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Robert W Janes

Publications and source records attributed to Robert W Janes.

10 recordsLinked to original sources
PubMed2006

Novel methods for secondary structure determination using low wavelength (VUV) circular dichroism spectroscopic data.

BACKGROUND: Circular Dichroism (CD) spectroscopy is a widely used method for studying protein structures in solution. Modern synchrotron radiation CD (SRCD) instruments have considerably higher photon fluxes than do conventional lab-based CD instruments, and hence have the ability to routinely measure CD data to much lower wavelengths. Recently a new reference dataset of SRCD spectra of proteins of known structure, designed to cover secondary structure and fold space, has been produced which includes low wavelength (vacuum ultraviolet - VUV) data. However, the existing algorithms used to calculate protein secondary structures from CD data have not been designed to take optimal advantage of the additional information in these low wavelength data. RESULTS: In this study, we have optimised secondary structure calculation methods based on the low wavelength CD data by examining existing algorithms and secondary structure assignment schemes, and then developing new methods which have produced clear improvements in prediction accuracy, especially for beta-sheet components. We have further shown that if precise measurements of protein concentrations, and therefore spectral magnitudes, are not available, the inclusion of the low wavelength data will significantly improve the analyses. However, we have also demonstrated that the new reference dataset, methods, and assignments can also improve the analyses of conventional circular dichroism data, even if the low wavelength data is not available. CONCLUSION: VUV CD data include important information on protein structure which can be exploited with the algorithms and methodologies described.

Algorithms↗
PubMed2006

Analysing the ability to retain sidechain hydrogen-bonds in mutant proteins.

MOTIVATION: Hydrogen bonds are one of the most important inter-atomic interactions in biology. Previous experimental, theoretical and bioinformatics analyses have shown that the hydrogen bonding potential of amino acids is generally satisfied and that buried unsatisfied hydrogen-bond-capable residues are destabilizing. When studying mutant proteins, or introducing mutations to residues involved in hydrogen bonding, one needs to know whether a hydrogen bond can be maintained. Our aim, therefore, was to develop a rapid method to evaluate whether a sidechain can form a hydrogen-bond. RESULTS: A novel knowledge-based approach was developed in which the conformations accessible to the residues involved are taken into account. Residues involved in hydrogen bonds in a set of high resolution crystal structures were analyzed and this analysis is then applied to a given protein. The program was applied to assess mutations in the tumour-suppressor protein, p53. This raised the number of distinct mutations identified as disrupting sidechain-sidechain hydrogen bonding from 181 in our previous analysis to 202 in this analysis.

Algorithms↗
PubMed2006

Protein Circular Dichroism Data Bank (PCDDB): data bank and website design.

The Protein Circular Dichroism Data Bank (PCDDB) is a new deposition data bank for validated circular dichroism spectra of biomacromolecules. Its aim is to be a resource for the structural biology and bioinformatics communities, providing open access and archiving facilities for circular dichroism and synchrotron radiation circular dichroism spectra. It is named in parallel with the Protein Data Bank (PDB), a long-existing valuable reference data bank for protein crystal and NMR structures. In this article, we discuss the design of the data bank structure and the deposition website located at http://pcddb.cryst.bbk.ac.uk. Our aim is to produce a flexible and comprehensive archive, which enables user-friendly spectral deposition and searching. In the case of a protein whose crystal structure and sequence are known, the PCDDB entry will be linked to the appropriate PDB and sequence data bank files, respectively. It is anticipated that the PCDDB will provide a readily accessible biophysical catalogue of information on folded proteins that may be of value in structural genomics programs, for quality control and archiving in industrial and academic labs, as a resource for programs developing spectroscopic structural analysis methods, and in bioinformatics studies.

Circular Dichroism↗
PubMed2005

Bioinformatics analyses of circular dichroism protein reference databases.

MOTIVATION: Circular dichroism (CD) spectroscopy has become established as a key method for determining the secondary structure contents of proteins which has had a significant impact on molecular biology. Many excellent mathematical protocols have been developed for this purpose and their quality is above question. However, reference database sets of proteins, with CD spectra matched to secondary structure components derived from X-ray structures, provide the key resource for this task. These databases were created many years ago, before most CD spectrophotometers became standardized and before it was commonplace to validate X-ray structures prior to publication. The analyses presented here were undertaken to investigate the overall quality of these reference databases in light of their extensive usage in determining protein secondary structure content from CD spectra. RESULTS: The analyses show that there are a number of significant problems associated with the CD reference database sets in current use. There are disparities between CD spectra for the same protein collected by different groups. These include differences in magnitudes, peak positions or both. However, many current reference sets are now amalgamations of spectra from these groups, introducing inconsistencies that can lead to inaccuracies in the determination of secondary structure components from the CD spectra. A number of the X-ray structures used fall short on the validation criteria now employed as standard for structure determination. Many have substantial percentages of residues in the disallowed regions of the Ramachandran plot. Hence their calculated secondary structure components, used as a foundation for the reference databases, are likely to be in error. Additionally, the coverage of secondary structure space in the reference datasets is poorly correlated to the secondary structure components found in the Protein Data Bank. A conclusion is that a new reference CD database with cross-correlated, machine-independent CD spectra and validated X-ray structures that cover more secondary structure components, including diverse protein folds, is now needed. However, that reasonably accurate values for the secondary structure content of proteins can be determined from spectra is a testament to CD spectroscopy being a very powerful technique.

Circular Dichroism↗
PubMed2005

Overcoming protein denaturation caused by irradiation in a high-flux synchrotron radiation circular dichroism beamline.

It has been established that the new circular dichroism beamline CD12 has sufficiently high flux at low wavelengths to cause apparent irradiation problems with protein samples while their synchrotron radiation circular dichroism (SRCD) spectra are being collected. The cause of this effect has been extensively investigated and is reported in an accompanying paper [Wien et al. (2005). J. Synchrotron Rad. 12, 517-523.]. Experiments suggest that localized heating of the protein sample, leading to denaturation, is the probable cause. Methods to circumvent this problem by limiting the beam flux are reported. This was achieved using either an attenuation cell of water placed beam-side of the sample cell, or limiting the beam cross-sectional area hitting the sample. Such methods are shown to result in substantial reduction or apparent complete removal of this protein denaturation over the course of collecting three successive spectra. Elimination of this denaturation problem enables multiple SRCD scans for protein samples to be collected, which are vital both for good practice and for statistically valid results.

Circular Dichroism↗
PubMed2005

alpha-Conotoxins as selective probes for nicotinic acetylcholine receptor subclasses.

alpha-Conotoxins are selective antagonists of neuromuscular or neuronal nicotinic acetylcholine receptors. Individual family members are often highly selective towards distinct receptor subclasses, most notably within neuronal nicotinic acetylcholine receptors. As such they are being used as tools to probe for the type and diversity of receptor subclasses in distinct parts of the central and peripheral nervous systems. Many new alpha-conotoxins are being identified every year, broadening the available armoury because small variations in their sequences and structures often confer altered selectivity towards receptor subunits and subclasses. Many neurological diseases are being associated wholly or in part with functional changes within specific subclasses of nicotinic acetylcholine receptors. Significantly, with more structures of alpha-conotoxins also becoming available this enables ready comparison of their similarities and, more notably, of their subtle differences, which dictate subclass selectivity. As such, alpha-conotoxins offer the potential to become templates for the creation, through rational drug design strategies, of pharmaceuticals highly selective for specific subclasses of nicotinic acetylcholine receptors.

Animals↗
PubMed2003

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.

Antineoplastic Agents↗
PubMed2003

Nicotinic acetylcholine receptors: alpha-conotoxins as templates for rational drug design.

Nicotinic acetylcholine receptors (nAChRs) mediate the passage of potassium and sodium ions across synaptic membranes. Two classes of receptors exist: the neuromuscular nAChRs, which mediate signals between nerve and muscle cells, and the neuronal nAChRs, which are found throughout the nervous system. For treatment of diseases involving nAChRs, drugs must be designed with a high level of selectivity towards only one of these classes or subclasses (in the case of neuronal receptors). alpha-Conotoxins, small polypeptides isolated from the venoms of marine snails, represent molecules with just this type of selectivity, with specificity even towards certain subclasses of nAChRs. The availability of high-resolution crystal structures of alpha-conotoxins provides the opportunity to examine the structural features that orchestrate their preferential blocking action. In the present study of a neuromuscular- and a neuronal-specific alpha-conotoxin, SI and EpI respectively, important and significant differences can be seen in the shapes of the molecules, which must reflect topological features of the different types of target receptor subunits. These then provide a template for computational docking studies with the homologous acetylcholine-binding protein, whose structure is known, so drug analogues of the naturally occurring toxins can be developed with the desired specificities.

Conotoxins↗
PubMed2003

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.

Animals↗