The Photosynthetic Reaction Center from the Purple Bacterium Rhodopseudomonas viridis

Photovoltaic Cells Using Composite Nanoclusters of Porphyrins and Fullerenes with Gold Nanoparticles

Novel organic solar cells have been prepared using quaternary self-organization of porphyrin (donor) and fullerene (acceptor) units by clusterization with gold nanoparticles on nanostructured SnO2 electrodes. First, porphyrin-alkanethiolate monolayer-protected gold nanoparticles (H2PCnMPC: n is the number of methylene groups in the spacer) are prepared (secondary organization) starting from the primary component (porphyrin-alkanethiol). These porphyrin-modified gold nanoparticles form complexes with fullerene molecules (tertiary organization), and they are clusterized in acetonitrile/toluene mixed solvent (quaternary organization). The highly colored composite clusters can then be assembled as three-dimensional arrays onto nanostructured SnO2 films to afford the OTE/SnO2/(H2PCnMPC+C60)m electrode using an electrophoretic deposition method. The film of the composite clusters with gold nanoparticle exhibits an incident photon-to-photocurrent efficiency (IPCE) as high as 54% and broad photocurrent action spectra (up to 1000 nm). The power conversion efficiency of the OTE/SnO2/(H2PC15MPC+C60)m composite electrode reaches as high as 1.5%, which is 45 times higher than that of the reference system consisting of the both single components of porphyrin and fullerene.

Tyrosyl radicals in Photosystem II

In PSII, there are two redox-active tyrosines, D and Z, with different midpoint potentials and different reduction kinetics. The factors responsible for these functional differences have not yet been elucidated. Recent model compound studies of tyrosinate and of tyrosine-containing dipeptides have demonstrated that perturbations of the amino and amide/imide group occur when the tyrosyl aromatic ring is oxidized [J. Am. Chem. Soc. 124 (2002) 5496]. Accompanying density functional calculations suggested that this perturbation is due to spin density delocalization from the aromatic ring onto the amino nitrogen. The implication of this finding is that spin density delocalization may occur in redox-active, tyrosine-containing enzymes, like Photosystem II. In this paper, we review the supporting evidence for the hypothesis that tyrosyl radical spin density delocalizes into the peptide bond in a conformationally sensitive, sequence-dependent manner. Our experimental measurements on tyrosyl radicals in dipeptides have suggested that the magnitude of the putative spin migration may be sequence-dependent. Vibrational spectroscopic studies on the tyrosyl radicals in Photosystem II, which are consistent with spin migration, are reviewed. Migration of the unpaired spin may provide a mechanism for control of the direction and possibly the rate of electron transfer.

Influence of cation-pi interactions in different folding types of membrane proteins

Cation-pi interactions play an important role to the stability of protein structures. In this work, we analyze the influence of cation-pi interactions in three-dimensional structures of membrane proteins. We found that transmembrane strand (TMS) proteins have more number of cation-pi interactions than transmembrane helical (TMH) proteins. In TMH proteins, both the positively charged residues Lys and Arg equally experience favorable cation-pi interactions whereas in TMS proteins, Arg is more likely than Lys to be in such interactions. There is no relationship between number of cation-pi interactions and number of residues in TMH proteins whereas a good correlation was observed in TMS proteins. The average cation-pi interaction energy for TMH proteins is -16 kcal/mol and that for TMS proteins is -27 kcal/mol. The pair-wise cation-pi interaction energy between aromatic and positively charged residues showed that Lys-Trp energy is stronger in TMS proteins than TMH proteins; Arg-Phe, Arg-Tyr and Lys-Phe have higher energy in TMH proteins than TMS proteins. The decomposition of energies into electrostatic and van der Waals revealed that the contribution from electrostatic energy is twice as that from van der Waals energy in both TMH and TMS proteins. The results obtained in the present study would be helpful to understand the contribution of cation-pi interactions to the stability of membrane proteins.

Electronic structure, chemical bond, and optical spectra of metal bis(porphyrin) complexes: a DFT/TDDFT study of the bis(porphyrin)M(IV) (M = Zr, Ce, Th) series

The electronic absorption spectra of the bis(porphyrin) sandwich complexes of the metals Zr, Ce, and Th are studied with time-dependent density functional theory (TDDFT). A ground-state electronic structure analysis reveals that the highest occupied one-electron levels are, as expected, composed of the porphyrin a(1u) and a(2u) highest occupied orbitals (the Gouterman orbitals), but the level pattern is not simply a pair of low-lying nearly degenerate in-phase combinations and a pair of high-lying approximately degenerate antibonding combinations. Instead, the a(1u) split strongly and the a(2u) do not. Since the calculated spectrum agrees very well with experiment, the assignment leaves little doubt that although the experimental spectrum has porphyrin-like features, such as the well-known Q and B bands, the actual composition of the states is rather different from that in porphyrin. In particular the strong mixing of a(1u) --> e(g) and a(2u) --> e(g) is absent, there is mixing with excitations of non-Gouterman type, and, in Ce, ring to metal charge-transfer transitions play an important role. The composition of the states as calculated in this work does not lead to a classification of the excitations as purely "excitonic" or "charge-resonance".

Bicelle crystallization: a new method for crystallizing membrane proteins yields a monomeric bacteriorhodopsin structure

Obtaining crystals of membrane proteins that diffract to high resolution remains a major stumbling block in structure determination. Here we present a new method for crystallizing membrane proteins from a bicelle forming lipid/detergent mixture. The method is flexible and simple to use. As a test case, bacteriorhodopsin (bR) from Halobacterium salinarum was crystallized from a bicellar solution, yielding a new bR crystal form. The crystals belong to space group P2(1) with unit cell dimensions of a=45.0 A, b=108.9 A, c=55.9 A, beta=113.58 degrees and a dimeric asymmetric unit. The structure was solved by molecular replacement and refined at 2.0 A resolution. In all previous bR structures the protein is organized as a parallel trimer, but in the crystals grown from bicelles, the individual bR subunits are arranged in an antiparallel fashion.

The influence of structure and redox state of prenylquinones on thermotropic phase behaviour of phospholipids in model membranes

Our study was aimed to investigate the significance of the isoprenoid side chain size as well as redox state of the quinone ring for interaction of two main classes of prenylquinones: plastoquinones (PQ) and ubiquinones (UQ) with lipid bilayers. By use of differential scanning calorimetry (DSC) we have followed the thermotropic behaviour of multilamellar vesicles prepared from dipalmitoylphosphatidylcholine (DPPC) upon incorporation of increasing amount (1.3-12 mol%) of quinone (quinol) molecules. Our studies reveal that as the side chain is shorter (from 9 to 2 isoprenoid units) the height of the calorimetric profiles is reduced and the temperature of the main transition of DPPC (T(m)) decreases (T(m)=39.4 degrees C for a sample with 12 mol% of PQ-2), and then increases up to 39.8 degrees C for PQ-1. For the samples containing quinols the effect is more pronounced even at lower concentration. The greater influence of the added prenylquinones on the pretransition demonstrates a stronger distortion of the DPPC packing in the gel state. It seems that this is the isoprenoid side chain length rather than the redox state of prenylquinones that determines their effectiveness in perturbation of thermotropic properties of lipid bilayer.

Scanning electrochemical microscopy of living cells. 3. Rhodobacter sphaeroides

The scanning electrochemical microscope (SECM) was used to probe the redox activity of individual purple bacteria (Rhodobacter sphaeroides). The approaches developed in our previous studies of mammalian cells were expanded to measure the rates and investigate the pathway of transmembrane charge transfer in bacteria. The two groups of redox mediators (i.e., hydrophilic and hydrophobic redox species) were used to shuttle the electrons between the SECM tip electrode in solution and the redox centers inside the cell. The analysis of the dependencies of the measured rate constant on formal potential and concentration of mediator species in solution yielded information about the permeability of the outer cell membrane to different ionic species and intracellular redox properties. The maps of redox reactivity of the cell surface were obtained with a micrometer or submicrometer spatial resolution.

Electrochemical reactions of redox cofactors in Rhodobacter sphaeroides reaction center proteins in lipid films

Cyclic voltammetry of thin films made from the lipid dimyristoylphosphatidyl choline and reaction centers from the purple bacterium Rhodobacter sphaeroides on pyrolytic graphite electrodes in bromide-free pH 8 buffers at 4 degrees C revealed an oxidation peak at 0.98 V and a reduction peak at -0.17 V vs. NHE. No reverse CV peaks were found, suggesting chemical irreversibility. The reduction peak disappeared for reaction centers depleted of quinones, suggesting that the peak represents reduction of this cofactor. The oxidation peak showed a catalytic current increase in the presence of small amounts of ferrous cytochrome c, and decreased by 85% when illuminated by visible light, suggesting assignment to the primary donor (P) cofactor. While oxidized primary donor P(+) is destroyed upon electrochemical formation in the film, reaction of ferrous cyt c with P(+) suggests its persistence in the films on the microsecond time scale.

Solid-state NMR structure determination of melittin in a lipid environment

Solid-state (13)C NMR spectroscopy was used to investigate the three-dimensional structure of melittin as lyophilized powder and in ditetradecylphosphatidylcholine (DTPC) membranes. The distance between specifically labeled carbons in analogs [1-(13)C]Gly3-[2-(13)C]Ala4, [1-(13)C]Gly3-[2-(13)C]Leu6, [1-(13)C]Leu13-[2-(13)C]Ala15, [2-(13)C]Leu13-[1-(13)C]Ala15, and [1-(13)C]Leu13-[2-(13)C]Leu16 was measured by rotational resonance. As expected, the internuclear distances measured in [1-(13)C]Gly3-[2-(13)C]Ala4 and [1-(13)C]Gly3-[2-(13)C]Leu6 were consistent with alpha-helical structure in the N-terminus irrespective of environment. The internuclear distances measured in [1-(13)C]Leu13-[2-(13)C]Ala15, [2-(13)C]Leu13-[1-(13)C]Ala15, and [1-(13)C]Leu13-[2-(13)C]Leu16 revealed, via molecular modeling, some dependence upon environment for conformation in the region of the bend in helical structure induced by Pro14. A slightly larger interhelical angle between the N- and C-terminal helices was indicated for peptide in dry or hydrated gel state DTPC (139 degrees -145 degrees ) than in lyophilized powder (121 degrees -139 degrees ) or crystals (129 degrees ). The angle, however, is not as great as deduced for melittin in aligned bilayers of DTPC in the liquid-crystalline state (approximately 160 degrees ). The study illustrates the utility of rotational resonance in determining local structure within peptide-lipid complexes.

Mutations within the putative membrane-spanning domain of the simian immunodeficiency virus transmembrane glycoprotein define the minimal requirements for fusion, incorporation, and infectivity

The membrane-spanning domain (MSD) of a number of retroviral transmembrane (TM) glycoproteins, including those from the human and simian immunodeficiency viruses (HIV and SIV), have been predicted to contain a charged arginine residue. The wild-type SIV TM glycoprotein is 354 amino acids long. The entire putative cytoplasmic domain of SIV (amino acids 193 to 354) is dispensable for virus replication in vitro, and such truncation-containing viruses are capable of reaching wild-type titers after a short delay. We show here that further truncation of eight additional amino acids to TM185 results in a protein that lacks fusogenicity but is, nevertheless, efficiently incorporated into budding virions. By analyzing a series of nonsense mutations between amino acids 193 and 185 in Env expression vectors and in the SIVmac239 proviral clone, a region of the SIV TM that contains the minimum requirement for glycoprotein-mediated cell-to-cell fusion and that for virus replication was identified. Virus entry and infectivity were evident in truncations to a minimum of 189 amino acids, whereas cell-cell fusion was observed for a protein of only 187 amino acids. Glycoprotein was efficiently incorporated into budding virions in truncations up to 185 amino acids, indicating that such proteins are membrane anchored and are transported to the cell surface. However, truncation of the TM to 180 amino acids resulted in a protein that displays a transport defect and may be retained in the endoplasmic reticulum. Based on our analyses of these mutants, an alternative model for the MSD of SIV is proposed. Our model suggests that membrane-imbedded charged residues can be neutralized by side-chain interactions with lipid polar head groups. As a consequence, the membrane-spanning region can be reduced by more than a helical turn. This new model accounts for the ability of truncations within the predicted MSD to remain membrane anchored and maintain biological activity.

Modeling the bacterial photosynthetic reaction center. 4. The structural, electrochemical, and hydrogen-bonding properties of 22 mutants of Rhodobacter sphaeroides

Site-directed mutagenesis has been employed by a number of groups to produce mutants of bacterial photosynthetic reaction centers, with the aim of tuning their operation by modifying hydrogen-bond patterns in the close vicinity of the "special pair" of bacteriochlorophylls P identical with P(L)P(M). Direct X-ray structural measurements of the consequences of mutation are rare. Attention has mostly focused on effects on properties such as carbonyl stretching frequencies and midpoint potentials to infer indirectly the induced structural modifications. In this work, the structures of 22 mutants of Rhodobacter sphaeroides have been calculated using a mixed quantum-mechanical molecular-mechanical method by modifying the known structure of the wild type. We determine (i) the orientation of the 2a-acetyl groups in the wild type, FY(M197), and FH(M197) series mutants of the neutral and oxidized reaction center, (ii) the structure of the FY(M197) mutant and possible water penetration near the special pair, (iii) that significant protein chain distortions are required to assemble some M160 series mutants (LS(M160), LN(M160), LQ(M160), and LH(M160) are considered), (iv) that there is competition for hydrogen-bonding between the 9-keto and 10a-ester groups for the introduced histidine in LH(L131) mutants, (v) that the observed midpoint potential of P for HL(M202) heterodimer mutants, including one involving also LH(M160), can be correlated with the change of electrostatic potential experienced at P(L), (vi) that hydrogen-bond cleavage may sometimes be induced by oxidation of the special pair, (vii) that the OH group of tyrosine M210 points away from P(M), and (viii) that competitive hydrogen-bonding effects determine the change in properties of NL(L166) and NH(L166) mutants. A new technique is introduced for the determination of ionization energies at the Koopmans level from QM/MM calculations, and protein-induced Stark effects on vibrational frequencies are considered.

Influence of bromide on electrochemistry of photosynthetic reaction center films on gold electrodes

A strong influence of bromide ion was found on voltammetry of layered films of photosynthetic reaction center (RC) protein and polyions on gold electrodes. Similar, but not identical, cyclic voltammetry peaks were observed for polyion films on gold with and without RC when the buffer solutions contained bromide ion. CVs of RC films were quite different in the absence of bromide. These new findings suggest that previously published results were biased by significant background peaks involving bromide ion adsorption/desorption.

Role of medium--and long-range interactions in discriminating globular and membrane proteins

The analysis of inter-residue interactions in protein structures provides considerable insight to understand their folding and stability. We have previously analyzed the role of medium- and long-range interactions in the folding of globular proteins. In this work, we study the distinct role of such interactions in the three-dimensional structures of membrane proteins. We observed a higher number of long-range contacts in the termini of transmembrane helical (TMH) segments, implying their role in the stabilization of helix-helix interactions. The transmembrane strand (TMS) proteins are having appreciably higher long-range contacts than that in all-beta class of globular proteins, indicating closer packing of the strands in TMS proteins. The residues in membrane spanning segments of TMH proteins have 1.3 times higher medium-range contacts than long-range contacts whereas that of TMS proteins have 14 times higher long-range contacts than medium-range contacts. Residue-wise analysis indicates that in TMH proteins, the residues Cys, Glu, Gly, Pro, Gln, Ser and Tyr have higher long-range contacts than medium-range contacts in contrast with all-alpha class of globular proteins. The charged residue pairs have higher medium-range contacts in all-alpha proteins, whereas hydrophobic residue pairs are dominant in TMH proteins. The information on the preference of residue pairs to form medium-range contacts has been successfully used to discriminate the TMH proteins from all-alpha proteins. The statistical significance of the results obtained from the present study has been verified using randomized structures of TMH and TMS protein templates.

Amino acid distributions in integral membrane protein structures

Advances in structure determination of membrane proteins enable analysis of the propensities of amino acids in extramembrane versus transmembrane locations to be performed on the basis of structure rather than of sequence and predicted topology. Using 29 available structures of integral membrane proteins with resolutions better than 4 A the distributions of amino acids in the transmembrane domains were calculated. The results were compared to analysis based on just the sequences of the same transmembrane alpha-helices and significant differences were found. The distribution of residues between transmembrane alpha-helices and beta-strands was also compared. Large hydrophobic (Phe, Leu, Ile, Val) residues showed a clear preference for the protein surfaces facing the lipids for beta-barrels, but in alpha-helical proteins no such preference was seen, with these residues equally distributed between the interior and the surface of the protein. A notable exception to this was alanine, which showed a slight preference for the interior of alpha-helical membrane proteins. Aromatic residues were found to follow saddle-like distributions preferring to be located in the lipid/water interfaces. The resultant 'aromatic belts' were spaced more closely for beta-barrel than for alpha-helical membrane proteins. Charged residues could be shown to generally avoid surfaces facing the bilayer although they were found to occur frequently in the transmembrane region of beta-barrels. Indeed detailed comparison between alpha-helical and beta-barrel proteins showed many qualitative differences in residue distributions. This suggests that there may be subtle differences in the factors stabilising beta-barrels in bacterial outer membranes and alpha-helix bundles in all other membranes.

Structure and Photophysics of β-Octafluoro-meso-tetraarylporphyrins

The structure of THF-coordinated [2,3,7,8,12,13,17,18-octafluoro-5,10,15,20-tetraphenylporphinato]zinc, Zn(F(8)TPP).THF, and photophysical studies of 2,3,7,8,12,13,17,18-octafluoro-5,10,15,20-tetraphenylporphyrin, F(8)TPP, Zn(F(8)TPP), 2,3,7,8,12,13,17,18-octafluoro-5,10,15,20-tetrakis(pentafluorophenyl)porphyrin, F(28)TPP, and [2,3,7,8,12,13,17,18-octafluoro-5,10,15,20-tetrakis(pentafluorophenyl)porphinato]zinc, Zn(F(28)TPP), in benzonitrile, are reported. A key point from these studies is that the octafluorinated F(8)TPP and perfluorinated F(28)TPP porphyrins possess similar absorption spectra, but dissimilar X-ray crystal structures and disparate photophysical characteristics. These data cannot be easily accommodated within currently accepted theories which relate macrocycle distortion and optoelectronic properties.

Molecular biology of weed control

The vast commercial effort to utilize chemical and molecular tools to solve weed control problems has had a major impact on the basic biological sciences as well as benefits to agriculture, and the first generation of transgenic products has been successful, while somewhat crude. More sophisticated products are envisaged and expected. Biotechnologically-derived herbicide-resistant crops have been a considerable benefit, yet in some cases there is a risk that the same useful transgenes may introgress into related weeds, specifically the weeds that are hardest to control without such transgenic crops. Biotechnology can also be used to mitigate the risks. Molecular tools should be considered for weed control without the use of, or with less chemicals, whether by enhancing crop competitiveness with weeds for light, nutrients and water, or via allelochemicals. Biocontrol agents may become more effective as well as more safe when rendered hypervirulent yet non-spreading by biotechnology. There might be ways to disperse deleterious transposons throughout weed populations, obviating the need to modify the crops.

Reaction centres of purple bacteria

The bacterial reaction centre is undoubtedly one of the most heavily studied electron transfer proteins and, as this article has tried to describe, it has made some unique contributions to our understanding of biological electron transfer and coupled protonation reactions, and has provided fascinating information in areas that concern basic properties such as protein heterogeneity and protein dynamics. Despite intensive study, much remains to be learned about how this protein catalyses the conversion of solar energy into a form that can be used by the cell. In particular, the dynamic roles played by the protein are still poorly understood. The wide range of time-scales over which the reaction centre catalyses electron transfer, and the relative ease with which electron transfer can be triggered and monitored, will ensure that the reaction centre will continue to be used as a laboratory for testing ideas about the nature of biological electron transfer for many years to come.

Incorporation of plastoquinone and ubiquinone into liposome membranes studied by HPLC analysis. The effect of side chain length and redox state of quinone

The efficiency of incorporation of plastoquinones and ubiquinones into phospholipid liposomes has been studied. The representatives of short (PQ1 and UQ1) middle (PQ4 and UQ4) and long (PQ9, UQ9 and UQ10) prenylquinones have been used to investigate the effect of quinone side chain length. The properties of hydroquinones have been also thoroughly examined in relation to the quinone forms. The extraction procedure was modified and further developed which enables removing of nonincorporated quinone by pentane washing and then determination of quinone content inside the lipid bilayer. The quantitatively evaluation of the amount of prenylquinone was assayed by means of HPLC analysis which offers much greater sensitivity and could be easily applied in case of hydroquinones. It has been found that PQ1 and UQ1 as well as their reduced forms were present mainly (about 80%) in the aqueous phase, when attempting to introduce them into phospholipid bilayer. In case of quinones having four and more isoprenyl units in side chain, a high level of quinone incorporation, ranging about 95%, was observed. The results pointed out that when comparing the effects of different exogenous quinones on membrane related processes, one has to consider the effectiveness of their incorporation within lipid bilayer.

Effects of detergents on specific activity and enantioselectivity of the epoxide hydrolase from Rhodotorula glutinis

The yeast Rhodotorula glutinis contains an enantioselective epoxide hydrolase. Previous work showed that the enzyme is a membrane-associated enzyme that can be solubilised from the membranes by a detergent treatment. Now, the effect of detergents on reaction rate and particularly enantioselectivity was investigated. Three types of detergents were tested: non-ionic, anionic and zwitterionic. Non-ionic detergents stimulated the specific activity of the enzyme. Enantioselectivity of the enzyme was strongly affected by several detergents. Thesit and sucrosemonolaurate had the most pronounced effects and enantiomeric ratios were strongly enhanced. The effects are most likely due to the ability of detergents to stabilise membrane-proteins by forming micelles and thus mimicking the membrane structure.

Re-emerging structures: continuing crystallography of the bacterial reaction centre

The reaction centre is nature's solar battery, and is found in a number of variations on a common theme in plants, algae and photosynthetic bacteria. During the last 20 years, a combination of X-ray crystallography, spectroscopy and mutagenesis has provided increasingly detailed insights into the mechanism of light energy transduction in the bacterial reaction centre. This mini-review looks at the application of X-ray crystallography to the bacterial reaction centre, focussing in particular on recent information on the structural consequences of site-directed mutagenesis, the roles played by water molecules in the reaction centre, the mechanism of ubiquinone reduction, and studies of the phospholipid environment of the protein.

Diversity and origin of alternative NADH:ubiquinone oxidoreductases

Mitochondria from various organisms, especially plants, fungi and many bacteria contain so-called alternative NADH:ubiquinone oxidoreductases that catalyse the same redox reaction as respiratory chain complex I, but do not contribute to the generation of transmembrane proton gradients. In eucaryotes, these enzymes are associated with the mitochondrial inner membrane, with their NADH reaction site facing either the mitochondrial matrix (internal alternative NADH:ubiquinone oxidoreductases) or the cytoplasm (external alternative NADH:ubiquinone oxidoreductases). Some of these enzymes also accept NADPH as substrate, some require calcium for activity. In the past few years, the characterisation of several alternative NADH:ubiquinone oxidoreductases on the DNA and on the protein level, of substrate specificities, mitochondrial import and targeting to the mitochondrial inner membrane has greatly improved our understanding of these enzymes. The present review will, with an emphasis on yeast model systems, illuminate various aspects of the biochemistry of alternative NADH:ubiquinone oxidoreductases, address recent developments and discuss some of the questions still open in the field.

Guidelines for membrane protein engineering derived from de novo designed model peptides

Notwithstanding great advances in the engineering and structural analysis of globular proteins, relatively limited success has been achieved with membrane proteins--due largely to their intrinsic high insolubility and the concomitant difficulty in obtaining crystals. Progress with de novo synthesis of model membrane-interactive peptides presents an opportunity to construct simpler peptides with definable structures, and permits one to approach an understanding of the properties of the membrane proteins themselves. In the present article, we review how our laboratory and others have used peptide approaches to assess the detailed interactions of peptides with membranes, and primary folding at membrane surfaces and in membranes. Structural studies of model peptides identified the existence of a "threshold hydrophobicity," which controls spontaneous peptide insertion into membranes. Related studies of the relative helicity of peptides in organic media such as n-butanol indicate that the helical propensity of individual residues--not simply their hydrophobicity--may dictate the conformations of peptides in membranes. The overall experimental results provide fundamental guidelines for membrane protein engineering.

Internal packing of helical membrane proteins

Helix packing is important in the folding, stability, and association of membrane proteins. Packing analysis of the helical portions of 7 integral membrane proteins and 37 soluble proteins show that the helices in membrane proteins have higher packing values (0.431) than in soluble proteins (0.405). The highest packing values in integral membrane proteins originate from small hydrophobic (G and A) and small hydroxyl-containing (S and T) amino acids, whereas in soluble proteins large hydrophobic and aromatic residues have the highest packing values. The highest packing values for membrane proteins are found in the transmembrane helix-helix interfaces. Glycine and alanine have the highest occurrence among the buried amino acids in membrane proteins, whereas leucine and alanine are the most common buried residue in soluble proteins. These observations are consistent with a shorter axial separation between helices in membrane proteins. The tight helix packing revealed in this analysis contributes to membrane protein stability and likely compensates for the lack of the hydrophobic effect as a driving force for helix-helix association in membranes.

Crystal structure of the vinculin tail suggests a pathway for activation

Vinculin plays a dynamic role in the assembly of the actin cytoskeleton. A strong interaction between its head and tail domains that regulates binding to other cytoskeletal components is disrupted by acidic phospholipids. Here, we present the crystal structure of the vinculin tail, residues 879-1066. Five amphipathic helices form an antiparallel bundle that resembles exchangeable apolipoproteins. A C-terminal arm wraps across the base of the bundle and emerges as a hydrophobic hairpin surrounded by a collar of basic residues, adjacent to the N terminus. We show that the C-terminal arm is required for binding to acidic phospholipids but not to actin, and that binding either ligand induces conformational changes that may represent the first step in activation.

Comparison of catalytic activity and inhibitors of quinone reactions of succinate dehydrogenase (Succinate-ubiquinone oxidoreductase) and fumarate reductase (Menaquinol-fumarate oxidoreductase) from Escherichia coli

Escherichia coli succinate-ubiquinone oxidoreductase (SQR) and menaquinol-fumarate reductase (QFR) are excellent model systems to understand the function of eukaryotic Complex II. They have structural and catalytic properties similar to their eukaryotic counterpart. An exception is that potent inhibitors of mammalian Complex II, such as thenoyltrifluoroacetone and carboxanilides, only weakly inhibit their bacterial counterparts. This lack of good inhibitors of quinone reactions and the higher level of side reactions in the prokaryotic enzymes has hampered the elucidation of the mechanism of quinone oxidation/reduction in E. coli Complex II. In this communication DT-diaphorase and an appropriate quinone are used to measure quinol-fumarate reductase activity and E. coli bo-oxidase and quinones are used to determine succinate-quinone reductase activity. Simple Michaelis kinetics are observed for both enzymes with ubiquinones and menaquinones in the succinate oxidase (forward) and fumarate reductase (reverse) reactions. The comparison of E. coli SQR and QFR demonstrates that 2-n-heptyl 4-hydroxyquinoline-N-oxide (HQNO) is a potent inhibitor of QFR in both assays; however, SQR is not sensitive to HQNO. A series of 2-alkyl-4,6-dinitrophenols and pentachlorophenol were found to be potent competitive inhibitors of both SQR and QFR. In addition, the isolated E. coli SQR complex demonstrates a mixed-type inhibition with carboxanilides, whereas the QFR complex is resistant to this inhibitor. The kinetic properties of SQR and QFR suggest that either ubiquinone or menaquinone operates at a single exchangeable site working in forward or reverse reactions. The pH activity profiles for E. coli QFR and SQR are similar showing maximal activity between pH 7.4 and 7.8, suggesting the importance of similar catalytic groups in quinol deprotonation and oxidation.

A simple method for predicting transmembrane alpha helices with better accuracy

The prediction of a protein's structure from its amino acid sequence has been a long-standing goal of molecular biology. In this work, a new set of conformational parameters for membrane spanning alpha helices was developed using the information from the topology of 70 membrane proteins. Based on these conformational parameters, a simple algorithm has been formulated to predict the transmembrane alpha helices in membrane proteins. A FORTRAN program has been developed which takes the amino acid sequence as input and gives the predicted transmembrane alpha-helices as output. The present method correctly identifies 295 transmembrane helical segments in 70 membrane proteins with only two overpredictions. Furthermore, this method predicts all 45 transmembrane helices in the photosynthetic reaction center, bacteriorhodopsin and cytochrome c oxidase to an 86% level of accuracy and so is better than all other methods published to date.