Tanveer Ali Dar

Protein and DNA destabilization by osmolytes: The other side of the coin

Osmolytes are naturally occurring small molecules accumulated intracellularly to protect organisms from various denaturing stresses. Similar to the two faces of a coin, several of these osmolytes are stabilizing and destabilizing proteins depending on the concentrations and/or solvent conditions. For example, the well known stabilizing osmolyte, trehalose destabilizes some proteins at high concentration and/or high pH. In spite of the fact that destabilizing aspects of osmolytes can modulate many cellular processes including regulation of protein homeostasis (proteostasis), protein-protein interaction, and protein-DNA interaction, researchers have mostly focused on the stabilizing aspects of osmolytes. Thus, it is important to look into both aspects of osmolytes to determine their precise role under physiological conditions. In this article, we have discussed both stabilizing and destabilizing/denaturant aspects of osmolytes to uncover both sides of the coin.

Glycine betaine may have opposite effects on protein stability at high and low pH values

The compatible osmolyte glycine betaine (GB) is the most efficient osmoprotectant and best excluder from the protein surface. It can reverse protein aggregation and correct mutant protein defects and counter the harmful effects of urea and salts in vivo and in vitro. In this study we have investigated the pH dependence of the stabilizing effect of GB on three different proteins, namely, alpha-lactalbumin (alpha-LA), lysozyme and ribonuclease-A (RNase-A). We show here that (a) GB stabilizes RNase-A at all pH values, and (b) GB has opposite effects on two proteins at high pH and low pH values, namely, alpha-LA and lysozyme. This conclusion was reached by determining T(m) (midpoint of denaturation), DeltaH(m) (denaturational enthalpy change at T(m)), DeltaC(p) (constant-pressure heat capacity change) and DeltaG(D)(o) (denaturational Gibbs energy change at 25 degrees C) of proteins in the presence of different GB concentrations. Another conclusion of this study is that DeltaH(m) and DeltaC(p) are not significantly changed in the presence of GB. This study suggests that other methylated glycine osmolytes may also behave in the same manner.

Forty Years of Research on Osmolyte-Induced Protein Folding and Stability

Most organisms that have adapted to environmental stresses have done so by production and accumulation of certain small organic molecules, known as osmolytes that arose by natural selection and have the ability to stabilize intracellular proteins against the environmental stress. It is well known that osmolytes stabilize proteins and induce folding of aberrant proteins and therefore, it is of therapeutic use for a large number of protein misfolding diseases. Thus, it is very important that the present knowledge of the ability and mechanism of osmolyte-induced protein folding and structural stabilization should reach to researchers working in different avenues. In around 40 years of research, we have gained great advances in various aspects of protein folding and structural stabilization induced by osmolytes. To summarize and discuss the original findings, many short review articles and few long reviews have also been available but almost all have focuses on specific aspects. To get a clear picture of the effect of osmolytes on protein folding and structural stabilization, it is necessary for the benefits of the general readers, to combine and discuss all findings made during its 40 years of life. This review article is therefore, designed to give a collective knowledge on almost all facets of the progresses made on osmolyte-protein interaction to-date.

Relationship between functional activity and protein stability in the presence of all classes of stabilizing osmolytes

We report the effects of stabilizing osmolytes (low molecular mass organic compounds that raise the midpoint of thermal denaturation) on the stability and function of RNase‐A under physiological conditions (pH 6.0 and 25 °C). Measurements of Gibbs free energy change at 25 °C (ΔGD°) and kinetic parameters, Michaelis constant (Km) and catalytic constant (kcat) of the enzyme mediated hydrolysis of cytidine monophosphate, enabled us to classify stabilizing osmolytes into three different classes based on their effects on kinetic parameters and protein stability. (a) Polyhydric alcohols and amino acids and their derivatives do not have significant effects on ΔGD° and functional activity (Km and kcat). (b) Methylamines increase ΔGD° and kcat, but decrease Km. (c) Sugars increase ΔGD°, but decrease both Km and kcat. These findings suggest that, among the stabilizing osmolytes, (a) polyols, amino acids and amino acid derivatives are compatible solutes in terms of both stability and function, (b) methylamines are the best refolders (stabilizers), and (c) sugar osmolytes stabilize the protein, but they apparently do not yield functionally active folded molecules.

Molecular Linkages Between Diabetes and Alzheimer's Disease: Current Scenario and Future Prospects

After the revolutionary Rotterdam study that suggested there was an increased risk of developing Alzheimers disease (AD) in patients with type-2 diabetes mellitus (T2DM), a number of studies have provided direct evidence for the linkage between AD and T2DM. In recent years, AD is considered as a neuroendocrine disorder, also referred as type-3 diabetes. There is a growing list of evidence to suggest that, in addition to impaired insulin signaling, there are a number of additional factors that may act as mechanistic links between AD and T2DM. These factors mainly include hypercholesterolemia, dyslipidemia, hypercystinemia, inflammation, impaired insulin signaling and impaired central nervous response to the adipose tissue-derived hormone leptin. Increased cholesterol plays a crucial role in the abnormal metabolism of the amyloid precursor protein, leading to the accumulation of β-amyloid. In addition to impaired insulin signaling, diabetes has been found to accelerate the appearance of cerebrovascular inflammation and β-amyloid peptide (Aβ) deposition. Increased oxidative stress and production of advanced glycation end products are other probable marker linkages. However, the details of many of these molecular links still require extensive investigation. It is possible that a number of common molecular linkages exist between T2DM and AD. Understanding and analyzing the various molecular linkages between AD and T2DM may shed light on new tools that can be used for the early diagnosis and treatment of AD and also accelerate the identification of T2DM patients who are at high risk of AD.

Living with urea stress

Intracellular organic osmolytes are present in certain organisms adapted to harsh environments. These osmolytes protect intracellular macromolecules against denaturing environmental stress. In contrast to the usually benign effects of most organic osmolytes, the waste product urea is a well-known perturbant of macromolecules. Although urea is a perturbing solute which inhibits enzyme activity and stability, it is employed by some species as a major osmolyte. The answer to this paradox was believed to be the discovery of protective osmolytes (methylamines). We review the current state of knowledge on the various ways of counteracting the harmful effects of urea in nature and the mechanisms for this. This review ends with the mechanistic idea that cellular salt (KCl/NaCl) plays a crucial role in counteracting the effects of urea, either by inducing required chaperones or methylamines, or by thermodynamic interactions with urea-destabilised proteins. We also propose future opportunities and challenges in the field.

In Vitro Antioxidant and Cytotoxic Activities of Arnebia benthamii (Wall ex. G. Don): A Critically Endangered Medicinal Plant of Kashmir Valley

Arnebia benthamii is a major ingredient of the commercial drug available under the name Gaozaban, which has antibacterial, antifungal, anti-inflammatory, and wound-healing properties. In the present study, in vitro antioxidant and anticancer activity of different extracts of Arnebia benthamii were investigated. Antioxidant potential of plant extracts was evaluated by means of total phenolics, DPPH, reducing power, microsomal lipid peroxidation, and hydroxyl radical scavenging activity. The highest phenolic content (TPC) of 780 mg GAE/g was observed in ethyl acetate, while the lowest TPC of 462 mg GAE/g was achieved in aqueous extract. At concentration of 700 µg/mL, DPPH radical scavenging activity was found to be highest in ethyl acetate extract (87.99%) and lowest in aqueous extract (73%). The reducing power of extracts increased in a concentration dependent manner. We also observed its inhibition on Fe2+/ascorbic acid-induced lipid peroxidation (LPO) on rat liver microsomes in vitro. In addition, Arnebia benthamii extracts exhibited antioxidant effects on Calf thymus DNA damage induced by Fenton reaction. Cytotoxicity of the extracts (10–100 µg/mL) was tested on five human cancer cell lines (lung, prostate, leukemia, colon, and pancreatic cell lines) using the Sulphorhodamine B assay.

A new method for determining the constant-pressure heat capacity change associated with the protein denaturation induced by guanidinium chloride (or urea)

Differential scanning calorimetry (DSC) provides authentic and accurate value of DeltaC(p)(X), the constant-pressure heat capacity change associated with the N (native state)<-->X (heat denatured state), the heat-induced denaturation equilibrium of the protein in the absence of a chemical denaturant. If X retains native-like buried hydrophobic interaction, DeltaC(p)(X) must be less than DeltaC(p)(D), the constant-pressure heat capacity change associated with the transition, N<-->D, where the state D is not only more unfolded than X but it also has its all groups exposed to water. One problem is that for most proteins D is observed only in the presence of chemical denaturants such as guanidinium chloride (GdmCl) and urea. Another problem is that DSC cannot yield authentic DeltaC(p)(D), for its measurement invokes the existence of putative specific binding sites for the chemical denaturants on N and D. We have developed a non-calorimetric method for the measurements of DeltaC(p)(D), which uses thermodynamic data obtained from the isothermal GdmCl (or urea)-induced denaturation and heat-induced denaturation in the presence of the chemical denaturant concentration at which significant concentrations of both N and D exist. We show that for each of the proteins (ribonuclease-A, lysozyme, alpha-lactalbumin and chymotrypsinogen) DeltaC(p)(D) is significantly higher than DeltaC(p)(X). DeltaC(p)(D) of the protein is also compared with that estimated using the known heat capacities of amino acid residues and their fractional area exposed on denaturation.

Unique Medicinal Properties of Withania somnifera: Phytochemical Constituents and Protein Component

Withania somnifera is an important medicinal herb that has been widely used for the treatment of different clinical conditions. The overall medicinal properties of Withania somnifera make it a viable therapeutic agent for addressing anxiety, cancer, microbial infection, immunomodulation, and neurodegenerative disorders. Biochemical constituents of Withania somnifera like withanolideA, withanolide D, withaferin A and withaniamides play an important role in its pharmacological properties. Proteins like Withania somnifera glycoprotein and withania lectin like-protein possess potent therapeutic properties like antimicrobial, anti-snake venom poison and antimicrobial. In this review, we have tried to present different pharmacological properties associated with different extract preparations, phytochemical constituents and protein component of Withania somnifera. Future insights in this direction have also been highlighted.

Targeting copper induced oxidative damage to proteins by ligation: a novel approach towards chelation therapy for oxidative stress disorders

Oxidative stress due to excessive accumulation of reactive oxygen species (ROS) triggers the onset of various pathological conditions in humans such as cancer, arthritis, muscular dystrophy (MD), Alzheimers and Parkinsons diseases. To date, the available therapeutic strategies have mainly focused on removal or sequestering of excessive ROS rather than preventing their generation. In the present study we hypothesize that the selective ligation of copper and iron ions in their inactive redox states with appropriate ligands can be a novel approach for prevention of free radical generation. To testify this hypothesis the present study was devised to explore the structural, conformational and electronic requirements of a potential biocompatible inhibitor of copper induced oxidative damage to proteins. A series of chemical compounds such as neocuproine, bathophenanthroline, thiourea, acetonitrile, bathocuproine, dimethylsulfoxide, mannitol, urea and histidine were tested for their impact on copper induced oxidative damage to proteins. To measure the oxidative damage, bovine serum albumin (BSA) was used as the model substrate to quantitate the conversion of its free amino groups to the carbonyl counterparts under the ROS induced oxidative stress. The observed complexation behavior of Cu with the investigated ligands revealed that a ligand with soft donor sites, donor sites placed at the corners of a tetrahedron or a good π-back acceptance character shall exhibit excellent potential to inhibit copper induced oxidative damage to proteins. To validate these facts we tested two bioactive molecules viz. 1,2-(diimino-4′-antipyrinyl)-1,2-diphenyl ethane (DIDE) and rhodanine whose distinctive molecular structure meets the hypothesized prerequisites, for their protective impact against Cu induced free radical-mediated oxidative damage. Expectedly both DIDE and rhodanine were found to offer excellent protection against copper-catalyzed oxidative damage to BSA. Furthermore, based on the thermodynamic, kinetic and computational investigations, we propose that the observed antioxidant activity of DIDE and rhodanine is due to the selective stabilization of Cu(I) by these bioactive and biofriendly molecules. To the best of our knowledge, the present study is the first of its kind to establish that the antioxidant activity of DIDE and rhodanine is an outcome of their ability to reduce the generation of ROS by binding copper into a redox inactive form.