Calcium fluoride micro cells for synchrotron radiation circular dichroism spectroscopy

De-mountable calcium fluoride micro cells have been developed for use in synchrotron radiation circular dichroism (SRCD) spectroscopy. They have the advantages that they require only very small sample volumes (as low as 1 microliter) and have short path lengths (as small as 2 micrometers). Highly reproducible spectra can be obtained in consecutive loadings with these spacer-free, fixed path length cells, which enable low wavelength data collection.

VUV irradiation effects on proteins in high-flux synchrotron radiation circular dichroism spectroscopy

Synchrotron radiation circular dichroism (SRCD) spectroscopy is emerging as an important new tool in structural molecular biology. Previously we had shown that in lower-flux SRCD instruments, such as UV1 at ISA and beamline 3.1 at the SRS, vacuum ultraviolet (VUV) radiation damage to proteins was not evident after exposure over a period of hours. No effects were detected in either the protein primary or the secondary structures. However, with the development of high-flux beamlines, such as CD12 at the SRS, this issue has been revisited because of changes observed in the SRCD spectra of consecutive scans of protein samples obtained on this high-flux beamline. Experiments have been designed to distinguish between two different possible mechanisms: (i) photoionization causing free radicals or secondary electrons producing degradation of the protein, and (ii) local heating of the sample resulting in protein denaturation. The latter appears to be the principal source of the signal deterioration.

Conductance studies on trichotoxin_A50E and implications for channel structure

Trichotoxin_A50E is an 18-residue peptaibol whose crystal structure has recently been determined. In this study, the conductance properties of trichotoxin_A50E have been investigated in neutral planar lipid bilayers. The macroscopic current-voltage curves disclose a moderate voltage-sensitivity and the concentration-dependence suggests the channels are primarily hexameric. Under ion gradients, shifts of the reversal potential indicate that cations are preferentially transported. Trichotoxin displays only one single-channel conductance state in a given experiment, but an ensemble of experiments reveals a distribution of conductance levels. This contrasts with the related peptaibol alamethicin, which produces multiple channel levels in a single experiment, indicative of recruitment of additional monomers into different multimeric-sized channels. Based on these conductance measurements and on the recently available crystal structure of trichotoxin_A50E, which is a shorter and straighter helix than alamethicin, a tightly-packed hexameric model structure has been constructed for the trichotoxin channel. It has molecular dimensions and surface electrostatic potential compatible with the observed conductance properties of the most probable and longer-lived channel.

Effects of deglycosylation of sodium channels on their structure and function

Voltage-gated sodium channels are important membrane proteins underlying electrical signaling in the nervous and muscular systems. They undergo rapid conformational changes between closed resting, activated, and inactivated states. Approximately 30% of the mass of the sodium channel is carbohydrate, present as glycoconjugate chains, mostly composed of N-acetylhexosamines and sialic acid. In this study, the effects of removing the carbohydrate on the functional and structural properties of highly purified sodium channels from Electrophorus electricus were investigated. After enzymatic deglycosylation, channels were reconstituted into planar lipid bilayers. In the presence of batrachotoxin, substates became evident and the single-channel conductance of the deglycosylated channels was slightly reduced relative to that of native channels, consistent with electrostatic effects due to the reduction in negative charge at the extracellular vestibule of the channel. The previously reported state-dependent changes in the circular dichroism spectra that are associated with the binding of the anticonvulsant drug Lamotrigine and batrachotoxin are also seen in the modified channels. Synchrotron radiation circular dichroism (SRCD) spectroscopy on the type of sugars found in the sodium channel showed that unlike most carbohydrates, these sugars produce a significant dichroic signal in the far-ultraviolet region. This can account for all of the measured SRCD-detected spectral differences between the native and deglycosylated channels, thereby indicating that no net change in protein secondary structure results from the deglycosylation procedure. Furthermore, thermal denaturation studies detected no significant differences in stability between native and deglycosylated channels. In summary, while the sugars of the voltage-gated sodium channels from electroplax are not essential for functional or structural integrity, they do appear to have a modulating effect on the conductance properties of these channels.

CDtool-an integrated software package for circular dichroism spectroscopic data processing, analysis, and archiving

CDtool is a software package written to facilitate circular dichroism (CD) spectroscopic studies on both conventional lab-based instruments and synchrotron beamlines. It takes format-independent input data from any type of CD instrument, enables a wide range of standard and advanced processing methods, and, in a single user-friendly graphics-based package, takes raw data through the entire processing procedure and, importantly, uses data-mining techniques to retain in the final output all the information associated with the processing. It permits the facile comparison of data obtained from different instruments without the need for reformatting and displays it in graphical formats suitable for publication. It also includes the ability to automatically archive the processed data. This latter feature may be especially useful in light of recent funding institution directives with regard to data sharing and archiving and requirements for "good practice" and "traceability" within the pharmaceutical industry. In addition, CDtool includes a means of interfacing with protein data bank coordinate files and calculating secondary structures from them using alternate definitions and algorithms. This feature, along with a function that permits the facile production of new reference databases, enables the creation of specialized databases for secondary structural analyses of specific types of proteins. Thus the CDtool software not only enables rapid data processing and analyses but also includes many enhanced features not available in other CD data processing/analysis packages.

Spectral magnitude effects on the analyses of secondary structure from circular dichroism spectroscopic data

The effects of spectral magnitude on the calculated secondary structures derived from circular dichroism (CD) spectra were examined for a number of the most commonly used algorithms and reference databases. Proteins with different secondary structures, ranging from mostly helical to mostly beta-sheet, but which were not components of existing reference databases, were used as test systems. These proteins had known crystal structures, so it was possible to ascertain the effects of magnitude on both the accuracy of determining the secondary structure and the goodness-of-fit of the calculated structures to the experimental data. It was found that most algorithms are highly sensitive to spectral magnitude, and that the goodness-of-fit parameter may be a useful tool in assessing the correct scaling of the data. This means that parameters that affect magnitude, including calibration of the instrument, the spectral cell pathlength, and the protein concentration, must be accurately determined to obtain correct secondary structural analyses of proteins from CD data using empirical methods.

The P23T Cataract Mutation Causes Loss of Solubility of Folded γD-Crystallin

Mutations in the human gammaD-crystallin gene have been linked to several types of congenital cataracts. In particular, the Pro23 to Thr (P23T) mutation of human gammaD crystallin has been linked to cerulean, lamellar, coralliform, and fasciculiform congenital cataracts. We have expressed and purified wild-type human gammaD, P23T, and the Pro23 to Ser23 (P23S) mutant. Our measurements show that P23T is significantly less soluble than wild-type human gammaD, with P23S having an intermediate solubility. Using synchrotron radiation circular dichroism spectroscopy, we have determined that the P23T mutant has a slightly increased content of beta-sheet, which may be attributed to the extension of an edge beta-strand due to the substitution of Pro23 with a residue able to form hydrogen bonds. Neither of the point mutations appears to have reduced the thermal stability of the protein significantly, nor its resistance to guanidine hydrochloride-induced unfolding. These results suggest that insolubility, rather than loss of stability, is the primary basis for P23T congenital cataracts.

The peptaibol database: a sequence and structure resource

The peptaibols are a large family of membrane-active peptides with considerable sequence homology, but with different biological properties and three-dimensional structures. They constitute a rich resource of naturally occurring 'mutants' which are potentially valuable for structure/function studies of ion channels. A searchable on-line database of sequences and structures of the peptaibols has been created at http://www.cryst.bbk.ac.uk/peptaibol, as a resource for the biological and structural community. In this paper, the contents and organization of the website are discussed as well as procedures for submission of new entries to the database. At present, more than 300 peptaibol sequences are stored in the database. Each sequence entry contains its full literature reference and information about its biological source. Tools are provided for searching for specific peptaibol sequences or groupings of sequences, and for locating peptaibols containing specified sequence motifs. In addition the website acts as a database for structural information. The coordinates of all currently available peptaibol x-ray and NMR structures are included and complemented, where appropriate. with molecular graphics illustrations. These include figures of model channel structures and comparisons between different peptaibol structures. The peptaibol database thus provides a tool for ready access to information and a means of investigating the sequences and structures of this class of polypeptides.

DICHROWEB, an online server for protein secondary structure analyses from circular dichroism spectroscopic data

The DICHROWEB web server enables on-line analyses of circular dichroism (CD) spectroscopic data, providing calculated secondary structure content and graphical analyses comparing calculated structures and experimental data. The server is located at http://www.cryst.bbk.ac.uk/cdweb and may be accessed via a password-limited user ID, available upon completion of a registration form. The server facilitates analyses using five popular algorithms and (currently) seven different reference databases by accepting data in a user-friendly manner in a wide range of formats, including those output by both commercial CD instruments and synchrotron radiation-based circular dichroism beamlines, as well as those produced by spectral processing software packages. It produces as output calculated secondary structures, a goodness-of-fit parameter for the analyses, and tabular and graphical displays of experimental, calculated and difference spectra. The web pages associated with the server provide information on CD spectroscopic methods and terms, literature references and aids for interpreting the analysis results.

The Peptaibol Database: a database for sequences and structures of naturally occurring peptaibols

The Peptaibol Database is a sequence and structure resource for the unusual class of peptides known as peptaibols. These peptides exhibit antibiotic and membrane channel-forming activities. The database includes sequence, biological source and bibliographical data for the naturally occurring peptaibols. Information is also collated for the growing number of peptaibol 3D structures determined by either crystallography or NMR spectroscopy. The database can be obtained as a whole or can be queried by name, group, sequence motif, biological origin and/or literature reference. The Peptaibol Database can be freely accessed at http://www.cryst.bbk.ac.uk/peptaibol.

Biomedical applications of synchrotron radiation circular dichroism spectroscopy: Identification of mutant proteins associated with disease and development of a reference database for fold motifs

Synchrotron radiation circular dichroism (SRCD) spectroscopy is an emerging technique in structural biology with particular value for accurate secondary structure determination, monitoring protein folding and kinetics, and drug discovery. This paper discusses new biomedical applications of SRCD, notably the identification of conformational changes associated with a mutant protein that causes disease, and the development of methods for identification of fold motifs in the context of structural genomics programmes. In addition, it presents for the first time, very low wavelength (below 154 nm) data for a protein in aqueous solution, demonstrating the presence of heretofore-unseen electronic transitions.

Analysis of peptaibol sequence composition: implications for in vivo synthesis and channel formation

The sequence entries in the Peptaibol Database were analysed to provide information on compositional features of this unusual family of peptides. The non-standard amino acid alpha-aminoisobutyric acid represents almost 40% of the residues in all the known sequences. Glutamine is the only significant polar residue in peptaibols, and the position and number of these residues appear to be related to their functional properties as ion channels. Aromatic residues are clustered at the termini, which may contribute to stabilization of the peptide vertically within the bilayer. The peptide chain length is strongly weighted towards the longer members of the family (16-20 residues) and likely to be an important feature in their mode of action as transmembrane permeabilizers. The significant skewing towards even numbers of residues and the bias in pairwise distributions of amino acids have implications for the nature of the in vivo synthesis of these peptides via large non-ribosomal protein complexes.

Circular dichroism and synchrotron radiation circular dichroism spectroscopy: tools for drug discovery

CD spectroscopy is an established and valuable technique for examining protein structure, dynamics and folding. Because of its ability to sensitively detect conformational changes, it has important potential for drug discovery, enabling screening for ligand and drug binding, and detection of potential candidates for new pharmaceuticals. The binding of the anti-tumour agent Taxol to the anti-apoptosis protein Bcl-2 [Rodi, Janes, Sanganee, Holton, Wallace and Makowski (1999) J. Mol. Biol. 285, 197-204] and the binding of the anti-epileptic drug lamotrigine to voltage-gated sodium channels [Cronin, O'Reilly, Duclohier and Wallace (2003) J. Biol. Chem. 278, 10675-10682] are used as examples to show changes detectable by CD involving secondary structure, and are contrasted with the binding of the agonist carbamylcholine to acetylcholine receptors [Mielke and Wallace (1988) J. Biol. Chem. 263, 8177-8182], an example where binding does not involve a secondary structural change. Synchrotron radiation CD spectroscopy offers significant enhancements with respect to conventional CD spectroscopy, which will enable its usage for high-throughput screening and as a tool in 'chemical genomics' or 'reverse chemical genetics' strategies for ligand identification. The lower wavelength data available enable more detailed, sensitive and accurate detection, the higher light intensity permits much smaller amounts of both proteins and drug candidates to be used in the screening, and future technological developments in sample handling and detection should enable automated high-throughput screening to be performed.

Analyses of circular dichroism spectra of membrane proteins

Circular dichroism (CD) spectroscopy is a valuable technique for the determination of protein secondary structures. Many linear and nonlinear algorithms have been developed for the empirical analysis of CD data, using reference databases derived from proteins of known structures. To date, the reference databases used by the various algorithms have all been derived from the spectra of soluble proteins. When applied to the analysis of soluble protein spectra, these methods generally produce calculated secondary structures that correspond well with crystallographic structures. In this study, however, it was shown that when applied to membrane protein spectra, the resulting calculations produce considerably poorer results. One source of this discrepancy may be the altered spectral peak positions (wavelength shifts) of membrane proteins due to the different dielectric of the membrane environment relative to that of water. These results have important consequences for studies that seek to use the existing soluble protein reference databases for the analyses of membrane proteins.

Binding of the anticonvulsant drug lamotrigine and the neurotoxin batrachotoxin to voltage-gated sodium channels induces conformational changes associated with block and steady-state activation

Voltage-gated sodium channels are dynamic membrane proteins characterized by rapid conformational changes that switch the molecule between closed resting, activated, and inactivated states. Sodium channels are specifically blocked by the anticonvulsant drug lamotrigine, which preferentially binds to the channel pore in the inactivated open state. Batrachotoxin is a lipid-soluble alkaloid that causes steady-state activation and binds in the inner pore of the sodium channel with overlapping but distinct molecular determinants from those of lamotrigine. Using circular dichroism spectroscopy on purified voltage-gated sodium channels from Electrophorus electricus, the secondary structures associated with the mixture of states present at equilibrium in the absence of these ligands were compared with specific stabilized states in their presence. As the channel shifts to open states, there appears to be a significant change in secondary structure to a more alpha-helical conformation. The observed changes are consistent with increased order involving the S6 segments that form the pore, the domain III-IV linker, and the P-loops that form the outer pore and selectivity filter. A molecular model has been constructed for the sodium channel based on its homology with the pore-forming regions of bacterial potassium channels, and automated docking of the crystal structure of lamotrigine with this model produces a structure in which the close contacts of the drug are with the residues previously identified by mutational studies as forming the binding site for this drug.

The temperature dependence of gramicidin conformational States in octanol

In lipid bilayers and organic solvents, the hydrophobic polypeptide gramicidin adopts a number of different conformations, some of which are capable of conducting monovalent cations across phospholipid membranes. The equilibria between conformations have been shown to be influenced by factors such as lipid chain length, solvent, concentration and salt. In this study, the temperature dependence of the equilibrium mixture of double helical ion-free gramicidin in octanol was examined using circular dichroism spectroscopy.

Solution NMR studies of antiamoebin, a membrane channel-forming polypeptide

Antiamoebin I is a membrane-active peptaibol produced by fungi of the species Emericellopsis which is capable of forming ion channels in membranes. Previous structure determinations by x-ray crystallography have shown the molecule is mostly helical, with a deep bend in the center of the polypeptide, and that the backbone structure is independent of the solvent used for crystallization. In this study, the solution structure of antiamoebin was determined by NMR spectroscopy in methanol, a solvent from which one of the crystal structures was determined. The ensemble of structures produced exhibit a right-handed helical C terminus and a left-handed helical conformation toward the N-terminus, in contrast to the completely right-handed helices found in the crystal structures. The NMR results also suggest that a "hinge" region exists, which gives flexibility to the polypeptide in the central region, and which could have functional implications for the membrane insertion process. A model for the membrane insertion and assembly process is proposed based on the antiamoebin solution and crystal structures, and is contrasted with the assembly and insertion mechanism proposed for other ion channel-forming polypeptides.

The peptaibol antiamoebin as a model ion channel: similarities to bacterial potassium channels

Antiamoebin (AAM) is a polypeptide antibiotic that is capable of forming ion channels in phospholipid membranes: planar bilayer studies have suggested the channels are octamers. The crystal structure of a monomeric form of AAM has provided the basis for molecular modelling of an octameric helical bundle channel. The channel model is funnel-shaped due to a substantial bend in the middle of the polypeptide chain caused by the presence of several imino acids. Inter-monomer hydrogen bonds orientate a ring of glutamine side chains to form a constriction in the pore lumen. The channel lumen is lined both by side chains of Gln11 and by polypeptide backbone carbonyl groups. Electrostatic calculations on the model are compatible with a channel that transports cations across membranes. The AAM channel model is compared with the crystal structures of two bacterial (KcsA andMthK) potassium channels. AAM and the potassium channels exhibit common functional features, such as cation-selectivity and similar single channel conductances. Common structural features include being multimers, each formed from a bundle of eight transmembrane helices, with lengths roughly comparable to the thickness of lipid bilayers. In addition, they all have aromatic amino acids that lie at the bilayer interfaces and which may aid in the stabilization of the transmembrane helices, as well as narrower constrictions that define the ion binding sites or selectivity filters in the pore lumen. The commonality of structural and functional features in these channels thus suggests that antiamoebin is a good, simple model for more complex bacterial and eukaryotic ion channels, capable of providing insight into details of the mechanisms of ion transport and multimeric channel stability.

Characterization and membrane assembly of the TatA component of the Escherichia coli twin-arginine protein transport system

Proteins bearing a signal peptide with a consensus twin-arginine motif are translocated via the Tat pathway, a multiprotein system consisting minimally of the integral inner membrane proteins TatA, TatB, and TatC. On a molar basis, TatA is the major pathway component. Here we show that TatA can be purified independently of the other Tat proteins as a 460 kDa homooligomeric complex. Homooligomer formation requires the amino-terminal membrane-anchoring domain of TatA. According to circular dichroism spectroscopy, approximately half of the TatA polypeptide forms alpha-helical secondary structure in both detergent solution and proteoliposomes. An expressed construct without the transmembrane segment is largely unstructured in aqueous solution but is able to insert into phospholipid monolayers and interacts with membrane bilayers. Protease accessibility experiments indicate that the extramembranous region of TatA is located at the cytoplasmic face of the cell membrane.

Model for a helical bundle channel based on the high-resolution crystal structure of trichotoxin_A50E

Trichotoxin_A50E is an 18-residue peptaibol antibiotic which forms multimeric transmembrane channels through self-association. The crystal structure of trichotoxin has been determined at a resolution of 0.9 A. The trichotoxin sequence contains nine helix-promoting Aib residues, which contribute to the formation of an entirely helical structure that has a central bend of 8-10 degrees located between residues 10-13. Trichotoxin is the first solved structure of the peptaibol family that is all alpha-helix as opposed to containing part or all 3(10)-helix. Gln residues in positions 6 and 17 produce a polar face, and are proposed to form the channel lumen. An octameric model channel has been constructed from the crystal structure. It has a central pore of approximately 4-5 A radius, a size sufficient to enable transport of ions, with a constricted region at one end, formed by a ring of Gln6 residues. Electrostatic calculations are consistent with it being a cationic channel.

Interactions of the type III secretion pathway proteins LcrV and LcrG from Yersinia pestis are mediated by coiled-coil domains

The type III secretion system is used by pathogenic Yersinia to translocate virulence factors into the host cell. A key component is the multifunctional LcrV protein, which is present on the bacterial surface prior to host cell contact and up-regulates translocation by blocking the repressive action of the LcrG protein on the cytosolic side of the secretion apparatus. The functions of LcrV are proposed to involve self-interactions (multimerization) and interactions with other proteins including LcrG. Coiled-coil motifs predicted to be present are thought to play a role in mediating these protein-protein interactions. We have purified recombinant LcrV, LcrG, and site-directed mutants of LcrV and demonstrated the structural integrity of these proteins using circular dichroism spectroscopy. We show that LcrV interacts both with itself and with LcrG and have obtained micromolar and nanomolar affinities for these interactions, respectively. The effects of LcrV mutations upon LcrG binding suggest that coiled-coil interactions indeed play a significant role in complex formation. In addition, comparisons of secretion patterns of effector proteins in Yersinia, arising from wild type and mutants of LcrV, support the proposed role of LcrG in titration of LcrV in vivo but also suggest that other factors may be involved.

Structure and function of voltage-dependent ion channel regulatory beta subunits

Voltage-dependent K(+), Ca(2+), and Na(+) channels play vital roles in basic physiological processes, including management of the action potential, signal transduction, and secretion. They share the common function of passively transporting ions across cell membranes; thus, it would not be surprising if they should exhibit similarities of both structure and mechanism. Indeed, the principal pore-forming (alpha) subunits of each show either exact or approximate 4-fold symmetry and share a similar transmembrane topology, and all are gated by changes in membrane potential. Furthermore, these channels all possess an auxiliary polypeptide, designated the beta subunit, which plays an important role in their regulation. Despite considerable functional semblences and abilities to interact with structurally similar alpha subunits, however, there is considerable structural diversity among the beta subunits. In this review, we discuss the similarities and differences in the structures and functions of the beta subunits of the voltage-dependent K(+), Ca(2+), and Na(+) channels.

DICHROWEB: an interactive website for the analysis of protein secondary structure from circular dichroism spectra

A user-friendly website for the analysis of protein secondary structures from Circular Dichroism (CD) and Synchrotron Radiation Circular Dichroism (SRCD) spectra has been created.

Synchrotron radiation circular dichroism spectroscopy of proteins: secondary structure, fold recognition and structural genomics

Recent developments in instrumentation and bioinformatics show that the technique of synchrotron radiation circular dichroism spectroscopy can provide novel information on protein secondary structures and folding motifs, and has the potential to play an important role in structural genomics studies, both as a means of target selection and as a high-throughput, low-sample-requiring screening method. This is possible because of the additional information content in the low-vacuum ultraviolet wavelength data obtainable with intense synchrotron radiation light sources, compared with that present in spectra from conventional lab-based circular dichroism instruments.