Toward an Alternative Intrinsic Probe for Spectroscopic Characterization of a Protein

Inhibitory Potential of Carnosine and Aminoguanidine Towards Glycation and Fibrillation of Albumin: In-vitro and Simulation Studies

Carnosine is beta-alanyl histidine, a dipeptide, endogenously produced in our body by the carnosine synthase enzyme. It is an antioxidant, thus protecting from the deleterious effect of advanced glycation end products (AGEs). Similarly, aminoguanidine (AG) also prevents AGEs formation by scavenging free radicals such as reactive oxygen species (ROS)/reactive carbonyl species (RCS). This study used experimental and computational techniques to perform a comparative analysis of carnosine and AG and their inhibiting properties against glycated human serum albumin (HSA). Fructose-mediated glycation of albumin produced fluorescent structures, such as pentosidine and malondialdehyde. These AGEs were significantly reduced by carnosine and AG. At 20 mM, carnosine and AG quenches pentosidine fluorescence by 66% and 83%, respectively. A similar inhibitory effect was observed for malondialdehyde. Protein hydrophobicity and tryptophan fluorescence were restored in the presence of carnosine and AG. Aminoguanidine decreased fibrillation in HSA, while carnosine did not significantly affect aggregation/fibrillation. In addition, molecular docking study observed binding scores of -5.90 kcal/mol and -2.59 kcal/mol by HSA-aminoguanidine and HSA-carnosine complex, respectively. Aminoguanidine forms one conventional hydrogen bond with ARG A:10 and a salt bridge with ASP A:13, ASP A:259, ASP A:255, and ASP A:256 from the amine group. Similarly, carnosine forms only hydrogen bonds with GLU A:501 and GLN A:508 from the amine and hydroxy group. The root mean square deviation (RMSD) calculated from simulation studies was 1 nm upto 70 ns for the HSA-aminoguanidine complex and the spectrum of HSA-carnosine was significantly deviated and not stabilized. The superior inhibitory activity of aminoguanidine could be due to additional salt bridge bonding with albumin. Conclusively, aminoguanidine can be the better treatment choice for diabetes-associated neurological diseases.

Ultrafast Spectroscopic Dynamics of Quinacrine-Riboflavin Binding Protein Interactions

Redox active cofactors play a dynamic role inside protein binding active sites because the amino acids responsible for binding participate in electron transfer (ET) reactions. Here, we use femtosecond transient absorption (FsTA) spectroscopy to examine the ultrafast ET between quinacrine (Qc), an antimalarial drug with potential anticancer activity, and riboflavin binding protein (RfBP) with a known K_d = 264 nM. Steady-state absorption reveals a ∼ 10 nm red-shift in the ground state when QcH₃²⁺ is titrated with RfBP, and a Stern-Volmer analysis shows ∼84% quenching and a blue-shift of the QcH₃²⁺ photoluminescence to form a 1:1 binding ratio of the QcH₃²⁺-RfBP complex. Upon selective photoexcitation of QcH₃²⁺ in the QcH₃²⁺-RfBP complex, we observe charge separation in 7 ps to form ¹[QcH_{3_red}^•+-RfBP^•+], which persists for 138 ps. The FsTA spectra show the spectroscopic identification of QcH_{3_red}^•+, determined from spectroelectrochemical measurements in DMSO. We correlate our results to literature and report lifetimes that are 10-20× slower than the natural riboflavin, Rf-RfBP, complex and are oxygen independent. Driving force (ΔG) calculations, corrected for estimated dielectric constants for protein hydrophobic pockets, and Marcus theory depict a favorable one-electron ET process between QcH₃²⁺ and nearby redox active tyrosine (Tyr) or tryptophan (Trp) residues.

Photostable Copper Nanoclusters: Compatible Förster Resonance Energy-Transfer Assays and a Nanothermometer

To address the concern of material chemists over the issue of stability and photoluminescent (PL) characteristics of Cu nanoclusters (NCs), herein we present an efficient protocol discussing PL Cu NCs (Cu/HSA) having blue emission and high photostability. These PL NCs were illustrated as efficient probes for Förster resonance energy transfer (FRET) with a compatible fluorophore (Coumarin 153). Our spectroscopic results were well complemented by our molecular docking calculations, which also favored our proposed mechanism for Cu NC formation. The beneficial aspect and uniqueness of these nontoxic Cu/HSA NCs highlights their temperature-dependent PL reversibility as well as the reversible FRET with Coumarin 153, which enables them to be used as a nanothermometer and a PL marker for sensitive biological samples.

Bio-NCs--the marriage of ultrasmall metal nanoclusters with biomolecules

Ultrasmall metal nanoclusters (NCs) have attracted increasing attention due to their fascinating physicochemical properties. Today, functional metal NCs are finding growing acceptance in biomedical applications. To achieve a better performance in biomedical applications, metal NCs can be interfaced with biomolecules, such as proteins, peptides, and DNA, to form a new class of biomolecule-NC composites (or bio-NCs in short), which typically show synergistic or novel physicochemical and physiological properties. This feature article focuses on the recent studies emerging at the interface of metal NCs and biomolecules, where the interactions could impart unique physicochemical properties to the metal NCs, as well as mutually regulate biological functions of the bio-NCs. In this article, we first provide a broad overview of key concepts and developments in the novel biomolecule-directed synthesis of metal NCs. A special focus is placed on the key roles of biomolecules in metal NC synthesis. In the second part, we describe how the encapsulated metal NCs affect the structure and function of biomolecules. Followed by that, we discuss several unique synergistic effects observed in the bio-NCs, and illustrate them with examples highlighting their potential biomedical applications. Continued interdisciplinary efforts are required to build up in-depth knowledge about the interfacial chemistry and biology of bio-NCs, which could further pave their ways toward biomedical applications.

Oxidation enhances human serum albumin thermal stability and changes the routes of amyloid fibril formation

Oxidative damages are linked to several aging-related diseases and are among the chemical pathways determining protein degradation. Specifically, interplay of oxidative stress and protein aggregation is recognized to have a link to the loss of cellular function in pathologies like Alzheimer's and Parkinson's diseases. Interaction between protein and reactive oxygen species may indeed induce small changes in protein structure and lead to the inhibition/modification of protein aggregation process, potentially determining the formation of species with different inherent toxicity. Understanding the temperate relationship between these events can be of utmost importance in unraveling the molecular basis of neurodegeneration. In this work, we investigated the effect of hydrogen peroxide oxidation on Human Serum Albumin (HSA) structure, thermal stability and aggregation properties. In the selected conditions, HSA forms fibrillar aggregates, while the oxidized protein undergoes aggregation via new routes involving, in different extents, specific domains of the molecule. Minute variations due to oxidation of single residues affect HSA tertiary structure leading to protein compaction, increased thermal stability, and reduced association propensity.

Protein-encapsulated gold cluster aggregates: the case of lysozyme

We report the evolution and confinement of atomically precise and luminescent gold clusters in a small protein, lysozyme (Lyz) using detailed mass spectrometric (MS) and other spectroscopic investigations. A maximum of 12 Au(0) species could be bound to a single Lyz molecule irrespective of the molar ratio of Lyz : Au(3+) used for cluster growth. The cluster-encapsulated protein also forms aggregates similar to the parent protein. Time dependent studies reveal the emergence of free protein and the redistribution of detached Au atoms, at specific Lyz to Au(3+) molar ratios, as a function of incubation time, proposing inter-protein metal ion transfer. The results are in agreement with the studies of inter-protein metal transfer during cluster growth in similar systems. We believe that this study provides new insights into the growth of clusters in smaller proteins.

Theoretical modeling of large molecular systems. Advances in the local self consistent field method for mixed quantum mechanics/molecular mechanics calculations

Molecular mechanics methods can efficiently compute the macroscopic properties of a large molecular system but cannot represent the electronic changes that occur during a chemical reaction or an electronic transition. Quantum mechanical methods can accurately simulate these processes, but they require considerably greater computational resources. Because electronic changes typically occur in a limited part of the system, such as the solute in a molecular solution or the substrate within the active site of enzymatic reactions, researchers can limit the quantum computation to this part of the system. Researchers take into account the influence of the surroundings by embedding this quantum computation into a calculation of the whole system described at the molecular mechanical level, a strategy known as the mixed quantum mechanics/molecular mechanics (QM/MM) approach. The accuracy of this embedding varies according to the types of interactions included, whether they are purely mechanical or classically electrostatic. This embedding can also introduce the induced polarization of the surroundings. The difficulty in QM/MM calculations comes from the splitting of the system into two parts, which requires severing the chemical bonds that link the quantum mechanical subsystem to the classical subsystem. Typically, researchers replace the quantoclassical atoms, those at the boundary between the subsystems, with a monovalent link atom. For example, researchers might add a hydrogen atom when a C-C bond is cut. This Account describes another approach, the Local Self Consistent Field (LSCF), which was developed in our laboratory. LSCF links the quantum mechanical portion of the molecule to the classical portion using a strictly localized bond orbital extracted from a small model molecule for each bond. In this scenario, the quantoclassical atom has an apparent nuclear charge of +1. To achieve correct bond lengths and force constants, we must take into account the inner shell of the atom: for an sp(3) carbon atom, we consider the two core 1s electrons and treat that carbon as an atom with three electrons. This results in an LSCF+3 model. Similarly, a nitrogen atom with a lone pair of electrons available for conjugation is treated as an atom with five electrons (LSCF+5). This approach is particularly well suited to splitting peptide bonds and other bonds that include carbon or nitrogen atoms. To embed the induced polarization within the calculation, researchers must use a polarizable force field. However, because the parameters of the usual force fields include an average of the induction effects, researchers typically can obtain satisfactory results without explicitly introducing the polarization. When considering electronic transitions, researchers must take into account the changes in the electronic polarization. One approach is to simulate the electronic cloud of the surroundings by a continuum whose dielectric constant is equal to the square of the refractive index. This Electronic Response of the Surroundings (ERS) methodology allows researchers to model the changes in induced polarization easily. We illustrate this approach by modeling the electronic absorption of tryptophan in human serum albumin (HSA).

Protein-directed synthesis of NIR-emitting, tunable HgS quantum dots and their applications in metal-ion sensing

The development of luminescent mercury sulfide quantum dots (HgS QDs) through the bio-mineralization process has remained unexplored. Herein, a simple, two-step route for the synthesis of HgS quantum dots in bovine serum albumin (BSA) is reported. The QDs are characterized by UV-vis spectroscopy, Fourier transform infrared (FT-IR) spectroscopy, luminescence, Raman spectroscopy, transmission electron microscopy (TEM), X-ray photoelectron spectroscopy (XPS), circular dichroism (CD), energy dispersive X-ray analysis (EDX), and picosecond-resolved optical spectroscopy. Formation of various sizes of QDs is observed by modifying the conditions suitably. The QDs also show tunable luminescence over the 680-800 nm spectral regions, with a quantum yield of 4-5%. The as-prepared QDs can serve as selective sensor materials for Hg(II) and Cu(II), based on selective luminescence quenching. The quenching mechanism is found to be based on Dexter energy transfer and photoinduced electron transfer for Hg(II) and Cu(II), respectively. The simple synthesis route of protein-capped HgS QDs would provide additional impetus to explore applications for these materials.

Development of an anti-influenza drug screening assay targeting nucleoproteins with tryptophan fluorescence quenching

Recent studies have shown that NP (nucleoprotein), which possesses multiple functions in the viral life cycle, is a new potential anti-influenza drug target. NP inhibitors reliably induce conformational changes in NPs, and these changes may confer inhibition of the influenza virus. The six conserved tryptophan residues in NP can be used as an intrinsic probe to monitor the change in fluorescence of the tryptophan residues in the protein upon binding to an NP inhibitor. In the present study, we found that the fluorescence of recombinant NP proteins was quenched following the binding of available NP inhibitors (such as nucleozin) in a concentration- and time-dependent manner, which suggests that the inhibitor induced conformational changes in the NPs. The minimal fluorescence-quenching effect and weak binding constant of nucleozin to the swine-origin influenza virus H1N1pdm09 (SOIV) NP revealed that the SOIV is resistant to nucleozin. We have used the fluorescence-quenching property of tryptophans in NPs that were bound to ligands in a 96-well-plate-based drug screen to assess the ability of promising small molecules to interact with NPs and have identified one new anti-influenza drug, CSV0C001018, with a high SI value. This convenient method for drug screening may facilitate the development of antiviral drugs that target viruses other than the influenza virus, such as HIV and HBV.

Protein-protected luminescent noble metal quantum clusters: an emerging trend in atomic cluster nanoscience

Noble metal quantum clusters (NMQCs) are the missing link between isolated noble metal atoms and nanoparticles. NMQCs are sub-nanometer core sized clusters composed of a group of atoms, most often luminescent in the visible region, and possess intriguing photo-physical and chemical properties. A trend is observed in the use of ligands, ranging from phosphines to functional proteins, for the synthesis of NMQCs in the liquid phase. In this review, we briefly overview recent advancements in the synthesis of protein protected NMQCs with special emphasis on their structural and photo-physical properties. In view of the protein protection, coupled with direct synthesis and easy functionalization, this hybrid QC-protein system is expected to have numerous optical and bioimaging applications in the future, pointers in this direction are visible in the literature.

Understanding the evolution of luminescent gold quantum clusters in protein templates

We show that the time-dependent biomineralization of Au(3+) by native lactoferrin (NLf) and bovine serum albumin (BSA) resulting in near-infrared (NIR) luminescent gold quantum clusters (QCs) occurs through a protein-bound Au(1+) intermediate and subsequent emergence of free protein. The evolution was probed by diverse tools, principally, using matrix-assisted laser desorption ionization mass spectrometry (MALDI MS), X-ray photoelectron spectroscopy (XPS), and photoluminescence spectroscopy (PL). The importance of alkaline pH in the formation of clusters was probed. At neutral pH, a Au(1+)-protein complex was formed (starting from Au(3+)) with the binding of 13-14 gold atoms per protein. When the pH was increased above 12, these bound gold ions were further reduced to Au(0) and nucleation and growth of cluster commenced, which was corroborated by the beginning of emission; at this point, the number of gold atoms per protein was ~25, suggesting the formation of Au(25). During the cluster evolution, at certain time intervals, for specific molar ratios of gold and protein, occurrence of free protein was noticed in the mass spectra, suggesting a mixture of products and gold ion redistribution. By providing gold ions at specific time of the reaction, monodispersed clusters with enhanced luminescence could be obtained, and the available quantity of free protein could be utilized efficiently. Monodispersed clusters would be useful in obtaining single crystals of protein-protected noble metal quantum clusters where homogeneity of the system is of primary concern.

Slow solvent relaxation dynamics of nanometer sized reverse micellar systems through tryptophan metabolite, kynurenine

Exploration of environmental dynamics using intrinsic biological probe tryptophan is very important; however, it suffers from various difficulties. An alternative probe, kynurenine (KN), has been found to be an efficient probe for the ultrafast dynamics in the biological environment (Goswami et al., [2010] J. Phys. Chem. B., 114, 15236-15243). In the present study, we have investigated the efficacy of KN for the exploration of relatively slower dynamics of biologically relevant environments. A detailed investigation involving UV-Vis, steady-state/time-resolved fluorescence spectroscopy and Förster resonance energy transfer (FRET) studies on KN compared to a well-known solvation probe, H33258, a DNA-minor groove binder in a model nonionic reverse micelle reveals that ultrafast internal conversion associated with the hydrogen-bonding dynamics masks KN to become a dynamical reporter of the immediate environments of the probe.