Robert W. Janes

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.

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.

A model for Batten disease protein CLN3: Functional implications from homology and mutations

In an attempt to understand the molecular nature of Batten disease, we have examined the amino acid sequence of the affected CLN3 gene product (The International Batten Disease Consortium (1995) Cell 82, 949–957) and the site‐specific mutations which give rise to the biological defect. Homology searches and molecular modeling have led to the development of a model for the folding and disposition of the protein, possibly within a mitochondrial membrane. High homology with a yeast protein of unknown function suggests a strong evolutionary conservation of function. We speculate that a possible role for the protein may be in chaperoning the folding/unfolding or assembly/disassembly of other proteins, specifically subunit c of the mitochondrial ATP synthase complex.

Calibration and Standardisation of Synchrotron Radiation Circular Dichroism and Conventional Circular Dichroism Spectrophotometers

Synchrotron radiation circular dichroism (SRCD) is an emerging technique in structural biology with particular value in protein secondary structure analyses since it permits the collection of data down to much lower wavelengths than conventional circular dichroism (cCD) instruments. Reference database spectra collected on different SRCD instruments in the future as well as current reference datasets derived from cCD spectra must be compatible. Therefore there is a need for standardization of calibration methods to ensure quality control. In this study, magnitude and optical rotation measurements on four cCD and three SRCD instruments were compared at 192.5, 219, 290 and 490 nm. At high wavelengths, all gave comparable results, however, at the lower wavelengths, some variations were observable. The consequences of these differences on the spectrum, and the calculated secondary structure, of a representative protein (myoglobin) are demonstrated. A method is proposed for standardising spectra obtained on any CD instrument, conventional or synchrotron-based, with respect to existing and future databases.

Light flux density threshold at which protein denaturation is induced by synchrotron radiation circular dichroism beamlines

New high-flux synchrotron radiation circular dichroism (SRCD) beamlines are providing important information for structural biology, but can potentially cause denaturation of the protein samples under investigation. This effect has been studied at the new CD1 dedicated SRCD beamline at ISA in Denmark, where radiation-induced thermal damage effects were observed, depending not only on the radiation flux but also on the focal spot size of the light. Comparisons with similar studies at other SRCD facilities worldwide has lead to the estimation of a flux density threshold under which SRCD beamlines should be operated when samples are to be exposed to low-wavelength vacuum ultraviolet radiation for extended periods of time.

Synchrotron Radiation Circular Dichroism (SRCD) spectroscopy: New beamlines and new applications in biology

New advances in instrumentation, demonstration of proof-of-principle studies, and development of new tools and methods for data analysis and interpretation have enabled the technique of Synchrotron Radiation Circular Dichroism (SRCD) spectroscopy to become a useful tool for structural and functional biology. This paper discusses the characterisation of two new SRCD beamlines, CD1 at the Institute for Storage Rings (ISA), Denmark and 4B8 at the Beijing Synchrotron Radiation Facility (BSRF), China, and new applications of the method for examining biological systems.

2Struc: the secondary structure server

Summary: The defined secondary structure of proteins method is often considered the gold standard for assignment of secondary structure from three-dimensional coordinates. However, there are alternative methods. ‘2Struc: The Secondary Structure Server’ has been created as a single point of access for eight different secondary structure assignment methods. It has been designed to enable comparisons between methods for analyzing the secondary structure content for a single protein. It also includes a second functionality, ‘Compare-the-Protein’ to enable comparisons of the secondary structure features from any one method to be made within a collection of nuclear magnetic resonance models, or between the crystal structures of two different proteins. Availability: http://2struc.cryst.bbk.ac.uk Contact: r.w.janes@qmul.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.

PCDDB: the protein circular dichroism data bank, a repository for circular dichroism spectral and metadata

The Protein Circular Dichroism Data Bank (PCDDB) is a public repository that archives and freely distributes circular dichroism (CD) and synchrotron radiation CD (SRCD) spectral data and their associated experimental metadata. All entries undergo validation and curation procedures to ensure completeness, consistency and quality of the data included. A web-based interface enables users to browse and query sample types, sample conditions, experimental parameters and provides spectra in both graphical display format and as downloadable text files. The entries are linked, when appropriate, to primary sequence (UniProt) and structural (PDB) databases, as well as to secondary databases such as the Enzyme Commission functional classification database and the CATH fold classification database, as well as to literature citations. The PCDDB is available at: http://pcddb.cryst.bbk.ac.uk.

The protein circular dichroism data bank, a Web-based site for access to circular dichroism spectroscopic data.

The Protein Circular Dichroism Data Bank (PCDDB) is a newly released resource for structural biology. It is a web-accessible (http://pcddb.cryst.bbk.ac.uk) data bank for circular dichroism (CD) and synchrotron radiation circular dichroism (SRCD) spectra and their associated experimental and secondary metadata, with links to protein sequence and structure data banks. It is designed to provide a public repository for CD spectroscopic data on macromolecules, to parallel the Protein Data Bank (PDB) for crystallographic, electron microscopic, and nuclear magnetic resonance spectroscopic data. Similarly to the PDB, it includes validation checking procedures to ensure good practice and the integrity of the deposited data. This paper reports on the first public release of the PCDDB, which provides access to spectral data that comprise standard reference datasets.

Tryptophans in Membrane Proteins

While tryptophans are generally found in low abundance in soluble proteins, in many integral membrane proteins they comprise a significantly higher proportion of the amino acid composition. Now that crystal structures are available for a number of membrane proteins, it has been possible to examine the distribution and disposition of the tryptophans within these structures. The tryptophan locations with respect to the lipid bilayer (along the direction normal to the membrane surface) are strikingly non-uniform in nearly all of the membrane proteins examined. They tend to cluster at the interface between the polar head group region and the hydrophobic interior, in a relatively uniform layer just below the surface. In many cases, their distributions with respect to the extra- and intra-cellular surfaces tend to be asymmetric. These observations provide evidence for possible structural roles for tryptophans in transmembrane sheets and helices, where they may play a part in the stabilization of the transmembrane segments and perhaps in the orientation and bilayer insertion processes.