MCR-ALS analysis of two-way UV resonance Raman spectra to resolve discrete protein secondary structural motifs.
ABSTRACT The ability of ultraviolet resonance Raman (UVRR) spectroscopy to monitor a host of structurally sensitive protein vibrational modes, the amide I, II, III and S regions, makes it a potentially powerful tool for the visualization of equilibrium and non-equilibrium secondary structure changes in even the most difficult peptide samples. However, it is difficult to unambiguously resolve discrete secondary structure-derived UVRR spectral signatures independently of one another as each contributes an unknown profile to each of the spectrally congested vibrational modes. This limitation is compounded by the presence of aromatic side chains, which introduce additional overlapping vibrational modes. To address this, we have exploited an often overlooked tool for alleviating this spectral overlap by utilizing the differential excitability of the vibrational modes associated with alpha-helices and coil moieties, in the deep UV. The differences in the resonance enhancements of the various structurally associated vibrational modes yields an added dimensionality in the spectral data sets making them multi-way in nature. Through a 'chemically relevant' shape-constrained multivariate curve resolution-alternating least squares (MCR-ALS) analysis, we were able to deconvolute the complex amide regions in the multi-excitation UVRR spectrum of the protein myoglobin, giving us potentially useful 'pure' secondary structure-derived contributions to these individual vibrational profiles.
- ChemBioChem 07/2011; 12(14):2125-8. · 3.74 Impact Factor
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ABSTRACT: Despite their presence in many aspects of biology, the study of membrane proteins lags behind that of their soluble counterparts. Improving structural analysis of membrane proteins is essential. Deep-UV resonance Raman (DUVRR) spectroscopy is an emerging technique in this area and has demonstrated sensitivity to subtle structural transitions and changes in protein environment. The pH low insertion peptide (pHLIP) has three distinct structural states: disordered in an aqueous environment, partially folded and associated with a lipid membrane, and inserted into a lipid bilayer as a transmembrane helix. While the soluble and membrane-inserted forms are well characterized, the partially folded membrane-associated state has not yet been clearly described. The amide I mode, known to be sensitive to protein environment, is the same in spectra of membrane-associated and membrane-inserted pHLIP, indicating comparable levels of backbone dehydration. The amide S mode, sensitive to helical structure, indicates less helical character in the membrane-associated form compared to the membrane-inserted state, consistent with previous findings. However, the structurally sensitive amide III region is very similar in both membrane-associated and membrane-inserted pHLIP, suggesting that the membrane-associated form has a large amount of ordered structure. Where before the membrane-associated state was thought to contain mostly unordered structure and reside in a predominantly aqueous environment, we have shown that it contains a significant amount of ordered structure and rests deeper within the lipid membrane.Biophysical chemistry 12/2013; 187-188C:1-6. · 2.28 Impact Factor
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ABSTRACT: The molten globule (MG) state can aid in the folding of a protein to a functional structure and is loosely defined as an increase in structural disorder with conservation of the ensemble secondary structure content. Simultaneous observation of persistent secondary structure content with increased disorder has remained experimentally problematic. As a consequence, modeling how the MG state remains stable and how it facilitates proper folding remains difficult due to a lack of amenable spectroscopic techniques to characterize this class of partially unfolded proteins. Previously, deep-UV resonance Raman (dUVRR) spectroscopy has proven useful in the resolution of global and local structural fluctuations in the secondary structure of proteins. In this work, dUVRR was employed to study the MG to ordered transition of a model four-helix bundle protein, HP7. Both the average ensemble secondary structure and types of local disorder were monitored, without perturbation of the solvent, pH, or temperature. The MG to ordered transition is induced by stepwise coordination of two heme molecules. Persistent dUVRR spectral features in the amide III region at 1295–1301 and 1335–1338 cm−1 confirm previous observations that HP7 remains predominantly helical in the MG versus the fully ordered state. Additionally, these spectra represent the first demonstration of conserved helical content in a MG protein. With successive heme binding, significant losses are observed in the spectral intensity of the amide III3 and S regions (1230–1260 and 1390 cm−1, respectively), which are known to be sensitive to local disorder. These observations indicate that there is a decrease in the structural populations able to explore various extended conformations with successive heme binding events. DUVRR spectra indicate that the first heme coordination between two helical segments diminishes exploration of more elongated backbone structural conformations in the inter-helical regions. A second heme coordination by the remaining two helices further restricts protein motion.Journal of Raman Spectroscopy 06/2013; · 2.68 Impact Factor