Excited-State Charge-Transfer Dynamics of Azurin, a Blue Copper Protein, from Resonance Raman Intensities

HYSCORE and QM/MM Studies of Second Sphere Variants of the Type 1 Copper Site in Azurin: Influence of Mutations on the Hyperfine Couplings of Remote Nitrogens

Secondary coordination sphere (SCS) interactions have been shown to play important roles in tuning reduction potentials and electron transfer (ET) properties of the Type 1 copper proteins, but the precise roles of these interactions are not fully understood. In this work, we examined the influence of F114P, F114N, and N47S mutations in the SCS on the electronic structure of the T1 copper center in azurin (Az) by studying the hyperfine couplings of (i) histidine remote Nε nitrogens and (ii) the amide Np using the two-dimensional (2D) pulsed electron paramagnetic resonance (EPR) technique HYSCORE (hyperfine sublevel correlation) combined with quantum mechanics/molecular mechanics (QM/MM) and DLPNO-CCSD calculations. Our data show that some components of hyperfine tensor and isotropic coupling in N47SAz and F114PAz (but not F114NAz) deviate by up to ∼±20% from WTAz, indicating that these mutations significantly influence the spin density distribution between the CuII site and coordinating ligands. Furthermore, our calculations support the assignment of Np to the backbone amide of residue 47 (both in Asn and Ser variants). Since the spin density distributions play an important role in tuning the covalency of the Cu-Scys bond of Type 1 copper center that has been shown to be crucial in controlling the reduction potentials, this study provides additional insights into the electron spin factor in tuning the reduction potentials and ET properties.

Metal-binding and circular permutation-dependent thermodynamic and kinetic stability of azurin

Native topology is known to determine the folding kinetics and the energy landscape of proteins. Furthermore, the circular permutation (CP) of proteins alters the order of the secondary structure connectivity while retaining the three-dimensional structure, making it an elegant and powerful approach to altering native topology. Previous studies elucidated the influence of CP in proteins with different folds such as Greek key β-barrel, β-sandwich, β-α-β, and all α-Greek key. CP mainly affects the protein stability and unfolding kinetics, while folding kinetics remains mostly unaltered. However, the effect of CP on metalloproteins is yet to be elaborately studied. The active site of metalloproteins poses an additional complexity in studying protein folding. Here, we investigate a CP variant (cpN42) of azurin-in both metal-free and metal-bound (holo) forms. As observed earlier in other proteins, apo-forms of wild-type (WT) and cpN42 fold with similar rates. In contrast, zinc-binding accelerates the folding of WT but decelerates the folding of cpN42. On zinc-binding, the spontaneous folding rate of WT increases by >250 times that of cpN42, which is unprecedented and the highest for any CP to date. On the other hand, zinc-binding reduces the spontaneous unfolding rate of cpN42 by ~100 times, making the WT and CP azurins unfold at similar rates. Our study demonstrates metal binding as a novel way to modulate the unfolding and folding rates of CPs compared to their WT counterparts. We hope our study increases the understanding of the effect of CP on the folding mechanism and energy landscape of metalloproteins.

Long-Range Charge Delocalization Mediates the Ultrafast Ligand-to-Metal Charge Transfer Dynamics at the Cu2+-Active Site in Azurin

The blue color metalloprotein in azurin has traditionally been attributed to the intense cysteine-to-Cu²⁺ ligand-to-metal charge transfer transition centered at 628 nm. Although resonance Raman measurements of the Cu²⁺ active site have implied that the LMCT transition electronically couples to the protein scaffold well beyond its primary metal-ligand coordination shell, the structural extent of this electronic coupling and visualization of the protein-mediated charge transfer dynamics have remained elusive. Here, using femtosecond broadband transient absorption and impulsive Raman spectroscopy, we provide direct evidence for a rapid relaxation between two distinct charge transfer states, having different spatial delocalization, within ∼300 fs followed by recombination of charges in subpicosecond time scales. We invoke the formation of a protein-centered radical cation, possibly Trp48 or a Phe residue, within 100 fs substantiating the long-range electronic coupling for the first time beyond the traditional copper active site. The Raman spectra of the excited CT state show the presence of protein-centric vibrations along with the vibrational modes assigned to the copper active site. Our results demonstrate a large delocalization length scale of the initially populated CT state, thereby highlighting the possibility of exploiting azurin photochemistry for energy conversion techniques.

Resonance Raman Excitation Profiles of Fe(II)-Terpyridine Complexes: Electronic Effects of Ligand Modifications

Metal 2,2':6',2″-terpyridine (tpy) complexes are readily used as building blocks in metallo-supramolecular polymers that stand out for their photophysical properties in solar energy assemblies. Furthermore, Resonance Raman (RR) excitation profiles are sensitive indicators of the electronic properties of chromophores. Previously, using RR spectroscopy, we studied the [Fe(tpy)₂]²⁺ complex and metallo-supramolecular polymers formed by tpy derivatives and Fe(II) ions. Here, we compare RR spectra of iron (Fe(II)) complexes with 4'-substituted tpy ligands─[Fe(4'-R-tpy)₂]²⁺, with R = H (1a), Cl (2a), 4-chlorophenyl (3a), and 2-thienyl (4a) to describe changes in their electronic structure after functionalization. By combining theoretical calculations, RR, and UV/vis spectra, we elucidated differences in the RR excitation profiles of 1a, 2a, and 4a complexes. In all Raman modes, complexes 1a and 2a showed maximal enhancement only at 532 nm excitation, whereas complex 4a exhibited maximal enhancement selectively at either 532 or 633 nm excitations. Based on our calculations, the mixed metal/ligand character of the highest occupied molecular orbital (HOMO) of 4a complex manifests itself through selective enhancement of vibration modes, mainly localized on the 2-thienyl unit at 633 nm excitation, which may explain the unique behavior of this complex. Therefore, complex 4a is a prospective candidate for further detailed photophysical explorations toward developing sensitizers for solar cells.

Ultrafast photoinduced energy and charge transfer

After presenting the basic theoretical models of excitation energy transfer and charge transfer, I describe some of the novel experimental methods used to probe them. Finally, I discuss recent results concerning ultrafast energy and charge transfer in biological systems, in chemical systems and in photovoltaics based on sensitized transition metal oxides.

Vibrational Changes Induced by Electron Transfer in Surface Bound Azurin Metalloprotein Studied by Tip-Enhanced Raman Spectroscopy and Scanning Tunneling Microscopy

The copper protein azurin, due to the peculiar coupling of its optical and vibronic properties with electron transfer (ET) and its biorecognition capabilities, is a very promising candidate for bioelectronic, bio-optoelectronic and biosensor applications. However, a complete understanding of the fundamental processes relating azurin ET and its optical and vibronic characteristics with the charge transport mechanisms occurring in proteins bound to a conductive surface, the typical scenario for a biosensor or bioelectronic component, is still lacking. We studied azurin proteins bound to a gold electrode surface by scanning tunneling microscopy combined with tip-enhanced Raman spectroscopy (STM-TERS). Robust TER spectra were obtained, and the protein's vibronic response under optical excitation in resonance with its ligand-to-metal charge transfer band was found to be affected by the tunneling parameters, indicating a direct involvement of the active site vibrations in the electron transport process.

Structure, Dynamics, and Electron Transfer of Azurin Bound to a Gold Electrode

Blue copper redox protein azurin (AZ) constitutes an ideal active element for building bionano-optoelectronic devices based on the intriguing interplay among its electron transfer (ET), vibrational, and optical properties. A full comprehension of its dynamical and functional behavior is required for efficient applications. Here, AZ bound to gold electrode via its disulfide bridge was investigated by a molecular dynamics simulation approach taking into account for gold electron polarization which provides a more realistic description of the protein-gold interaction. Upon binding to gold, AZ undergoes slight changes in its secondary structure with the preservation of the copper-containing active site structure. Binding of AZ to gold promotes new collective motions, with respect to free AZ, as evidenced by essential dynamics. Analysis of the ET from the AZ copper ion to the gold substrate, performed by the Pathways model, put into evidence the main residues and structural motifs of AZ involved in the ET paths. During the dynamical evolution of the bionanosystem, transient contacts between some lateral protein atoms and the gold substrate occurred; concomitantly, the opening of additional ET channels with much higher rates was registered. These results provide new and detailed insights on the dynamics and ET properties of the AZ-gold system, by also helping to rationalize some imaging and conductive experimental evidences and also to design new bionanodevices with tailored features.

Resonance Raman Intensities Demonstrate that C5 Substituents Affect the Initial Excited-State Structural Dynamics of Uracil More than C6 Substituents

Resonance Raman derived initial excited-state structural dynamics provide insight into the photochemical mechanisms of pyrimidine nucleobases, in which the photochemistry appears to be dictated by the C5 and C6 substituents. The absorption and resonance Raman spectra and excitation profiles of 5,6-dideuterouracil were measured to further test this photochemical dependence on the C5 and C6 substituents. The resulting set of excited-state reorganization energies of the observed internal coordinates were calculated and compared to those of other 5- and 6-substituted uracils. The results show that the initial excited-state dynamics along the C5C6 stretch responds to changes in mass at C5 and C6 in the same manner but that the in-plane bends at C5 and C6 are more sensitive to substituents at the C5 position than at the C6 position. In addition, the presence of two deuterium substituents at C5 and C6 decreases the initial excited-state structural dynamics along these in-plane bends, in contrast to what is observed in the presence of two CH3 groups on C5 and C6. The results are discussed in the context of DNA nucleobase photochemistry.

Fusion protein bilayer fabrication composed of recombinant azurin/cytochrome P450 by the sortase-mediated ligation method

Recently, the fabrication of protein bilayer has been required for the development of protein or enzyme complex formation. In the present study, we fabricated a fusion protein bilayer composed of recombinant azurin-cytochrome P450, which was synthesized by a site-specific sortase-mediated ligation method. The Pseudomonas aeruginosa azurin was modified by DNA recombinant technique, for enzymatic ligation and immobilization. The Pseudomonas putida cytochrome P450 was also modified for enzymatic ligation. The recombinant metalloproteins were conjugated via the sortase A. The conjugation was confirmed by SDS-PAGE and UV-vis. Then, the prepared fusion protein was immobilized on Au substrate, by the self-assembly method. The Azu-P450 (recombinant azurin-cytochrome P450) fusion protein layer was confirmed by AFM (Atomic Force Microscopy) and SERS (Surface-enhanced Raman Spectroscopy), to confirm the fusion protein bilayer orientation. Moreover, the electrochemical property of Azu-P450 was observed by cyclic voltammetry (CV). As a result, the Azu-P450 fusion protein bilayer shows good orientation on the Au substrate. Also, the original redox property of this fusion protein bilayer has been well maintained. The proposed fusion protein bilayer can.

Initial excited-state structural dynamics of thymine derivatives

Thymine is one of the pyrimidine nucleobases found in DNA. Upon absorption of UV light, thymine forms a number of photoproducts, including the cyclobutyl photodimer, the pyrimidine pyrimidinone [6-4] photoproduct and the photohydrate. Here, we use UV resonance Raman spectroscopy to measure the initial excited-state structural dynamics of the N(1)-substituted thymine derivatives N(1)-methylthymine, thymidine, and thymidine 5'-monophosphate in an effort to understand the role of the N1 substituent in determining the excited-state structural dynamics and the subsequent photochemistry. The UV resonance Raman spectrum of thymidine and thymidine 5'-monophosphate are similar to that of thymine, suggesting that large masses at N(1) effectively isolate the vibrations of the nucleobase. However, the UV resonance Raman spectrum of N(1)-methylthymine is significantly different, suggesting that the methyl group couples into the thymine ring vibrations. The resulting resonance Raman intensities and absorption spectra are self-consistently simulated with a time-dependent expression to quantitatively extract the initial excited-state slopes, homogeneous and inhomogeneous linewidths, and electronic parameters. These results are discussed in the context of the known photochemistry of thymine and its derivatives.

Analysis of resonance Raman data on the blue copper site in pseudoazurin: excited state π and σ charge transfer distortions and their relation to ground state reorganization energy

The short Cu(2+)-S(Met) bond in pseudoazurin (PAz) results in the presence of two relatively intense S(p)(π) and S(p)(σ) charge transfer (CT) transitions. This has enabled resonance Raman (rR) data to be obtained for each excited state. The rR data show very different intensity distribution patterns for the vibrations in the 300-500 cm(-1) region. Time-dependent density functional theory (TDDFT) calculations have been used to determine that the change in intensity distribution between the S(p)(π) and S(p)(σ) excited states reflects the differential enhancement of S(Cys) backbone modes with Cu-S(Cys)-C(β) out-of-plane (oop) and in-plane (ip) bend character in their respective potential energy distributions (PEDs). The rR excited state distortions have been related to ground state reorganization energies (λ s) and predict that, in addition to M-L stretches, the Cu-S(Cys)-C(β) oop bend needs to be considered. DFT calculations predict a large distortion in the Cu-S(Cys)-C(β) oop bending coordinate upon reduction of a blue copper (BC) site; however, this distortion is not present in the X-ray crystal structures of reduced BC sites. The lack of Cu-S(Cys)-C(β) oop distortion upon reduction corresponds to a previously unconsidered constraint on the thiolate ligand orientation in the reduced state of BC proteins and can be considered as a contribution to the entatic/rack nature of BC sites.

A review on the fabrication of substrates for surface enhanced Raman spectroscopy and their applications in analytical chemistry

This work reviews different types of substrates used for surface-enhanced Raman scattering (SERS) that have been developed in the last 10 years. The different techniques of self-assembly to immobilize metallic nanoparticles on solid support are covered. An overview of SERS platforms developed using nanolithography methods, including electron-beam (e-beam) lithography and focused ion beam (FIB) milling are also included, together with several examples of template-based methodologies to generate metallic nano-patterns. The potential of SERS to impact several aspects of analytical chemistry is demonstrated by selected examples of applications in electrochemistry, biosensing, environmental analysis, and remote sensing. This review shows that highly enhancing SERS substrates with a high degree of reliability and reproducibility can now be fabricated at relative low cost, indicating that SERS may finally realize its full potential as a very sensitive tool for routine analytical applications.

The role of ligand-containing loops at copper sites in proteins

Many approaches are being used to engineer metalloproteins, with most of these informed by, and aiming to further elucidate, the basic structural requirements for biological metal centers. Cupredoxins are type 1 (T1) copper-containing electron transfer (ET) proteins with a -barrel fold that is thought to constrain metal site structure. The T1 copper ion is bound by ligands mainly originating from a single active site loop whose length and structure varies. This Highlight article will focus on protein engineering studies which have investigated the role of the metal-binding loop for active site integrity and functionality. Scaffold differences are present within the cupredoxin family and their influence has also been assessed. Given the widespread occurrence of -barrel domains in nature, and the array of metal sites in proteins composed of loop regions, the studies described on this model system have implications for a variety of metalloproteins.

Determination of the Fe−CO Bond Energy in Myoglobin Using Heterodyne-Detected Transient Thermal Phase Grating Spectroscopy

The bond energies at active sites of proteins are intimately coupled to the structure-function relationship in biological systems. Due to the unknown nature of the protein relaxation along a reaction coordinate, it has not been possible to directly determine bond energies relevant to protein function. By embedding proteins in trehalose glasses, it is possible to freeze out protein relaxation on short time scales and determine the bond energies of photolabile ligands using photothermal spectroscopies. As a prototypical example, the photodissociation dynamics and energetics of carboxy-myoglobin (MbCO) in a trehalose glass matrix at room temperature were studied by transient absorption (or pump-probe) and transient thermal phase grating spectroscopy to determine the CO recombination dynamics and associated energetics, respectively. Both the initial energetics of the bond breaking and the energy released upon bond reformation could be used, on a time scale faster than significant protein relaxation, to determine the Fe-CO bond energy as 34 +/- 4 kcal/mol. This bond energy is significantly larger than that typically cited (25 kcal/mol) on the basis of indirect measurements but is in good agreement with recent theoretical predictions (35 kcal/mol) (Rovira, C.; Parrinello, M. Int. J. Quantum Chem. 2000, 80, 1172). This result in combination with the theoretical study suggests that protein structure plays a significant role in the bond energies at active sites which in turn provides a tuning element of the effective barrier heights independent to the transition state region.

Ligand and loop variations at type 1 copper sites: influence on structure and reactivity

Type 1 (T1) copper sites promote biological electron transfer and are found in the cupredoxins and a number of copper-containing enzymes including the multi-copper oxidases. A T1 copper site usually has a distorted tetrahedral geometry with strong ligands provided by the thiolate sulfur of a Cys and the imidazole nitrogens of two His residues. The active site structure is typically completed by a weak axial Met ligand (a second weak axial interaction is found in azurin resulting in a trigonal bipyramidal geometry). The axial Met is not conserved and Gln, Phe, Leu and Val are also found in this position. Three of the four ligands at a T1 copper site are situated on a single C-terminal loop whose length and structure varies. Studies are discussed which investigate both the influence of physiologically relevant axial ligand alterations, and also of mutations to the length and structure of the ligand-containing loop, on the properties of T1 copper sites.

Conformation of microcontact-printed proteins by atomic force microscopy molecular sizing

We investigated the structural changes occurring in proteins patterned via microcontact printing. This was done by molecular sizing using atomic force microscopy to observe the structure of printed individual metalloprotein molecules in the unlabeled and untreated states. We observed that the size of the printed proteins were more than 2-fold smaller than the native shape, which indicates that some deformations take place upon the contact-assisted adsorption on silanized silicon dioxide. This can be attributed to simultaneously occurring effects, and particularly to the sandwiching between surfaces of very different hydrophilic/hydrophobic properties during contact lithography.

Single-molecule detection of yeast cytochrome c by Surface-Enhanced Raman Spectroscopy

The giant enhancement of Raman signal near silver colloidal nanoparticles is exploited to study the Raman spectrum of Cytochrome c from Saccharomyces cerevisiae (Yeast Cytochrome c--YCc) in the limit of single-molecule. The investigation is performed on proteins both in solution and immobilised onto a glass slide using a quasi resonant laser line as exciting source with low excitation intensity. In both cases, spectra acquired at different times exhibit dramatic temporal fluctuations in both the total spectrum and in the specific line intensity, even though averaging of several individual spectra reproduces the main Raman features of bulk YCc. Analysis of the spectral intensity fluctuations from solutions reveals a multimodal distribution of some specific Raman lines, consistent with the approaching of single molecule regime. Among other results, the statistical analysis of the spectra from immobilised samples seems to indicate dynamical processes involving the reorientational of the heme with respect to the metal surface.