Structural characterization and functional activity of an exopolysaccharide secreted by Rhodopseudomonas palustris GJ-22.

One water exopolysaccharide, designated G-EPS, was secreted by Rhodopseudomonas palustris GJ-22 culture media. The structure of G-EPS was characterized with HPGPC, GC-MS, methylation, 1D and 2D NMR, along with UV and FT-IR spectrum. The G-EPS molecular weight was 10.026 kilodalton, and is composed of D-mannose (92.8%) and d-glucose (7.2%). The purified G-EPS promoted plant growth and induced systemic resistance against TMV in Nicotiana benthamiana. These results suggested that G-EPS is an important active component of the bio-control capacity of GJ-22.

Preparation and biological activities of an extracellular polysaccharide from Rhodopseudomonas palustris.

The photosynthetic bacterium, Rhodopseudomonas palustris has been widely used as probiotics in aquaculture, while the molecular basis underlying the probiotic properties of this organism remains largely unknown. In this study, a novel extracellular polysaccharides (RPEPS-30) extracted from the fermentation of Rhodopseudomonas palustris was characterized. Results illustrated that RPEPS-30 was an α-mannan with a molecular weight of 46.82 kDa, which possessed a backbone consisted of 1, 2-linked and 1, 4-linked mannose residues, with side chains composed of 1 → 6 linked and 1 → 2,6 linked mannose residues and substitution at O-6. The in vitro immunomodulatory tests revealed that RPEPS-30 could enhance phagocytic capacity, NO release and mRNA expression of cytokines in macrophages. In addition, RPEPS-30 was shown to promote the growth of resident beneficial gut microbiotasuch as Lactobacillus reuteri, Bacteroides thetaiotaomicron and Akkermansia muciniphila. These findings might help us to partially understand the molecular mechanism concerning the probiotic properties of Rhodopseudomonas palustris, in which the extracellular polysaccharide RPEPS-30 stimulated host immune response and favored the growth of specific benificial micriobiota in the gut.

Chromophore binding to two cysteines increases quantum yield of near-infrared fluorescent proteins.

Phytochromes are red/far-red light sensing photoreceptors employing linear tetrapyrroles as chromophores, which are covalently bound to a cysteine (Cys) residue in the chromophore-binding domain (CBD, composed of a PAS and a GAF domain). Recently, near-infrared (NIR) fluorescent proteins (FPs) engineered from bacterial phytochromes binding biliverdin IXα (BV), such as the iRFP series, have become invaluable probes for multicolor fluorescence microscopy and in vivo imaging. However, all current NIR FPs suffer from relatively low brightness. Here, by combining biochemical, spectroscopic and resonance Raman (RR) assays, we purified and characterized an iRFP variant that contains a BV chromophore simultaneously bound to two cysteines. This protein with the unusual double-Cys attached BV showed the highest fluorescence quantum yield (FQY) of 16.6% reported for NIR FPs, whereas the initial iRFP appeared to be a mixture of species with a mean FQY of 11.1%. The purified protein was also characterized with 1.3-fold higher extinction coefficient that together with FQY resulted in almost two-fold brighter fluorescence than the original iRFP as isolated. This work shows that the high FQY of iRFPs with two cysteines is a direct consequence of the double attachment. The PAS-Cys, GAF-Cys and double-Cys attachment each entails distinct configurational constraints of the BV adduct, which can be identified by distinct RR spectroscopic features, i.e. the marker band including the C=C stretching coordinate of the ring A-B methine bridge, which was previously identified as being characteristic for rigid chromophore embedment and high FQY. Our findings can be used to rationally engineer iRFP variants with enhanced FQYs.

Postnovo: Postprocessing Enables Accurate and FDR-Controlled de Novo Peptide Sequencing.

De novo sequencing offers an alternative to database search methods for peptide identification from mass spectra. Since it does not rely on a predetermined database of expected or potential sequences in the sample, de novo sequencing is particularly appropriate for samples lacking a well-defined or comprehensive reference database. However, the low accuracy of many de novo sequence predictions has prevented the widespread use of the variety of sequencing tools currently available. Here, we present a new open-source tool, Postnovo, that postprocesses de novo sequence predictions to find high-accuracy results. Postnovo uses a predictive model to rescore and rerank candidate sequences in a manner akin to database search postprocessing tools such as Percolator. Postnovo leverages the output from multiple de novo sequencing tools in its own analyses, producing many times the length of amino acid sequence information (including both full- and partial-length peptide sequences) at an equivalent false discovery rate (FDR) compared to any individual tool. We present a methodology to reliably screen the sequence predictions to a desired FDR given the Postnovo sequence score. We validate Postnovo with multiple data sets and demonstrate its ability to identify proteins that are missed by database search even in samples with paired reference databases.

The Lipid†A from Rhodopseudomonas palustris Strain BisA53 LPS Possesses a Unique Structure and Low Immunostimulant Properties.

The search for novel lipid A analogues from any biological source that can act as antagonists, displaying inhibitory activity towards the production of pro-inflammatory cytokines, or as immunomodulators in mammals, is a very topical issue. To this aim, the structure and immunological properties of the lipopolysaccharide lipid A from the purple nonsulfur bacterium Rhodopseudomonas palustris strain BisA53 have been determined. This lipid A displays a unique structural feature, with a non-phosphorylated skeleton made up of the tetrasaccharide Manp-α-(1→4)-GlcpN3N-ß-1→6-GlcpN3N-α-(1→1)-α-GalpA, and four primary amide-linked 14:0(3-OH) and, as secondary O-acyl substituents, a 16:0 and the very long-chain fatty acid 26:0(25-OAc), appended on the GlcpN3N units. This lipid A architecture is definitely rare, so far identified only in the genus Bradyrhizobium. Immunological tests on both murine bone-marrow-derived and human monocyte-derived macrophages revealed an extremely low immunostimulant capability of this LPS lipid A.

Kinetically and Crystallographically Guided Mutations of a Benzoate CoA Ligase (BadA) Elucidate Mechanism and Expand Substrate Permissivity.

A benzoate CoA ligase (BadA), isolated from the bacterium Rhodopseudomonas palustris, catalyzes the conversion of benzoate to benzoyl CoA on the catabolic pathway of aromatic carboxylic acids. Herein, apparent Michaelis constants K(app)cat and K(app)M were determined for an expanded array of 31 substrates chosen to systematically probe the active site architecture of the enzyme and provide a baseline for expansion of wild-type substrate specificity. Acyl CoA products were observed for 25 of the 31 substrates; in general, BadA converted ortho-substituted substrates better than the corresponding meta and para regioisomers, and the turnover number was more affected by steric rather than electronic effects. The kinetic data are interpreted in relation to six crystal structures of BadA in complex with several substrates and a benzoyl-AMP reaction intermediate. In contrast to other known natural substrate-bound benzoate ligase structures, all substrate-bound BadA structures adopted the thiolation conformation instead of the adenylation conformation. We also observed all the aryl carboxylates to be uniquely oriented within the active site, relative to other structures. Together, the kinetics and structural data suggested a mechanism that involves substrate binding in the thiolation conformation, followed by substrate rotation to an active orientation upon the transition to the adenylation conformation. On the basis of this hypothesis and the structural data, sterically demanding active site residues were mutated, and the substrate specificity was expanded substantially versus that of BadA. Novel activities were seen for substrates with larger substituents, including phenyl acetate. Additionally, the mutant Lys427Ala identified this nonconserved residue as essential for the thiolation step of BadA, but not adenylation. These variously acylated CoAs can serve as novel substrates of acyl CoA-dependent acyltransferases in coupled enzyme assays to produce analogues of bioactive natural products.

The structure of a novel electron-transfer ferredoxin from Rhodopseudomonas palustris HaA2 which contains a histidine residue in its iron-sulfur cluster-binding motif.

Rhodopseudomonas palustris HaA2 contains a gene, RPB3630, encoding a ferredoxin, HaPuxC, with an atypical CXXHXXC(X)nCP iron-sulfur cluster-binding motif. The ferredoxin gene is associated with a cytochrome P450 (CYP) monooxygenase-encoding gene, CYP194A3, an arrangement which is conserved in several strains of bacteria. Similar ferredoxin genes are found in other bacteria, such as Mycobacterium tuberculosis, where they are also associated with CYP genes. The crystal structure of HaPuxC has been solved at 2.3 Å resolution. The overall fold of this [3Fe-4S] cluster-containing ferredoxin is similar to other [3Fe-4S] and [4Fe-4S] species, with the loop around the iron-sulfur cluster more closely resembling those of [3Fe-4S] ferredoxins. The side chain of His17 from the cluster-binding motif in HaPuxC points away from the vacant site of the cluster and interacts with Glu61 and one of the sulfide ions of the cluster. This is the first cytochrome P450 electron-transfer partner of this type to be structurally characterized and will provide a better understanding of the electron-transfer processes between these ferredoxins and their CYP enzymes.

MAIN software for density averaging, model building, structure refinement and validation.

MAIN is software that has been designed to interactively perform the complex tasks of macromolecular crystal structure determination and validation. Using MAIN, it is possible to perform density modification, manual and semi-automated or automated model building and rebuilding, real- and reciprocal-space structure optimization and refinement, map calculations and various types of molecular structure validation. The prompt availability of various analytical tools and the immediate visualization of molecular and map objects allow a user to efficiently progress towards the completed refined structure. The extraordinary depth perception of molecular objects in three dimensions that is provided by MAIN is achieved by the clarity and contrast of colours and the smooth rotation of the displayed objects. MAIN allows simultaneous work on several molecular models and various crystal forms. The strength of MAIN lies in its manipulation of averaged density maps and molecular models when noncrystallographic symmetry (NCS) is present. Using MAIN, it is possible to optimize NCS parameters and envelopes and to refine the structure in single or multiple crystal forms.

Molecular origins and consequences of High-800 LH2 in Roseobacter denitrificans.

Roseobacter denitrificans is a marine bacterium capable of using a wide variety of different metabolic schemes and in particular is an anoxygenic aerobic photosynthetic bacterium. In the work reported here we use a deletion mutant that we have constructed to investigate the structural origin of the unusual High-800 light-harvesting complex absorption in this bacterium. We suggest that the structure is essentially unaltered when compared to the usual nonameric complexes but that a change in the environment of the C(13:1) carbonyl group is responsible for the change in spectrum. We tentatively relate this change to the presence of a serine residue in the α-polypeptide. Surprisingly, the low spectral overlap between the peripheral and core light-harvesting systems appears not to compromise energy collection efficiency too severely. We suggest that this may be at the expense of maintaining a low antenna size.

The light intensity under which cells are grown controls the type of peripheral light-harvesting complexes that are assembled in a purple photosynthetic bacterium.

The differing composition of LH2 (peripheral light-harvesting) complexes present in Rhodopseudomonas palustris 2.1.6 have been investigated when cells are grown under progressively decreasing light intensity. Detailed analysis of their absorption spectra reveals that there must be more than two types of LH2 complexes present. Purified HL (high-light) and LL (low-light) LH2 complexes have mixed apoprotein compositions. The HL complexes contain PucAB(a) and PucAB(b) apoproteins. The LL complexes contain PucAB(a), PucAB(d) and PucB(b)-only apoproteins. This mixed apoprotein composition can explain their resonance Raman spectra. Crystallographic studies and molecular sieve chromatography suggest that both the HL and the LL complexes are nonameric. Furthermore, the electron-density maps do not support the existence of an additional Bchl (bacteriochlorophyll) molecule; rather the density is attributed to the N-termini of the α-polypeptide.

Single-molecule spectroscopy reveals that individual low-light LH2 complexes from Rhodopseudomonas palustris 2.1.6. have a heterogeneous polypeptide composition.

Rhodopseudomonas palustris belongs to the group of purple bacteria that have the ability to produce LH2 complexes with unusual absorption spectra when they are grown at low-light intensity. This ability is often related to the presence of multiple genes encoding the antenna apoproteins. Here we report, for the first time to our knowledge, direct evidence that individual low-light LH2 complexes have a heterogeneous alphabeta-apoprotein composition that modulates the site energies of Bchl a molecules, producing absorption bands at 800, 820, and 850 nm. The arrangement of the Bchl a molecules in the "tightly coupled ring" can be modeled by nine alphabeta-Bchls dimers, such that the Bchls bound to six alphabeta-pairs have B820-like site energies and the remaining Bchl a molecules have B850-like site energies. Furthermore, the experimental data can only be satisfactorily modeled when these six alphabeta-pairs with B820 Bchl a molecules are distributed such that the symmetry of the assembly is reduced to C(3). It is also clear from the measured single-molecule spectra that the energies of the electronically excited states in the mixed B820/850 ring are mainly influenced by diagonal disorder.

Role of cysteine residues in 4-oxalomesaconate hydratase from Pseudomonas ochraceae NGJ1.

4-Oxalomesaconate hydratase from Pseudomonas ochraceae NGJ1 is unstable in the absence of reducing reagents such as dithiothreitol, and strongly inhibited by 5,5'-dithiobis(2-nitrobenzoic acid) (DTNB). To study the role of cysteine residues in enzyme catalysis, the eight individual cysteine residues of the enzyme were replaced with serine residues by site-directed mutagenesis. The catalytic properties and chemical modification of wild- and mutant type-enzymes by DTNB showed that (i) none of eight cysteine residues was essential for enzyme catalysis; (ii) the inhibition by DTNB was mostly due to modification of Cys-186; (iii) Cys-96 might be another residue reacting with DTNB, and its modification caused an increase in the K(m)-value for 4-oxalomesaconate; (iv) the other six cysteine residues were inaccessible to DTNB, but susceptible to HgCl(2); and (v) only replacement of Cys-186 remarkably improved the stability of the enzyme in the absence of reducing reagent.

Expressed peptide tags: an additional layer of data for genome annotation.

While genome sequencing is becoming ever more routine, genome annotation remains a challenging process. Identification of the coding sequences within the genomic milieu presents a tremendous challenge, especially for eukaryotes with their complex gene architectures. Here, we present a method to assist the annotation process through the use of proteomic data and bioinformatics. Mass spectra of digested protein preparations of the organism of interest were acquired and searched against a protein database created by a six-frame translation of the genome. The identified peptides were mapped back to the genome, compared to the current annotation, and then categorized as supporting or extending the current genome annotation. We named the classified peptides Expressed Peptide Tags (EPTs). The well-annotated bacterium Rhodopseudomonas palustris was used as a control for the method and showed a high degree of correlation between EPT mapping and the current annotation, with 86% of the EPTs confirming existing gene calls and less than 1% of the EPTs expanding on the current annotation. The eukaryotic plant pathogens Phytophthora ramorum and Phytophthora sojae, whose genomes have been recently sequenced and are much less well-annotated, were also subjected to this method. A series of algorithmic steps were taken to increase the confidence of EPT identification for these organisms, including generation of smaller subdatabases to be searched against, and definition of EPT criteria that accommodates the more complex eukaryotic gene architecture. As expected, the analysis of the Phytophthora species showed less correlation between EPT mapping and their current annotation. While approximately 76% of Phytophthora EPTs supported the current annotation, a portion of them (7.7% and 12.9% for P. ramorum and P. sojae, respectively) suggested modification to current gene calls or identified novel genes that were missed by the current genome annotation of these organisms.

MASPIC: intensity-based tandem mass spectrometry scoring scheme that improves peptide identification at high confidence.

Algorithmic search engines bridge the gap between large tandem mass spectrometry data sets and the identification of proteins associated with biological samples. Improvements in these tools can greatly enhance biological discovery. We present a new scoring scheme for comparing tandem mass spectra with a protein sequence database. The MASPIC (Multinomial Algorithm for Spectral Profile-based Intensity Comparison) scorer converts an experimental tandem mass spectrum into a m/z profile of probability and then scores peak lists from potential candidate peptides using a multinomial distribution model. The MASPIC scoring scheme incorporates intensity, spectral peak density variations, and m/z error distribution associated with peak matches into a multinomial distribution. The scoring scheme was validated on two standard protein mixtures and an additional set of spectra collected on a complex ribosomal protein mixture from Rhodopseudomonas palustris. The results indicate a 5-15% improvement over Sequest for high-confidence identifications. The performance gap grows as sequence database size increases. Additional tests on spectra from proteinase-K digest data showed similar performance improvements demonstrating the advantages in using MASPIC for studying proteins digested with less specific proteases. All these investigations show MASPIC to be a versatile and reliable system for peptide tandem mass spectral identification.

Toll-like receptor 6-independent signaling by diacylated lipopeptides.

Bacterial lipopeptides are strong immune modulators that activate early host responses after infection as well as initiating adjuvant effects on the adaptive immune system. These lipopeptides induce signaling in cells of the immune system through Toll-like receptor 2 (TLR2)-TLR1 or TLR2-TLR6 heteromers. So far it has been thought that triacylated lipopeptides, such as the synthetic N-palmitoyl-S-[2,3-bis(palmitoyloxy)-(2RS)-propyl]-(R)-cysteine (Pam3)-CSK4, signal through TLR2-TLR1 heteromers, whereas diacylated lipopeptides, like the macrophage-activating lipopeptide from Mycoplasma fermentans (MALP2) or S-[2,3-bis(palmitoyloxy)-(2RS)-propyl]-(R)-cysteine (Pam2)-CGNNDESNISFKEK, induce signaling through TLR2-TLR6 heteromers. Using new synthetic lipopeptide derivatives we addressed the contribution of the lipid and, in particular, the peptide moieties with respect to TLR2 heteromer usage. In contrast to the current model of receptor usage, not only triacylated lipopeptides, but also diacylated lipopeptides like Pam2CSK4 and the elongated MALP2 analog Pam2CGNNDESNISFKEK-SK4 (MALP2-SK4) induced B lymphocyte proliferation and TNF-alpha secretion in macrophages in a TLR6-independent manner as determined with cells from TLR6-deficient mice. Our results indicate that both the lipid and the N-terminal peptides of lipoproteins contribute to the specificity of recognition by TLR2 heteromers and are responsible for the ligand-receptor interaction on host cells.

Iron(II) carboxylate complexes based on a tetraimidazole ligand as models of the photosynthetic non-heme ferrous sites: synthesis, crystal structure, and Mössbauer and magnetic studies.

The preparations, X-ray structures, and detailed physical characterization are presented for new complexes involving an iron(II) center, a tetraimidazole ligand (TIM), and different carboxylates. [Fe(TIM)(C(6)H(5)CH(2)CO(2))](ClO(4)) (1) crystallizes in the Pbca space group with a = 10.8947(13), b = 20.343(2), and c = 22.833(3) A, Z = 8, and V = 5060.6(11) A(3). [Fe(TIM)(CH(3)CO(2))](ClO(4)) (2) crystallizes in the Ia space group with a = 17.117(2), b = 10.3358(12), and c = 25.658(3) A, beta = 90.301(13) degrees, Z = 8, and V = 4539.5(9) A(3). In both structures, the iron(II) is hexacoordinated to the four N(imidazole) donors of the TIM ligand and the two O donors of a bidentate carboxylate. The flexibility of the carboxylate bidentate coordination, symmetrical or more or less asymmetrical, associated with the steric demand of the TIM ligand results in a remarkable versatility of the Fe(II)N(4)O(2) coordination geometry. The diversity in carboxylate bidentate coordination modes has allowed us to clearly show the importance of the structural and electronic effects, through IR and Mössbauer spectroscopy, of this apparently tenuous carboxylate shift. Comparison of the structural and Mössbauer properties of these complexes with the non-heme ferrous site of photosynthetic systems (i) shows that the metric parameters of site 2b, including the symmetrically chelated bidentate carboxylate, are closer to those of the non-heme ferrous site in the bacterial reaction centers of Rhodopseudomonas viridis and R. sphaeroides and (ii) suggests that the ligand environment of the non-heme ferrous center of PS 2 is close to the axially distorted octahedral symmetry resulting from an asymmetrical bidentate coordination of the -CO(2) motif, as in complex 1.

Membrane protein stability: high pressure effects on the structure and chromophore-binding properties of the light-harvesting complex LH2.

Using the bacteriochlorophyll a (Bchl) cofactors as intrinsic probes to monitor changes in membrane protein structure, we investigate the response to high-pressure of the LH2 complexes from the photosynthetic bacteria Rhodobacter sphaeroides 2.4.1 and Rhodopseudomonas acidophila 10050. By FT-Raman spectroscopy, we demonstrate that high pressure does not induce significant distortion of the protein-bound 850 nm-absorbing bacteriochlorophyll molecules, or break of the hydrogen bond they are involved in. This indicates in particular that the oligomerization of the polypeptides is not perturbed up to 0.6 GPa. The pressure-induced changes in the Bchl absorption spectra are attributed to pigment-pigment interactions. In contrast, the loss of 800 nm-absorbing bacteriochlorophyll reflects pressure-induced alterations to the tertiary structure of the protein in proximity to the membrane/cytosol interface. This suggests that the LH2 protein does have two independent structural domains. The first domain is pressure independent and comprises mostly the C-terminal domain. The second domain located on the N-terminal side exhibits sensitivity to pressure and pH reminiscent of soluble proteins. The LH2 thus constitutes a suitable model system for studying in detail the stability of membrane-embedded hydrophobic helices and helices located at or close to the solvent/membrane interface.

The 7.5-A electron density and spectroscopic properties of a novel low-light B800 LH2 from Rhodopseudomonas palustris.

A novel low-light (LL) adapted light-harvesting complex II has been isolated from Rhodopseudomonas palustris. Previous work has identified a LL B800-850 complex with a heterogeneous peptide composition and reduced absorption at 850 nm. The work presented here shows the 850 nm absorption to be contamination from a high-light B800-850 complex and that the true LL light-harvesting complex II is a novel B800 complex composed of eight alpha beta(d) peptide pairs that exhibits unique absorption and circular dichroism near infrared spectra. Biochemical analysis shows there to be four bacteriochlorophyll molecules per alpha beta peptide rather than the usual three. The electron density of the complex at 7.5 A resolution shows it to be an octamer with exact 8-fold rotational symmetry. A number of bacteriochlorophyll geometries have been investigated by simulation of the circular dichroism and absorption spectra and compared, for consistency, with the electron density. Modeling of the spectra suggests that the B850 bacteriochlorophylls may be arranged in a radial direction rather than the usual tangential arrangement found in B800-850 complexes.

Cleavage of the iron-methionine bond in c-type cytochromes: crystal structure of oxidized and reduced cytochrome c(2) from Rhodopseudomonas palustris and its ammonia complex.

The three-dimensional structures of the native cytochrome c(2) from Rhodopseudomonas palustris and of its ammonia complex have been obtained at pH 4.4 and pH 8.5, respectively. The structure of the native form has been refined in the oxidized state at 1.70 A and in the reduced state at 1.95 A resolution. These are the first high-resolution crystal structures in both oxidation states of a cytochrome c(2) with relatively high redox potential (+350 mV). The differences between the two oxidation states of the native form, including the position of internal water molecules, are small. The unusual six-residue insertion Gly82-Ala87, which precedes the heme binding Met93, forms an isolated 3(10)-helix secondary structural element not previously observed in other c-type cytochromes. Furthermore, this cytochrome shows an external methionine residue involved in a strained folding near the exposed edge of the heme. The structural comparison of the present cytochrome c(2) with other c-type cytochromes has revealed that the presence of such a residue, with torsion angles phi and psi of approximately -140 and -130 degrees, respectively, is a typical feature of this family of proteins. The refined crystal structure of the ammonia complex, obtained at 1.15 A resolution, shows that the sulphur atom of the Met93 axial ligand does not coordinate the heme iron atom, but is replaced by an exogenous ammonia molecule. This is the only example so far reported of an X-ray structure with the heme iron coordinated by an ammonia molecule. The detachment of Met93 is accompanied by a very localized change in backbone conformation, involving mainly the residues Lys92, Met93, and Thr94. Previous studies under typical denaturing conditions, including high-pH values and the presence of exogenous ligands, have shown that the detachment of the Met axial ligand is a basic step in the folding/unfolding process of c-type cytochromes. The ammonia adduct represents a structural model for this important step of the unfolding pathway. Factors proposed to be important for the methionine dissociation are the strength of the H-bond between the Met93 and Tyr66 residues that stabilizes the native form, and the presence in this bacterial cytochrome c(2) of the rare six-residue insertion in the helix 3(10) conformation that increases Met loop flexibility.

Hydrophobicity and prediction of the secondary structure of membrane proteins and peptides.

Reliability of the hydropathy method to predict the formation of membrane-spanning alpha-helices by integral membrane proteins and peptides whose structure is known from X-ray crystallography is analysed. It is shown that Kyte-Doolittle hydropathy plots do not predict accurately 22 transmembrane alpha-helices in the reaction centres (RC) of the photosynthetic bacteria Rhodopseudomonas viridis and Rhodobacter sphaeroides (R-26). The accuracy of prediction for these proteins was improved using an optimised Kyte-Doolittle hydrophobicity scale. However, this hydrophobicity scale did not improve the predictions for the alphabeta-peptides of the B800-850 (LH2) complexes of the photosynthetic bacteria Rhodopseudomonas acidophila and Rhodospirillum molischianum, which were excluded from the optimisation procedure. The best and worst predictions of membrane-spanning alpha-helices for the RC proteins and LH2 peptides, respectively, were obtained with a propensity scale (PRC) calculated from the amino acid sequences and X-ray data for the RC proteins. A propensity scale (PLH) obtained using the amino acid sequences and X-ray data for the alphabeta-peptides of the LH2 complexes did not give an acceptable prediction of the transmembrane segments in the LH2 peptides; moreover, it markedly contradicted the PRC scale. Amino acids have been concluded to have no significant preference to localisation in transmembrane segments. Therefore, the predictive ability of the hydropathy methodology appears to be limited: the number of transmembrane segments can be correctly calculated for the best case only, and the lengths and positions of membrane-spanning alpha-helices in a protein amino acid sequence can not be predicted exactly.