Ultraviolet Resonance Raman and Fluorescence Studies of Folded and Unfolded Conformations of the Membrane Protein OmpA

Ultraviolet Resonance Raman and Fluorescence Studies of Folded and Unfolded Conformations of the Membrane Protein OmpA
Author: Katheryn Marie Sanchez
Publisher:
Total Pages: 230
Release: 2010
Genre:
ISBN: 9781109691238

This dissertation focuses on the folding dynamics of a bacterial membrane protein, Outer Membrane Protein A (OmpA), using fluorescence and Ultraviolet resonance Raman spectroscopy. Our model [Beta]-barrel membrane protein, OmpA, contains five native anchoring Tryptophan residues. The spectroscopic properties of trp residues are highly sensitive to the local environment, making it an ideal probe for membrane protein folding studies. Utilizing trp fluorescence, refolding studies were performed on single trp mutants of OmpA to determine the thermodynamic stability of these trp mutants. The important noncovalent interactions that promote stability in OmpA are pairwise aromatic interactions and hydrogen bonds with the N1H moiety of trp. Refolding studies were also performed on truncated single-trp mutants, in which the soluble domain of the protein was removed. These studies resulted in increased stability relative to the full-length protein and suggest the absence of the soluble domain may destabilize the unfolded transmembrane domain. Ultraviolet resonance Raman spectroscopy (UVRR) is a powerful vibrational technique that can selectively probe different biological chromophores depending on excitation wavelength. Excitation wavelength dependence studies were performed on OmpA using wavelengths from 206.5 nm - 236.5 nm. This study determined an optimal excitation wavelength of 228-nm to selectively enhance signal from trp residues in OmpA. Additionally, UVRR was used to monitor changes in trp environmental hydrophobicity, hydrogen bonding, and dihedral torsion angle in different conformations of OmpA. The first UVRR spectra were collected of OmpA in a highly scattering environment and show differences in folded and unfolded conformations of the protein, showing the applicability of this technique to study membrane protein folding. UVRR spectra were collected of trp mutants of OmpA at different time points in the folding/insertion process to determine the types of noncovalent interactions with trp residues, and the folding timescales these interactions occur. Our results indicate noncovalent interactions start to form within the first 20 minutes after initiation of folding into DMPC vesicles and continue to show subtle changes over the course of the folding process. Additionally, there is evidence for interactions between trp residues and lipids, inter-residue hydrogen bonding, and amino-aromatic interactions.

Fluorescence and Energy Transfer Studies of Membrane Protein Folding

Fluorescence and Energy Transfer Studies of Membrane Protein Folding
Author: Guipeun Kang
Publisher:
Total Pages: 179
Release: 2015
Genre:
ISBN: 9781321852677

Approximately 30 % of human genes encode for membrane proteins. Membrane proteins play important roles in cells as ion pumps, ligand receptors, and ion channels, and are targets for approximately 60 % of all therapeutic drugs. Despite their relevance in biology and biochemistry, membrane proteins account for only 1 % of the total number of reported protein structures (RCSB Protein Data Bank), and only 16 % of all protein folding literature is related to membrane protein folding (literature search from 1990 -- 2015, Web of Science). This dissertation presents spectroscopic studies of the in vitro folding mechanisms of outer membrane protein A (OmpA). Several optical tools are utilized, including circular dichroism (CD), tryptophan fluorescence, Förster resonance energy transfer (FRET), and ultraviolet resonance Raman (UVRR) spectroscopy. An improved method to determine free energies of unfolding of OmpA based on spectral decomposition is presented. Dynamics of OmpA folding in synthetic lipid bilayers of small unilamellar vesicles (SUVs) are investigated through studies of secondary and tertiary structures. CD and FRET data indicate that secondary and tertiary structures are formed within the first hour of folding, and strand extension and equilibration continues on a longer timescale. UVRR data complement the CD and FRET results, and reveal evolution of molecular interactions during folding. In particular, a tryptophan residue in the extra-vesicle portion of the pore (position 129) displays unusually intense Raman activity in the hydrogen-out-of-plane (HOOP) region. The increase in HOOP intensity is hypothesized to reflect perturbation of the indole ring electron density because of a nearby charged residue or hydroxyl group on neighboring threonine residue. More likely, hydrogen bonding of [pi] electrons on tryptophan with hydroxyl group contributes to the overall stability in addition to hydrophobic contacts by neighboring hydrophobic residues. A relatively new folding environment of nanodiscs is also explored. Preliminary FRET and UVRR data show that OmpA folds and inserts into nanodiscs. Collectively, these measurements elucidate changes in secondary and tertiary structures as well as molecular interactions of tryptophan residues during membrane protein folding.

Studies of Membrane Protein Folding by Bimolecular Fluorescence Quenching

Studies of Membrane Protein Folding by Bimolecular Fluorescence Quenching
Author: Ivan Andrew Kozachenko
Publisher:
Total Pages: 164
Release: 2016
Genre:
ISBN:

This project investigates changes in protein solvation during the folding reaction of Outer membrane protein A (OmpA) of Escherichia Coli, and correlates this dehydration process with shifts in local polarity. Changes in solvent accessibility were probed by fluorescence quenching experiments and Stern-Volmer analysis while polarity was monitored via emission maxima; site-specific insights were gained by probing single tryptophan OmpA mutants (W7, W15, W57, W102, W129, and W143). Fluorescence experiments were performed on OmpA denatured in 8.0 M urea, folded in small unilamellar vesicles (SUVs), adsorbed on SUVs, and aggregated in 0.5 M urea. Time resolved experiments were performed during the folding reaction. The Stern-Volmer quenching constant (KSV) and fluorescence maxima ([lambda] max) showed a correlation where high values of KSV corresponded to red-shifted [lambda] max. KSV and [lambda] max values decayed from unfolded values of 8.6-10 M-1 and 351-354 nm to folded values of 0.6-2.0 M-1 and 325-338 nm. Double exponential fits to the KSV and [lambda] max data showed fast (t ~ 3–11 minutes) and slow components (t ~ 26–49 minutes). The majority of [lambda] max shift occurs in the fast step, while the majority of dehydration occurs in the slower step. The fast component was attributed to a transition of the trp residues of unfolded OmpA to a partially adsorbed state in the bilayer headgroup. A slower, dehydration event took place in which the protein fully inserted into the bilayer. These results complement previously proposed mechanisms of concerted folding, and provided insights into changes in solvation that accompanies formation of native structure.

Protein Folding Handbook, 5 Volume Set

Protein Folding Handbook, 5 Volume Set
Author: Johannes Buchner
Publisher: Wiley-VCH
Total Pages: 2623
Release: 2005-03-11
Genre: Science
ISBN: 9783527307845

How a polypeptide chain folds into a stable and functional protein is probably the most important question in present-day molecular biology. Reliably predicting the folding process allows to deduce protein function from genomic information alone and will bring about a revolution in structural genomics. Understanding the way in which proper protein folding is controlled by the cell is required to find a cure for Alzheimer's and other diseases caused by misfolded proteins. This unique handbook contains the expertise from more than 60 research groups, covering the entire range of topics in protein folding - from biophysics to molecular medicine. The first part explains the principles and factors governing protein stability, and how this knowledge may be used to predict folding pathways. It also surveys important techniques used to study the protein folding process, including spectroscopic, chemical and biological techniques. The second part is devoted to protein folding, unfolding, and misfolding in the cellular context, introducing chaperones and other enzymes involved in protein folding, as well as a study of the pathophysiology of misfolded proteins in amyloid and other disease states. The whole is rounded off by a discussion of the possibility of interfering with the protein folding process by genetic engineering. The comprehensiveness and outstanding quality of the carefully selected contents make this the ultimate reference for every scientist with an interest in protein folding.