Location of the Heme in Horse Heart Ferricytochrome c by X-Ray Diffraction

The first resolution revolution in protein structure analysis: X-ray diffraction of polypeptide conformations and globular protein folds in 1950s and 1960s

Although determination of structures of biological molecules became a real possibility after the first X-ray analyses of crystals by the William Henry Bragg and his son Lawrence in 1913, the crystal structure determination of globular proteins became a possibility only in 1934 with the demonstration of X-ray diffraction from pepsin by J D Bernal and Dorothy Crowfoot, later Hodgkin, who had realised the importance of maintaining an aqueous environment for proteins in crystals. After a further 20 years of hard work by Max Perutz, John Kendrew and others the structures of haemoglobin and myoglobin emerged. Further innovation resulted in a revolution in X-ray diffraction studies in the 1960s, which focused first on polypeptides with alpha helix, beta strand and collagen polyproline helix structures, described in a review by David Davies in 1965 in the journal Progress in Biophysics, later to become Progress in Biophysics and Molecular Biology. It was followed in 1969 by a further detailed review by Tony North and David Phillips in the same journal on crystal structure a nalyses of globular proteins that successfully emerged soon after that of myoglobin. These included the structure of the first enzyme, lysozyme, followed by structures of chymotrypsin, trypsin, carboxypeptidase and many others. This first resolution revolution in X-ray analysis described in the two reviews is the subject of this retrospective analysis just over five decades later.

Study of cytochrome c-DNA interaction--evaluation of binding sites on the redox protein

Artificial assemblies consisting of the cationic cytochrome c (cyt c) and double-stranded DNA are interesting for the field of biohybrid systems because of the high electro-activity of the incorporated redox protein. However, little is known about the interactions between these two biomolecules. Here, the complex of reduced cyt c and a 41 base pair oligonucleotide was characterized in solution as a function of pH and ionic strength. Persistent cyt c-DNA agglomerates were observed by UV-vis and DLS (dynamic light scattering) at pH 5.0 and low ionic strength. The strength of the interaction was attenuated by raising the pH or the ionic strength. At pH 7.0 agglomerates were not formed, allowing interaction analysis by NMR spectroscopy. Using TROSY (transverse relaxation-optimized spectroscopy)-HSQC (heteronuclear single quantum coherence) experiments it was possible to identify the DNA binding site on the cyt c surface. Numerous residues surrounding the exposed heme edge of cyt c were involved in transient binding to DNA under these conditions. This result was supported by SEC (size exclusion chromatography) experiments at pH 7.0 showing that the interaction is sufficient for co-elution of cyt c and DNA.

Electrical characteristics of the ionic psn-junction as a model of the resting axon membrane

As a model for the resting axon membrane, we propose the ionic psn-junction. Its electrical characteristics can be determined in close analogy to the corresponding electronic semiconductor junction. Using the "semianalytic approximation", we calculated the electrical capacity and the ionic currents. In contrast to the abrupt pn-junction, the electrical capacity of the psn-junction turns out to be practically voltage-independent, as it is observed for the squid axon membrane. The passive ionic fluxes for K(+), Na(+) and Cl(-), as the main contributions to the total charge flux, are calculated and compared with literature data on the ion fluxes through the resting squid axon membrane as measured by use of radioactive tracers. From this comparison, the ionic permeabilities can be evaluated and used to compute the resting membrane conductivity, which is found to be close to the experimental value. Further evidence in favor of the proposed asymmetrical membrane structure and possible ways of its test by the methods of protein chemistry are discussed.

Protein surface recognition by porphyrin-based receptors

Protein surface recognition is largely unexplored owing to the large solvent exposed surface and lack of proper molecular scaffolds to match the binding residues. This review describes the design, synthesis, and fluorescence binding studies of functionalized porphyrins aimed at targeting surface residues of proteins through complementary recognition. The pattern of lysine residues surrounding the heme-edge of horse heart cytochrome c has been targeted by tetraphenylporphyrin and tetrabiphenylporphyrin receptors that bind with nano- and sub-nanomolar affinity. Other designed porphyrin-based receptors also recognize potassium channel as a target. The strategies for protein surface recognition offer a new use for porphyrins as molecular scaffolds.

Spectroscopic identification of heme axial ligands in HtsA that are involved in heme acquisition by Streptococcus pyogenes

The heme-binding proteins Shp and HtsA of Streptococcus pyogenes are part of the heme acquisition machinery in which Shp directly transfers its heme to HtsA. Mutagenesis and spectroscopic analyses were performed to identify the heme axial ligands in HtsA and to characterize axial mutants of HtsA. Replacements of the M79 and H229 residues, not the other methionine and histidine residues, with alanine convert UV-vis spectra of HtsA with a low-spin, hexacoordinate heme iron into spectra of high-spin heme complexes. Ferrous M79A and H229A HtsA mutants possess magnetic circular dichroism (MCD) spectra that are similar with those of proteins with pentacoordinate heme iron. Ferric M79A HtsA displays UV-vis, MCD, and resonance Raman (RR) spectra that are typical of a hexacoordinate heme iron with histidine and water ligands. In contrast, ferric H229A HtsA has UV-vis, MCD, and RR spectra that represent a pentacoordinate heme iron complex with a methionine axial ligand. Imidazole readily forms a low-spin hexacoordinate adduct with M79A HtsA with a K(d) of 40.9 muM but not with H229A HtsA, and cyanide binds to M79A and H229A with K(d) of 0.5 and 19.1 microM, respectively. The ferrous mutants rapidly bind CO and form simple CO complexes. These results establish the H229 and M79 residues as the axial ligands of the HtsA heme iron, indicate that the M79 side is more accessible to the solvent than the H229 side of the bound heme in HtsA, and provide unique spectral features for a protein with pentacoordinate, methionine-ligated heme iron. These findings will facilitate elucidation of the molecular mechanism and structural basis for rapid and direct heme transfer from Shp to HtsA.

The effect of ionic strength on the electron-transfer rate of surface immobilized cytochrome C

Horse heart cytochrome c was immobilized on four different self-assembled monolayer (SAM) films. The electron tunneling kinetics were studied in the different assemblies as a function of the ionic strength of the buffer solution using cyclic voltammetry. When cytochrome c is electrostatically immobilized, the standard electron exchange rate constant k0 decreases with the increase of the solution's ionic strength. In contrast, the protein covalently attached or ligated has a rate constant independent of the ionic strength. The inhomogeneity of electrostatically immobilized cytochrome c increases with the increase of the solution's ionic strength whereas that of the covalently attached protein is independent of the ionic strength. A comparison of these different electron-transfer behaviors suggests that the thermodynamically stable geometry of cytochrome c in the electrostatic assemblies is also an electron transfer favorable one. It suggests that the surface charges of cytochrome c are capable of guiding it into geometries in which its front surface faces the electron-transfer partner. The inhomogeneity observed in this study indicates that a distribution of cytochrome c orientations and thus a distribution of electron transfer rate constants exists.

Assemblies of dendrimers and proteins on carbon and gold electrodes

Dendritic macromolecules of two adjacent (G3.5 and G4) generations have been used to modify gold or carbon electrodes. The structure and stability of deposited films have been explored by quartz crystal microbalance (QCM), Surface Plasma Resonance (SPR) and electrochemistry. Dendrimers have been shown to adsorb spontaneously on electrode materials as compressed macromolecular films. They are able to inhibit (G3.5) or promote (G4) electroactive anionic species such as Fe(CN)(6)(3-/4-) used as a probe system. Mixed protein/dendrimer assemblies have been constructed with proteins differing in charge, nature of the prosthetic groups and sizes such as lysozyme, cytochrome c, polyhemic cytochrome c(3) or glucose oxidase. Generally, the stability of adsorbed films seems to be limited to one dendrimer/protein bilayer. Owing to the satisfactory stability of composite cytochrome c(3)/G3.5 or glucose oxidase/G4 films, biosensing applications are described for metal bioremediation and glucose detection, respectively.

Order Parameters and Orientation Distributions of Solution Adsorbed and Microcontact Printed Cytochrome c Protein Films on Glass and ITO

The structure of solution adsorbed and microcontact printed (muCP) cytochrome c (cyt c) films on glass and indium tin oxide (ITO) was investigated using attenuated total reflectance (ATR) and total internal reflectance fluorescence (TIRF) spectroscopies to determine the orientation of the heme groups in the films. The second and fourth order parameters of the heme as well as information on the angle between the absorption and emission dipoles of the heme, gamma, were experimentally determined. The order parameters of the heme are related to the order parameters of the protein molecule using the known angle between the heme plane and the electrostatic dipole moment of the cyt c protein. The effect of the surface roughness of the substrates (glass and ITO) was also taken into account quantitatively using AFM data. Physically possible order parameters were obtained for the heme group in both solution adsorbed and muCP films, but not for the electrostatic dipole moment of the protein. In addition, the experimental values of {cos2 gamma} for immobilized zinc-substituted cyt c are greater than the values of {cos2 gamma} determined in viscous solutions, which could be an indication that the environment of the heme groups changes upon adsorption. The electron transfer behavior of solution adsorbed and muCP films on ITO, determined using electrochemical methods, is compared to their orientation distribution and surface coverage as determined by spectroscopic methods.

Determination of Anisotropic Optical Constants and Surface Coverage of Molecular Films Using Polarized Visible ATR Spectroscopy. Application to Adsorbed Cytochrome c Films

This article describes a method to determine the anisotropic optical constants and surface coverage of molecular films using polarized attenuated total reflectance (ATR) absorbance measurements. We have extended the transfer-matrix formalism to describe birefringent and dichroic films in ATR geometries and have combined it with an iterative numerical procedure to determine the anisotropic values of both the real (n) and imaginary (k) parts of the complex refractive index of the film under investigation. Anisotropic values of the imaginary part of the refractive index (k) allow for the determination of the surface coverage and one order parameter of the film. To illustrate this approach, we have used cytochrome c (cyt c) protein films adsorbed to glass and indium tin oxide (ITO) surfaces. Experimental results show that cyt c films on these surfaces, which were formed under identical conditions, have significant differences in their surface coverages (11.2 +/- 0.4 pmol/cm(2) on glass and 21.7 +/- 0.9 pmol/cm(2) on ITO); however, their order parameters <cos(2)theta> are similar (0.30 +/- 0.02 on glass and 0.36 +/- 0.04 on ITO).

Buildup of polyelectrolyte-protein multilayer assemblies on gold electrodes. Role of the hydrophobic effect

The buildup of layer-by-layer assemblies onto gold surfaces from water-soluble charged polyelectrolytes and proteins is examined using quartz crystal microgravimetry (QCM) and electrochemical techniques. Polyelectrolytes such as poly(styrenesulfonate) and poly(ester sulfonic acid) (Eastman AQ-29D polymer) adsorb spontaneously onto gold, contrary to poly(ethyleneimine). From the modification of the gold surface with a thiol and specific adsorption of polymers under polarization conditions, it is concluded that the hydrophobicity of the gold surface seems to be a determining factor in the adsorption process. Alternate adsorption onto gold resonators first coated with AQ-29D polymer gives stable multilayer films in the case of positively charged lysozyme (pI = 11) or polyheme Desulfovibrio vulgaris Hildenborough cytochrome c3 (pI = 10.5). QCM frequency changes with the number of adsorption steps suggest that a linear increase in film mass occurs. Desulfomicrobium norvegicum polyheme cytochrome c3 (pI = 7), which has a null global charge at neutral pH, is shown to give also stable multilayer AQ-29D/cytochrome c3 films, suggesting that several types of interactions, especially the hydrophobic effect, are involved in the buildup process.

29-Methylidene-2,3-oxidosqualene derivatives as stereospecific mechanism-based inhibitors of liver and yeast oxidosqualene cyclase

Two pairs of isomers (18Z)- (8), (18E)-29-methylidene-2,3-oxidohexanorsqualene (21), and (18Z)- (31), (18E)-29-methylidene-2,3-oxidosqualene (34), have been obtained in a fully stereospecific manner, as inhibitors of rat and yeast oxidosqualene cyclase. A new method for the synthesis of C22 squalene aldehyde 2,3-epoxide is reported, as well as that of other 19-modified 2,3-oxidosqualene analogues. We found that the activity is the opposite in the two series: the (E)-hexanormethylidene 21 and the (Z)-methylidene 31 are potent and irreversible inhibitors of oxidosqualene cyclase, while (Z)-hexanormethylidene 8 and (E)-methylidene 34 are almost completely inactive. Reduction of the 18,19-double bond, such as in 39, eliminates the activity, while removal of both of the 19-linked groups such as in heptanor derivative 40 greatly reduces inhibition of the enzyme. (E)-Hexanormethylidene 21 results the first irreversible inhibitor of the series toward the yeast enzyme.

Linear dichroism spectroscopy of nucleic acids

This review will consider solution studies of structure and interactions of DNA and DNA complexes using linear dichroism spectroscopy, with emphasis on the technique of orientation by flow. The theoretical and experimental background to be given may serve, in addition, as a general introduction into the state of the art of linear dichroism spectroscopy, particularly as it is applied to biophysical problems.

Lipid/myelin basic protein multilayers. A model for the cytoplasmic space in central nervous system myelin

A multilayered complex forms when a solution of myelin basic protein is added to single-bilayer vesicles formed by sonicating myelin lipids. Vesicles and multilayers have been studied by electron microscopy, biochemical analysis, and X-ray diffraction. Freeze-fracture electron microscopy shows well-separated vesicles before myelin basic protein is added, but afterward there are aggregated, possibly multilayered, vesicles and extensive planar multilayers. The vesicles aggregate and fuse within seconds after the protein is added, and the multilayers form within minutes. No intra-bilayer particles are seen, with or without the protein. Some myelin basic protein, but no lipid, remains in the supernatant after the protein is added and the complex sedimented for X-ray diffraction. A rather variable proportion of the protein is bound. X-ray diffraction patterns show that the vesicles are stable in the absence of myelin basic protein, even under high g-forces. After the protein is added, however, lipid/myelin basic protein multilayers predominate over single-bilayer vesicles. The protein is in every space between lipid bilayers. Thus the vesicles are torn open by strong interaction with myelin basic protein. The inter-bilayer spaces in the multilayers are comparable to the cytoplasmic spaces in central nervous system myelins . The diffraction indicates the same lipid bilayer thickness in vesicles and multilayers, to within 1 A. By comparing electron-density profiles of vesicles and multilayers, most of the myelin basic protein is located in the inter-bilayer space while up to one-third may be inserted between lipid headgroups. When cytochrome c is added in place of myelin basic protein, multilayers also form. In this case the protein is located entirely outside the unchanged bilayer. Comparison of the various profiles emphasizes the close and extensive apposition of myelin basic protein to the lipid bilayer. Numerous bonds may form between myelin basic protein and lipids. Cholesterol may enhance binding by opening gaps between diacyl-lipid headgroups.

A study of the redox potentials and electron transfer rates of several naturally occurring and synthetic iron porphyrins in DMF

The reduction potentials and formal electron transfer rate constants of several iron porphyrins were measured in DMF by the technique of cyclic voltammetry. The ease of each reduction was found to be a function of porphyrin ring basicity and was dependent on the type of electrode reaction. Greatest effects of ring basicity were observed for pi anion radical formation whil smaller effects were obtained for reactions involving the central metal. Electron transfer rate constants for the ferric-ferrous reaction also varied with ring basicity and paralled trends in the redox potentials, that is, the most basic porphyrin yielded the most difficult reduction, both kinetically and thermo-dynamically, while the least basic prophyrin yielded the most facile kinetic and thermodynamic reduction. Based on this data a mechanism of ferric-ferrous electron transfer involving transfer via the pi ring system is proposed.

[Structure and function of the endoplasmic reticulum]

After a general review of enzyme topology and the molecular architecture of endoplasmic reticulum the latest research results are discussed. Microsomal enzymes do not occur in specialized regions of the endoplasmic reticulum but are uniformly distributed over the entire membrane system. Functionally associated enzymes are also located in the direct vicinity of the membrane. It has been shown that the catalytic activity of integral enzyme proteins depends on phospholipid and membrane structure. These membrane-bound lipoproteid complexes exert specific effects as vectorial enzyme catalysts. The endoplasmic reticulum is active is active in the intracellular transport of metabolites.