Alcohol and Temperature Induced Conformational Transitions in Ervatamin B: Sequential Unfolding of Domains

Kundu, Suman,Sundd, Monica,Jagannadham, Medicherla V. Korean Society for Biochemistry and Molecular Biol 2002 Journal of biochemistry and molecular biology Vol.35 No.2

The structural aspects of ervatamin B have been studied in different types of alcohol. This alcohol did not affect the structure or activity of ervatamin B under neutral conditions. At a low pH (3.0), different kinds of alcohol have different effects. Interestingly, at a certain concentration of non-fluorinated, aliphatic, monohydric alcohol, a conformational switch from the predominantly $\alpha$-helical to $\beta$-sheeted state is observed with a complete loss of tertiary structure and proteolytic activity. This is contrary to the observation that alcohol induces mostly the $\alpha$helical structure in proteins. The O-state of ervatamin B in 50% methanol at pH 3.0 has enhanced the stability towards GuHCl denaturation and shows a biphasic transition. This suggests the presence of two structural parts with different stabilities that unfold in steps. The thermal unfolding of ervatamin B in the O-state is also biphasic, which confirms the presence of two domains in the enzyme structure that unfold sequentially. The differential stabilization of the structural parts may also be a reflection of the differential stabilization of local conformations in methanol. Thermal unfolding of ervatamin B in the absence of alcohol is cooperative, both at neutral and low pH, and can be fitted to a two state model. However, at pH 2.0 the calorimetric profiles show two peaks, which indicates the presence of two structural domains in the enzyme with different thermal stabilities that are denatured more or less independently. With an increase in pH to 3.0 and 4.0, the shape of the DSC profiles change, and the two peaks converge to a predominant single peak. However, the ratio of van't Hoff enthalpy to calorimetric enthalpy is approximated to 2.0, indicating non-cooperativity in thermal unfolding.

Dynamics and risk assessment of SARS-CoV-2 in urban areas: a geographical assessment on Kolkata Municipal Corporation, India

Paul Suman,Bhattacharya Subhasis,Mandal Buddhadev,Haldar Subrata,Mandal Somnath,Kundu Sanjit,Biswas Anupam 대한공간정보학회 2021 Spatial Information Research Vol.29 No.3

SARS-CoV-2 has been transmitted and outbreak took place in India during the last week before nationwide 1st lockdown took place. Urban areas found more vulnerable and reported nearly 65% of cases during every phase of lockdown. Mumbai, among four metropolitan cities found huge number of containment zones with nearly 30% of SARS-CoV-2 cases indicating clustering of cases. Most of the containment zones of SARS-CoV-2 cases in Kolkata Municipal Corporation found a significant relation with slum areas. The study primarily tries considering the nature of SARS-CoV-2 cases in different urban centres with the help of cartographic techniques. AHP method has been used to determine the factors responsible for such concentration of SARS-CoV-2 cases with vulnerability assessment (exposure, sensitivity and resilience) and risks. Before nationwide lockdown starts, the share of urban centres found 25% which has been transformed into nearly 60% at the end of 3rd phase of lockdown. Growth rate of SARS-CoV-2 cases found very high for Chennai and Thane with less number of doubling time to nation. Slum concentration and containment density shows a higher degree of correlation in Kolkata Municipal Corporation. Risk map also shows the concentration of cases in central and north Kolkata with higher degree of diseases exposure and sensitivity. Control measures must be taken by the central and state Government to minimise the transmission rate of SARS-CoV-2 mainly urban areas. As urban area contributing a higher share of SARS-CoV-2 cases, a proper management plan must be enforce.

Unfolding of Ervatamin C in the Presence of Organic Solvents: Sequential Transitions of the Protein in the O-state

Sundd, Monica,Kundu, Suman,Dubey, Vikash Kumar,Jagannadham, Medicherla V. Korean Society for Biochemistry and Molecular Biol 2004 Journal of biochemistry and molecular biology Vol.37 No.5

The folding of ervatamin C was investigated in the presence of various fluorinated and non-fluorinated organic solvents. The differences in the unfolding of the protein in the presence of various organic solvents and the stabilities of O-states were interpreted. At pH 2.0, non-fluorinated alkyl alcohols induced a switch from the native $\alpha$-helix to a $\beta$-sheet, contrary to the $\beta$-sheet to $\alpha$-helix conversion observed for many proteins. The magnitude of ellipticity at 215 nm, used as a measure of $\beta$-content, was found to be dependent on the concentration of the alcohol. Under similar conditions of pH, fluorinated alcohol enhanced the intrinsic a-helicity of the protein molecule, whereas the addition of acetonitrile reduced the helical content. Ervatamin C exhibited high stability towards GuHCl induced unfolding in different O-states. Whereas the thermal unfolding of O-states was non-cooperative, contrary to the cooperativity seen in the absence of the organic solvents under similar conditions. Moreover, the differential scanning calorimetry endotherms of the protein acquired at pH 2.0 were deconvoluted into two distinct peaks, suggesting two cooperative transitions. With increase in pH, the shape of the thermogram changed markedly to exhibit a major and a minor transition. The appearance of two distinct peaks in the DSC together with the non-cooperative thermal transition of the protein in O-states indicates that the molecular structure of ervatamin C consists of two domains with different stabilities.

Acid and Chemical Induced Conformational Changes of Ervatamin B. Presence of Partially Structured Multiple Intermediates

Sundd, Monica,Kundu, Suman,Jagannadham, Medicherla V. Korean Society for Biochemistry and Molecular Biol 2002 Journal of biochemistry and molecular biology Vol.35 No.2

The structural and functional aspects of ervatamin B were studied in solution. Ervatamin B belongs to the $\alpha+\beta$ class of proteins. The intrinsic fluorescence emission maximum of the enzyme was at 350 nm under neutral conditions, and at 355 nm under denaturing conditions. Between pH 1.0-2.5 the enzyme exists in a partially unfolded state with minimum or no tertiary structure, and no proteolytic activity. At still lower pH, the enzyme regains substantial secondary structure, which is predominantly $\beta$-sheet conformation and shows a strong binding to 8-anilino-1-napthalene-sulfonic acid (ANS). In the presence of salt, the enzyme attains a similar state directly from the native state. Under neutral conditions, the enzyme was stable in urea, while the guanidine hydrochloride (GuHCl) induced equilibrium unfolding was cooperative. The GuHCl induced unfolding transition curves at pH 3.0 and 4.0 were non-coincidental, indicating the presence of intermediates in the unfolding pathway. This was substantiated by strong ANS binding that was observed at low concentrations of GuHCl at both pH 3.0 and 4.0. The urea induced transition curves at pH 3.0 were, however, coincidental, but non-cooperative. This indicates that the different structural units of the enzyme unfold in steps through intermediates. This observation is further supported by two emission maxima in ANS binding assay during urea denaturation. Hence, denaturant induced equilibrium unfolding pathway of ervatamin B, which differs from the acid induced unfolding pathway, is not a simple two-state transition but involves intermediates which probably accumulate at different stages of protein folding and hence adds a new dimension to the unfolding pathway of plant proteases of the papain superfamily.

Acid and Chemical Induced Conformational Changes of Ervatamin B. Presence of Partially Structured Multiple Intermediates

Sundd, Monica,Kundu, Suman,Jagannadham, Medicherla V . 생화학분자생물학회 1998 BMB Reports Vol.35 No.2

The structural and functional aspects of ervatamin B were studied in solution. Ervatamin B belongs to the α+β class of proteins. The intrinsic fluorescence emission maximum of the enzyme was at 350 nm under neutral conditions, and at 355 nm under denaturing conditions. Between pH 1.0-2.5 the enzyme exists in a partially unfolded state with minimum or no tertiary structure, and no proteolytic activity. At still lower pH, the enzyme regains substantial secondary structure, which is predominantly a β-sheet conformation and shows a strong binding to 8-anilino-l-napthalene-sulfonic acid (ANS). In the presence of salt, the enzyme attains a similar state directly from the native state. Under neutral conditions, the enzyme was stable in urea, while the guanidine hydrochloride (GuHCI) induced equilibrium unfolding was cooperative. The GuHCI induced unfolding transition curves at pH 3.0 and 4.0 were non-coincidental, indicating the presence of intermediates in the unfolding pathway. This was substantiated by strong ANS binding that was observed at low concentrations of GuHCI at both pH 3.0 and 4.0. The urea induced transition curves at pH 3.0 were, however, coincidental, but non-cooperative. This indicates that the different structural units of the enzyme unfold in steps through intermediates. This observation is further supported by two emission maxima in ANS binding assay during urea denaturation. Hence, denaturant induced equilibrium unfolding pathway of ervatamin B, which differs from the acid induced unfolding pathway, is not a simple two-state transition but involves intermediates which probably accumulate at different stages of protein folding and hence adds a new dimension to the unfolding pathway of plant proteases of the papain superfamily.

Alcohol and Temperature Induced Conformational Transitions in Ervatamin B - Sequential Unfolding of Domains

Sundd, Monica,Kundu, Suman,Jagannadham, Medicherla V . 생화학분자생물학회 1998 BMB Reports Vol.35 No.2

The structural aspects of ervatamin B have been studied in different types of alcohol. This alcohol did not affect the structure or activity of ervatamin B under neutral conditions. At a low pH (3.0), different kinds of alcohol have different effects. Interestingly, at a certain concentration of non-fluorinated, aliphatic, monohydric alcohol, a conformational switch from the predominantly α-helical to β-sheeted state is observed with a complete loss of tertiary structure and proteolytic activity. This is contrary to the observation that alcohol induces mostly the α-helical structure in proteins. The O-state of ervatamin B in 50 % methanol at pH 3.0 has enhanced the stability towards GuHCl denaturation and shows a biphasic transition. This suggests the presence of two structural parts with different stabilities that unfold in steps. The thermal unfolding of ervatamin B in the O-state is also biphasic, which confirms the presence of two domains in the enzyme structure that unfold sequentially. The differential stabilization of the structural parts may also be a reflection of the differential stabilization of local conformations in methanol. Thermal unfolding of ervatamin B in the absence of alcohol is cooperative, both at neutral and low pH, and can be fitted to a two state model. However, at pH 2.0 the calorimetric profiles show two peaks, which indicates the presence of two structural domains in the enzyme with different thermal stabilities that are denatured more or less independently. With an increase in pH to 3.0 and 4.0, the shape of the DSC profiles change, and the two peaks converge to a predominant single peak. However, the ratio of van't Hoff enthalpy to calorimetric enthalpy is approximated to 2.0, indicating non-cooperativity in thermal unfolding.

Unfolding of Ervatamin C in the Presence of Organic Solvents: Sequential Transitions of the Protein in the O-state

( Monica Sundd ),( Suman Kundu ),( Vikash Kumar Dubey ),( Medicherla V. Jagannadham ) 생화학분자생물학회 2004 BMB Reports Vol.37 No.5

The folding of ervatamin C was investigated in the presence of various fluorinated and non-fluorinated organic solvents. The differences in the unfolding of the protein in the presence of various organic solvents and the stabilities of 0-states were interpreted. At pH 2.0, non-fluorinated alkyl alcohols induced a switch from the native α-helix to a β-sheet, contrary to the β-sheet to α-helix conversion observed for many proteins. The magnitude of ellipticity at 215 nm, used as a measure of β-content, was found to be dependent on the concentration of the alcohol. Under similar conditions of pH, fluorinated alcohol enhanced the intrinsic a-helicity of the protein molecule, whereas the addition of acetonitrile reduced the helical content. Ervatamin C exhibited high stability towards GuHC1 induced unfolding in different 0-states. Whereas the thermal unfolding of 0-states was non-cooperative, contrary to the cooperativity seen in the absence of the organic solvents under similar conditions. Moreover, the differential scanning calorimetry endotherms of the protein acquired at pH 2.0 were deconvoluted into two distinct peaks, suggesting two cooperative transitions. With increase in pH, the shape of the thermogram changed markedly to exhibit a major and a minor transition. The appearance of two distinct peaks in the DSC together with the non-cooperative thermal transition of the protein in 0-states indicates that the molecular structure of ervatamin C consists of two domains with different stabilities.

Mechanism of Lipid Induced Insulin Resistance: An Overview

Samir Bhattacharya,Rakesh Kundu,Suman Dasgupta,Sushmita Bhattacharya 대한내분비학회 2012 Endocrinology and metabolism Vol.27 No.1

Type 2 diabetes (T2D) is rapidly spreading throughout the world. It’s an insidious disease and still treated in an indirect manner without having specific drug target. In majority cases T2D is treated with drugs that address type 1 diabetes, majority of drugs aim to increase insulin release although the root cause for T2D is not the dearth of insulin release, it occurs in the later stage of disease development. T2D silently progressed in the patient; it begins with insulin resistance that takes place due to the loss of insulin sensitivity. Though insulin resistance is the centre of pathogenesis, our treatment of the disease has not yet addressed it. It is now a fact that insulin resistance is manifested by lipid and fatty acids (FAs) play a critical role in blunting insulin sensitivity. Our understanding is still poor in deciphering how lipid impose insulin insensitivity, majority of workers suggest it is because of insulin signaling defects which implements insulin function in inhibiting glucose to the cell from circulation. Number of long chain saturated FA has been shown to produce insulin signaling defects. However, we really need further investigation to find specific target(s) for FA induced damage. In addition to these information, a new dimension of T2D is getting attractive is fetuin-A/α2-Heremans-Schmid Glycoprotein,a secretary protein from liver. Its gene locus has been identified as T2D susceptible. Fetuin-A’s excess expression occurs by FA and it disrupts adipocyte function. It has been shown to be associated with T2D especially in obesity. In this review, we briefly discuss the present status on the mechanistic understanding of lipid induced insulin resistance that leads to T2D. More we understand the mechanism; opportunity to fight the battle with T2D will be increasing. Since, this field is now vast; we covered a few major events.