A. and Slater, E.C. (1982) J. Biol. Chem. 256, 11996–11998) is formed at the same rate as that of the reduction of all species of cytochrome b. In this case cytochrome b is reduced in a single phase. (5) The reversible change of the line shape of the EPR spectrum of the [2Fe-2S] cluster 1 is caused by ubiquinone bound in the vicinity of this cluster. (6) The experimental results are consistent with the basic principles of the Q cycle. Because of the multiplicity, stoicheiometry and heterogeneous kinetics of the prosthetic groups, a Q cycle model describing the pathway of electrons through a dimeric QH₂:cytochrome c oxidoreductase is proposed.     

Crystals of glutamine synthetase from Escherichia coli.

Further details are given of crystals of glutamine synthetase prepared from Escherichia coli. Crystals of two kinds have been observed: (1) rhombic dodecahedra which correspond to the morphology of the crystals studied by Eisenberg et al. (1971) (and which were found by them to contain dodecamers), and (2) rhombohedra, reported here. Cell dimensions and packing considerations led to the consideration of two possible structures for the rhombohedral crystals. These we have called the “T = 7 structure” and the “B.C.C. structure”. The T = 7 structure would be related to that derived by Eisenberg and would contain dodecamers, but is inconsistent with our X-ray intensity data. The B.C.C. structure is considered more probable. It is built of cubic octomers or square tetramers. Electron micrographs of our glutamine synthetase preparations show a wide variety of aggregates, including dodecamers and tetramers. The unit cell dimensions of our crystals are $\text{a = 140 ± 2}\text{A}\text{̊}$, and $\text{c = 148 ± 2}\text{A}\text{̊}$. The Laue symmetry group is $\text{3}\text{̄}$m P3₁.