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

Mechanisms of Biomolecular Self-Assembly Investigated Through In Situ Observations of Structures and Dynamics

Biomolecular self-assembly of hierarchical materials is a precise and adaptable bottom-up approach to synthesizing across scales with considerable energy, health, environment, sustainability, and information technology applications. To achieve desired functions in biomaterials, it is essential to directly observe assembly dynamics and structural evolutions that reflect the underlying energy landscape and the assembly mechanism. This review will summarize the current understanding of biomolecular assembly mechanisms based on in situ characterization and discuss the broader significance and achievements of newly gained insights. In addition, we will also introduce how emerging deep learning/machine learning-based approaches, multiparametric characterization, and high-throughput methods can boost the development of biomolecular self-assembly. The objective of this review is to accelerate the development of in situ characterization approaches for biomolecular self-assembly and to inspire the next generation of biomimetic materials.

Computational Methods and Deep Learning for Elucidating Protein Interaction Networks

Protein interactions play a critical role in all biological processes, but experimental identification of protein interactions is a time- and resource-intensive process. The advances in next-generation sequencing and multi-omics technologies have greatly benefited large-scale predictions of protein interactions using machine learning methods. A wide range of tools have been developed to predict protein-protein, protein-nucleic acid, and protein-drug interactions. Here, we discuss the applications, methods, and challenges faced when employing the various prediction methods. We also briefly describe ways to overcome the challenges and prospective future developments in the field of protein interaction biology.

Structure of whey protein hydrolysate used as emulsifier in wet and dried oil delivery systems: Effect of pH and drying processing

The secondary structure of whey protein concentrate hydrolysate (WPCH), used as an emulsifier in oil delivery systems, was investigated using Synchrotron Radiation Circular Dichroism (SRCD). The effect of pH on the conformation of peptides in solution and adsorbed at the oil/water interface, as well as the thermal stability of the systems was studied. Furthermore, oil-loaded microcapsules were produced by spray-drying or electrospraying to investigate the influence of encapsulating agents (glucose syrup, maltodextrin) and drying technique on the secondary structure of WPCH at the oil/water interface. Enzymatic hydrolysis resulted in peptides with a highly unordered structure (∼60% turns and unordered regions) in solution. However, WPCH adsorption onto the oil/water interface increased the α-helical content resulting in an improved thermal stability. The encapsulating agents and spray-drying process did not modify the conformation of WPCH at the oil/water interface. Nonetheless, electrospraying affected the SRCD spectra obtained for WPCH adsorbed at the oil/water interface.

Spectroscopy of model-membrane liposome-protein systems: complementarity of linear dichroism, circular dichroism, fluorescence and SERS

A range of membrane models have been developed to study components of cellular systems. Lipid vesicles or liposomes are one such artificial membrane model which mimics many properties of the biological system: they are lipid bilayers composed of one or more lipids to which other molecules can associate. Liposomes are thus ideal to study the roles of cellular lipids and their interactions with other membrane components to understand a wide range of cellular processes including membrane disruption, membrane transport and catalytic activity. Although liposomes are much simpler than cellular membranes, they are still challenging to study and a variety of complementary techniques are needed. In this review article, we consider several currently used analytical methods for spectroscopic measurements of unilamellar liposomes and their interaction with proteins and peptides. Among the variety of spectroscopic techniques seeing increasing application, we have chosen to discuss: fluorescence based techniques such as FRET (fluorescence resonance energy transfer) and FRAP (fluorescence recovery after photobleaching), that are used to identify localisation and dynamics of molecules in the membrane; circular dichroism (CD) and linear dichroism (LD) for conformational and orientation changes of proteins on membrane binding; and SERS (Surface Enhanced Raman Spectroscopy) as a rapidly developing ultrasensitive technique for site-selective molecular characterisation. The review contains brief theoretical basics of the listed techniques and recent examples of their successful applications for membrane studies.

Bayesian inference assessment of protein secondary structure analysis using circular dichroism data - how much structural information is contained in protein circular dichroism spectra?

Circular dichroism spectroscopy is an important tool for determining the structural characteristics of biomolecules, particularly the secondary structure of proteins. In this paper we propose a Bayesian model that estimates the covariance structure within a measured spectrum and quantifies the uncertainty associated with the inferred secondary structures and characteristic spectra associated with each secondary structure type. Furthermore, we used tools from Bayesian model selection to determine the best secondary structure classification scheme and illustrate a technique for comparing whether or not two or more measured protein spectra share the same secondary structure. Our findings suggest that it is not possible to identify more than 3 distinct secondary structure classes from CD spectra above 175 nm. The inclusion of data from wavelengths between 175 and 200 nm did not substantially affect the ability to determine secondary structure fractions.

Chiroptical characterization tools for asymmetric small molecules - experimental and computational approaches for electronic circular dichroism (ECD) and anisotropy spectroscopy

Synchrotron radiation electronic circular dichroism (SRECD) and anisotropy spectroscopy for both enantiomers of a group of small non-planar chiral molecules are reported here. The experimental SRECD spectra are compared to computational ECD spectra generated using time-dependent density functional theory and a thermal averaging over relevant molecular configurations. The combination of these experimental and computational characterization methodologies for such molecules enables the prediction and understanding of the spectral behavior of other small molecules, in addition to chiroptically characterizing members of the mandelic acid family substructure. Enantiomeric purity of samples can be evaluated in comparison with these spectra and the extent of photolytic enantioinduction can also be predicted using these experimental/calculated SRECD and anisotropy spectra.

Experimental and computational electronic circular dichroism spectra are used in conjunction with anisotropy spectra to chiroptically characterize mandelic acid and its derivatives into the vacuum UV.

BeStSel: a web server for accurate protein secondary structure prediction and fold recognition from the circular dichroism spectra

Circular dichroism (CD) spectroscopy is a widely used method to study the protein secondary structure. However, for decades, the general opinion was that the correct estimation of β-sheet content is challenging because of the large spectral and structural diversity of β-sheets. Recently, we showed that the orientation and twisting of β-sheets account for the observed spectral diversity, and developed a new method to estimate accurately the secondary structure (PNAS, 112, E3095). BeStSel web server provides the Beta Structure Selection method to analyze the CD spectra recorded by conventional or synchrotron radiation CD equipment. Both normalized and measured data can be uploaded to the server either as a single spectrum or series of spectra. The originality of BeStSel is that it carries out a detailed secondary structure analysis providing information on eight secondary structure components including parallel-β structure and antiparallel β-sheets with three different groups of twist. Based on these, it predicts the protein fold down to the topology/homology level of the CATH protein fold classification. The server also provides a module to analyze the structures deposited in the PDB for BeStSel secondary structure contents in relation to Dictionary of Secondary Structure of Proteins data. The BeStSel server is freely accessible at http://bestsel.elte.hu.

Synchrotron-radiation vacuum-ultraviolet circular dichroism spectroscopy in structural biology: an overview

Circular dichroism spectroscopy is widely used for analyzing the structures of chiral molecules, including biomolecules. Vacuum-ultraviolet circular dichroism (VUVCD) spectroscopy using synchrotron radiation can extend the short-wavelength limit into the vacuum-ultraviolet region (down to ~160 nm) to provide detailed and new information about the structures of biomolecules in combination with theoretical analysis and bioinformatics. The VUVCD spectra of saccharides can detect the high-energy transitions of chromophores such as hydroxy and acetal groups, disclosing the contributions of inter- or intramolecular hydrogen bonds to the equilibrium configuration of monosaccharides in aqueous solution. The roles of hydration in the fluctuation of the dihedral angles of carboxyl and amino groups of amino acids can be clarified by comparing the observed VUVCD spectra with those calculated theoretically. The VUVCD spectra of proteins markedly improves the accuracy of predicting the contents and number of segments of the secondary structures, and their amino acid sequences when combined with bioinformatics, for not only native but also nonnative and membrane-bound proteins. The VUVCD spectra of nucleic acids confirm the contributions of the base composition and sequence to the conformation in comparative analyses of synthetic poly-nucleotides composed of selected bases. This review surveys these recent applications of synchrotron-radiation VUVCD spectroscopy in structural biology, covering saccharides, amino acids, proteins, and nucleic acids.

UV-Denaturation Assay to Assess Protein Photostability and Ligand-Binding Interactions Using the High Photon Flux of Diamond B23 Beamline for SRCD

Light irradiation with high photon flux in the vacuum and far-UV region is known to denature the conformation of biopolymers. Measures are in place at Diamond Light Source B23 beamline for Synchrotron Radiation Circular Dichroism (SRCD) to control and make this effect negligible. However, UV denaturation of proteins can also be exploited as a novel method for assessing biopolymer photostability as well as ligand-binding interactions. Usually, host–ligand binding interactions can be assessed monitoring CD changes of the host biopolymer upon ligand addition. The novel method of identifying ligand binding monitoring the change of relative rate of UV denaturation using SRCD is especially important when there are very little or insignificant secondary structure changes of the host protein upon ligand binding. The temperature study, another method used to determine molecular interactions, can often be inconclusive when the thermal effect associated with the displacement of the bound solvent molecules by the ligand is also small, making the determination of the binding interaction inconclusive. Herein we present a review on the UV-denaturation assay as a novel method to determine the relative photostability of protein formulations as well as the screening of ligand-binding interactions using the high photon flux Diamond B23 beamline for SRCD.

Reversible Assembly of a Drug Peptide into Amyloid Fibrils: A Dynamic Circular Dichroism Study

The common view on the amyloid fibril formation is that it is a multistep process that involves many oligomeric intermediate species, which leads to a high degree of polymorphism. This view derives from numerous kinetic studies whose vast majority was carried out with amyloid β fragments or other pathological amyloidogenic sequences. Yet, it is not clear whether the mechanisms inferred from these studies are universal and also apply to functional amyloids, in particular to peptide hormones which form reversible amyloid structures. In the present work, we study the self-assembly properties of atosiban, a nonapeptide drug, whose sequence is very close to those of the oxytocin and vasopressin hormones. We show that this very soluble peptide consistently self-assembles into 7 nm wide amyloid fibrils above a critical aggregation concentration (2-10 w/w % depending on the buffer conditions). The peptide system is characterized in details, from the monomeric to the assembled form, with osmotic concentration measurements, transmission electron microscopy, small-angle X-ray scattering, infrared and fluorescence spectroscopy, and circular dichroism (CD). We have followed in situ the fibril assembly with fluorescence and synchrotron radiation CD and noticed that the peptide undergoes conformational changes during the process. However, several lines of evidence point toward the association of monomers and dimers into fibrils without passing through oligomeric intermediate species contrary to what is usually reported for pathogenic amyloids. The native β-hairpin conformation of the monomer could explain the straightforward assembly. The tyrosine stacking is also shown to play an important role.

Predictive and Experimental Approaches for Elucidating Protein-Protein Interactions and Quaternary Structures

The elucidation of protein-protein interactions is vital for determining the function and action of quaternary protein structures. Here, we discuss the difficulty and importance of establishing protein quaternary structure and review in vitro and in silico methods for doing so. Determining the interacting partner proteins of predicted protein structures is very time-consuming when using in vitro methods, this can be somewhat alleviated by use of predictive methods. However, developing reliably accurate predictive tools has proved to be difficult. We review the current state of the art in predictive protein interaction software and discuss the problem of scoring and therefore ranking predictions. Current community-based predictive exercises are discussed in relation to the growth of protein interaction prediction as an area within these exercises. We suggest a fusion of experimental and predictive methods that make use of sparse experimental data to determine higher resolution predicted protein interactions as being necessary to drive forward development.

PDB2CD visualises dynamics within protein structures

Proteins tend to have defined conformations, a key factor in enabling their function. Atomic resolution structures of proteins are predominantly obtained by either solution nuclear magnetic resonance (NMR) or crystal structure methods. However, when considering a protein whose structure has been determined by both these approaches, on many occasions, the resultant conformations are subtly different, as illustrated by the examples in this study. The solution NMR approach invariably results in a cluster of structures whose conformations satisfy the distance boundaries imposed by the data collected; it might be argued that this is evidence of the dynamics of proteins when in solution. In crystal structures, the proteins are often in an energy minimum state which can result in an increase in the extent of regular secondary structure present relative to the solution state depicted by NMR, because the more dynamic ends of alpha helices and beta strands can become ordered at the lower temperatures. This study examines a novel way to display the differences in conformations within an NMR ensemble and between these and a crystal structure of a protein. Circular dichroism (CD) spectroscopy can be used to characterise protein structures in solution. Using the new bioinformatics tool, PDB2CD, which generates CD spectra from atomic resolution protein structures, the differences between, and possible dynamic range of, conformations adopted by a protein can be visualised.

Advantages of synchrotron radiation circular dichroism spectroscopy to study intrinsically disordered proteins

The unordered secondary structural content of an intrinsically disordered protein (IDP) is susceptible to conformational changes induced by many different external factors, such as the presence of organic solvents, removal of water, changes in temperature, binding to partner molecules, and interaction with lipids and/or other ligands. In order to characterize the high-flexibility nature of an IDP, circular dichroism (CD) spectroscopy is a particularly useful method due to its capability of monitoring both subtle and remarkable changes in different environments, relative ease in obtaining measurements, the small amount of sample required, and the capability for sample recovery (sample not damaged) and others. Using synchrotron radiation as the light source for CD spectroscopy represents the state-of-the-art version of this technique with feasibility of accessing the lower wavelength UV region, and therefore presenting a series of advantages over conventional circular dichroism (cCD) to monitor a protein conformational behavior, check protein stability, detect ligand binding, and many others. In this paper, we have performed a comparative study using cCD and SRCD methods for investigating the secondary structure and the conformational behavior of natively unfolded proteins: MEG-14 and soybean trypsin inhibitor. We show that the SRCD technique greatly improves the analysis and accuracy of the studies on the conformations of IDPs.

Environmental Factors Modulating the Stability and Enzymatic Activity of the Petrotoga mobilis Esterase (PmEst)

Enzymes isolated from thermophilic organisms found in oil reservoirs can find applications in many fields, including the oleochemical, pharmaceutical, bioenergy, and food/dairy industries. In this study, in silico identification and recombinant production of an esterase from the extremophile bacteria Petrotoga mobilis (designated PmEst) were performed. Then biochemical, bioinformatics and structural characterizations were undertaken using a combination of synchrotron radiation circular dichroism (SRCD) and fluorescence spectroscopies to correlate PmEst stability and hydrolytic activity on different substrates. The enzyme presented a high Michaelis-Menten constant (KM 0.16 mM) and optimum activity at ~55°C for p-nitrophenyl butyrate. The secondary structure of PmEst was preserved at acid pH, but not under alkaline conditions. PmEst was unfolded at high concentrations of urea or guanidine through apparently different mechanisms. The esterase activity of PmEst was preserved in the presence of ethanol or propanol and its melting temperature increased ~8°C in the presence of these organic solvents. PmEst is a mesophilic esterase with substrate preference towards short-to medium-length acyl chains. The SRCD data of PmEst is in agreement with the prediction of an α/β protein, which leads us to assume that it displays a typical fold of esterases from this family. The increased enzyme stability in organic solvents may enable novel applications for its use in synthetic biology. Taken together, our results demonstrate features of the PmEst enzyme that indicate it may be suitable for applications in industrial processes, particularly, when the use of polar organic solvents is required.

Circular dichroism spectroscopy of membrane proteins

Circular dichroism spectra of helical bundle (red), beta barrel (blue), and mixed helical/sheet/unordered (green) membrane proteins.

Quadruplex DNA-Stabilising Dinuclear Platinum(II) Terpyridine Complexes with Flexible Linkers

Four dinuclear terpyridineplatinum(II) (Pt-terpy) complexes were investigated for interactions with G-quadruplex DNA (QDNA) and duplex DNA (dsDNA) by synchrotron radiation circular dichroism (SRCD), fluorescent intercalator displacement (FID) assays and fluorescence resonance energy transfer (FRET) melting studies. Additionally, computational docking studies were undertaken to provide insight into potential binding modes for these complexes. The complexes demonstrated the ability to increase the melting temperature of various QDNA motifs by up to 17 °C and maintain this in up to a 600-fold excess of dsDNA. This study demonstrates that dinuclear Pt-terpy complexes stabilise QDNA and have a high degree of selectivity for QDNA over dsDNA.

A Versatile Strategy for Production of Membrane Proteins with Diverse Topologies: Application to Investigation of Bacterial Homologues of Human Divalent Metal Ion and Nucleoside Transporters

Membrane proteins play key roles in many biological processes, from acquisition of nutrients to neurotransmission, and are targets for more than 50% of current therapeutic drugs. However, their investigation is hampered by difficulties in their production and purification on a scale suitable for structural studies. In particular, the nature and location of affinity tags introduced for the purification of recombinant membrane proteins can greatly influence their expression levels by affecting their membrane insertion. The extent of such effects typically depends on the transmembrane topologies of the proteins, which for proteins of unknown structure are usually uncertain. For example, attachment of oligohistidine tags to the periplasmic termini of membrane proteins often interferes with folding and drastically impairs expression in Escherichia coli. To circumvent this problem we have employed a novel strategy to enable the rapid production of constructs bearing a range of different affinity tags compatible with either cytoplasmic or periplasmic attachment. Tags include conventional oligohistidine tags compatible with cytoplasmic attachment and, for attachment to proteins with a periplasmic terminus, either tandem Strep-tag II sequences or oligohistidine tags fused to maltose binding protein and a signal sequence. Inclusion of cleavage sites for TEV or HRV-3C protease enables tag removal prior to crystallisation trials or a second step of purification. Together with the use of bioinformatic approaches to identify members of membrane protein families with topologies favourable to cytoplasmic tagging, this has enabled us to express and purify multiple bacterial membrane transporters. To illustrate this strategy, we describe here its use to purify bacterial homologues of human membrane proteins from the Nramp and ZIP families of divalent metal cation transporters and from the concentrative nucleoside transporter family. The proteins are expressed in E. coli in a correctly folded, functional state and can be purified in amounts suitable for structural investigations.

Introducing DInaMo: A Package for Calculating Protein Circular Dichroism Using Classical Electromagnetic Theory

The dipole interaction model is a classical electromagnetic theory for calculating circular dichroism (CD) resulting from the π-π* transitions of amides. The theoretical model, pioneered by J. Applequist, is assembled into a package, DInaMo, written in Fortran allowing for treatment of proteins. DInaMo reads Protein Data Bank formatted files of structures generated by molecular mechanics or reconstructed secondary structures. Crystal structures cannot be used directly with DInaMo; they either need to be rebuilt with idealized bond angles and lengths, or they need to be energy minimized to adjust bond lengths and bond angles because it is common for crystal structure geometries to have slightly short bond lengths, and DInaMo is sensitive to this. DInaMo reduces all the amide chromophores to points with anisotropic polarizability and all nonchromophoric aliphatic atoms including hydrogens to points with isotropic polarizability; all other atoms are ignored. By determining the interactions among the chromophoric and nonchromophoric parts of the molecule using empirically derived polarizabilities, the rotational and dipole strengths are determined leading to the calculation of CD. Furthermore, ignoring hydrogens bound to methyl groups is initially explored and proves to be a good approximation. Theoretical calculations on 24 proteins agree with experiment showing bands with similar morphology and maxima.

Accurate secondary structure prediction and fold recognition for circular dichroism spectroscopy

Circular dichroism (CD) spectroscopy is a widely used technique for the study of protein structure. Numerous algorithms have been developed for the estimation of the secondary structure composition from the CD spectra. These methods often fail to provide acceptable results on α/β-mixed or β-structure-rich proteins. The problem arises from the spectral diversity of β-structures, which has hitherto been considered as an intrinsic limitation of the technique. The predictions are less reliable for proteins of unusual β-structures such as membrane proteins, protein aggregates, and amyloid fibrils. Here, we show that the parallel/antiparallel orientation and the twisting of the β-sheets account for the observed spectral diversity. We have developed a method called β-structure selection (BeStSel) for the secondary structure estimation that takes into account the twist of β-structures. This method can reliably distinguish parallel and antiparallel β-sheets and accurately estimates the secondary structure for a broad range of proteins. Moreover, the secondary structure components applied by the method are characteristic to the protein fold, and thus the fold can be predicted to the level of topology in the CATH classification from a single CD spectrum. By constructing a web server, we offer a general tool for a quick and reliable structure analysis using conventional CD or synchrotron radiation CD (SRCD) spectroscopy for the protein science research community. The method is especially useful when X-ray or NMR techniques fail. Using BeStSel on data collected by SRCD spectroscopy, we investigated the structure of amyloid fibrils of various disease-related proteins and peptides.

Improved DNA equilibrium binding affinity determinations of platinum(ii) complexes using synchrotron radiation circular dichroism

The DNA binding affinity of a range of Pt(ii) complexes was reinvestigated using SRCD and a new method was implemented for determining the binding constant, saving time and minimising data collection.

The collagen-like protein gp12 is a temperature-dependent reversible binder of SPP1 viral capsids

Icosahedral capsids of viruses are lattices of defined geometry and homogeneous size. The (quasi-)equivalent organization of their protein building blocks provides, in numerous systems, the binding sites to assemble arrays of viral polypeptides organized with nanometer precision that protrude from the capsid surface. The capsid of bacterial virus (bacteriophage) SPP1 exposes, at its surface, the 6.6-kDa viral polypeptide gp12 that binds to the center of hexamers of the major capsid protein. Gp12 forms an elongated trimer with collagen-like properties. This is consistent with the fold of eight internal GXY repeats of gp12 to build a stable intersubunit triple helix in a prokaryotic setting. The trimer dissociates and unfolds at near physiological temperatures, as reported for eukaryotic collagen. Its structural organization is reacquired within seconds upon cooling. Interaction with the SPP1 capsid hexamers strongly stabilizes gp12, increasing its Tm to 54 °C. Above this temperature, gp12 dissociates from its binding sites and unfolds reversibly. Multivalent binding of gp12 trimers to the capsid is highly cooperative. The capsid lattice also provides a platform to assist folding and association of unfolded gp12 polypeptides. The original physicochemical properties of gp12 offer a thermoswitchable system for multivalent binding of the polypeptide to the SPP1 capsid surface.

Effect of ultrasound on the activity and conformation of α-amylase, papain and pepsin

The effect of ultrasound on the activity of α-amylase, papain and pepsin was investigated and the mechanism of the effect was explored by determining their conformational changes. With the irradiation of power ultrasound, the activity of α-amylase and papain was inhibited, while the activity of pepsin was activated. According to the analysis of circular dichroism, Fourier transform infrared and fluorescence spectroscopy, the πo → π(∗) amide transitions and secondary structural components, especially β-sheet, of these three enzymes were significantly influenced by ultrasound. The tryptophan fluorescence intensity of the three enzymes was also observed to be affected by sonication. Furthermore, it was found that the pepsin molecule might gradually be resistant to prolonged ultrasonic treatment and recover from the ultrasound-induced damage to its original structure. The results suggested that the activity of α-amylase, papain and pepsin could be modified by ultrasonic treatment mainly due to the variation of their secondary and tertiary structures.

Interaction between a cationic surfactant-like peptide and lipid vesicles and its relationship to antimicrobial activity

We investigate the properties of an antimicrobial surfactant-like peptide (Ala)6(Arg), A6R, containing a cationic headgroup. The interaction of this peptide with zwitterionic (DPPC) lipid vesicles is investigated using a range of microscopic, X-ray scattering, spectroscopic, and calorimetric methods. The β-sheet structure adopted by A6R is disrupted in the presence of DPPC. A strong effect on the small-angle X-ray scattering profile is observed: the Bragg peaks from the DPPC bilayers in the vesicle walls are eliminated in the presence of A6R and only bilayer form factor peaks are observed. All of these observations point to the interaction of A6R with DPPC bilayers. These studies provide insight into interactions between a model cationic peptide and vesicles, relevant to understanding the action of antimicrobial peptides on lipid membranes. Notably, peptide A6R exhibits antimicrobial activity without membrane lysis.

MS-desi, a desiccation-related protein in the floral nectar of the evergreen velvet bean (Mucuna sempervirens Hemsl): molecular identification and characterization

Plant desiccation-related proteins (DRPs) were first identified as pcC13-62 from the resurrection plant Craterostigma plantagineum and it has been suggested they are involved in plant desiccation tolerance. We identified and characterized a plant DRP, which we called MS-desi, in the floral nectar of a subtropical bean species, Mucuna sempervirens (MS). MS-desi is a major nectar protein (nectarin) of the bean plant and expresses exclusively in the stylopodium, where the nectary is located. The full-length MS-desi gene encodes for a protein of 306 amino acids with a molecular mass of 33,248 Da, and possesses a ferritin-like domain and a signal peptide of 30 amino acids. Structural and phylogenetic analysis demonstrated MS-desi has high similarity to members of the plant DRPs, including pcC 13-62 protein. MS-desi has a similar hydropathy profile to that of pcC13-62 with a grand average of hydropathy index of 0.130 for MS-desi and 0.106 for pcC13-62 protein, which is very different from those of dehydrins and late embryogenesis abundant proteins. The protein's secondary structures, both predicted from the amino acid sequence and directly analysed by far UV circular dichroism, showed that MS-desi is mainly composed of alpha helices and is relatively temperature dependent. The structure change is reversible within a wide range of temperatures. Purified MS-desi and raw MS floral nectar showed dose-dependent citrate synthase inhibition activity, but insensitivity to lactate dehydrogenase, suggesting that, unlike dehydrins, it does not act as a chaperone. The overall results constitute, to our knowledge, the first study on a desiccation-related protein in plant floral nectar.

DichroMatch: a website for similarity searching of circular dichroism spectra

Circular dichroism (CD) spectroscopy is a widely used method for examining the structure, folding and conformational changes of proteins. A new online CD analysis server (DichroMatch) has been developed for identifying proteins with similar spectral characteristics by detecting possible structurally and functionally related proteins and homologues. DichroMatch includes six different methods for determining the spectral nearest neighbours to a query protein spectrum and provides metrics of how similar these spectra are and, if corresponding crystal structures are available for the closest matched proteins, information on their secondary structures and fold classifications. By default, DichroMatch uses all the entries in the Protein Circular Dichroism Data Bank (PCDDB) for its comparison set, providing the broadest range of publicly available protein spectra to match with the unknown protein. Alternatively, users can download or create their own specialized data sets, thereby enabling comparisons between the structures of related proteins such as wild-type versus mutants or homologues or a series of spectra of the same protein under different conditions. The DichroMatch server is freely available at http://dichromatch.cryst.bbk.ac.uk.

Nanosecond T-jump experiment in poly(glutamic acid): a circular dichroism study

Poly(glutamic acid) has been studied with a nanosecond T-jump experiment. A new experimental set-up based on the frequency-quadrupling of an 82 MHz Titanium-Sapphire laser allows rapid CD measurements to be performed. Combining time-resolved absorption and circular dichroism at 204 and 220 nm, we are able to measure precisely the unfolding relaxation time as well as the helical fraction evolution. We show that only CD at 220 nm is relevant to observe the unfolding of an alpha helix whereas no change is observed for CD at 204 nm. Conversely, both absorptions yield information on the dynamics of the process.

Optical properties of Yeast Cytochrome c monolayer on gold: an in situ spectroscopic ellipsometry investigation

The adsorption of Yeast Cytochrome c (YCC) on well defined, flat gold substrates has been studied by Spectroscopic Ellipsometry (SE) in the 245-1000 nm wavelength range. The investigation has been performed in aqueous ambient at room temperature, focusing on monolayer-thick films. In situ δΨ and δΔ difference spectra have shown reproducibly well-defined features related to molecular optical absorptions typical of the so-called heme group. The data have been reproduced quantitatively by a simple isotropic optical model, accounting for the molecular absorption spectrum and film-substrate interface effects. The simulations allowed a reliable estimate of the film thickness and the determination of the position and the shape of the so-called Soret absorption peak that, within the experimental uncertainty, is the same found for molecules in liquid. These findings suggest that YCC preserves its native structure upon adsorption. The same optical model was able to reproduce also ex situ results on rinsed and dried samples, dominated by the spectral features associated to the polypeptide chain that tend to overwhelm the heme absorption features.

Spectroscopic Characterization of Intermolecular Interaction of Amyloid β Promoted on GM1 Micelles

Clusters of GM1 gangliosides act as platforms for conformational transition of monomeric, unstructured amyloid β (Aβ) to its toxic β-structured aggregates. We have previously shown that Aβ(1–40) accommodated on the hydrophobic/hydrophilic interface of lyso-GM1 or GM1 micelles assumes α-helical structures under ganglioside-excess conditions. For better understanding of the mechanisms underlying the α-to-β conformational transition of Aβ on GM1 clusters, we performed spectroscopic characterization of Aβ(1–40) titrated with GM1. It was revealed that the thioflavin T- (ThT-) reactive β-structure is more populated in Aβ(1–40) under conditions where the Aβ(1–40) density on GM1 micelles is high. Under this circumstance, the C-terminal hydrophobic anchor Val³⁹-Val⁴⁰ shows two distinct conformational states that are reactive with ThT, while such Aβ species were not generated by smaller lyso-GM1 micelles. These findings suggest that GM1 clusters promote specific Aβ-Aβ interactions through their C-termini coupled with formation of the ThT-reactive β-structure depending on sizes and curvatures of the clusters.

Synchrotron radiation circular dichroism (SRCD) spectroscopy: an enhanced method for examining protein conformations and protein interactions

CD (circular dichroism) spectroscopy is a well-established technique in structural biology. SRCD (synchrotron radiation circular dichroism) spectroscopy extends the utility and applications of conventional CD spectroscopy (using laboratory-based instruments) because the high flux of a synchrotron enables collection of data at lower wavelengths (resulting in higher information content), detection of spectra with higher signal-to-noise levels and measurements in the presence of absorbing components (buffers, salts, lipids and detergents). SRCD spectroscopy can provide important static and dynamic structural information on proteins in solution, including secondary structures of intact proteins and their domains, protein stability, the differences between wild-type and mutant proteins, the identification of natively disordered regions in proteins, and the dynamic processes of protein folding and membrane insertion and the kinetics of enzyme reactions. It has also been used to effectively study protein interactions, including protein-protein complex formation involving either induced-fit or rigid-body mechanisms, and protein-lipid complexes. A new web-based bioinformatics resource, the Protein Circular Dichroism Data Bank (PCDDB), has been created which enables archiving, access and analyses of CD and SRCD spectra and supporting metadata, now making this information publicly available. To summarize, the developing method of SRCD spectroscopy has the potential for playing an important role in new types of studies of protein conformations and their complexes.

Biochemical and biophysical characterization of succinate: quinone reductase from Thermus thermophilus

Enzymes serving as respiratory complex II belong to the succinate:quinone oxidoreductases superfamily that comprises succinate:quinone reductases (SQRs) and quinol:fumarate reductases. The SQR from the extreme thermophile Thermus thermophilus has been isolated, identified and purified to homogeneity. It consists of four polypeptides with apparent molecular masses of 64, 27, 14 and 15kDa, corresponding to SdhA (flavoprotein), SdhB (iron-sulfur protein), SdhC and SdhD (membrane anchor proteins), respectively. The existence of [2Fe-2S], [4Fe-4S] and [3Fe-4S] iron-sulfur clusters within the purified protein was confirmed by electron paramagnetic resonance spectroscopy which also revealed a previously unnoticed influence of the substrate on the signal corresponding to the [2Fe-2S] cluster. The enzyme contains two heme b cofactors of reduction midpoint potentials of -20mV and -160mV for b(H) and b(L), respectively. Circular dichroism and blue-native polyacrylamide gel electrophoresis revealed that the enzyme forms a trimer with a predominantly helical fold. The optimum temperature for succinate dehydrogenase activity is 70°C, which is in agreement with the optimum growth temperature of T. thermophilus. Inhibition studies confirmed sensitivity of the enzyme to the classical inhibitors of the active site, as there are sodium malonate, sodium diethyl oxaloacetate and 3-nitropropionic acid. Activity measurements in the presence of the semiquinone analog, nonyl-4-hydroxyquinoline-N-oxide (NQNO) showed that the membrane part of the enzyme is functionally connected to the active site. Steady-state kinetic measurements showed that the enzyme displays standard Michaelis-Menten kinetics at a low temperature (30°C) with a K(M) for succinate of 0.21mM but exhibits deviation from it at a higher temperature (70°C). This is the first example of complex II with such a kinetic behavior suggesting positive cooperativity with k' of 0.39mM and Hill coefficient of 2.105. While the crystal structures of several SQORs are already available, no crystal structure of type A SQOR has been elucidated to date. Here we present for the first time a detailed biophysical and biochemical study of type A SQOR-a significant step towards understanding its structure-function relationship.

From structure to cellular mechanism with infrared microspectroscopy

Current efforts in structural biology aim to integrate structural information within the context of cellular organization and function. X-rays and infrared radiation stand at opposite ends of the electromagnetic spectrum and act as complementary probes for achieving this goal. Intense and bright beams are produced by synchrotron radiation, and are efficiently used in the wavelength domain extending from hard X-rays to the far-infrared (or THz) regime. While X-ray crystallography provides exquisite details on atomic structure, Fourier transform infrared microspectroscopy (FTIRM) is emerging as a spectroscopic probe and imaging tool for correlating molecular structure to biochemical dynamics and function. In this manuscript, the role of synchrotron FTIRM in bridging the gap towards 'functional biology' is discussed based upon recent achievements, with a critical assessment of the contributions to biological and biomedical research.

Protein characterisation by synchrotron radiation circular dichroism spectroscopy

Circular dichroism (CD) spectroscopy is a well-established technique for the study of proteins. Synchrotron radiation circular dichroism (SRCD) spectroscopy extends the utility of conventional CD spectroscopy (i.e. using laboratory-based instruments) because the high light flux from a synchrotron enables collection of data to lower wavelengths, detection of spectra with higher signal-to-noise levels and measurements in the presence of strongly absorbing non-chiral components such as salts, buffers, lipids and detergents. This review describes developments in instrumentation, methodologies and bioinformatics that have enabled new applications of the SRCD technique for the study of proteins. It includes examples of the use of SRCD spectroscopy for providing static and dynamic structural information on molecules, including determinations of secondary structures of intact proteins and domains, assessment of protein stability, detection of conformational changes associated with ligand and drug binding, monitoring of environmental effects, examination of the processes of protein folding and membrane insertion, comparisons of mutant and modified proteins, identification of intermolecular interactions and complex formation, determination of the dispositions of proteins in membranes, identification of natively disordered proteins and their binding partners and examination of the carbohydrate components of glycoproteins. It also discusses how SRCD can be used in conjunction with macromolecular crystallography and other biophysical techniques to provide a more complete picture of protein structures and functions, including how proteins interact with other macromolecules and ligands. This review also includes a discussion of potential new applications in structural and functional genomics using SRCD spectroscopy and future instrumentation and bioinformatics developments that will enable such studies. Finally, the appendix describes a number of computational/bioinformatics resources for secondary structure analyses that take advantage of the improved data quality available from SRCD. In summary, this review discusses how SRCD can be used for a wide range of structural and functional studies of proteins.

Comprehensive secondary-structure analysis of disulfide variants of lysozyme by synchrotron-radiation vacuum-ultraviolet circular dichroism

To elucidate the effects of specific disulfide bridges (Cys6-Cys127, Cys30-Cys115, Cys64-Cys80, and Cys76-Cys94) on the secondary structure of hen lysozyme, the vacuum-ultraviolet circular dichroism (VUVCD) spectra of 13 species of disulfide-deficient variants in which Cys residues were replaced with Ala or Ser residues were measured down to 170 nm at pH 2.9 and 25 degrees C using a synchrotron-radiation VUVCD spectrophotometer. Each variant exhibited a VUVCD spectrum characteristic of a considerable amount of residual secondary structures depending on the positions and numbers of deleted disulfide bridges. The contents of alpha-helices, beta-strands, turns, and unordered structures were estimated with the SELCON3 program using the VUVCD spectra and PDB data of 31 reference proteins. The numbers of alpha-helix and beta-strand segments were also estimated from the VUVCD data. In general, the secondary structures were more effectively stabilized through entropic forces as the number of disulfide bridges increased and as they were formed over larger distances in the primary structure. The structures of three-disulfide variants were similar to that of the wild type, but other variants exhibited diminished alpha-helices with a border between the ordered and disordered structures around the two-disulfide variants. The sequences of the secondary structures were predicted for all the variants by combining VUVCD data with a neural-network method. These results revealed the characteristic role of each disulfide bridge in the formation of secondary structures.

Membrane-induced conformational change of alpha1-acid glycoprotein characterized by vacuum-ultraviolet circular dichroism spectroscopy

The tertiary structure of alpha1-acid glycoprotein (AGP) remains unresolved despite its novel function because AGP is a hard target in X-ray and NMR analyses. To elucidate the membrane-induced conformational change of AGP, the vacuum-ultraviolet circular dichroism (VUVCD) spectra of AGP and its constituent sugars were measured down to 160 nm in the presence or absence of phosphoglyceride liposome using a synchrotron-radiation VUVCD spectrophotometer. The secondary-structure contents and numbers of segments of AGP were estimated from the VUVCD spectra of the protein moiety obtained by subtracting the contributions of the glycan moiety. Further, the positions of secondary structures on the amino acid sequence were predicted by combining the VUVCD data with a neural network algorithm. These comprehensive secondary-structure analyses revealed that AGP consists of 11.4% alpha-helices (3 segments) and 39.9% beta-strands (12 segments) in the absence of liposome (pH 4.5), which are close to the proportions in the secondary structure of native AGP (pH 7.4) predicted by homology modeling, and that it consists of 47.5% alpha-helices (7 segments) and 2.7% beta-strands (2 segments) in the presence of liposome (pH 4.5). Detailed characterization of these alpha-helices of AGP bound to liposome suggested that two alpha-helices (residues 15-27 and 161-175) in the N- and C-terminal regions strongly interact with liposome. Most of the progesterone-binding residues of AGP were involved in the sequences transferring from beta-strands to alpha-helices or unordered structures, which coincided with the large decrease in progesterone-binding capacity of liposome-bound AGP. These results provide the first sequence-level information on the membrane-binding mechanism and structure-function relationship of AGP.

Cations modulate polysaccharide structure to determine FGF-FGFR signaling: a comparison of signaling and inhibitory polysaccharide interactions with FGF-1 in solution

For heparan sulfate (HS) to bind and regulate the activity of proteins, the polysaccharide must present an appropriate sequence and adopt a suitable conformation. The conformations of heparin derivatives, as models of HS, are altered via a change in the associated cations, and this can drastically modify their FGF signaling activities. Here, we report that changing the cations associated with an N-acetyl-enriched heparin polysaccharide, from sodium to copper(II), converted it from supporting signaling through the fibroblast growth factor receptor (FGF-1-FGFR1c) tyrosine kinase signaling system to being inhibitory in a cell-based BaF3 assay. Nuclear magnetic resonance and synchrotron radiation circular dichroism (SRCD) spectroscopy demonstrated that the polysaccharide conformation differed in the presence of sodium or copper(II) cations. Electron paramagnetic resonance confirmed the environment of the copper(II) ion on the N-acetyl-enriched polysaccharide was distinct from that previously observed with intact heparin, which supported signaling. Secondary structures in solution complexes of polysaccharides with FGF-1 (which either supported signaling through FGFR1c or were inhibitory) were determined by SRCD. This allowed direct comparison of the two FGF-1-polysaccharide complexes in solution, containing identical molecular components and differing only in their cation content. Subtle structural differences were revealed, including a reduction in the level of disordered structure in the inhibitory complex.