Global analysis of predicted proteomes: functional adaptation of physical properties

Identification of subtelomeric cluster-genes associated to sexual stage in Toxoplasma gondii

Toxoplasma gondii is an obligate intracellular parasite with sexual reproduction in the intestinal epithelium of felines. The depletion of two gene repressors, AP2XI-2 and AP2XII-1, induces merozoite formation and gene expression towards sexual commitment. Based on RNA-seq datasets of AP2XI-2 and AP2XII-1 knock downs we identified subtelomeric (ST) TgB12 and hypothetical (HP) genes upregulated. Some of the differentially expressed genes (DEGs) are arranged in ST clusters. These DEG products are characterized by high isoelectric points (pI) and may encode small proteins. The potential roles of these clusters of DEG ST genes in environmental resistance or parasite sexual development of T. gondii is discussed.

Exploring the Combined Action of Adding Pertuzumab to Branded Trastuzumab versus Trastuzumab Biosimilars for Treating HER2+ Breast Cancer

The binding activity of various trastuzumab biosimilars versus the branded trastuzumab towards the glycosylated extracellular domain of the human epidermal growth factor receptor 2 (HER2) target in the presence of pertuzumab was investigated. We employed size exclusion chromatography with tetra-detection methodology to simultaneously determine absolute molecular weight, concentration, molecular size, and intrinsic viscosity. All trastuzumab molecules in solution exhibit analogous behavior in their binary action towards HER2 regardless of the order of addition of trastuzumab/pertuzumab. This analogous behavior of all trastuzumab molecules, including biosimilars, highlights the robustness and consistency of their binding activity towards HER2. Furthermore, the addition of HER2 to a mixture of trastuzumab and pertuzumab leads to increased formation of high-order HER2 complexes, up to concentrations of one order of magnitude higher than in the case of sequential addition. The observed increase suggests a potential synergistic effect between these antibodies, which could enhance their therapeutic efficacy in HER2-positive cancers. These findings underscore the importance of understanding the complex interplay between therapeutic antibodies and their target antigens, providing valuable insights for the development of more effective treatment strategies.

The study of acidic/basic nature of metallothioneins and other metal-binding biomolecules in the soluble hepatic fraction of the northern pike (Esox lucius)

Since fish metalloproteins are still not thoroughly characterized, the aim of this study was to investigate the acidic/basic nature of biomolecules involved in the sequestration of twelve selected metals in the soluble hepatic fraction of an important aquatic bioindicator organism, namely the fish species northern pike (Esox lucius). For this purpose, the hyphenated system HPLC-ICP-MS was applied, with chromatographic separation based on anion/cation-exchange principle at physiological pH (7.4). The results indicated predominant acidic nature of metal-binding peptides/proteins in the studied hepatic fraction. More than 90 % of Ag, Cd, Co, Cu, Fe, Mo, and Pb were eluted with negatively charged biomolecules, and >70 % of Bi, Mn, and Zn. Thallium was revealed to bind equally to negatively and positively charged biomolecules, and Cs predominantly to positively charged ones. The majority of acidic (negatively charged) metalloproteins/peptides were coeluted within the elution time range of applied standard proteins, having pIs clustered around 4-6. Furthermore, binding of several metals (Ag, Cd, Cu, Zn) to two MT-isoforms was assumed, with Cd and Zn preferentially bound to MT1 and Ag to MT2, and Cu evenly distributed between the two. The results presented here are the first of their kind for the important bioindicator species, the northern pike, as well as one of the rare comprehensive studies on the acidic/basic nature of metal-binding biomolecules in fish, which can contribute significantly to a better understanding of the behaviour and fate of metals in the fish organism, specifically in liver as main metabolic and detoxification organ.

Physicochemical classification of organisms

The hypervariable residues that compose the major part of proteins’ surfaces are generally considered outside evolutionary control. Yet, these “nonconserved” residues determine the outcome of stochastic encounters in crowded cells. It has recently become apparent that these encounters are not as random as one might imagine, but carefully orchestrated by the intracellular electrostatics to optimize protein diffusion, interactivity, and partner search. The most influential factor here is the protein surface-charge density, which takes different optimal values across organisms with different intracellular conditions. In this study, we examine how far the net-charge density and other physicochemical properties of proteomes will take us in terms of distinguishing organisms in general. The results show that these global proteome properties not only follow the established taxonomical hierarchy, but also provide clues to functional adaptation. In many cases, the proteome–property divergence is even resolved at species level. Accordingly, the variable parts of the genes are not as free to drift as they seem in sequence alignment, but present a complementary tool for functional, taxonomic, and evolutionary assignment.

In silico structural, phylogenetic and drug target analysis of putrescine monooxygenase from Shewanella putrefaciens-95

BACKGROUND

The enormous and irresponsible use of antibiotics has led to the emergence of resistant strains of bacteria globally. A new approach to combat this crisis has been nutritional immunity limiting the availability of nutrients to pathogens. Targeting the siderophore biosynthetic pathway that helps in iron acquisition, an essential microelement in the bacterial system has been the topic of interest in recent days that backs the concept of nutritional immunity. Supporting this view, we have chosen to study a key enzyme in the biosynthetic pathway of putrebactin called putrescine monooxygenase (SpPMO) from Shewanella putrefaciens. In our previous study, we co-expressed putrescine monooxygenase recombinantly in Escherichia coli BL21 Star (DE3). The bioinformatic analysis and screening of inhibitors will broaden the scope of SpPMO as a drug target.

RESULTS

In the present study, we have analysed the physicochemical properties of the target enzyme and other N-hydroxylating monooxygenases (NMOs) using ExPASy server. The target enzyme SpPMO and most of the selected NMOs have a slightly acidic isoelectric point and are medially thermostable and generally insoluble. The multiple sequence alignment identified the GXGXX(N/A), DXXXFATGYXXXXP motives and conserved amino acids involved in FAD binding, NADP binding, secondary structure formation and substrate binding. The phylogenetic analysis indicated the distribution of the monooxygenases into different clades according to their substrate specificity. Further, a 3D model of SpPMO was predicted using I-TASSER online tool with DfoA from Erwinia amylovora as a template. The model was validated using the SAVES server and deposited to the Protein Model Database with the accession number PM0082222. The molecular docking analysis with different substrates revealed the presence of a putrescine binding pocket made of conserved amino acids and another binding pocket present on the surface of the protein wherein all other ligands interact with high binding affinity. The molecular docking of naturally occurring inhibitor molecules with SpPMO 3D model identified curcumin and niazirin with 1.83 and 2.81 μM inhibition constants as two promising inhibitors. Further studies on kinetic parameters of curcumin and niazirin inhibitors in vitro determined the Ki to be 2.6±0.0036 μM and 18.38±0.008 μM respectively.

CONCLUSION

This analysis will help us understand the structural, phylogenetic and drug target aspects of putrescine monooxygenase from Shewanella putrefaciens-95 in detail. It sheds light on the precautionary measures that can be developed to inhibit the enzyme and thereby the secondary infections caused by them.

Protein pI and Intracellular Localization

The protein isoelectric point (pI) can be calculated from an amino acid sequence using computational analysis in a good agreement with experimental data. Availability of whole-genome sequences empowers comparative studies of proteome-wide pI distributions. It was found that the whole-proteome distributions of protein pI values are multimodal in different species. It was further hypothesized that the observed multimodality is associated with subcellular localization-specific differences in local pI distributions. Here, we overview the multimodality of proteome-wide pI distributions in different organisms focusing on the relationships between protein pI and subcellular localization. We also discuss the probable factors responsible for variation of the intracellular localization-specific pI profiles.

Virtual 2-D map of the fungal proteome

The molecular weight and isoelectric point (pI) of the proteins plays important role in the cell. Depending upon the shape, size, and charge, protein provides its functional role in different parts of the cell. Therefore, understanding to the knowledge of their molecular weight and charges is (pI) is very important. Therefore, we conducted a proteome-wide analysis of protein sequences of 689 fungal species (7.15 million protein sequences) and construct a virtual 2-D map of the fungal proteome. The analysis of the constructed map revealed the presence of a bimodal distribution of fungal proteomes. The molecular mass of individual fungal proteins ranged from 0.202 to 2546.166 kDa and the predicted isoelectric point (pI) ranged from 1.85 to 13.759 while average molecular weight of fungal proteome was 50.98 kDa. A non-ribosomal peptide synthase (RFU80400.1) found in Trichoderma arundinaceum was identified as the largest protein in the fungal kingdom. The collective fungal proteome is dominated by the presence of acidic rather than basic pI proteins and Leu is the most abundant amino acid while Cys is the least abundant amino acid. Aspergillus ustus encodes the highest percentage (76.62%) of acidic pI proteins while Nosema ceranae was found to encode the highest percentage (66.15%) of basic pI proteins. Selenocysteine and pyrrolysine amino acids were not found in any of the analysed fungal proteomes. Although the molecular weight and pI of the protein are of enormous important to understand their functional roles, the amino acid compositions of the fungal protein will enable us to understand the synonymous codon usage in the fungal kingdom. The small peptides identified during the study can provide additional biotechnological implication.

Localization-specific distributions of protein pI in human proteome are governed by local pH and membrane charge

Background

Whole-proteome distributions of protein isoelectric point (pI) values in different organisms are bi- or trimodal with some variations. It was suggested that the observed multimodality of the proteome-wide pI distributions is associated with subcellular localization-specific differences in the local pI distributions. However, the factors responsible for variation of the intracellular localization-specific pI profiles have not been investigated in detail.

Results

In this work, we explored proteome-wide pI distributions of 32,138 human proteins predicted to reside in 10 subcellular compartments, as well as the pI distributions of experimentally observed lysosomal and Golgi proteins. The distributions were found to differ significantly, although all of them adhered to the major recurrent bimodal pattern. Grossly, acid-biased and alkaline-biased patterns with various minor statistical features were observed at different subcellular locations. Bioinformatics analysis revealed the existence of strong statistically significant correlations between protein pI and subcellular localization. Most markedly, protein pI was found to correlate positively with nuclear and mitochondrial locations and negatively with cytoskeletal, cytoplasmic, lysosomal and peroxisomal environment. Further analysis demonstrated that subcellular compartment-specific pI distributions are greatly influenced by local pH and organelle membrane charge. Multiple nonlinear regression analysis identified a polynomial function of the two variables that best fitted the mean pI values of the localization-specific pI distributions. A high coefficient of determination calculated for this regression (R² = 0.98) suggests that local pH and organelle membrane charge are the major factors responsible for variation of the intracellular localization-specific pI profiles.

Conclusions

Our study demonstrates that strong correlations exist between protein pI and subcellular localization. The specific pI distributions at different subcellular locations are defined by local environment. Predominantly, it is the local pH and membrane charge that shape the organelle-specific protein pI patterns. These findings expand our understanding of spatial organization of the human proteome.

Electronic supplementary material

The online version of this article (10.1186/s12860-019-0221-4) contains supplementary material, which is available to authorized users.

The molecular mass and isoelectric point of plant proteomes

Background

Cell contain diverse array of proteins with different molecular weight and isoelectric point (pI). The molecular weight and pI of protein play important role in determining the molecular biochemical function. Therefore, it was important to understand the detail regarding the molecular weight and pI of the plant proteins.

Results

A proteome-wide analysis of plant proteomes from 145 species revealed a pI range of 1.99 (epsin) to 13.96 (hypothetical protein). The spectrum of molecular mass of the plant proteins varied from 0.54 to 2236.8 kDa. A putative Type-I polyketide synthase (22244 amino acids) in Volvox carteri was found to be the largest protein in the plant kingdom. However, Type-I polyketide synthase was not found in higher plant species. Titin (806.46 kDa) and misin/midasin (730.02 kDa) were the largest proteins identified in higher plant species. The pI and molecular weight of the plant proteins showed a trimodal distribution. An acidic pI (56.44% of proteins) was found to be predominant over a basic pI (43.34% of proteins) and the abundance of acidic pI proteins was higher in unicellular algae species relative to multicellular higher plants. In contrast, the seaweed, Porphyra umbilicalis, possesses a higher proportion of basic pI proteins (70.09%). Plant proteomes were also found to contain selenocysteine (Sec), amino acid that was found only in lower eukaryotic aquatic plant lineage. Amino acid composition analysis showed Leu was high and Trp was low abundant amino acids in the plant proteome. Additionally, the plant proteomes also possess ambiguous amino acids Xaa (unknown), Asx (asparagine or aspartic acid), Glx (glutamine or glutamic acid), and Xle (leucine or isoleucine) as well.

Conclusion

The diverse molecular weight and isoelectric point range of plant proteome will be helpful to understand their biochemical and functional aspects. The presence of selenocysteine proteins in lower eukaryotic organism is of interest and their expression in higher plant system can help us to understand their functional role.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5983-8) contains supplementary material, which is available to authorized users.

Misprediction of Structural Disorder in Halophiles

Whereas the concept of intrinsic disorder derives from biophysical observations of the lack of structure of proteins or protein regions under native conditions, many of our respective concepts rest on proteome-scale bioinformatics predictions. It is established that most predictors work reliably on proteins commonly encountered, but it is often neglected that we know very little about their performance on proteins of microorganisms that thrive in environments of extreme temperature, pH, or salt concentration, which may cause adaptive sequence composition bias. To address this issue, we predicted structural disorder for the complete proteomes of different extremophile groups by popular prediction methods and compared them to those of the reference mesophilic group. While significant deviations from mesophiles could be explained by a lack or gain of disordered regions in hyperthermophiles and radiotolerants, respectively, we found systematic overprediction in the case of halophiles. Additionally, examples were collected from the Protein Data Bank (PDB) to demonstrate misprediction and to help understand the underlying biophysical principles, i.e., halophilic proteins maintain a highly acidic and hydrophilic surface to avoid aggregation in high salt conditions. Although sparseness of data on disordered proteins from extremophiles precludes the development of dedicated general predictors, we do formulate recommendations for how to address their disorder with current bioinformatics tools.

The Biologics Revolution and Endotoxin Test Concerns

The advent of “at will” production of biologics in lieu of harvesting animal proteins (i.e. insulin) or human cadaver proteins (i.e. growth hormone) has revolutionized the treatment of disease. While the fruits of the biotechnology revolution are widely acknowledged, the realization of the differences in the means of production and changes in the manner of control of potential impurities and contaminants in regard to the new versus the old are less widely appreciated. This chapter is an overview of the biologics revolution in terms of the rigors of manufacturing required to produce them, their mechanism of action, and caveats of endotoxin control. It is a continulation of the previous chapter that established a basic background knowledge of adaptive immune principles necessary to understand the mode of action of both disease causation and biologics therapeutic treatment via immune modulation.

Marginal protein stability drives subcellular proteome isoelectric point

There exists a positive correlation between the pH of subcellular compartments and the median isoelectric point (pI) for the associated proteomes. Proteins in the human lysosome-a highly acidic compartment in the cell-have a median pI of ∼6.5, whereas proteins in the more basic mitochondria have a median pI of ∼8.0. Proposed mechanisms reflect potential adaptations to pH. For example, enzyme active site general acid/base residue pKs are likely evolved to match environmental pH. However, such effects would be limited to a few residues on specific proteins, and might not affect the proteome at large. A protein model that considers residue burial upon folding recapitulates the correlation between proteome pI and environmental pH. This correlation can be fully described by a neutral evolution process; no functional selection is included in the model. Proteins in acidic environments incur a lower energetic penalty for burying acidic residues than basic residues, resulting in a net accumulation of acidic residues in the protein core. The inverse is true under alkaline conditions. The pI distributions of subcellular proteomes are likely not a direct result of functional adaptations to pH, but a molecular spandrel stemming from marginal stability.

Local and global anatomy of antibody-protein antigen recognition

Deciphering antibody-protein antigen recognition is of fundamental and practical significance. We constructed an antibody structural dataset, partitioned it into human and murine subgroups, and compared it with nonantibody protein-protein complexes. We investigated the physicochemical properties of regions on and away from the antibody-antigen interfaces, including net charge, overall antibody charge distributions, and their potential role in antigen interaction. We observed that amino acid preference in antibody-protein antigen recognition is entropy driven, with residues having low side-chain entropy appearing to compensate for the high backbone entropy in interaction with protein antigens. Antibodies prefer charged and polar antigen residues and bridging water molecules. They also prefer positive net charge, presumably to promote interaction with negatively charged protein antigens, which are common in proteomes. Antibody-antigen interfaces have large percentages of Tyr, Ser, and Asp, but little Lys. Electrostatic and hydrophobic interactions in the Ag binding sites might be coupled with Fab domains through organized charge and residue distributions away from the binding interfaces. Here we describe some features of antibody-antigen interfaces and of Fab domains as compared with nonantibody protein-protein interactions. The distributions of interface residues in human and murine antibodies do not differ significantly. Overall, our results provide not only a local but also a global anatomy of antibody structures.

In silico physicochemical characterization and topology analysis of Respiratory burst oxidase homolog (Rboh) proteins from Arabidopsis and rice

NADPH oxidase (NOX) is a key enzyme involved in the production of apoplastic superoxide (O2-), a type of reactive oxygen species (ROS). Plant Noxes are the homologs of mammalian NADPH oxidase's catalytic subunit and are documented as respiratory burst oxidase homologs (Rbohs). A number of studies have reported their diverse functions in combating various stresses and in plant growth and development. In the present study, a total of 19 Rboh proteins (10 from Arabidopsis thaliana and 9 from Oryza sativa Japonica) were analyzed. We employed in silico approaches to compute the physiochemical properties (molecular weight, isoelectric point, total number of negatively and positively charged residues, extinction coefficient, half-life, instability and aliphatic index, grand average of hydropathicity, amino acid percentage). We observed a lot of variability in these parameters among the Rbohs accounting for their functional diversification. Their topological analysis, subcellular localization and signal peptide detection are also performed. To the best of our knowledge, the present study report on in silico physiochemical characterization, topology analysis, subcellular localization and signal peptide detection of Rboh proteins within two model plants. The study elucidates the variations in the key properties among Rbohs proteins, which may be responsible for their functional multiplicity.

Corona Discharge Suppression in Negative Ion Mode Nanoelectrospray Ionization via Trifluoroethanol Addition

Negative ion mode nanoelectrospray ionization (nESI) is often utilized to analyze acidic compounds, from small molecules to proteins, with mass spectrometry (MS). Under high aqueous solvent conditions, corona discharge is commonly observed at emitter tips, resulting in low ion abundances and reduced nESI needle lifetimes. We have successfully reduced corona discharge in negative ion mode by trace addition of trifluoroethanol (TFE) to aqueous samples. The addition of as little as 0.2% TFE increases aqueous spray stability not only in nESI direct infusion, but also in nanoflow liquid chromatography (nLC)/MS experiments. Negative ion mode spray stability with 0.2% TFE is approximately 6× higher than for strictly aqueous samples. Upon addition of 0.2% TFE to the mobile phase of nLC/MS experiments, tryptic peptide identifications increased from 93 to 111 peptides, resulting in an average protein sequence coverage increase of 18%.

The physical characteristics of human proteins in different biological functions

The physical properties of gene products are the foundation of their biological functions. In this study, we systematically explored relationships between physical properties and biological functions. The physical properties including origin time, evolution pressure, mRNA and protein stability, molecular weight, hydrophobicity, acidity/alkaline, amino acid compositions, and chromosome location. The biological functions are defined from 4 aspects: biological process, molecular function, cellular component and cell/tissue/organ expression. We found that the proteins associated with basic material and energy metabolism process originated earlier, while the proteins associated with immune, neurological system process etc. originated later. Tissues may have a strong influence on evolution pressure. The proteins associated with energy metabolism are double-stable. Immune and peripheral cell proteins tend to be mRNA stable/protein unstable. There are very few function items with double-unstable of mRNA and protein. The proteins involved in the cell adhesion tend to consist of large proteins with high proportion of small amino acids. The proteins of organic acid transport, neurological system process and amine transport have significantly high hydrophobicity. Interestingly, the proteins involved in olfactory receptor activity tend to have high frequency of aromatic, sulfuric and hydroxyl amino acids.

Improvement of Mitochondria Extract from Saccharomyces cerevisiae Characterization in Shotgun Proteomics Using Sheathless Capillary Electrophoresis Coupled to Tandem Mass Spectrometry

In this work, we describe the characterization of a quantity-limited sample (100 ng) of yeast mitochondria by shotgun bottom-up proteomics. Sample characterization was carried out by sheathless capillary electrophoresis, equipped with a high sensitivity porous tip and coupled to tandem mass spectrometry (CESI-MS-MS) and concomitantly with a state-of-art nano flow liquid chromatography coupled to a similar mass spectrometry (MS) system (nanoLC-MS-MS). With single injections, both nanoLC-MS-MS and CESI-MS-MS 60 min-long separation experiments allowed us to identify 271 proteins (976 unique peptides) and 300 proteins (1,765 unique peptides) respectively, demonstrating a significant specificity and complementarity in identification depending on the physicochemical separation employed. Such complementary, maximizing the number of analytes detected, presents a powerful tool to deepen a biological sample's proteomic characterization. A comprehensive study of the specificity provided by each separating technique was also performed using the different properties of the identified peptides: molecular weight, mass-to-charge ratio (m/z), isoelectric point (pI), sequence coverage or MS-MS spectral quality enabled to determine the contribution of each separation. For example, CESI-MS-MS enables to identify larger peptides and eases the detection of those having extreme pI without impairing spectral quality. The addition of peptides, and therefore proteins identified by both techniques allowed us to increase significantly the sequence coverages and then the confidence of characterization. In this study, we also demonstrated that the two yeast enolase isoenzymes were both characterized in the CESI-MS-MS data set. The observation of discriminant proteotypic peptides is facilitated when a high number of precursors with high-quality MS-MS spectra are generated.

Limitation of tuning the antibody-antigen reaction by changing the value of pH and its consequence for hyperthermia

Distribution of the isoelectric point (pI) was calculated for the hypervariable regions of Fab fragments of the antibody molecules, which structure is annotated in the structural antibody database SabDab. The distribution is consistent with the universal for all organisms dividing the proteome into two sets of acidic and basic proteins. It shows the additional fine structure in a form of the narrow-sized peaks of pI values. This is an explanation why a small change of the environmental pH can have a strong effect on the antibody-antigen affinity. To show this, a typical enzyme-linked immunospecific assay experiment for testing the reaction of goat anti-human IgA antibodies with human IgA immunoglobulins of saliva as antigens was modified in such a way that Fe3O4magnetic nanoparticles were added to PBS buffer. The magnetic nanoparticles were remotely heated by the radio frequency magnetic field providing the local change of temperature and pH. It was observed that short times of the heating were significantly increasing the antibody-antigen binding strength while it was not the case for a longer time. The finding discussed in the study can be useful for biopharmaceuticals using antibodies, the immunoassay techniques as well as for control over the use of hyperthermia.

Interactions of proteins with biogenic iron oxyhydroxides and a new culturing technique to increase biomass yields of neutrophilic, iron-oxidizing bacteria

Neutrophilic, bacterial iron-oxidation remains one of the least understood energy-generating biological reactions to date. One of the reasons it remains under-studied is because there are inherent problems with working with iron-oxidizing bacteria (FeOB), including low biomass yields and interference from the iron oxides in the samples. In an effort to circumvent the problem of low biomass, a new large batch culturing technique was developed. Protein interactions with biogenic iron oxides were investigated confirming that such interactions are strong. Therefore, a protein extraction method is described to minimize binding of proteins to biogenic iron oxides. The combination of these two methods results in protein yields that are appropriate for activity assays in gels and for proteomic profiling.

Function-valued traits in evolution

Many biological characteristics of evolutionary interest are not scalar variables but continuous functions. Given a dataset of function-valued traits generated by evolution, we develop a practical, statistical approach to infer ancestral function-valued traits, and estimate the generative evolutionary process. We do this by combining dimension reduction and phylogenetic Gaussian process regression, a non-parametric procedure that explicitly accounts for known phylogenetic relationships. We test the performance of methods on simulated, function-valued data generated from a stochastic evolutionary model. The methods are applied assuming that only the phylogeny, and the function-valued traits of taxa at its tips are known. Our method is robust and applicable to a wide range of function-valued data, and also offers a phylogenetically aware method for estimating the autocorrelation of function-valued traits.

Activated ion negative electron transfer dissociation of multiply charged peptide anions

We report the implementation and evaluation of activated ion negative electron transfer dissociation (AI-NETD) in order to enhance the analytical capabilities of NETD for the elucidation of doubly deprotonated peptide anions. The analytical figures-of-merit and fragmentation characteristics are compared for NETD alone and with supplemental collisional activation of the charge reduced precursors or infrared photoactivation of the entire ion population during the NETD reaction period. The addition of supplemental collisional activation of charge reduced precursor ions or infrared photoactivation of the entire ion population concomitant with the NETD reaction period significantly improves sequencing capabilities for peptide anions as evidenced by the greater abundances of product ions and overall sequence coverage. Neither of these two AI-NETD methods significantly alters the net fragmentation efficiencies relative to NETD; however, the sequence ion conversion percentages with respect to formation of diagnostic product ions are notably higher. Supplemental infrared photoactivation outperforms collisional activation for most of the peptide fragmentation metrics evaluated.

Protein charge and mass contribute to the spatio-temporal dynamics of protein-protein interactions in a minimal proteome

We constructed and simulated a "minimal proteome" model using Langevin dynamics. It contains 206 essential protein types that were compiled from the literature. For comparison, we generated six proteomes with randomized concentrations. We found that the net charges and molecular weights of the proteins in the minimal genome are not random. The net charge of a protein decreases linearly with molecular weight, with small proteins being mostly positively charged and large proteins negatively charged. The protein copy numbers in the minimal genome have the tendency to maximize the number of protein-protein interactions in the network. Negatively charged proteins that tend to have larger sizes can provide a large collision cross-section allowing them to interact with other proteins; on the other hand, the smaller positively charged proteins could have higher diffusion speed and are more likely to collide with other proteins. Proteomes with random charge/mass populations form less stable clusters than those with experimental protein copy numbers. Our study suggests that "proper" populations of negatively and positively charged proteins are important for maintaining a protein-protein interaction network in a proteome. It is interesting to note that the minimal genome model based on the charge and mass of Escherichia coli may have a larger protein-protein interaction network than that based on the lower organism Mycoplasma pneumoniae.

Proteomic properties reveal phyloecological clusters of Archaea

In this study, we propose a novel way to describe the variety of environmental adaptations of Archaea. We have clustered 57 Archaea by using a non-redundant set of proteomic features, and verified that the clusters correspond to environmental adaptations to the archaeal habitats. The first cluster consists dominantly of hyperthermophiles and hyperthermoacidophilic aerobes. The second cluster joins together halophilic and extremely halophilic Archaea, while the third cluster contains mesophilic (mostly methanogenic) Archaea together with thermoacidophiles. The non-redundant subset of proteomic features was found to consist of five features: the ratio of charged residues to uncharged, average protein size, normalized frequency of beta-sheet, normalized frequency of extended structure and number of hydrogen bond donors. We propose this clustering to be termed phyloecological clustering. This approach could give additional insights into relationships among archaeal species that may be hidden by sole phylogenetic analysis.

Systematic comparison of ultraviolet photodissociation and electron transfer dissociation for peptide anion characterization

Ultraviolet photodissociation at 193 nm (UVPD) and negative electron transfer dissociation (NETD) were compared to establish their utility for characterizing acidic proteomes with respect to sequence coverage distributions (a measure of product ion signals across the peptide backbone), sequence coverage percentages, backbone cleavage preferences, and fragmentation differences relative to precursor charge state. UVPD yielded significantly more diagnostic information compared with NETD for lower charge states (n ≤ 2), but both methods were comparable for higher charged species. While UVPD often generated a more heterogeneous array of sequence-specific products (b-, y-, c-, z-, Y-, d-, and w-type ions in addition to a- and x- type ions), NETD usually created simpler sets of a/x-type ions. LC-MS/UVPD and LC-MS/NETD analysis of protein digests utilizing high pH mobile phases coupled with automated database searching via modified versions of the MassMatrix algorithm was undertaken. UVPD generally outperformed NETD in stand-alone searches due to its ability to efficiently sequence both lower and higher charge states with rapid activation times. However, when combined with traditional positive mode CID, both methods yielded complementary information with significantly increased sequence coverage percentages and unique peptide identifications over that of just CID alone.

A theoretical and experimental proteome map of Pseudomonas aeruginosa PAO1

A total proteome map of the Pseudomonas aeruginosa PAO1 proteome is presented, generated by a combination of two-dimensional gel electrophoresis and protein identification by mass spectrometry. In total, 1128 spots were visualized, and 181 protein spots were characterized, corresponding to 159 different protein entries. In particular, protein chaperones and enzymes important in energy conversion and amino acid biosynthesis were identified. Spot analysis always resulted in the identification of a single protein, suggesting sufficient spot resolution, although the same protein may be detected in two or more neighboring spots, possibly indicating posttranslational modifications. Comparison to the theoretical proteome revealed an underrepresentation of membrane proteins, though the identified proteins cover all predicted subcellular localizations and all functional classes. These data provide a basis for subsequent comparative studies of the biology and metabolism of P. aeruginosa, aimed at unraveling global regulatory networks.

Studies of T.pallidum proteome for the purpose of improving laboratory assessments for the syphilis diagnostics

The review covers problems related to the ways of development of modern methods of laboratory assessment used for syphilis diagnostics on the basis of the use of specific antigens of the pathogenic agent. Results of studies of some immune proteome proteins of T.pallidum have been provided. The data on the possibility of their use for the development of new laboratory methods based on the detection of antibodies to Т. pallidum target proteins in blood serum samples of patients with different clinical forms of syphilis.

Stage-specific proteomic expression patterns of the human filarial parasite Brugia malayi and its endosymbiont Wolbachia

Global proteomic analyses of pathogens have thus far been limited to unicellular organisms (e.g., protozoa and bacteria). Proteomic analyses of most eukaryotic pathogens (e.g., helminths) have been restricted to specific organs, specific stages, or secretomes. We report here a large-scale proteomic characterization of almost all the major mammalian stages of Brugia malayi, a causative agent of lymphatic filariasis, resulting in the identification of more than 62% of the products predicted from the Bm draft genome. The analysis also yielded much of the proteome of Wolbachia, the obligate endosymbiont of Bm that also expressed proteins in a stage-specific manner. Of the 11,610 predicted Bm gene products, 7,103 were definitively identified from adult male, adult female, blood-borne and uterine microfilariae, and infective L3 larvae. Among the 4,956 gene products (42.5%) inferred from the genome as "hypothetical," the present study was able to confirm 2,336 (47.1%) as bona fide proteins. Analysis of protein families and domains coupled with stage-specific expression highlight the important pathways that benefit the parasite during its development in the host. Gene set enrichment analysis identified extracellular matrix proteins and those with immunologic effects as enriched in the microfilarial and L3 stages. Parasite sex- and stage-specific protein expression identified those pathways related to parasite differentiation and demonstrates stage-specific expression by the Bm endosymbiont Wolbachia as well.

Molecular aspects of bacterial pH sensing and homeostasis

Diverse mechanisms for pH sensing and cytoplasmic pH homeostasis enable most bacteria to tolerate or grow at external pH values that are outside the cytoplasmic pH range they must maintain for growth. The most extreme cases are exemplified by the extremophiles that inhabit environments with a pH of below 3 or above 11. Here, we describe how recent insights into the structure and function of key molecules and their regulators reveal novel strategies of bacterial pH homeostasis. These insights may help us to target certain pathogens more accurately and to harness the capacities of environmental bacteria more efficiently.

argC Orthologs from Rhizobiales show diverse profiles of transcriptional efficiency and functionality in Sinorhizobium meliloti

Several factors can influence ortholog replacement between closely related species. We evaluated the transcriptional expression and metabolic performance of ortholog substitution complementing a Sinorhizobium meliloti argC mutant with argC from Rhizobiales (Agrobacterium tumefaciens, Rhizobium etli, and Mesorhizobium loti). The argC gene is necessary for the synthesis of arginine, an amino acid that is central to protein and cellular metabolism. Strains were obtained carrying plasmids with argC orthologs expressed under the speB and argC (S. meliloti) and lac (Escherichia coli) promoters. Complementation analysis was assessed by growth, transcriptional activity, enzymatic activity, mRNA levels, specific detection of ArgC proteomic protein, and translational efficiency. The argC orthologs performed differently in each complementation, reflecting the diverse factors influencing gene expression and the ability of the ortholog product to function in a foreign metabolic background. Optimal complementation was directly related to sequence similarity with S. meliloti, and was inversely related to species signature, with M. loti argC showing the poorest performance, followed by R. etli and A. tumefaciens. Different copy numbers of genes and amounts of mRNA and protein were produced, even with genes transcribed from the same promoter, indicating that coding sequences play a role in the transcription and translation processes. These results provide relevant information for further genomic analyses and suggest that orthologous gene substitutions between closely related species are not completely functionally equivalent.

The oligodeoxynucleotide sequences corresponding to never-expressed peptide motifs are mainly located in the non-coding strand

BACKGROUND

We study the usage of specific peptide platforms in protein composition. Using the pentapeptide as a unit of length, we find that in the universal proteome many pentapeptides are heavily repeated (even thousands of times), whereas some are quite rare, and a small number do not appear at all. To understand the physico-chemical-biological basis underlying peptide usage at the proteomic level, in this study we analyse the energetic costs for the synthesis of rare and never-expressed versus frequent pentapeptides. In addition, we explore residue bulkiness, hydrophobicity, and codon number as factors able to modulate specific peptide frequencies. Then, the possible influence of amino acid composition is investigated in zero- and high-frequency pentapeptide sets by analysing the frequencies of the corresponding inverse-sequence pentapeptides. As a final step, we analyse the pentadecamer oligodeoxynucleotide sequences corresponding to the never-expressed pentapeptides.

RESULTS

We find that only DNA context-dependent constraints (such as oligodeoxynucleotide sequence location in the minus strand, introns, pseudogenes, frameshifts, etc.) provide a coherent mechanistic platform to explain the occurrence of never-expressed versus frequent pentapeptides in the protein world.

CONCLUSIONS

This study is of importance in cell biology. Indeed, the rarity (or lack of expression) of specific 5-mer peptide modules implies the rarity (or lack of expression) of the corresponding n-mer peptide sequences (with n < 5), so possibly modulating protein compositional trends. Moreover the data might further our understanding of the role exerted by rare pentapeptide modules as critical biological effectors in protein-protein interactions.

High-throughput expression and purification of membrane proteins

High-throughput (HT) methodologies have had a tremendous impact on structural biology of soluble proteins. High-resolution structure determination relies on the ability of the macromolecule to form ordered crystals that diffract X-rays. While crystallization remains somewhat empirical, for a given protein, success is proportional to the number of conditions screened and to the number of variants trialed. HT techniques have greatly increased the number of targets that can be trialed and the rate at which these can be produced. In terms of number of structures solved, membrane proteins appear to be lagging many years behind their soluble counterparts. Likewise, HT methodologies for production and characterization of these hydrophobic macromolecules are only now emerging. Presented here is an HT platform designed exclusively for membrane proteins that has processed over 5000 targets.

Characterization and serologic analysis of the Treponema pallidum proteome

Treponema pallidum subsp. pallidum is the causative agent of syphilis, a sexually transmitted disease characterized by widespread tissue dissemination and chronic infection. In this study, we analyzed the proteome of T. pallidum by the isoelectric focusing (IEF) and nonequilibrating pH gel electrophoresis (NEPHGE) forms of two-dimensional gel electrophoresis (2DGE), coupled with matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) analysis. We determined the identity of 148 T. pallidum protein spots, representing 88 T. pallidum polypeptides; 63 of these polypeptides had not been identified previously at the protein level. To examine which of these proteins are important in the antibody response to syphilis, we performed immunoblot analysis using infected rabbit sera or human sera from patients at different stages of syphilis infection. Twenty-nine previously described antigens (predominantly lipoproteins) were detected, as were a number of previously unidentified antigens. The reactivity patterns obtained with sera from infected rabbits and humans were similar; these patterns included a subset of antigens reactive with all serum samples tested, including CfpA, MglB-2, TmpA, TmpB, flagellins, and the 47-kDa, 17-kDa, and 15-kDa lipoproteins. A unique group of antigens specifically reactive with infected human serum was also identified and included the previously described antigen TpF1 and the hypothetical proteins TP0584, TP0608, and TP0965. This combined proteomic and serologic analysis further delineates the antigens potentially useful as vaccine candidates or diagnostic markers and may provide insight into the host-pathogen interactions that occur during T. pallidum infection.

Structural genomics target selection for the New York consortium on membrane protein structure

The New York Consortium on Membrane Protein Structure (NYCOMPS), a part of the Protein Structure Initiative (PSI) in the USA, has as its mission to establish a high-throughput pipeline for determination of novel integral membrane protein structures. Here we describe our current target selection protocol, which applies structural genomics approaches informed by the collective experience of our team of investigators. We first extract all annotated proteins from our reagent genomes, i.e. the 96 fully sequenced prokaryotic genomes from which we clone DNA. We filter this initial pool of sequences and obtain a list of valid targets. NYCOMPS defines valid targets as those that, among other features, have at least two predicted transmembrane helices, no predicted long disordered regions and, except for community nominated targets, no significant sequence similarity in the predicted transmembrane region to any known protein structure. Proteins that feed our experimental pipeline are selected by defining a protein seed and searching the set of all valid targets for proteins that are likely to have a transmembrane region structurally similar to that of the seed. We require sequence similarity aligning at least half of the predicted transmembrane region of seed and target. Seeds are selected according to their feasibility and/or biological interest, and they include both centrally selected targets and community nominated targets. As of December 2008, over 6,000 targets have been selected and are currently being processed by the experimental pipeline. We discuss how our target list may impact structural coverage of the membrane protein space.

Evidence for the adaptation of protein pH-dependence to subcellular pH

BACKGROUND

The availability of genome sequences, and inferred protein coding genes, has led to several proteome-wide studies of isoelectric points. Generally, isoelectric points are distributed following variations on a biomodal theme that originates from the predominant acid and base amino acid sidechain pKas. The relative populations of the peaks in such distributions may correlate with environment, either for a whole organism or for subcellular compartments. There is also a tendency for isoelectric points averaged over a subcellular location to not coincide with the local pH, which could be related to solubility. We now calculate the correlation of other pH-dependent properties, calculated from 3D structure, with subcellular pH.

RESULTS

For proteins with known structure and subcellular annotation, the predicted pH at which a protein is most stable, averaged over a location, gives a significantly better correlation with subcellular pH than does isoelectric point. This observation relates to the cumulative properties of proteins, since maximal stability for individual proteins follows the bimodal isoelectric point distribution. Histidine residue location underlies the correlation, a conclusion that is tested against a background of proteins randomised with respect to this feature, and for which the observed correlation drops substantially.

CONCLUSION

There exists a constraint on protein pH-dependence, in relation to the local pH, that is manifested in the pKa distribution of histidine sub-proteomes. This is discussed in terms of protein stability, pH homeostasis, and fluctuations in proton concentration.

Proteomic strategies to elucidate pathogenic mechanisms of spirochetes

Spirochetes are a unique group of bacteria that include several motile and highly invasive pathogens that cause a multitude of acute and chronic disease processes. Nine genomes of spirochetes have been completed, which provide significant insights into pathogenic mechanisms of disease and reflect an often complex lifestyle associated with a wide range of environmental and host factors encountered during disease transmission and infection. Characterization of the outer membrane of spirochetes is of particular interest since it interacts directly with the host and environs during disease and likely contains candidate vaccinogens and diagnostics. In concert with appropriate fractionation techniques, the tools of proteomics have rapidly evolved to characterize the proteome of spirochetes. Of greater significance, studies have confirmed the differential expression of many proteins, including those of the outer membrane, in response to environmental signals encountered during disease transmission and infection. Characterization of the proteome in response to such signals provides novel insights to understand pathogenic mechanisms of spirochetes.

Analysis of the mouse liver proteome using advanced mass spectrometry

We report a large-scale analysis of mouse liver tissue comprising a novel fractionation approach and high-accuracy mass spectrometry techniques. Two fractions enriched for soluble and membrane proteins from 20 mg of frozen tissue were separated by one-dimensional electrophoresis followed by LC-MS/MS on the hybrid linear ion trap (LTQ)-Orbitrap mass spectrometer. Confident identification of 2210 proteins relied on at least two peptides. We combined this proteome with our previously reported organellar map (Foster et al. Cell 2006, 125, 187-199) to generate a very high confidence mouse liver proteome of 3244 proteins. The identified proteins represent the liver proteome with no discernible bias due to protein physicochemical properties, subcellular distribution, or biological function. Forty-seven percent of identified proteins were annotated as membrane-bound, and for 35.3%, transmembrane domains were predicted. For potential application in toxicology or clinical studies, we demonstrate that it is possible to consistently identify more than 1000 proteins in a single run.

The relationships between the isoelectric point and: length of proteins, taxonomy and ecology of organisms

Background

The distribution of isoelectric point (pI) of proteins in a proteome is universal for all organisms. It is bimodal dividing the proteome into two sets of acidic and basic proteins. Different species however have different abundance of acidic and basic proteins that may be correlated with taxonomy, subcellular localization, ecological niche of organisms and proteome size.

Results

We have analysed 1784 proteomes encoded by chromosomes of Archaea, Bacteria, Eukaryota, and also mitochondria, plastids, prokaryotic plasmids, phages and viruses. We have found significant correlation in more than 95% of proteomes between the protein length and pI in proteomes – positive for acidic proteins and negative for the basic ones. Plastids, viruses and plasmids encode more basic proteomes while chromosomes of Archaea, Bacteria, Eukaryota, mitochondria and phages more acidic ones. Mitochondrial proteomes of Viridiplantae, Protista and Fungi are more basic than Metazoa. It results from the presence of basic proteins in the former proteomes and their absence from the latter ones and is related with reduction of metazoan genomes. Significant correlation was found between the pI bias of proteomes encoded by prokaryotic chromosomes and proteomes encoded by plasmids but there is no correlation between eukaryotic nuclear-coded proteomes and proteomes encoded by organelles. Detailed analyses of prokaryotic proteomes showed significant relationships between pI distribution and habitat, relation to the host cell and salinity of the environment, but no significant correlation with oxygen and temperature requirements. The salinity is positively correlated with acidicity of proteomes. Host-associated organisms and especially intracellular species have more basic proteomes than free-living ones. The higher rate of mutations accumulation in the intracellular parasites and endosymbionts is responsible for the basicity of their tiny proteomes that explains the observed positive correlation between the decrease of genome size and the increase of basicity of proteomes. The results indicate that even conserved proteins subjected to strong selectional constraints follow the global trend in the pI distribution.

Conclusion

The distribution of pI of proteins in proteomes shows clear relationships with length of proteins, subcellular localization, taxonomy and ecology of organisms. The distribution is also strongly affected by mutational pressure especially in intracellular organisms.

Membrane protein prediction methods

We survey computational approaches that tackle membrane protein structure and function prediction. While describing the main ideas that have led to the development of the most relevant and novel methods, we also discuss pitfalls, provide practical hints and highlight the challenges that remain. The methods covered include: sequence alignment, motif search, functional residue identification, transmembrane segment and protein topology predictions, homology and ab initio modeling. In general, predictions of functional and structural features of membrane proteins are improving, although progress is hampered by the limited amount of high-resolution experimental information available. While predictions of transmembrane segments and protein topology rank among the most accurate methods in computational biology, more attention and effort will be required in the future to ameliorate database search, homology and ab initio modeling.

Simple proteomic checks for detecting noncoding RNA

Proper validation can accelerate sequence-based discovery of proteins and protein-coding genes. Databases currently contain a backlog of experimentally unverified gene models and tentative assignments of observed transcripts to coding or noncoding RNA. We present and apply a general principle, founded on base composition and the genetic code and validated here by bulk 2-D gels, that can improve the reliability of such classifications and of the algorithms or pipelines that lead to them.

How do we compare hundreds of bacterial genomes?

The genomic revolution is fully upon us in 2006 and the pace of discovery is set to accelerate with the emergence of ultra-high-throughput sequencing technologies. Our complete genome collection of bacteria and archaea continues to grow in number and diversity, as genome sequencing is applied to an array of new problems, from the characterization of the pan-genome to the detection of mutation after experimentation and the exploration of microbial communities in unprecedented detail. The benefits of large-scale comparative genomic analyses are driving the community to think about how to manage our public collections of genomes in novel ways.

Comparative proteome analysis of subcellular fractions from Borrelia burgdorferi by NEPHGE and IPG

Borrelia burgdorferi, the cause of Lyme disease, produces excessive amounts of membrane lipoproteins such as outer surface protein A (OspA) when grown in vitro, and consequently many low or moderately abundant proteins are underrepresented when cell lysates are examined by 2-DE. We analyzed the B. burgdorferi B31 proteome computationally and by IPG or modified NEPHGE after subcellular fractionation into membrane-associated and soluble proteins. The B. burgdorferi B31 theoretical proteome is comprised of 1623 proteins and has a mean pI of 8.36 and a median pI of 9.03 with 68% of the proteome possessing a pI >/=7.5. Separation of soluble proteins by IPG resulted in 205 individual spots and identification of 78 protein spots by MALDI-TOF MS. Separation by modified NEPHGE routinely resulted in approximately 185 soluble and 160 membrane protein spots with the identification of 88 individual protein spots combined by MALDI-TOF MS. Homologues to GroEL and aminopeptidase I were present in greater amounts in the membrane faction, with enolase at nearly equivalent amounts in the soluble and membrane fractions. Identification of proteins isolated and separated by such methods will enable future determination of proteome changes in membrane and soluble protein fractions as spirochetes adapt to their changing environments.

Subcellular pH and predicted pH-dependent features of proteins

A characteristic of two-dimensional proteomics gels is a general bimodal distribution of isoelectric (pI) values. Discussion of this feature has focussed on the balance of acidic and basic ionisable residues, and potential relationships between pI distributions and organism classification or protein subcellular location. Electrostatics calculations on a set of protein structures with known subcellular location show that predicted folded state pI are similar to those calculated from sequence alone, but adjusted according to a general stabilising effect from interactions between ionisable groups. Bimodal distributions dominate both pI and the predicted pH of maximal stability. However, there are significant differences between these features. The average pH of maximal stability generally follows organelle pH. Average pI values are well removed from organelle pH in most subcellular environments, consistent with the view that proteins have evolved to carry (on average) net charge in a given subcellular location, and relevant to discussion of solubility in crowded environments. Correlation of the predicted pH of maximum stability with subcellular pH suggests an evolutionary pressure to adjust folded state interactions according to environment. Finally, our analysis of ionisable group contributions to stability suggests that Golgi proteins have the largest such term, although this dataset is small.

Does the proteome encode organellar pH?

Inherent to the proteome itself, may be information that enables proteins to buffer pH at a level that promotes their own function within a specialized compartment. We observe that the distribution of computed isoelectric points in the yeast proteome matches experimentally derived organellar pH estimates across distinct subcellular compartments. This raises an interesting evolutionary question: did the pI of proteins and the pH of organelles co-evolve to optimize function?

Multi-modality of pI distribution in whole proteome

Multi-modality of pI distribution is a common feature in different whole proteomes. Some researchers considered it relate to the proteins with different subcellular locations, indicating the result of natural selection. We explored the pI distribution of predicted proteomes (including animals, plants, bacterium, archaeans) and random proteome [random protein sequences constructed according to the special amino acid composition and molecular weight (MW) distribution of human predicted proteome]. Our results suggest that the multi-modality is the result of discrete pK(R) values for different amino acids. Amino acid composition and MW distribution of a proteome also contributes to the specific pI distribution. Although protein subcellular location was related to pI value, our analyses revealed that comparing with the random proteome, neither the multi-modality phenomenon nor the distribution bias of pI values is caused by subcellular location. It seems that the multi-modality distribution is just a mathematical fun. The blank region near the neutral pI was caused by the absence of amino acids with neutral pK(R), and suggests that the selection of amino acids with ionizable side chain might be restricted by the requirement for a special pH environment during the origin of life. From this point of view, the special distribution was the result of natural selection.

The genome of Salinibacter ruber: convergence and gene exchange among hyperhalophilic bacteria and archaea

Saturated thalassic brines are among the most physically demanding habitats on Earth: few microbes survive in them. Salinibacter ruber is among these organisms and has been found repeatedly in significant numbers in climax saltern crystallizer communities. The phenotype of this bacterium is remarkably similar to that of the hyperhalophilic Archaea (Haloarchaea). The genome sequence suggests that this resemblance has arisen through convergence at the physiological level (different genes producing similar overall phenotype) and the molecular level (independent mutations yielding similar sequences or structures). Several genes and gene clusters also derive by lateral transfer from (or may have been laterally transferred to) haloarchaea. S. ruber encodes four rhodopsins. One resembles bacterial proteorhodopsins and three are of the haloarchaeal type, previously uncharacterized in a bacterial genome. The impact of these modular adaptive elements on the cell biology and ecology of S. ruber is substantial, affecting salt adaptation, bioenergetics, and photobiology.

Amino acid variation in cellular processes in 108 bacterial proteomes

We have analysed 108 bacterial proteomes in the KEGG database to explore the variation of amino acid composition with respect to protein function. The ratio between the observed amino acid composition and that predicted based on mononucleotide composition was calculated for each functional category. This indicated whether the compositional variation arose from mutation or selection pressure. The results showed that charged amino acids (Lys, Arg and Glu), were found more frequently than expected in proteins involved in genetic information processing (i.e. transcription, translation, etc.) Similarly, in the proteins involved in processing environmental information (e.g. signal transduction), the hydrophobic amino acid Leu was found in excess of values expected from the base composition in the genes.

Analysing proteomic data

The rapid growth of proteomics has been made possible by the development of reproducible 2D gels and biological mass spectrometry. However, despite technical improvements 2D gels are still less than perfectly reproducible and gels have to be aligned so spots for identical proteins appear in the same place. Gels can be warped by a variety of techniques to make them concordant. When gels are manipulated to improve registration, information is lost, so direct methods for gel registration which make use of all available data for spot matching are preferable to indirect ones. In order to identify proteins from gel spots a property or combination of properties that are unique to that protein are required. These can then be used to search databases for possible matches. Molecular mass, pI, amino acid composition and short sequence tags can all be used in database searches. Currently the method of choice for protein identification is mass spectrometry. Proteins are eluted from the gels and cleaved with specific endoproteases to produce a series of peptides of different molecular mass. In peptide mass fingerprinting, the peptide profile of the unknown protein is compared with theoretical peptide libraries generated from sequences in the different databases. Tandem mass spectroscopy (MS/MS) generates short amino acid sequence tags for the individual peptides. These partial sequences combined with the original peptide masses are then used for database searching, greatly improving specificity. Increasingly protein identification from MS/MS data is being fully or partially automated. When working with organisms, which do not have sequenced genomes (the case with most helminths), protein identification by database searching becomes problematical. A number of approaches to cross species protein identification have been suggested, but if the organism being studied is only distantly related to any organism with a sequenced genome then the likelihood of protein identification remains small. The dynamic nature of the proteome means that there really is no such thing as a single representative proteome and a complete set of metadata (data about the data) is going to be required if the full potential of database mining is to be realised in the future.