Zinc porphyrin as a donor for FRET in Zn(II)cytochrome c

Enzyme-activated probes in optical imaging: a focus on atherosclerosis

Enzyme-activated probes enable complex biological processes to be studied in real-time. A wide range of enzymes are modulated in diseases, including cancer, inflammatory diseases and cardiovascular disease, and have the potential to act as vital diagnostic and prognostic biomarkers to monitor and report on disease progression. In this perspective article, we discuss suitable design characteristics of enzyme-activated fluorescent probes for ex vivo and in vivo optical imaging applications. With a particular focus on atherosclerosis imaging, we highlight recent approaches to report on the activity of cathepsins (K and B), matrix metalloproteinases (MMP-2 and MMP-9), thrombin, heme oxygenase-1 (HO-1) and myeloperoxidase (MPO).

A Coumarin-Porphyrin FRET Break-Apart Probe for Heme Oxygenase-1

Heme oxygenase-1 (HO-1) is a vital enzyme in humans that primarily regulates free heme concentrations. The overexpression of HO-1 is commonly associated with cardiovascular and neurodegenerative diseases including atherosclerosis and ischemic stroke. Currently, there are no known chemical probes to detect HO-1 activity, limiting its potential as an early diagnostic/prognostic marker in these serious diseases. Reported here are the design, synthesis, and photophysical and biological characterization of a coumarin-porphyrin FRET break-apart probe to detect HO-1 activity, Fe-L1. We designed Fe-L1 to "break-apart" upon HO-1-catalyzed porphyrin degradation, perturbing the efficient FRET mechanism from a coumarin donor to a porphyrin acceptor fluorophore. Analysis of HO-1 activity using Escherichia coli lysates overexpressing hHO-1 found that a 6-fold increase in emission intensity at 383 nm was observed following incubation with NADPH. The identities of the degradation products following catabolism were confirmed by MALDI-MS and LC-MS, showing that porphyrin catabolism was regioselective at the α-position. Finally, through the analysis of Fe-L2, we have shown that close structural analogues of heme are required to maintain HO-1 activity. It is anticipated that this work will act as a foundation to design and develop new probes for HO-1 activity in the future, moving toward applications of live fluorescent imaging.

Successive energy transfer within multiple photosensitizers assembled in a hexameric hemoprotein scaffold

An assembly of multiple photosensitizers is demonstrated by development of a hexameric hemoprotein (HTHP) scaffold as a light harvesting model to replicate the successive energy transfer occuring within photosensitizer assemblies of natural systems. In our model, six zinc protoporphyrin IX (ZnPP) molecules are arrayed at the heme binding site of HTHP by supramolecular interactions and five fluorescein (Flu) molecules and one Texas Red (Tex) molecule as donor and acceptor photosensitizers, respectively, are attached to the HTHP protein surface with covalent linkages. The flow of excited energy from photoexcited Flu to Tex occurs via two pathways: direct energy transfer from Flu to Tex (path 1) and energy transfer via ZnPP (path 2). Steady state and time-resolved fluorescence measurements reveal that the energy transfer ratio of these pathways (path 1 : path 2) is 39 : 61. These findings indicate that the excited energy originating at five Flu and six ZnPP molecules is collected at one Tex molecule as a funnel-like bottom for light harvesting. The present system using the hexameric hemoprotein scaffold is a promising candidate for construction of an artificial light harvesting system having multiple photosensitizers to promote efficient use of solar energy.

Intramolecular Transfer of Singlet Oxygen

The intramolecular transfer of energy (FRET) and electrons (Dexter) are of great interest for the scientific community and are well-understood. In contrast, the intramolecular transfer of singlet oxygen ((1)O2), a reactive and short-lived oxygen species, has until now been unknown. This process would be very interesting because (1)O2 plays an important role in photodynamic therapy (PDT). Herein, we present the first successful intramolecular transfer of (1)O2 from a donor to acceptor. Also, we found a dependence of conformation and temperature comparable with those of FRET. We provide several pieces of evidence for the intramolecular character of this transfer, including competition experiments. Our studies should be interesting not only from the theoretical and mechanistic point of view but also for the design of new (1)O2 donors and applications in PDT.

Nitrogen-Nitrogen Bonds Undermine Stability of N-Doped Graphene

Two-dimensional alloys of carbon and nitrogen draw strong interest due to prospective applications in nanomechanical and optoelectronic devices. The stability of these chemical structures can vary greatly as a function of chemical composition and structure. The present study employs hybrid density functional theory and reactive molecular dynamics simulations to elucidate how many nitrogen atoms can be incorporated into the graphene sheet without destroying it. We conclude that (1) the C/N = 56:29 structure and all nitrogen-poorer structures maintain stability at 1000 K; (2) the stability suffers greatly in the presence of N-N bonds; and (3) distribution of electron density depends heavily on the structural pattern in the N-doped graphene. Our calculations support the experimental efforts aimed at production of highly N-doped graphene and generate important insights into the mechanisms of tuning graphene mechanical and optoelectronic properties. The theoretical prediction can be tested directly by chemical synthesis.

Biological significance and applications of heme c proteins and peptides

Hemes are ubiquitous in biology and carry out a wide range of functions. The heme group is largely invariant across proteins with different functions, although there are a few variations seen in nature. The most common variant is heme c, which is formed by a post-translational modification in which heme is covalently linked to two Cys residues on the polypeptide via thioether bonds. In this Account, the influence of this covalent attachment on heme c properties and function is discussed, and examples of how covalent attachment has been used in selected applications are presented. Proteins that bind heme c are among the most well-characterized proteins in biochemistry. Most of these proteins are cytochromes c (cyts c) that serve as electron carriers in photosynthesis and respiration. Despite the intense study of cyts c, the functional significance of heme covalent attachment has remained elusive. One observation is that heme c reaches a lower reduction potential in nature than its noncovalently linked counterpart, heme b, when comparing proteins with the same axial ligands. Furthermore, covalent attachment is known to enhance protein stability and allow the heme to be relatively solvent exposed. However, an inorganic chemistry perspective on the effects of covalent attachment has been lacking. Spectroscopic measurements and computations on cyts c and model systems reveal a number of effects of covalent attachment on heme electronic structure and reactivity. One is that the predominant nonplanar ruffling distortion seen in heme c lowers heme reduction potential. Another is that covalent attachment influences the interaction of the heme iron with the proximal His ligand. Heme ruffling also has been shown to influence electronic coupling to redox partners and, therefore, electron transfer rates by altering the distribution of the orbital hole on the porphyrin in oxidized cyt c. Another consequence of heme covalent attachment is the strong vibrational coupling seen between the iron and the protein surface as revealed by nuclear resonance vibrational spectroscopy studies. Finally, heme covalent attachment is proposed to be an important feature supporting multiple roles of cyt c in programmed cell death (apoptosis). Heme covalent attachment is not only vital for the biological functions of cyt c but also provides a useful handle in a number of applications. For one, the engineering of heme c onto an exposed portion of a protein of interest has been shown to provide a visible affinity purification tag. In addition, peptides with covalently attached heme, known as microperoxidases, have been studied as model compounds and oxidation catalysts and, more recently, in applications for energy conversion and storage. The wealth of insight gained about heme c through fundamental studies of cyts c forms a basis for future efforts toward engineering natural and artificial cytochromes for a variety of applications.

Direct conversion of cytochrome c spectral shifts to fluorescence using photochromic FRET

Photochromic fluorescence resonance energy transfer (pcFRET) was used to monitor the redox activity of non-fluorescent heme protein. Venus fluorescent protein was used as a donor where its emission intensity was reversibly modulated by the absorption change of Cytochrome c.

Cytochrome c causes pore formation in cardiolipin-containing membranes

The release of cytochrome c from mitochondria is a key signaling mechanism in apoptosis. Although extramitochondrial proteins are thought to initiate this release, the exact mechanisms remain unclear. Cytochrome c (cyt c) binds to and penetrates lipid structures containing the inner mitochondrial membrane lipid cardiolipin (CL), leading to protein conformational changes and increased peroxidase activity. We describe here a direct visualization of a fluorescent cyt c crossing synthetic, CL-containing membranes in the absence of other proteins. We observed strong binding of cyt c to CL in phospholipid vesicles and bursts of cyt c leakage across the membrane. Passive fluorescent markers such as carboxyfluorescein and a 10-kDa dextran polymer crossed the membrane simultaneously with cyt c, although larger dextrans did not. The data show that these bursts result from the opening of lipid pores formed by the cyt c-CL conjugate. Pore formation and cyt c leakage were significantly reduced in the presence of ATP. We suggest a model, consistent with these findings, in which the formation of toroidal lipid pores is driven by initial cyt c-induced negative spontaneous membrane curvature and subsequent protein unfolding interactions. Our results suggest that the CL-cyt c interaction may be sufficient to allow cyt c permeation of mitochondrial membranes and that cyt c may contribute to its own escape from mitochondria during apoptosis.

Origin of the conformational heterogeneity of cardiolipin-bound cytochrome C

Interactions of cytochrome c (cyt c) with cardiolipin (CL) partially unfold the protein, activating its peroxidase function, a critical event in the execution of apoptosis. However, structural features of the altered protein species in the heterogeneous ensemble are difficult to probe with ensemble averaging. Analyses of the dye-to-heme distance distributions P(r) from time-resolved FRET (TR-FRET) have uncovered two distinct types of CL-bound cyt c conformations, extended and compact. We have combined TR-FRET, fluorescence correlation spectroscopy (FCS), and biolayer interferometry to develop a systematic understanding of the functional partitioning between the two conformations. The two subpopulations are in equilibrium with each other, with a submillisecond rate of conformational exchange reflecting the protein folding into a compact non-native state, as well as protein interactions with the lipid surface. Electrostatic interactions with the negatively charged lipid surface that correlate with physiologically relevant changes in CL concentrations strongly affect the kinetics of cyt c binding and conformational exchange. A predominantly peripheral binding mechanism, rather than deep protein insertion into the membrane, provides a rationale for the general denaturing effect of the CL surface and the large-scale protein unfolding. These findings closely relate to cyt c folding dynamics and suggest a general strategy for extending the time window in monitoring the kinetics of folding.

Fluorescence resonance energy transfer (FRET)-based biosensors: visualizing cellular dynamics and bioenergetics

Förster (or fluorescence) resonance energy transfer (FRET) is a process involving the radiation-less transfer of energy from a "donor" fluorophore to an "acceptor" fluorophore. FRET technology enables the quantitative analysis of molecular dynamics in biophysics and in molecular biology, such as the monitoring of protein-protein interactions, protein-DNA interactions, and protein conformational changes. FRET-based biosensors have been utilized to monitor cellular dynamics not only in heterogeneous cellular populations, but also at the single-cell level in real time. Lately, applications of FRET-based biosensors range from basic biological to biomedical disciplines. Despite the diverse applications of FRET, FRET-based sensors still face many challenges. There is an increasing need for higher fluorescence resolution and improved specificity of FRET biosensors. Additionally, as more FRET-based technologies extend to medical diagnostics, the affordability of FRET reagents becomes a significant concern. Here, we will review current advances and limitations of FRET-based biosensor technology and discuss future FRET applications.

Conformational properties of cardiolipin-bound cytochrome c

Interactions of cytochrome c (cyt c) with cardiolipin (CL) are important for both electron transfer and apoptotic functions of this protein. A sluggish peroxidase in its native state, when bound to CL, cyt c catalyzes CL peroxidation, which contributes to the protein apoptotic release. The heterogeneous CL-bound cyt c ensemble is difficult to characterize with traditional structural methods and ensemble-averaged probes. We have employed time-resolved FRET measurements to evaluate structural properties of the CL-bound protein in four dansyl (Dns)-labeled variants of horse heart cyt c. The Dns decay curves and extracted Dns-to-heme distance distributions P(r) reveal a conformational diversity of the CL-bound cyt c ensemble with distinct populations of the polypeptide structures that vary in their degree of protein unfolding. A fraction of the ensemble is substantially unfolded, with Dns-to-heme distances resembling those in the guanidine hydrochloride-denatured state. These largely open cyt c structures likely dominate the peroxidase activity of the CL-bound cyt c ensemble. Site variations in P(r) distributions uncover structural features of the CL-bound cyt c, rationalize previous findings, and implicate the prime role of electrostatic interactions, particularly with the protein C terminus, in the CL-induced unfolding.

Communication: Systematic shifts of the lowest unoccupied molecular orbital peak in x-ray absorption for a series of 3d metal porphyrins

Porphyrins are widely used as dye molecules in solar cells. Knowing the energies of their frontier orbitals is crucial for optimizing the energy level structure of solar cells. We use near edge x-ray absorption fine structure (NEXAFS) spectroscopy to obtain the energy of the lowest unoccupied molecular orbital (LUMO) with respect to the N(1s) core level of the molecule. A systematic energy shift of the N(1s) to LUMO transition is found along a series of 3d metal octaethylporphyrins and explained by density functional theory. It is mainly due to a shift of the N(1s) level rather than a shift of the LUMO or a change in the electron-hole interaction of the core exciton.

Photophysical properties of Zn-substituted cytochrome c investigated by single-molecule and ensemble-averaged spectroscopy

The study of the structural reorganization and photophysical properties of Zn-Cytc using the single-molecule and ensemble-averaged spectroscopy shows that the photoblinking behaviors of single-Zn-Cytc depend on the folded and unfolded structures, whereas the fluorescence dynamics of Zn-Cytc observed in the bulk phase are hardly affected by the conformational change of a protein.