Krishnananda Chattopadhyay

A Facile Synthesis of PEG-Coated Magnetite (Fe3O4) Nanoparticles and Their Prevention of the Reduction of Cytochrome C

We report here a facile and green synthetic approach to prepare magnetite (Fe(3)O(4)) nanoparticles (NPs) with magnetic core and polyethylene glycol (PEG) surface coating. The interaction of the bare and PEG-coated Fe(3)O(4) NPs with cytochrome c (cyt c, an important protein with direct role in the electron transfer chain) is also reported in this study. With ultrasonication as the only peptization method and water as the synthesis medium, this method is easy, fast, and environmentally benign. The PEG coated NPs are highly water dispersible and stable. The bare NPs have considerable magnetism at room temperature; surface modification by PEG has resulted in softening the magnetization. This approach can very well be applicable to prepare biocompatible, surface-modified soft magnetic materials, which may offer enormous utility in the field of biomedical research. Detailed characterizations including XRD, FTIR, TG/DTA, TEM, and VSM of the PEG-coated Fe(3)O(4) NPs were carried out in order to ensure the future applicability of this method. Although the interaction of bare NPs with cyt c shows reduction of the protein, efficient surface modification by PEG prevents its reduction.

Measurement of microsecond dynamic motion in the intestinal fatty acid binding protein by using fluorescence correlation spectroscopy

Fluorescence correlation spectroscopy (FCS) measurements have been carried out on the intestinal fatty acid binding protein (IFABP) to study microsecond dynamics of the protein in its native state as well as in pH-induced intermediates. IFABP is a small (15 kDa) protein that consists mostly of antiparallel β-strands enclosing a large central cavity into which the ligand binds. Because this protein does not contain cysteine, two cysteine mutants (Val60Cys and Phe62Cys) have been prepared and covalently modified with fluorescein. Based on fluorescence measurements, one of the mutants (Val60Flu) has the fluorescein moiety inside the cavity of the protein, whereas the fluorescein is exposed to solvent in the other (Phe62Flu). The protein modified at position 60 demonstrates the presence of a conformational event on the order of 35 μsec, which is not seen in the other mutant (Phe62Flu). The amplitude of this fast conformational event decreases sharply at low pH as the protein unfolds. Experiments measuring the diffusion as a function of pH indicate the formation of a compact state distinct from the native state at about pH 3.5. Steady state fluorescence and far-UV CD indicates that unfolding occurs at pH values below pH 3.

Effect of arginine on protein aggregation studied by fluorescence correlation spectroscopy and other biophysical methods.

Arginine has been used extensively as an excipient in the formulation development of protein-based biopharmaceuticals. We investigate the role of arginine in suppressing protein aggregation and its mechanism by using bovine serum albumin as a model system. By using sedimentation velocity and other analytical techniques, we show that the use of arginine inhibits temperature-induced aggregation of the protein. We use fluorescence correlation spectroscopy and other spectroscopic techniques to show that arginine inhibits accumulation of partially folded intermediates, potentially involved in the aggregation process. The hydrodynamic radii of the protein in its native, unfolded, and intermediate states have been determined using fluorescence correlation spectroscopy at single-molecule resolution. A possible mechanism of the effects of arginine and its role as an aggregation suppressor has been discussed.

Direct electrochemistry of heme proteins: effect of electrode surface modification by neutral surfactants

Direct electrochemical studies on horse heart myoglobin and horseradish peroxidase (HRP) have been carried out using tin-doped indium oxide (ITO) and surfactant modified glassy carbon working electrodes. These proteins show very slow electron transfer kinetics at metal or untreated electrodes. Moreover, small amounts of surface-active impurity were drastically affects the electrode reaction of these proteins. The results showed that modification of the electrode surface with neutral surfactants significantly improves the electrochemical response of myoglobin as well as of HRP. The electrode response was found to depend on the structure of the surfactants. The amount of surfactant required per unit area of the electrode surface to promote the maximum electron transfer rate constants was found to be constant. This indicated that the surfactant molecules interacted with the electrode surface in a specific manner and anchored the protein molecules to align in the suitable orientation. The hydrophobicity of the surfactants rather than their charge was found to be crucial in promoting the electrode response of these proteins at the glassy carbon electrode.

Role of Protein Stabilizers on the Conformation of the Unfolded State of Cytochrome c and Its Early Folding Kinetics INVESTIGATION AT SINGLE MOLECULAR RESOLUTION

An insight into the conformation and dynamics of unfolded and early intermediate states of a protein is essential to understand the mechanism of its aggregation and to design potent inhibitor molecules. Fluorescence correlation spectroscopy has been used to study the effects of several model protein stabilizers on the conformation of the unfolded state and early folding dynamics of tetramethyl rhodamine-labeled cytochrome c from Saccharomyces cerevisiae at single molecular resolution. Special attention has been given to arginine, which is a widely used stabilizer for improving refolding yield of different proteins. The value of the hydrodynamic radius (rH) obtained by analyzing the intensity fluctuations of the diffusing molecules has been found to increase in a two-state manner as the protein is unfolded by urea. The results further show that the presence of arginine and other protein stabilizers favors a relatively structured conformation of the unfolded states (rH of 29 Å) over an extended one (rH of 40 Å), which forms in their absence. Also, the time constant of a kinetic component (τR) of about 30 μs has been observed by analyzing the correlation functions, which represents formation of a collapsed state. This time constant varies with urea concentration representing an inverted Chevron plot that shows a roll-over and behavior in the absence of arginine. To the best of our knowledge, this is one of the first applications of fluorescence correlation spectroscopy to study direct folding kinetics of a protein.

Ag−TiO2 Nanoparticle Codoped SiO2 Films on ZrO2 Barrier-Coated Glass Substrates with Antibacterial Activity in Ambient Condition

Anatase TiO2 and Ag nanoparticles (NPs) codoped SiO2 films were prepared by the sol-gel method. Proportionate amounts of 3-(glycidoxypropyl)trimethoxysilane (GLYMO), tetraethylorthosilicate (TEOS) and 3-(methacryloxypropyl)trimethoxysilane (MEMO) derived inorganic-organic silica sol, commercially available dispersed anatase TiO2 NPs, and AgNO3 were used to prepare the sols. The films were prepared on ZrO2 (cubic) precoated soda-lime glass substrates by a single-dipping technique and heat-treated at 450 °C in air and H2/Ar atmosphere to obtain hard, relatively porous, and transparent coatings of thickness>600 nm. The ZrO2 barrier layer was previously applied on soda-lime glass to restrict the diffusion of Ag into the substrate. The Ag-TiO2 NPs incorporated SiO2 films were intense yellow in color and found to be fairly stable at ambient condition for several days under fluorescent light. These films show a considerable growth inhibition on contact with the gram negative bacteria E. coli.

What fluorescence correlation spectroscopy can tell us about unfolded proteins

Publisher Summary Fluorescence correlation spectroscopy (FCS) measures rates of diffusion, chemical reaction, and other dynamic processes of fluorescent molecules. Studies of unfolded proteins benefit from the fact that FCS can provide information about rates of protein conformational change both by a direct readout from conformation-dependent fluorescence changes and by changes in diffusion coefficient. Although the diffusion coefficient is relatively insensitive to protein conformation changes, it can be measured with high accuracy by FCS and so can be useful for monitoring structural changes that occur as the protein passes among partially unfolded states. As the protein takes on more compact or more extended conformations, the hydrodynamic radius and consequently the diffusion coefficient change correspondingly; if these changes are large enough, they can be observed in FCS measurements. Among kinetics approaches used to study dynamics within the unfolded state, FCS is closely related to relaxation methods in which small free energy perturbations displace the equilibrium point of a reaction system. The kinetic parameters are deduced from the rate of relaxation to the new equilibrium.

Interconnection of Salt-induced Hydrophobic Compaction and Secondary Structure Formation Depends on Solution Conditions REVISITING EARLY EVENTS OF PROTEIN FOLDING AT SINGLE MOLECULE RESOLUTION

Background: Early events of protein folding are difficult to follow. Results: The unfolded state may have extended and compact conformers, which interconvert at early microsecond. Conclusion: Hydrophobic compaction and secondary structure formation do not occur simultaneously in aqueous solution. They occur simultaneously in the presence of urea. Significance: Hydrophobic collapse has been monitored at single molecular resolution. What happens in the early stage of protein folding remains an interesting unsolved problem. Rapid kinetics measurements with cytochrome c using submillisecond continuous flow mixing devices suggest simultaneous formation of a compact collapsed state and secondary structure. These data seem to indicate that collapse formation is guided by specific short and long range interactions (heteropolymer collapse). A contrasting interpretation also has been proposed, which suggests that the collapse formation is rapid, nonspecific, and a trivial solvent related compaction, which could as well be observed by a homopolymer (homopolymer collapse). We address this controversy using fluorescence correlation spectroscopy (FCS), which enables us to monitor the salt-induced compaction accompanying collapse formation and the associated time constant directly at single molecule resolution. In addition, we follow the formation of secondary structure using far UV CD. The data presented here suggest that both these models (homopolymer and heteropolymer) could be applicable depending on the solution conditions. For example, the formation of secondary structure and compact state is not simultaneous in aqueous buffer. In aqueous buffer, formation of the compact state occurs through a two-state co-operative transition following heteropolymer formalism, whereas secondary structure formation takes place gradually. In contrast, in the presence of urea, a compaction of the protein radius occurs gradually over an extended range of salt concentration following homopolymer formalism. The salt-induced compaction and the formation of secondary structure take place simultaneously in the presence of urea.

Subtle change in the charge distribution of surface residues may affect the secondary functions of cytochrome c

Background: The cardiolipin (CDL) binding and the peroxidase activity of cytochrome c (cyt c) vary with the protein source. Results: The CDL binding and the peroxidase activity of cyt c depend on conformational heterogeneity and oligomerization. Conclusion: Subtle variations in the surface residues of cyt c influence its conformational dynamics and stability. Significance: Secondary functions of cyt c have been studied at single-molecule resolution. Although the primary function of cytochrome c (cyt c) is electron transfer, the protein caries out an additional secondary function involving its interaction with membrane cardiolipin (CDL), its peroxidase activity, and the initiation of apoptosis. Whereas the primary function of cyt c is essentially conserved, its secondary function varies depending on the source of the protein. We report here a detailed experimental and computational study, which aims to understand, at the molecular level, the difference in the secondary functions of cyt c obtained from horse heart (mammalian) and Saccharomyces cerevisiae (yeast). The conformational landscape of cyt c has been found to be heterogeneous, consisting of an equilibrium between the compact and extended conformers as well as the oligomeric species. Because the determination of relative populations of these conformers is difficult to obtain by ensemble measurements, we used fluorescence correlation spectroscopy (FCS), a method that offers single-molecule resolution. The population of different species is found to depend on multiple factors, including the protein source, the presence of CDL and urea, and their concentrations. The complex interplay between the conformational distribution and oligomerization plays a crucial role in the variation of the pre-apoptotic regulation of cyt c observed from different sources. Finally, computational studies reveal that the variation in the charge distribution at the surface and the charge reversal sites may be the key determinant of the conformational stability of cyt c.

The Presence of the Iron-Sulfur Motif Is Important for the Conformational Stability of the Antiviral Protein, Viperin

Viperin, an antiviral protein, has been shown to contain a CX3CX2C motif, which is conserved in the radical S-adenosyl-methionine (SAM) enzyme family. A triple mutant which replaces these three cysteines with alanines has been shown to have severe deficiency in antiviral activity. Since the crystal structure of Viperin is not available, we have used a combination of computational methods including multi-template homology modeling and molecular dynamics simulation to develop a low-resolution predicted structure. The results show that Viperin is an α -β protein containing iron-sulfur cluster at the center pocket. The calculations suggest that the removal of iron-sulfur cluster would lead to collapse of the protein tertiary structure. To verify these predictions, we have prepared, expressed and purified four mutant proteins. In three mutants individual cysteine residues were replaced by alanine residues while in the fourth all the cysteines were replaced by alanines. Conformational analyses using circular dichroism and steady state fluorescence spectroscopy indicate that the mutant proteins are partially unfolded, conformationally unstable and aggregation prone. The lack of conformational stability of the mutant proteins may have direct relevance to the absence of their antiviral activity.