POTAMOS mass spectrometry calculator: computer aided mass spectrometry to the post-translational modifications of proteins. A focus on histones

Mass spectrometry is a widely used technique for protein identification and it has also become the method of choice in order to detect and characterize the post-translational modifications (PTMs) of proteins. Many software tools have been developed to deal with this complication. In this paper we introduce a new, free and user friendly online software tool, named POTAMOS Mass Spectrometry Calculator, which was developed in the open source application framework Ruby on Rails. It can provide calculated mass spectrometry data in a time saving manner, independently of instrumentation. In this web application we have focused on a well known protein family of histones whose PTMs are believed to play a crucial role in gene regulation, as suggested by the so called "histone code" hypothesis. The PTMs implemented in this software are: methylations of arginines and lysines, acetylations of lysines and phosphorylations of serines and threonines. The application is able to calculate the kind, the number and the combinations of the possible PTMs corresponding to a given peptide sequence and a given mass along with the full set of the unique primary structures produced by the possible distributions along the amino acid sequence. It can also calculate the masses and charges of a fragmented histone variant, which carries predefined modifications already implemented. Additional functionality is provided by the calculation of the masses of fragments produced upon protein cleavage by the proteolytic enzymes that are most widely used in proteomics studies.

A structural approach to understanding the iron-binding properties of phylogenetically different frataxins

Friedreich's ataxia (FRDA), an autosomal recessive cardio- and neurodegenerative disease, is caused by low expression of frataxin, a small mitochondrial protein, encoded in the nucleus. At the biochemical level, the lack of frataxin leads to dysregulation of mitochondrial iron homeostasis and oxidative damage, which eventually causes neuronal death. It is, however, still unclear whether frataxin is directly involved in iron binding, since the yeast orthologue, but not the human protein, has been shown to form large aggregates in the presence of large iron excess. We have compared the properties of three proteins from the frataxin family--the bacterial CyaY from Escherichia coli, the yeast Yfh1 and human frataxin--as representative of organisms of increasing complexity. We show that the three proteins have the same fold but different thermal stabilities and iron-binding properties. While human frataxin has no tendency to bind iron, CyaY forms iron-promoted aggregates with a behaviour similar to that of yeast frataxin. However, aggregation can be competed by chelator agents or by ionic strength. At physiological salt conditions, almost no aggregation is observed. The design of mutants produced to identify the protein surface involved in iron-promoted aggregation allows us to demonstrate that the process is mediated by a negatively charged surface ridge. Mutation of three of these residues is sufficient to convert CyaY in a protein with properties similar to those of human frataxin. On the other hand, mutation of the exposed surface of the beta sheet, which contains most of the conserved residues, does not affect aggregation, suggesting that iron binding is a non-conserved part of a more complex cellular function of frataxins.

A structural characterization of the interactions between titin Z-repeats and the alpha-actinin C-terminal domain

Titin and alpha-actinin, two modular muscle proteins, are with actin the major components of the Z-band in vertebrate striated muscles where they serve to organize the antiparallel actin filament arrays in adjacent sarcomeres and to transmit tension between sarcomeres during activation. Interactions between titin and alpha-actinin have been mainly localized in a 45-amino acid multiple motif (Z-repeat) in the N-terminal region of titin and the C-terminal region of alpha-actinin. In this study, we provide the first quantitative characterization of alpha-actinin-Z-repeat recognition and dissect the interaction to its minimal units. Different complementary techniques, such as circular dichroism, calorimetry, and nuclear magnetic spectroscopy, were used. Two overlapping alpha-actinin constructs (Act-EF34 and Act-EF1234) containing two and four EF-hand motifs, respectively, were produced, and their folding properties were examined. Complex formation of Act-EF34 and Act-EF1234 with single- and double-Z-repeat constructs was studied. Act-EF34 was shown quantitatively to be necessary and sufficient for binding to Z-repeats, excluding the presence of additional high-affinity binding sites in the remaining part of the domain. The binding affinities of the different Z-repeats for Act-EF34 range from micromolar to millimolar values. The strongest of these interactions are comparable to those observed in troponin C-troponin I complexes. The binding affinities for Act-EF34 are maximal for Zr1 and Zr7, the two highly homologous sequences present in all muscle isoforms. No cooperative or additional contributions to the interaction were observed for Z-repeat double constructs. These findings have direct relevance for evaluating current models of Z-disk assembly.

Protein secretion biotechnology using Streptomyces lividans: large-scale production of functional trimeric tumor necrosis factor alpha

We evaluated the feasibility of large-scale production of biopharmaceuticals expressed as heterologous polypeptides from the Gram-positive bacterium Streptomyces lividans. As a model protein we used murine tumor necrosis factor alpha (mTNFalpha). mTNFalpha fused C-terminally to the secretory signal peptide of the subtilisin-inhibitor protein from Streptomyces venezuelae. Under appropriate fermentation conditions, significant amounts of mature mTNFalpha (80-120 mg/L) can be recovered from spent growth media. Efficient downstream processing allowing rapid purification of mTNFalpha from culture supernatants was developed. Importantly, the protein is recovered from the spent growth medium in its native trimeric state as judged by biophysical analysis. Further, mTNFalpha secreted by S. lividans is significantly more active in an in vitro apoptosis tissue culture assay than a corresponding polypeptide produced in Escherichia coli. This pilot study provides the first validation of S. lividans protein secretion as an alternative bioprocess for large-scale production of oligomeric proteins of potential therapeutic value.

Dynamic associations of heterochromatin protein 1 with the nuclear envelope

To study the dynamics of mammalian HP1 proteins we have microinjected recombinant forms of mHP1alpha, M31 and M32 into the cytoplasm of living cells. As could be expected from previous studies, the three fusion proteins were efficiently transported into the nucleus and targeted specific chromatin areas. However, before incorporation into these areas the exogenous proteins accumulated in a peripheral zone and associated closely with the nuclear envelope. This transient association did not occur when the cells were treated with deacetylase inhibitors, indicating an acetylation-inhibited interaction. In line with these observations, recombinant HP1 proteins exhibited saturable binding to purified nuclear envelopes and stained the nuclei of detergent-permeabilized cells in a rim-like fashion. Competition experiments with various M31 mutants allowed mapping of the nuclear envelope-binding site within an N-terminal region that includes the chromodomain. A His(6)-tagged peptide representing this region inhibited recruitment of LAP2beta and B-type lamins around the surfaces of condensed chromosomes, suggesting involvement of HP1 proteins in nuclear envelope reassembly.

A molecular switch in SecA protein couples ATP hydrolysis to protein translocation

SecA, the dimeric ATPase subunit of bacterial protein translocase, catalyses translocation during ATP-driven membrane cycling at SecYEG. We now show that the SecA protomer comprises two structural modules: the ATPase N-domain, containing the nucleotide binding sites NBD1 and NBD2, and the regulatory C-domain. The C-domain binds to the N-domain in each protomer and to the C-domain of another protomer to form SecA dimers. NBD1 is sufficient for single rounds of SecA ATP hydrolysis. Multiple ATP turnovers at NBD1 require both the NBD2 site acting in cis and a conserved C-domain sequence operating in trans. This intramolecular regulator of ATP hydrolysis (IRA) mediates N-/C-domain binding and acts as a molecular switch: it suppresses ATP hydrolysis in cytoplasmic SecA while it releases hydrolysis in SecY-bound SecA during translocation. We propose that the IRA switch couples ATP binding and hydrolysis to SecA membrane insertion/deinsertion and substrate translocation by controlling nucleotide-regulated relative motions between the N-domain and the C-domain. The IRA switch is a novel essential component of the protein translocation catalytic pathway.

SH3 in muscles: solution structure of the SH3 domain from nebulin

The huge modular protein nebulin is located in the thin filament of striated muscle in vertebrates and is thought to bind and stabilize F-actin. The C-terminal part of human nebulin is anchored in the sarcomeric Z-disk and contains an SH3 domain, the first of such motifs to be identified in a myofibrillar protein. We have determined the nebulin SH3 sequence from several species and found it strikingly conserved. We have also shown that the SH3 transcripts are constitutively expressed in skeletal muscle tissues. As the first step towards a molecular understanding of nebulin's cellular role we have determined the three-dimensional structure of the human nebulin SH3 domain in solution by nuclear magnetic resonance (NMR) spectroscopy and compared it with other known SH3 structures. The nebulin SH3 domain has a well-defined structure in solution with a typical SH3 topology, consisting of a beta-sandwich of two triple-stranded, antiparallel beta-sheets arranged at right angles to each other and of a single turn of a 310-helix. An additional double-stranded antiparallel beta-sheet in the RT loop bends over the beta-sandwich. The derived structure reveals a remarkable similarity with a distinct subset of SH3 domains, especially in the structural features of the exposed hydrophobic patch that is thought to be the site of interaction with polyproline ligands. On the basis of this similarity, we have modelled the interaction with an appropriate polyproline ligand and attempted to delineate the characteristics of the physiological SH3-binding partner in the Z-disk. Our results represent the first step in reconstructing the structure of nebulin and are expected to contribute to our understanding of nebulin's functional role in myofibrillar assembly.

When a module is also a domain: the rôle of the N terminus in the stability and the dynamics of immunoglobulin domains from titin

In the course of a structural study of titin, a giant modular protein from muscle, we have reported that N-terminal extension of immunoglobulin-like (Ig-like) domains from titin stabilizes this fold. In order to investigate the structural basis of such an effect, we have solved the structure of NEXTM5, which has six amino acids added to the sequence of M5, a domain for which full structure determination has been previously achieved. In the present work, the structures and the dynamics of M5 and NEXTM5 are compared in the light of data collected for these and other titin domains. In NEXTM5, three out of the six added residues are structured and pack against the nearby BC and FG loops. As a consequence, three new backbone hydrogen bonds are formed with the B strand, extending the A strand by two residues and decreasing the exposed surface area of the loops. Additional contacts which involve the side-chains give rise to a remarkable pH dependence of the stability. Interestingly, no correlation is observed on the NMR time-scale between the overall dynamics of the extended domain and its increased stability. The most noticeable differences between the two constructs are localised around the N terminus, which becomes more rigid upon extension. Since a similar pattern of contacts is observed for other domains of the immunoglobulin I-set, our results are of general relevance for this protein family. Our work might also inspire a more rational approach to the investigation of domain boundaries and their influence on module stability.

Immunoglobulin-like modules from titin I-band: extensible components of muscle elasticity

BACKGROUND

The giant muscle protein titin forms a filament which spans half of the sarcomere and performs, along its length, quite diverse functions. The region of titin located in the sarcomere I-band is believed to play a major role in extensibility and passive elasticity of muscle. In the I-band, the titin sequence consists mostly of repetitive motifs of tandem immunoglobulin-like (Ig) modules intercalated by a potentially non-globular region. The highly repetitive titin architecture suggests that the molecular basis of its mechanical properties be approached through the characterization of the isolated components of the I-band and their interfaces. In the present paper, we report on the structure determination in solution of a representative Ig module from the I-band (I27) as solved by NMR techniques.

RESULTS

The structure of I27 consists of a beta sandwich formed by two four-stranded sheets (named ABED and A'GFC). This fold belongs to the intermediate frame (I frame) of the immunoglobulin superfamily. Comparison of I27 with another titin module from the region located in the M-line (M5) shows that two loops (between the B and C and the F and G strands) are shorter in I27, conferring a less elongated appearance to this structure. Such a feature is specific to the Ig domains in the I-band and might therefore be related to the functions of the protein in this region. The structure of tandem Ig domains as modeled from I27 suggests the presence of hinge regions connecting contiguous modules.

CONCLUSIONS

We suggest that titin Ig domains in the I-band function as extensible components of muscle elasticity by stretching the hinge regions.

The elastic I-band region of titin is assembled in a "modular" fashion by weakly interacting Ig-like domains

The vertebrate striated muscle protein titin is thought to play a critical rôle in myofibril assembly and passive tension. The recently determined complete primary structure of titin revealed a modular architecture that opens the way to a structural characterisation and the understanding of essential properties of this molecule through dissection into units that are structurally and/or functionally relevant. To understand the assembly process of titin, and ultimately the molecular basis of its elastic behaviour, we studied the thermodynamic properties of module pairs, the smallest structural unit that includes a module-module interface. Thus, selected module pairs and their component single modules from the I-band part of the titin molecule were expressed in Escherichia coli and their heat-induced and denaturant-induced unfolding was investigated with a combination of techniques (circular dichroism, fluorescence spectroscopy and nuclear magnetic resonance). The stabilities of single modules and pairs were determined from denaturation experiments. The module interface was also modelled on the basis of the sequence alignment of all approximately 40 immunoglobulin like modules from the I-band and the known structure of one of them. Our results show that all modules and module pairs examined are independently folded in solution. When covalently linked, although weakly interacting, they still behave as autonomous co-operative units upon unfolding. These observations lead us to suggest that folding of titin in vitro is a hierarchical event and that weak interactions between its adjacent modules must only partly account for its presumed elastic function.

The folding and stability of titin immunoglobulin-like modules, with implications for the mechanism of elasticity

Titin (first known as connectin) is a vast modular protein found in vertebrate striated muscle. It is thought to assist myofibrillogenesis and to provide a passive elastic restoring force that helps to keep the thick filaments properly centered in the sarcomere. We show that representative titin modules do indeed fold independently, and report their stabilities (i.e., delta G of unfolding and melting temperature) as measured by circular dichroism, fluorescence, and nuclear magnetic resonance spectroscopies. We find that there is a region-dependent variation in stability, although we find no evidence to support a proposed elastic mechanism based on a molten-globular-like equilibrium folding intermediate, nor do our calculations support any mechanism based on the configurational entropy of the molecule itself; instead we suggest a model based on hydrophobic hinge regions that would not be strongly dependent on the precise folding pattern of the chain.

Secondary structure determination by NMR spectroscopy of an immunoglobulin-like domain from the giant muscle protein titin

We present the complete 15N and 1H NMR assignment and the secondary structure of an immunoglobulin-like domain from the giant muscle protein titin. The assignment was obtained using homonuclear and 15N heteronuclear 2D and 3D experiments. The complementarity of 3D TOCSY-NOESY and 3D 15N NOESY-HSQC experiments, using WATERGATE for water suppression, allowed an efficient assignment of otherwise ambiguous cross peaks and was helpful in overcoming poor TOCSY transfer for some amino acids. The secondary structure is derived from specific NOEs between backbone alpha- and amide protons, secondary chemical shifts of alpha-protons and chemical exchange for the backbone amide protons. It consists of eight beta-strands, forming two beta-sheets with four strands each, similar to the classical beta-sandwich of the immunoglobulin superfamily, as previously predicted by sequence analysis. Two of the beta-strands are connected by type II beta-turns; the first beta-strand forms a beta-bulge. The whole topology is very similar to the only intracellular immunoglobulin-like domain for which a structure has been determined so far, i.e., telokin.

Immunoglobulin-type domains of titin are stabilized by amino-terminal extension

We have recently suggested that similarly folded titin modules located at different sarcomeric regions have distinct molecular properties and stability. Could our selection of module boundaries have potentially influenced our conclusions? To address this question we expressed amino-terminally extended versions of the same modules and determined, with the use of CD and Fluorescence techniques, key thermodynamic parameters characterizing their stability. We present here our results which confirm our previous observations and show that, while amino-terminal extension has a profound effect on the stability of individual modules, it does not affect at all their folding pattern or their relative stabilities. Moreover, our data suggest that the selection of module boundaries can be of critical importance for the structural analysis of modular proteins in general, especially when a well-defined intron-exon topography is absent and proteolytic methods are inconclusive.

Immunoglobulin-type domains of titin: same fold, different stability?

Titin is a 3-MDa protein thought to form a fibrous intracellular system in vertebrate striated muscle and to play an important role in sarcomere alignment during muscle contraction. It has also been implicated as a "molecular ruler", regulating the assembly and the precise length of the thick filaments [Whiting, A. J., Wardale, J., & Trinick, J. (1989) J. Mol. Biol. 205, 163-169]. Partial sequencing of titin-encoding cDNAs suggests that the protein is organized in a modular fashion, containing two classes of approximately 100-residue repeats [Labeit, S., Barlow, D. P., Gautel, M., Gibson, T., Holt, J., Hsieh, C. L., Francke, U., Leonard, K., Wardale, J., Whiting, A., & Trinick, J. (1990) Nature 345, 273-276]. These motifs, referred to as type I and type II modules, show sequence homology to the fibronectin III and immunoglobulin C2 superfamilies, respectively. Since the type II modules represent the most widely occurring motifs along the titin molecule, we expressed in Escherichia coli three domains of this type spanning different regions of the sarcomere (A-band and M-line) and studied their structure and stability. Using circular dichroism, nuclear magnetic resonance, and fluorescence spectroscopy, we showed that all the fragments examined are independently folded in solution and possess a beta-sheet conformation. Furthermore, employing NMR analysis, we identified an overall folding pattern present in all modules and related to the Ig fold, as previously suggested by theoretical predictions. The stability of the modules over a range of conditions was investigated by measuring key thermodynamic parameters for both thermal and chemical denaturation and by monitoring amide proton exchange as a function of time.(ABSTRACT TRUNCATED AT 250 WORDS)