An Infrared Spectroscopic Study of the Secondary Structure of Protein Kinase Cα and Its Thermal Denaturation

Advancements of two dimensional correlation spectroscopy in protein researches

The developments of two-dimensional correlation spectroscopy (2DCOS) applications in protein studies are discussed, especially for the past two decades. The powerful utilities of 2DCOS combined with various analytical techniques in protein studies are summarized. The emphasis is on the vibration spectroscopic techniques including IR, NIR, Raman and optical activity (ROA), as well as vibration circular dichroism (VCD) and fluorescence spectroscopy. In addition, some new developments, such as hetero-spectral 2DCOS, moving-window correlation, and model based correlation, are also reviewed for their utility in the investigation of the secondary structure, denaturation, folding and unfolding changes of protein. Finally, the new possibility and challenges of 2DCOS in protein research are highlighted as well.

Two-dimensional correlation spectroscopy in protein science, a summary for past 20years

Two-dimensional correlation spectroscopy (2DCOS) has been widely used to Infrared, Raman, Near IR, Optical Activity (ROA), Vibrational Circular Dichroism (VCD) and Fluorescence spectroscopy. In addition, several new developments, such as 2D hetero-correlation analysis, moving-window two-dimensional (MW2D) correlation, model based correlation (βν and kν correlation analyses) have also well incorporated into protein research. They have been used to investigate secondary structure, denaturation, folding and unfolding changes of protein, and have contributed greatly to the field of protein science. This review provides an overview of the applications of 2DCOS in the field of protein science for the past 20 year, especially to memory our old friend, Dr. Boguslawa Czarnik-Matusewicz, for her great contribution in this research field. The powerful utility of 2DCOS combined with various analytical techniques in protein studies is summarized. The noteworthy developments and perspective of 2DCOS in this field are highlighted finally.

Investigation of the Effect of Bilayer Composition on PKCα-C2 Domain Docking Using Molecular Dynamics Simulations

The protein kinase Cα (PKCα) enzyme is a member of a broad family of serine/threonine kinases, which are involved in varied cellular signaling pathways. The initial step of PKCα activation involves the C2 subunit docking with the cell membrane, which is followed by interactions of the C1 domains with diacylglycerol (DAG) in the membrane. Notably, the molecular mechanisms of these interactions remain poorly understood, especially what effects, if any, DAG may have on the initial C2 docking. To further understand this process, we have performed a series of conventional molecular dynamics simulations to systematically investigate the interaction between PKCα-C2 domains and lipid bilayers with different compositions to examine the effects of POPS, PIP2, and 1-palmitoyl-2-oleoyl-sn-glycerol (POG) on domain docking. Our results show that the PKCα-C2 domain does not interact with the bilayer surface in the absence of POPS and PIP2. In contrast, the inclusion of POPS and PIP2 to the bilayer resulted in strong domain docking in both perpendicular and parallel orientations, whereas the further inclusion of POG resulted in only parallel domain docking. In addition, lysine residues in the C2 domain formed hydrogen bonds with PIP2 molecule bilayers containing POG. These effects were further explored with umbrella sampling calculations to estimate the free energy of domain docking to the lipid bilayer in the presence of one or two PIP2 molecules. The results show that the binding of one or two PIP2 molecules is thermodynamically favorable, although stronger in bilayers lacking POG. However, in POG-containing bilayers, the binding mode of the C2 domain appears to be more flexible, which may have implications for activation of full-length PKCα. Together, our results shed new insights into the process of C2 bilayer binding and suggest new mechanisms for the roles of different phospholipids in the activation process of PKCα.

Signaling through C2 domains: more than one lipid target

C2 domains are membrane-binding modules that share a common overall fold: a single compact Greek-key motif organized as an eight-stranded anti-parallel β-sandwich consisting of a pair of four-stranded β-sheets. A myriad of studies have demonstrated that in spite of sharing the common structural β-sandwich core, slight variations in the residues located in the interconnecting loops confer C2 domains with functional abilities to respond to different Ca(2+) concentrations and lipids, and to signal through protein-protein interactions as well. This review summarizes the main structural and functional findings on Ca(2+) and lipid interactions by C2 domains, including the discovery of the phosphoinositide-binding site located in the β3-β4 strands. The wide variety of functions, together with the different Ca(2+) and lipid affinities of these domains, converts this superfamily into a crucial player in many functions in the cell and more to be discovered. This Article is Part of a Special Issue Entitled: Membrane Structure and Function: Relevance in the Cell's Physiology, Pathology and Therapy.

Phosphatidylinositol 4,5-bisphosphate decreases the concentration of Ca2+, phosphatidylserine and diacylglycerol required for protein kinase C α to reach maximum activity

The C2 domain of PKCα possesses two different binding sites, one for Ca(2+) and phosphatidylserine and a second one that binds PIP2 with very high affinity. The enzymatic activity of PKCα was studied by activating it with large unilamellar lipid vesicles, varying the concentration of Ca(2+) and the contents of dioleylglycerol (DOG), phosphatidylinositol 4,5-bisphosphate (PIP2) and phosphadidylserine (POPS) in these model membranes. The results showed that PIP2 increased the Vmax of PKCα and, when the PIP2 concentration was 5 mol% of the total lipid in the membrane, the addition of 2 mol% of DOG did not increase the activity. In addition PIP2 decreases K0.5 of Ca(2+) more than 3-fold, that of DOG almost 5-fold and that of POPS by a half. The K0.5 values of PIP2 amounted to only 0.11 µM in the presence of DOG and 0.39 in its absence, which is within the expected physiological range for the inner monolayer of a mammalian plasma membrane. As a consequence, PKCα may be expected to operate near its maximum capacity even in the absence of a cell signal producing diacylglycerol. Nevertheless, we have shown that the presence of DOG may also help, since the K0.5 for PIP2 notably decreases in its presence. Taken together, these results underline the great importance of PIP2 in the activation of PKCα and demonstrate that in its presence, the most important cell signal for triggering the activity of this enzyme is the increase in the concentration of cytoplasmic Ca(2+).

Fe2+-catalyzed non-enzymatic glycosylation alters collagen conformation during AGE-collagen formation in vitro

Advanced glycation end-products (AGEs) are one of the major factors of hyperglycemia related complications for diabetic patients. We studied the formation of AGEs in type I collagen after Fe2+-catalyzed non-enzymatic glycosylation in vitro. Type I collagen isolated from rat tail tendon was incubated with glucose and increasing concentrations of iron ions Fe2+. After 4 weeks incubation, cytotoxity of AGEs was indicated by the cytotoxity assay of primary human umbilical vein endothelial cells and primary human monocytes cultured with glycosylated collagen AGEs. Fourier transform infrared spectroscopy analysis revealed that structural changes of functional groups in glycosylated collagen are accelerated by the catalyst Fe2+. Using two-dimensional Fourier-transform infrared correlation spectroscopy analyses, for the first time, we demonstrated that the order of structural changes of these functional groups is -CH->Amide I>Amide II>Amide III>nu(C=O) the carboxylic group of Asn, Gln or polyproline amino acid residue in the course of AGE-collagen formation. Knowing the positions of these functional groups in collagen, this order of changes indicates that during glycation of collagen, the structure of the main chain residues in collagen changed first, and then the side chain changed gradually, which may lead to more carboxylic groups exposed to glucose for further formation of AGE-collagen irreversibly. The findings presented may support the design of new therapeutic strategies to prevent or slow down the Fe2+-catalyzed glycosylation of collagen and other matrix proteins.

The Influence of Fluoroquinolone Drugs on the Bacterial Growth of S. epidermidis Utilizing the Unique Potential of Vibrational Spectroscopy

Increasing resistance of many antibiotics has made the design of new drugs necessary. To assist a target-oriented search for new structures and for the elucidation of the mode of action of existing drugs, powerful analytical techniques are required. In this work, vibrational spectroscopy is used to shed more light on the as-yet elusive interaction of gyrase inhibitors of the fluoroquinolone type with their biological target inside the Gram-positive bacterium Staphylococcus epidermidis by investigating whole-cell changes that occur as a result of the presence of the drug moxifloxacin. IR absorption and Raman spectra with excitation off resonance (lambda exc = 532 nm) and in resonance with the biological targets DNA and the aromatic amino acids of gyrase (lambda exc = 244 nm) were recorded for unperturbed bacteria and bacteria in varying drug concentrations (0.08, 0.16, 0.27, and 0.62 microg moxifloxacin/mL bacterial culture). The spectral changes caused by the action of the drug were analyzed with the help of statistical methods, such as hierarchical cluster analysis (HCA), principal component analysis (PCA), and Fisher's linear discriminant analysis (LDA) combined with variable selection. The wavenumbers mostly affected by the action of the drug could be assigned to protein and DNA moieties, supporting the proposed mechanisms of a tertiary complex of the fluoroquinolone, the enzyme gyrase, and DNA.

Structural study of the catalytic domain of PKCzeta using infrared spectroscopy and two-dimensional infrared correlation spectroscopy

The secondary structure of the catalytic domain from protein kinase C zeta was studied using IR spectroscopy. In the presence of the substrate MgATP, there was a significant change in the secondary structure. After heating to 80 degrees C, a 14% decrease in the alpha-helix component was observed, accompanied by a 6% decrease in the beta-pleated sheet; no change was observed in the large loops or in 3(10)-helix plus associated loops. The maximum increase with heating was observed in the aggregated beta-sheet component, with an increase of 14%. In the presence of MgATP, and compared with the sample heated in its absence, there was a substantial decrease in the 3(10)-helix plus associated loops and an increase in alpha-helix. Synchronous 2D-IR correlation showed that the main changes occurred at 1617 cm(-1), which was assigned to changes in the intermolecular aggregated beta-sheet of the denaturated protein. This increase was mainly correlated with the change in alpha-helix. In the presence of MgATP, the main correlation was between aggregated beta-sheet and the large loops component. The asynchronous 2D-correlation spectrum indicated that a number of components are transformed in intermolecularly aggregated beta-sheet, especially the alpha-helix and beta-sheet components. It is interesting that changes in 3(10)-helix plus associated loops and in alpha-helix preceded changes in large loops, which suggests that the open loops structure exists as an intermediate state during denaturation. In summary, IR spectroscopy revealed an important effect of MgATP on the secondary structure and on the thermal unfolding process when this was induced, whereas 2D-IR correlation spectroscopy allowed us to show the establishment of the denaturation pathway of this protein.

Interaction of alcohols with serum LDL

The interaction of low molecular weight alcohols with low density lipoprotein (LDL) has been studied using amide I band-fitting, thermal profiling and two-dimensional infrared correlation spectroscopy (2D-IR). At 0.3 M alcohol, no changes in secondary structure are observed. In the presence of 1 M alcohol, ethanol and propanol decreases protein denaturation temperature and produces changes in the amide I thermal profiles of protein components and in the lipid bands. The 2D-IR synchronous map corresponding to protein or lipid component at 20-37 degrees C suggests differences in the presence of propanol. The asynchronous map corresponding to the lipid component indicates changes in bandwidth, compatible with a more fluid environment. In the 37-80 degrees C temperature range the thermal profile is different in the presence of propanol, both for the lipid and protein components. The results presented show that when alcohols affect the protein component, the lipid spectrum also varies pointing to an effect on the lipid-protein interaction.

Uncoupled Peptide Bond Vibrations in α-Helical and Polyproline II Conformations of Polyalanine Peptides

We examined the 204-nm UV resonance Raman (UVR) spectra of the polyproline II (PPII) and alpha-helical states of a 21-residue mainly alanine peptide (AP) in different H2O/D2O mixtures. Our hypothesis is that if the amide backbone vibrations are coupled, then partial deuteration of the amide N will perturb the amide frequencies and Raman cross sections since the coupling will be interrupted; the spectra of the partially deuterated derivatives will not simply be the sum of the fully protonated and deuterated peptides. We find that the UVR spectra of the AmIII and AmII' bands of both the PPII conformation and the alpha-helical conformation (and also the PPII AmI, AmI', and AmII bands) can be exactly modeled as the linear sum of the fully N-H protonated and N-D deuterated peptides. Negligible coupling occurs for these vibrations between adjacent peptide bonds. Thus, we conclude that these peptide bond Raman bands can be considered as being independently Raman scattered by the individual peptide bonds. This dramatically simplifies the use of these vibrational bands in IR and Raman studies of peptide and protein structure. In contrast, the AmI and AmI' bands of the alpha-helical conformation cannot be well modeled as a linear sum of the fully N-H protonated and N-D deuterated derivatives. These bands show evidence of coupling between adjacent peptide bond vibrations. Care must be taken in utilizing the AmI and AmI' bands for monitoring alpha-helical conformations since these bands are likely to change as the alpha-helical length changes and the backbone conformation is perturbed.

Vibrational Spectroscopic Studies on the Disulfide Formation and Secondary Conformational Changes of Captopril–HSA Mixture after UV-B Irradiation

The effects of pH and ultraviolet-B (UV-B) irradiation on the secondary structure of human serum albumin (HSA) in the absence or presence of captopril were investigated by an attenuated total reflection (ATR)/Fourier transform infrared (FTIR) spectroscopy. The UV-B exposure affecting the stability of captopril before and after captopril-HSA interaction was also examined by using confocal Raman microspectroscopy. The results indicate that the transparent pale-yellow solution for captopril-HSA mixture in all pH buffer solutions, except pH 5.0 approximately 7.0, changed into a viscous form then a gel form with UV-B exposure time. The secondary structural transformation of HSA in the captopril-HSA mixture with or without UV-B irradiation was found to shift the maxima amide I peak in IR spectra from 1652 cm(-1) assigned to alpha-helix structure to 1622 cm(-1) because of a beta-sheet structure, which was more evident in pH 3.0, 8.0 or 9.0 buffer solutions. The Raman shift from 1653 cm(-1) (alpha-helix) to 1670 cm(-1) (beta-sheet) also confirmed this result. Captopril dissolved in distilled water with or without UV-B irradiation was determined to form a captopril disulfide observed from the Raman spectra of 512 cm(-1), which was exacerbated by UV-B irradiation. There was little disulfide formation in the captopril-HSA mixture even with long-term UV-B exposure, but captopril might interact with HSA to change the protein secondary structure of HSA whether there was UV-B irradiation or not. The pH of the buffer solution and captopril-HSA interaction may play more important roles in transforming the secondary structure of HSA from alpha-helix to beta-sheet in the corresponding captopril-HSA mixture than UV-B exposure. The present study also implies that HSA has the capability to protect the instability of captopril in the course of UV-B irradiation. In addition, a partial unfolding of HSA induced by pH or captopril-HSA interaction under UV-B exposure is proposed.