Methods to investigate nucleosome structure and dynamics with single-molecule FRET.

The nucleosome is the fundamental building block of chromatin. Changes taking place at the nucleosome level are the molecular basis of chromatin transactions with various enzymes and factors. These changes are directly and indirectly regulated by chromatin modifications such as DNA methylation and histone post-translational modifications including acetylation, methylation, and ubiquitylation. Nucleosomal changes are often stochastic, unsynchronized, and heterogeneous, making it very difficult to monitor with traditional ensemble averaging methods. Diverse single-molecule fluorescence approaches have been employed to investigate the structure and structural changes of the nucleosome in the context of its interactions with various enzymes such as RNA Polymerase II, histone chaperones, transcription factors, and chromatin remodelers. We utilize diverse single-molecule fluorescence methods to study the nucleosomal changes accompanying these processes, elucidate the kinetics of these processes, and eventually learn the implications of various chromatin modifications in directly regulating these processes. The methods include two- and three-color single-molecule fluorescence resonance energy transfer (FRET), single-molecule fluorescence correlation spectroscopy, and fluorescence (co-)localization. Here we report the details of the two- and three-color single-molecule FRET methods we currently use. This report will help researchers design their single-molecule FRET approaches to investigating chromatin regulation at the nucleosome level.

The Effects of Histone H2B Ubiquitylations on the Nucleosome Structure and Internucleosomal Interactions.

Eukaryotic gene compaction takes place at multiple levels to package DNA to chromatin and chromosomes. Two of the most fundamental levels of DNA packaging are at the nucleosome and dinucleosome stacks. The nucleosome is the basic gene-packing unit and is composed of DNA wrapped around a histone core. Nucleosomes stack with one another for further compaction of DNA. The first stacking step leads to dinucleosome formation, which is driven by internucleosomal interactions between various parts of two nucleosomes. Histone proteins are rich targets for post-translational modifications, some of which affect the structure of the nucleosome and the interactions between nucleosomes. These effects are often implicated in the regulation of various genomic transactions. In particular, histone H2B ubiquitylation has been associated with facilitated transcription and hexasome formation. Here, we employed semi-synthetically ubiquitylated histone H2B and single-molecule FRET to investigate the effects of H2B ubiquitylations at lysine 34 (H2BK34) and lysine 120 (H2BK120) on the structure of the nucleosome and the interactions between two nucleosomes. Our results suggest that H2BK34 ubiquitylation widens the DNA gyre gap in the nucleosome and stabilizes long- and short-range internucleosomal interactions while H2BK120 ubiquitylation does not affect the nucleosome structure or internucleosomal interactions. These results suggest potential roles for H2B ubiquitylations in facilitated transcription and hexasome formation while maintaining the structural integrity of chromatin.

PCNA Monoubiquitination Is Regulated by Diffusion of Rad6/Rad18 Complexes along RPA Filaments.

Translesion DNA synthesis (TLS) enables DNA replication through damaging modifications to template DNA and requires monoubiquitination of the proliferating cell nuclear antigen (PCNA) sliding clamp by the Rad6/Rad18 complex. This posttranslational modification is critical to cell survival following exposure to DNA-damaging agents and is tightly regulated to restrict TLS to damaged DNA. Replication protein A (RPA), the major single-strand DNA (ssDNA) binding protein complex, forms filaments on ssDNA exposed at TLS sites and plays critical yet undefined roles in regulating PCNA monoubiquitination. Here, we utilize kinetic assays and single-molecule FRET microscopy to monitor PCNA monoubiquitination and Rad6/Rad18 complex dynamics on RPA filaments, respectively. Results reveal that a Rad6/Rad18 complex is recruited to an RPA filament via Rad18·RPA interactions and randomly translocates along the filament. These translocations promote productive interactions between the Rad6/Rad18 complex and the resident PCNA, significantly enhancing monoubiquitination. These results illuminate critical roles of RPA in the specificity and efficiency of PCNA monoubiquitination and represent, to the best of our knowledge, the first example of ATP-independent translocation of a protein complex along a protein filament.

Monomerization and aggregation of ß-lactoglobulin under adverse condition: A fluorescence correlation spectroscopic investigation.

ß-Lactoglobulin is one of the major components of bovine milk and it remains in a dimeric form under physiological conditions. The present contribution elucidates the structural change of ß-lactoglobulin at pH7.4 under the action of guanidine hydrochloride (GnHCl) and heat at the single molecular level. The only free cysteine (Cys-121) of ß-lactoglobulin has been tagged with 7-diethylamino-3-(4-maleimidophenyl)-4-methylcoumarin (CPM) for this purpose. The dimeric structure of ß-lactoglobulin found to undergoes a monomerization prior to the unfolding process upon being subjected to GnHCl. The hydrodynamic diameter of the native dimer, native monomer and the unfolded monomer has been estimated as ~55Å, ~29Å and ~37Å, respectively. The free energy change for the monomerization and denaturation are respectively 1.57kcalmol-1 and 8.93kcalmol-1. With change in temperature, development of two types of aggregates (small aggregates and large aggregates) was observed, which is triggered by the formation of the monomeric structure of ß-lactoglobulin. The hydrodynamic diameters of the smaller and larger aggregates have been estimated to be ~77Å and ~117Å, respectively. The formation of small aggregates turns out to be reversible whereas that of larger aggregates is irreversible. The free energy associated with these two steps are 0.69kcalmol-1 and 9.09kcalmol-1. Based on the size parameters, the smaller and larger aggregates have been proposed to contain ~twenty and ~sixty monomeric units. It has also been concluded that the monomeric subunits retain their native like secondary structure in these aggregates.

Calmidazolium Chloride and Its Complex with Serum Albumin Prevent Huntingtin Exon1 Aggregation.

Huntington's disease (HD) is a genetic disorder caused by a CAG expansion mutation in Huntingtin gene leading to polyglutamine (polyQ) expansion in the N-terminus side of Huntingtin (Httex1) protein. Neurodegeneration in HD is linked to aggregates formed by Httex1 bearing an expanded polyQ. Initiation and elongation steps of Httex1 aggregation are potential target steps for the discovery of therapeutic molecules for HD, which is currently untreatable. Here we report Httex1 aggregation inhibition by calmidazolium chloride (CLC) by acting on the initial aggregation event. Because it is hydrophobic, CLC was adsorbed to the vial surface and could not sustain an inhibition effect for a longer duration. The use of bovine serum albumin (BSA) prevented CLC adsorption by forming a BSA-CLC complex. This complex showed improved Httex1 aggregation inhibition by interacting with the aggregation initiator, the NT17 part of Httex1. Furthermore, biocompatible CLC-loaded BSA nanoparticles were made which reduced the polyQ aggregates in HD-150Q cells.

Differential lipid metabolism in monocytes and macrophages: influence of cholesterol loading.

The influence of the hypercholesterolemia associated with atherosclerosis on monocytes is poorly understood. Monocytes are exposed to high concentrations of lipids, particularly cholesterol and lysophosphatidylcholine (lyso-PC). Indeed, in line with recent reports, we found that monocytes accumulate cholesteryl esters (CEs) in hypercholesterolemic mice, demonstrating the need for studies that analyze the effects of lipid accumulation on monocytes. Here we analyze the effects of cholesterol and lyso-PC loading in human monocytes and macrophages. We found that cholesterol acyltransferase and CE hydrolase activities are lower in monocytes. Monocytes also showed a different expression profile of cholesterol influx and efflux genes in response to lipid loading and a different pattern of lyso-PC metabolism. In monocytes, increased levels of CE slowed the conversion of lyso-PC into PC. Interestingly, although macrophages accumulated glycerophosphocholine, phosphocholine was the main water-soluble choline metabolite being generated in monocytes, suggesting a role for mono- and diacylglycerol in the chemoattractability of these cells. In summary, monocytes and macrophages show significant differences in lipid metabolism and gene expression profiles in response to lipid loading. These findings provide new insights into the mechanisms of atherosclerosis and suggest potentials for targeting monocyte chemotactic properties not only in atherosclerosis but also in other diseases.

Startling temperature effect on proteins when confined: single molecular level behaviour of human serum albumin in a reverse micelle.

The present work reports the effect of confinement, and temperature therein, on the conformational fluctuation dynamics of domain-I of human serum albumin (HSA) by fluorescence correlation spectroscopy (FCS). The water-pool of a sodium bis(2-ethylhexyl)sulfosuccinate (AOT) reverse micelle has been used as the confined environment. It was observed that the conformational fluctuation time is about 6 times smaller compared to bulk medium when confined in a water-pool of 3.5 nm radius. On increasing the size of the water-pool the conformational fluctuation time was found to increase monotonically and approaches the bulk value. The effect of confinement is on par with the general belief about the restricted motion of a macromolecule upon confinement. However, the effect of temperature was found to be surprising. An increase in the temperature from 298 K to 313 K induces a larger change in the conformational fluctuation time in HSA, when confined. In the bulk medium, apparently there is no change in the conformational fluctuation time in the aforementioned temperature range, whereas, when HSA is present in an AOT water-pool of radius 3.5 nm, about an 88% increase in the fluctuation time was observed. The observed prominent thermal effect on the conformational dynamics of domain-I of HSA in the water-pool of an AOT reverse micelle as compared to in the bulk medium was concluded to arise from the confined solvent effect.

Elucidation of the local dynamics of domain-III of human serum albumin over the ps-µs time regime using a new fluorescent label.

The ps-µs dynamics of domain-III of human serum albumin (HSA) has been investigated using a new fluorescent marker selectively labeled to the Tyr-411 residue. The location of the marker has been confirmed using Förster resonance energy transfer (FRET) study. Steady state, time-resolved and single molecular level fluorescence techniques have been employed to understand the dynamics within the domain-III of HSA. It is found that solvent reorganization dynamics in domain-III is 1.7 times faster than that in domain-I. The timescale of the local rotational dynamics of domain-III is found to be 2.3 times faster than that of domain-I. Fluorescence correlation spectroscopic experiments reveal that domain-III of HSA has more conformational flexibility than domain-I. Together, the results deliver useful details of the local environment around the domain-III of HSA, which have not been explored earlier, mainly because of a lack of a suitable fluorescent marker for domain-III. The newly synthesized probe serves well as a site specific fluorescent marker for HSA, and can be used for further investigation of the ligand binding properties and enzymatic activity of domain-III of HSA.

A next-generation BRAF inhibitor overcomes resistance to BRAF inhibition in patients with BRAF-mutant cancers using pharmacokinetics-informed dose escalation.

RAF inhibitors have transformed treatment for BRAF V600-mutant cancer patients, but clinical benefit is limited by adaptive induction of ERK signaling, genetic alterations that induce BRAF V600 dimerization, and poor brain penetration. Next-generation pan-RAF dimer inhibitors are limited by narrow therapeutic index. PF-07799933 (ARRY-440) is a brain-penetrant, selective, pan-mutant BRAF inhibitor. PF-07799933 inhibited signaling in vitro, disrupted endogenous mutant-BRAF:wild-type-CRAF dimers, and spared wild-type ERK signaling. PF-07799933 ± binimetinib inhibited growth of mouse xenograft tumors driven by mutant BRAF that functions as dimers and by BRAF V600E with acquired resistance to current RAF inhibitors. We treated patients with treatment-refractory BRAF-mutant solid tumors in a first-in-human clinical trial (NCT05355701) that utilized a novel, flexible, pharmacokinetics-informed dose escalation design that allowed rapid achievement of PF-07799933 efficacious concentrations. PF-07799933 ± binimetinib was well-tolerated and resulted in multiple confirmed responses, systemically and in the brain, in BRAF-mutant cancer patients refractory to approved RAF inhibitors.

Novel technique for generating macrophage foam cells for in vitro reverse cholesterol transport studies.

Generation of foam cells, an essential step for reverse cholesterol transport studies, uses the technique of receptor-dependent macrophage loading with radiolabeled acetylated LDL. In this study, we used the ability of a biologically relevant detergent molecule, lysophosphatidylcholine (lyso-PtdCho), to form mixed micelles with cholesterol or cholesteryl ester (CE) to generate macrophage foam cells. Fluorescent or radiolabeled cholesterol/lyso-PtdCho mixed micelles were prepared and incubated with RAW 264.7 or mouse peritoneal macrophages. Results showed that such micelles were quite stable at 4°C and retained the solubilized cholesterol during one month of storage. Macrophages incubated with cholesterol or CE (unlabeled, fluorescently labeled, or radiolabeled)/lyso-PtdCho mixed micelles accumulated CE as documented by microscopy, lipid staining, labeled oleate incorporation, and by TLC. Such foam cells unloaded cholesterol when incubated with HDL but not with oxidized HDL. We propose that stable cholesterol or CE/lyso-PtdCho micelles would offer advantages over existing methods.

Effects of Histone H2B Ubiquitylations and H3K79me3 on Transcription Elongation.

Post-translational modifications of histone proteins often mediate gene regulation by altering the global and local stability of the nucleosome, the basic gene-packing unit of eukaryotes. We employed semisynthetic approaches to introduce histone H2B ubiquitylations at K34 (H2BK34ub) and K120 (H2BK120ub) and H3K79 trimethylation (H3K79me3). With these modified histones, we investigated their effects on the kinetics of transcription elongation by RNA polymerase II (Pol II) using single-molecule FRET. Pol II pauses at several locations within the nucleosome for a few seconds to minutes, which governs the overall transcription efficiency. We found that H2B ubiquitylations suppress pauses and shorten the pause durations near the nucleosome entry while H3K79me3 shortens the pause durations and increases the rate of RNA elongation near the center of the nucleosome. We also found that H2BK34ub facilitates partial rewrapping of the nucleosome upon Pol II passage. These observations suggest that H2B ubiquitylations promote transcription elongation and help maintain the chromatin structure by inducing and stabilizing nucleosome intermediates and that H3K79me3 facilitates Pol II progression possibly by destabilizing the local structure of the nucleosome. Our results provide the mechanisms of how these modifications coupled by a network of regulatory proteins facilitate transcription in two different regions of the nucleosome and help maintain the chromatin structure during active transcription.

The Effects of Histone H2B ubiquitylations and H3K79me 3 on Transcription Elongation.

Post-translational modifications of histone proteins often mediate gene regulation by altering the global and local stability of the nucleosome, the basic gene-packing unit of eukaryotes. We employed semi-synthetic approaches to introduce histone H2B ubiquitylations at K34 (H2BK34ub) and K120 (H2BK120ub) and H3 K79 trimethylation (H3K79me3). With these modified histones, we investigated their effects on the kinetics of transcription elongation by RNA Polymerase II (Pol II) using single-molecule FRET. Pol II pauses at several locations within the nucleosome for a few seconds to minutes, which governs the overall transcription efficiency. We found that H2B ubiquitylations suppress pauses and shorten the pause durations near the nucleosome entry while H3K79me3 shortens the pause durations and increases the rate of RNA elongation near the center of the nucleosome. We also found that H2BK34ub facilitates partial rewrapping of the nucleosome upon Pol II passage. These observations suggest that H2B ubiquitylations promote transcription elongation and help maintain the chromatin structure by inducing and stabilizing nucleosome intermediates and that H3K79me3 facilitates Pol II progression possibly by destabilizing the local structure of the nucleosome. Our results provide the mechanisms of how these modifications coupled by a network of regulatory proteins facilitate transcription in two different regions of the nucleosome and help maintain the chromatin structure during active transcription.

Clinicopathological investigation of secretory carcinoma cases including a successful treatment outcome using entrectinib for high-grade transformation: a case report.

BACKGROUND: Secretory carcinoma (SC) of the salivary gland is a recently described malignant tumor harboring characteristic ETV6-NTRK3 gene fusion. SC generally has a favorable clinical course, and is currently regarded as a low-grade carcinoma. However, a small subset of SCs demonstrates aggressive clinical features with histologically high-grade transformed morphology, the molecular pathogenesis of which has not yet been elucidated. In this study, we performed a clinicopathological and molecular genetic study of patients with SC of the head and neck displaying various clinical characteristics to investigate the differences of pathological and molecular genetics between low-grade and high-grade components of SC. CASE PRESENTATION: Three cases with SC of the head and neck, including a conventional low-grade SC and two high-grade transformed SCs are described. High-grade transformed SCs with histological features such as nuclear polymorphism, distinctive nucleoli and increased mitotic activity developed locoregional recurrence and distant metastasis. Immunohistochemical analysis revealed that low- and high-grade components showed different expression patterns for S-100 protein and mammaglobin, whereas all examined components were positive for p-STAT5. p53-positive cell population was markedly higher in one case with high-grade transformed SC. The proliferative activity of high-grade components was markedly increased, with the Ki-67 labeling index ranging up to 30-32%. A fluorescence in situ hybridization study with an ETV6 (12p13) break apart probe revealed split signals in the nuclei in all 3 cases. A targeted next-generation sequencing-based fusion assay demonstrated that all 6 clinical samples from the 3 patients showed the presence of the ETV6-NTRK3 fusion transcripts. One patient with high-grade transformed SC showed a dramatic clinical response to the pan-TRK inhibitor, entrectinib, for the treatment of locoregional recurrence and pulmonary metastasis. CONCLUSIONS: High-grade transformed SC showed aggressive clinical and pathological features with increased Ki-67 labeling index. Molecular genetic study of gene rearrangement appears to be beneficial treatment as the presence of ETV6-NTRK3 translocation may represent a therapeutic target in SC, particularly the high-grade transformed type.

A study on knowledge and practice related to bird flu in a rural community of Hooghly District of West Bengal.

For last few years in the early spring bird flu poses a threat to India. The causative agent H5N1 virus is also getting robust day by day acquiring an ability to cross the species barrier. It is now known as (H5N1) which is emerging as killer virus to man. Although human casualty is yet to be recorded from India, but the threat is not over. The present study had been undertaken in the village of Hakimpur of Singur Block of District Hooghly, West Bengal, with a population 862 of 215 families. The objective of the study was to assess the knowledge of the study population regarding bird flu and to study their practice regarding poultry maintenance. The head of the family from each family was interviewed. A house to house survey in the census method on a pre-designed, pre-tested, semi-structured schedule was done. Information regarding socio-demographic profile, poultry keeping, correct knowledge about bird flu, mode of transmission, culling, etc was recorded. The data were collected and analyzed by relevant statistical methods. The results showed that 46% respondents knew what bird flu is, 62.8% knew the mode of transmission, and 35.3% knew the procedure of culling. Out of literates about 53% and out of the illiterates only 0.93% were aware of the transmission of the virus through body fluids. The predominant source of information was mass media. 57.14% of the families rearing poultry, kept the birds in shed, 40.48% in cage, and 2.38% in living room.

Fluorescence correlation spectroscopy as a tool to investigate the directionality of proteolysis.

Enzymatic proteolysis or protein digestion is the fragmentation of protein into smaller peptide units under the action of peptidase enzymes. In this contribution, the directionality of proteolysis has been studied using fluorescence correlation spectroscopy (FCS), taking human serum albumin (HSA) as the model protein and papain, chymotrypsin and trypsin as the model enzymes. Domain-I of HSA has been tagged with tetramethylrhodamine-5-maleimide (TMR) and domain-III with p-nitrophenylcoumarin ester (NPCE) separately and subjected to proteolysis. Following the change in hydrodynamic radius, as monitored by FCS, it has been confirmed that under similar experimental conditions the order of efficiency of digestion is papain > trypsin > chymotrypsin. More interestingly, a faster decrease of hydrodynamic radius was observed when the fluorescence from domain-I was monitored in FCS, compared to that of domain-III. This observation clearly indicates that all these enzymes prefer to start cleaving HSA from domain-I. We assign this preference to the hydrophilic natures of the enzyme active site and domain-I surface. The dependence of the proteolysis on temperature and enzyme concentration has also been studied for papain using the same approach. Reverse-phase HPLC results are found to be in line with the FCS results and validates the applicability of our proposed method.

Domain-Specific Stabilization of Structural and Dynamic Responses of Human Serum Albumin by Sucrose.

BACKGROUND: Human Serum Albumin (HSA) is the most abundant protein present in human blood plasma. It is a large multi-domain protein with 585 amino acid residues. Due to its importance in human body, studies on the interaction of HSA with different external agent is of vital interest. The denaturation and renaturation of HSA in presence of external agents are of particular interest as they affect the biological activity of the protein. OBJECTIVE: The objective of this work is to study the domain-specific and overall structural and dynamical changes occurring to HSA in the presence of a denaturing agent, urea and a renaturing agent, sucrose. METHODS: In order to carry out the domain-specific studies, HSA has been tagged using N-(7- dimethylamino-4-methylcoumarin-3-yl) iodoacetamide (DACIA) at Cys-34 of domain-I and pnitrophenyl coumarin ester (NPCE) at Tyr-411 site in domain-III, separately. Steady-state absorption, emission and solvation dynamic measurements have been carried out in order to monitor the domain-specific alteration of HSA caused by the external agents. The overall structural change of HSA have been monitored using circular dichroism spectroscopy. RESULTS: The α-helicity of HSA was found to decrease from 65% to 11% in presence of urea and was found to further increase to 25% when sucrose is added, manifesting the denaturing and renaturing effects of urea and sucrose, respectively. The steady state studies show that domain-III is more labile towards denaturation as compared to domain-I. The presence of an intermediate state is observed during the denaturation process. The stabilization of this intermediate state in presence of sucrose is attributed as the reason for the stabilization of HSA by sucrose. From solvation dynamics studies, it could be seen that the solvation time of DACIA inside domain-I of HSA decreases and increases regularly with increasing concentrations of urea and sucrose, respectively, while in the case of NPCE-tagged domain-III, the effect of sucrose on solvation time is evident only at high concentrations of urea. CONCLUSION: The denaturing and renaturing effects of urea and sucrose could be clearly seen from the steady state studies and circular dichroism spectroscopy measurements. A regular change in solvation time could only be observed in the case of domain-I and not in domain-III. The results indicate that the renaturing effect of sucrose on domain-III is not very evident when protein is in its native state, but is evident in when the protein is denatured.

Direct Observation of Intermediate State(s) in the Mechanistic Investigation of Domain Specific Protein-Surfactant Interaction.

INTRODUCTION: Interaction of surfactants with proteins can decipher important information regarding the stability and behavior of proteins. For multi-domain proteins, these interactions vary domain wise and these details are crucial in understanding the contribution of different domains of the protein in its overall activity. OBJECTIVE: The objective of the present work is to study the interaction of surfactants with domain III of Human Serum Albumin (HSA) and to compare the same with the global interaction. METHODS: Interaction of the anionic Sodium Dodecyl Sulphate (SDS) and the Cationic Cetyltrimethylammonium Bromide (CTAB) surfactants with domain III of Human Serum Albumin (HSA) has been studied using 8-Anilino-1-Naphthalene-Sulphonate (ANS) as a fluorescent marker. Circular Dichroism (CD) spectroscopy has been used to study the protein-surfactant interaction for the overall protein. RESULTS: SDS is found to interact sequentially with domain III of HSA having two detectable intermediate states in the binding process. In case of CTAB, we have observed only one intermediate state for its interaction with domain III. Although Quantum yield measurement can reflect the presence of such intermediate state, the overall conformational change of the HSA on addition of surfactants, studied by Circular Dichroism (CD) spectroscopy, and the ANS-Trp distance measurement by FRET could not resolve the presence of such intermediate states. The esterase activity of HSA in presence of different amount of surfactants is also in accordance with our above observation. CONCLUSION: The interaction of both the surfactants with HSA is found to be sequential in nature. The most important conclusion revealed from our study is that the nature of protein-surfactant interaction is not same throughout the entire protein. Our study reveals that different parts of the multi-domain HSA have different affinity to the surfactant molecules.

Region-Specific Double Denaturation of Human Serum Albumin: Combined Effects of Temperature and GnHCl on Structural and Dynamical Responses.

In this work, we have investigated the effects of denaturing agents, guanidine hydrochloride (GnHCl) and temperature, on the overall structure, domain-I, and domain-III of human serum albumin (HSA) using circular dichroism (CD) spectroscopy and steady-state, time-resolved fluorescence spectroscopy. We have tagged Cys-34 of HSA, located at domain-I, using N-(7-dimethylamino-4-methylcoumarin-3-yl)iodoacetamide and Tyr-411 of HSA, located at domain-III, using p-nitrophenyl coumarin ester, for this purpose. The CD spectroscopy studies reveal the overall denaturation of the protein. The denaturation follows the expected direction in which the protein is denatured with an increase in the concentration of GnHCl or temperature. The α-helicity of the native state of HSA was found to be 64.2%, and the minimum value of α-helicity was found to be 14.8% in the presence of 6 M GnHCl at room temperature. Steady-state emission studies were carried out on domain-I and domain-III of the protein using site-specific fluorescent tags. The degree of folding of the two domains at different combinations of temperature and GnHCl concentration was calculated and was found to follow a slightly different course of denaturation. Solvation dynamics was found to be quite different for these two domains. The domain-I of HSA has a maximum solvation time of 0.39 ns, and the solvation time tends to decrease with the action of either temperature or GnHCl. On the other hand, the domain-III of HSA showed a much higher solvation time (1.42 ns) and does not show any regular change at higher temperatures or in the presence of GnHCl. This difference could be attributed to the different microenvironment inside the protein cores of the two domains.

Elucidation of µs dynamics of domain-III of human serum albumin during the chemical and thermal unfolding: A fluorescence correlation spectroscopic investigation.

The local structural dynamics and denaturation profile of domain-III of HSA against guanidine hydrochloride (GnHCl) and temperature has been studied using a coumarin based solvatochromic fluorescent probe p-nitrophenyl coumarin ester (NPCE), covalently tagged to Tyr-411 residue. By the steady state, time-resolved and single molecular level fluorescence studies it has been established that the domain-III of HSA is very sensitive to GnHCl but somewhat resistant to temperature and the domain specific unfolding proceeds in an altered way as compared to the overall unfolding of HSA. While the overall denaturation of HSA is a two-state process for both GnHCl and heat, domain-III adopts two intermediate states for GnHCl induced denaturation and one intermediate state for temperature induced denaturation. Fluorescence correlation spectroscopic investigation divulges the conformational dynamics of domain-III of HSA in the native, intermediates and denatured state.

Single Molecular Level Probing of Structure and Dynamics of Papain Under Denaturation.

INTRODUCTION: Papain is a cysteine protease enzyme present in papaya and known to help in digesting peptide. Thus the structure and function of the active site of papain is of interest. OBJECTIVE: The objective of present study is to unveil the overall structural transformation and the local structural change around the active site of papain as a function of chemical denaturant. METHODS: Papain has been tagged at Cys-25 with a thiol specific fluorescence probe N-(7- dimethylamino-4-methylcoumarin-3-yl) iodoacetamide (DACIA). Guanidine hydrochloride (GnHCl) has been used as the chemical denaturant. Steady state, time-resolved, and single molecular level fluorescence techniques was applied to map the change in the local environment. RESULTS: It is found that papain undergoes a two-step denaturation in the presence of GnHCl. Fluorescence correlation spectroscopic (FCS) data indicate that the size (hydrodynamic diameter) of native papain is ~36.8 Å, which steadily increases to ~53 Å in the presence of 6M GnHCl. FCS study also reveals that the conformational fluctuation time of papain is 6.3 µs in its native state, which decreased to 2.7 µs in the presence of 0.75 M GnHCl. Upon further increase in GnHCl concentration the conformational fluctuation time increase monotonically till 6 M GnHCl, where the time constant is measured as 14 µs. On the other hand, the measurement of ellipticity, hence the helical structure, by circular dichroism spectroscopy is found to be incapable to capture such structural transformation. CONCLUSION: It is concluded that in the presence of small amount of GnHCl the active site of papain takes up a more compact structure (although the overall size increases) than in the native state, which has been designated as the intermediate state.