Aabgeena Naeem - Academia.edu (original) (raw)

Papers by Aabgeena Naeem

International journal of biological macromolecules, Mar 1, 2024

Gut, 1995

Attachment of Giardia lamblia trophozoites to enterocytes is essential for colonisation of the sm... more Attachment of Giardia lamblia trophozoites to enterocytes is essential for colonisation of the small intestine and is considered a prerequisite for giardia induced enterocyte damage. The precise mechanisms involved are still being debated and some earlier work has been performed in models of uncertain biological relevance. In this study, co-incubation of giardia with enterocyte-like differentiated Caco-2 celis was used as a model to study the influence of physical and chemical factors on attachment. Giardia attachment was maximal between one and eight hours and stable over pH 7.2-8.2 but it was reduced by acidification. Attachment was dependent on temperature and was maximal at 370 and virtually abolished at 4°C. It was reduced compared with controls (p<0.05) by EDTA 2.5 mM (mean (SEM) 32 (4)%/o), colchicine 12.5 ,M (35 (5)0/o), mebendazole 10 pg/ml (30 (3)%), and cytochalasin B 1 ,g/ml (34 (3)%/o).

Journal of Glycomics & Lipidomics, 2015

The understanding of folding of proteins into their compact three-dimensional structures, example... more The understanding of folding of proteins into their compact three-dimensional structures, example of complex biological self-assembly process, will provide an insight into the way in which evolutionary selection has influenced the properties of a molecular system for functional advantage. Once regarded as a grand challenge, protein folding has seen much progress in recent years. Protein folding pathways are of great interest not only in themselves, but also because understanding them is important for both protein structure predictions and for de novo protein design. Protein misfolding is a ubiquitous phenomenon associated with a wide range of diseases. Aggregation of misfolded proteins that escape the cellular quality-control mechanisms is a common feature of a wide range of highly debilitating and increasingly prevalent diseases. We hope that this review will stimulate further research in this area and catalyze increased collaboration at the interface of chemistry and biology to decipher the mechanisms and roles of protein folding, misfolding and aggregation in the fields of health and disease.

Annals of the New York Academy of Sciences, 2008

Several factors have been incriminated in the genesis of diabetic nephropathy. To elucidate their... more Several factors have been incriminated in the genesis of diabetic nephropathy. To elucidate their interplay, we have used a hypertensive, obese, diabetic rat model with nephropathy (SHR/NDmcr‐cp) that mimics human type 2 diabetes. This model is characterized by hypertension, obesity with the metabolic syndrome, diabetes with insulin resistance, and intrarenal advanced glycation end product (AGE) accumulation. In order to achieve renoprotection, which was evaluated by histology and albuminuria, various therapeutic approaches were used: caloric restriction, antihypertensive agents (angiotensin II receptor blocker [ARB] and calcium channel blocker), lipid‐ (bezafibrate) or glucose‐lowering (insulin and pioglitazone) agents, and cobalt chloride (a hypoxia‐inducible factor activator). Altogether, renoprotection is not necessarily associated with blood pressure or glycemic control. By contrast, it is almost always associated with decreased AGE formation, with the exception of insulin, whi...

Journal of Molecular Recognition, May 19, 2021

Macromolecular crowding plays an inevitable role in all biological processes influencing associat... more Macromolecular crowding plays an inevitable role in all biological processes influencing association, conformation, and other characteristics of proteins. Present study is based on the effect of macromolecular crowding on structure of horseradish peroxidase (HRP) enzyme. Concentration‐dependent conformational changes induced by crowding agents, dextran 70 and polyethylene glycol (PEG)‐4000, were monitored employing a range of biophysical techniques. The intrinsic fluorescence spectra showed transition of protein from native to unfolded state. Marked increase in 8‐Anilino‐1‐naphthalene‐sulphonoic acid and Thioflavin T fluorescence indicated presence of non‐native moieties with 80 mg/mL dextran. Enhanced absorbance in turbidity, Soret, and Congo red in corroboration with scattering intensity at 350nm results revealed incidence of HRP aggregates. A new peak around 218 nm in CD spectra pointed towards change in secondary structure towards β‐sheets. Significant loss of enzyme activity upon structural disruption was seen. Comet assay demonstrated DNA damage and genotoxic nature of HRP aggregates, supporting spectroscopic, and fluorescence results. The normalized results were obtained with 120 mg/mL PEG‐4000 close to that of native HRP implying no disruptive effect on structure. It can be hypothesized that macromolecular crowding is a vital element, which can have diverse effects. In this study, dextran 70 was observed to have pro‐aggregatory effect while enhanced stability of native enzyme was witnessed with PEG. Hence, it can be stated that PEG has potentially better crowder as it helps retain the native enzyme structure. Routine addition of crowding agents is recommended if biological molecules are to be studied under more physiologically appropriate environments.

Journal of Fluorescence, Jun 22, 2021

Biomacromolecules evolve and function inside the cell under crowded conditions. The effect of mac... more Biomacromolecules evolve and function inside the cell under crowded conditions. The effect of macromolecular crowding and confinement on nature and interactions of biomacromolecules cannot be ruled out. This study demonstrates the effect of volume exclusion due to macromolecular crowding on refolding rate of Gn-HCl induced unfolded hemoglobin. The in vivo like crowding milieu was created using dextran 70. Unfolding of Hb was followed by the absorbance at 280 nm and intrinsic fluorescence intensity along with a bathochromic shift that shows the destabilization of Hb in the presence of the denaturing agent. This was supported by a decrease in soret absorbance, increased hydrodynamic radii and loss in secondary structure, evidenced from dynamic light scattering and circular dichroism experiments respectively. Refolding process of Hb was followed by an increase in soret absorbance, decrease in intrinsic fluorescence intensity with a hypsochromic shift, decreased hydrodynamic radii and gain in secondary structural content. The results revealed that the effect of confinement and volume exclusion is insignificant on the process of Hb refolding.

Journal of Molecular Liquids, 2021

Background: Amyloid fibrils associated with neurodegenerative diseases can be considered biologic... more Background: Amyloid fibrils associated with neurodegenerative diseases can be considered biologically relevant failures of cellular quality control mechanisms. It is known that in vivo human Tau protein, human prion protein, and human copper, zinc superoxide dismutase (SOD1) have the tendency to form fibril deposits in a variety of tissues and they are associated with different neurodegenerative diseases, while rabbit prion protein and hen egg white lysozyme do not readily form fibrils and are unlikely to cause neurodegenerative diseases. In this study, we have investigated the contrasting effect of macromolecular crowding on fibril formation of different proteins. Methodology/Principal Findings: As revealed by assays based on thioflavin T binding and turbidity, human Tau fragments, when phosphorylated by glycogen synthase kinase-3b, do not form filaments in the absence of a crowding agent but do form fibrils in the presence of a crowding agent, and the presence of a strong crowding agent dramatically promotes amyloid fibril formation of human prion protein and its two pathogenic mutants E196K and D178N. Such an enhancing effect of macromolecular crowding on fibril formation is also observed for a pathological human SOD1 mutant A4V. On the other hand, rabbit prion protein and hen lysozyme do not form amyloid fibrils when a crowding agent at 300 g/l is used but do form fibrils in the absence of a crowding agent. Furthermore, aggregation of these two proteins is remarkably inhibited by Ficoll 70 and dextran 70 at 200 g/l. Conclusions/Significance: We suggest that proteins associated with neurodegenerative diseases are more likely to form amyloid fibrils under crowded conditions than in dilute solutions. By contrast, some of the proteins that are not neurodegenerative disease-associated are unlikely to misfold in crowded physiological environments. A possible explanation for the contrasting effect of macromolecular crowding on these two sets of proteins (amyloidogenic proteins and non-amyloidogenic proteins) has been proposed.

Cell Biochemistry and Biophysics, Mar 18, 2014

Protein folding is a very complex process, and recognition of the molecular mechanisms responsibl... more Protein folding is a very complex process, and recognition of the molecular mechanisms responsible for protein folding is one of the demanding queries in biochemistry. Protein molecules have a fixed propensity either to misfold or unable to sustain their precisely folded states, under assured conditions. Taking into account that the protein misfolding and aggregation are central in the pathogenesis of protein conformational disorders, a therapy focussed to the root of the disease should target to restrain and/or undo the conformational alterations that lead to the development of the pathological protein conformer. In future, an understanding of the causes of protein aggregation and genetic and environmental vulnerability features of an exact individual may offer an enhanced prospect for a successful therapeutic intrusion. Dealing with these and related problems not only provides great prospects for involvement with numerous, presently fatal diseases but will also ultimately disclose the basically essential association between proteostasis and prolonged existence.

International Journal of Biological Macromolecules, Aug 1, 2015

Trifluoroethanol (TFE) mimics the membrane environments as it simulates the hydrophobic environme... more Trifluoroethanol (TFE) mimics the membrane environments as it simulates the hydrophobic environment and better stabilizes the secondary structures in peptides owing to its hydrophobicity and hydrogen bondforming properties. Its dielectric constant approximates that of the interior of proteins and is one-third of that of water. HSA is a biological transporter. The effect of TFE on HSA gives the clue about the conformational changes taking place in HSA on transport of ligands across the biological membranes. At 25% (v/v) and 60% (v/v) TFE, human serum albumin (HSA) exhibits non-native ␤-sheet, altered tryptophan fluorescence, exposed hydrophobic clusters, increased thioflavin T fluorescence and prominent red shifted Congo red absorbance, and large hydrodynamic radii suggesting the aggregate formation. Isothermal titration calorimetric results indicate weak binding of TFE and HSA. This suggests that solvent-mediated effects dominate the interaction of TFE and HSA. TEM confirmed prefibrillar at 25% (v/v) and fibrillar aggregates at 60% (v/v) TFE. Comet assay of prefibrillar aggregates showed DNA damage causing cell necrosis hence confirming cytotoxic nature. On increasing concentration of TFE to 80% (v/v), HSA showed retention of native-like secondary structure, increase Trp and ANS fluorescence, a transition from ␤-sheet to ␣-helix. Thus, TFE at high concentration possess anti aggregating potency.

Biopolymers, 2006

A systematic investigation of the effects of detergents [Sodium dodecyl sulphate (SDS), hexa decy... more A systematic investigation of the effects of detergents [Sodium dodecyl sulphate (SDS), hexa decyltrimethyl ammonium bromide (CTAB) and Tween-20] on the structure of acid-unfolded papain (EC.3.4.22.2) was made using circular dichroism (CD), intrinsic tryptophan fluorescence, and 1-anilino 8-sulfonic acid (ANS) binding. At pH 2, papain exhibits a substantial amount of secondary structure and is relatively less denatured compared with 6 M GdnHCl (guanidine hydrochloride) but loses the persistent tertiary contacts of the native state. Addition of detergents caused an induction of a-helical structure as evident from the increase in the mean residue ellipticity value at 208 and 222 nm. Near-UV CD spectra also showed the regain of native-like spectral features in the presence of 8 mM SDS and 3.5 mM CTAB. Induction of structure in acid-unfolded papain was greater in the presence SDS followed by CTAB and Tween-20. Intrinsic tryptophan fluorescence studies indicate the change in the environment of tryptophan residues upon addition of detergents to acid-unfolded papain. Addition of 8 mM SDS resulted in the loss of ANS binding sites exhibited by a decrease in ANS fluorescence intensity, suggesting the burial of hydrophobic patches. Maximum ANS binding was obtained in the presence of 0.1 mM Tween-20 followed by CTAB, indicating a compact ''molten-globule''-like conformation with enhanced exposure of hydrophobic surface area. Acidunfolded papain in the presence of detergents showed the partial recovery of enzymatic activity. These results suggest that papain at low pH and in the presence of SDS exists in a partially folded state characterized by native-like secondary structure and tertiary folds. While in the presence of Tween, acidunfolded papain exists as a compact intermediate with molten-globule-like characteristics, viz. enhanced hydrophobic surface area and retention of secondary structure. While in the presence of CTAB it exists as a compact intermediate with regain of native-like secondary and partial tertiary structure as well as high ANS binding with the partially recovered enzymatic activity, i.e., a molten globule state with tertiary folds.

International Journal of Biological Macromolecules, Dec 1, 2020

Cell interior is extremely congested with tightly packed biological macromolecules that exerts ma... more Cell interior is extremely congested with tightly packed biological macromolecules that exerts macromolecular crowding effect, influencing biophysical properties of proteins. To have a deeper insight into it we studied consequences of crowding on aggregation susceptibility and structural stability of α-chymotrypsinogen-A, proenzyme of serine protease family, upon addition of co-solvent reported to exert stress on polypeptides crafting favourable conditions for aggregation. Hexafluoropropan-2-ol (HFIP), a fluorinated alcohol caused structural disruption at 5% v/v unveiled by reduced intrinsic intensity and blue shifted ANS spectra. Significantly enhanced, red-shifted ThT and Congo red spectra sustained conformational changes concomitant with aggregation. FTIR and CD results confirmed transition of native structure to non-native extended, cross-linked beta-sheets. Transmission electron micrographs visibly exhibited incidence of amorphous aggregates. Macromolecular crowding, typically mimicked by concentrated solutions of dextran 70, was noticeably witnessed to defend conformational stability under denaturing condition. The native structure was retained maximally in presence of 100 mg/ml followed by 200 and 300 mg/ml dextran indicating concentration dependent deceleration of aggregate formation. It can be established that explicit consideration of crowding effects using relevant range of inert crowding agents must be a requisite for presumptions on intracellular conformational behaviour of proteins deduced from in vitro experiments.

International Journal of Biological Macromolecules, Oct 1, 2018

Misfolded proteins that escape cellular quality control check lay the foundation for several prog... more Misfolded proteins that escape cellular quality control check lay the foundation for several progressively widespread neurodegenerative diseases, diabetes and others. Here, crotonic and citric acid are employed to study aggregation behaviour of hemoglobin (Hb). A systematic investigation on varying concentrations of acids from 0-60 mM on Hb gives an idea that transition is taking place in the vicinity of 10-30 mM. Hb showed increased intrinsic Trp fluorescence in the presence of both acids. A red shift of 10 nm in presence of citric acid contrary to a blue shift of 5 nm in presence of crotonic acid is observed. ANS and ThT fluorescence marked aggregation at 50 mM, supported by Congo red and Soret absorbance spectroscopy. CD, RLS and DLS studies also validate the findings. Molecular docking analysis exhibited the binding mode of Hb with acids. Aggregates were dense, beaded structure as visualised under TEM. Crotonic and citric acid at 20 and 30 mM, respectively, induced structural changes in Hb which transmutes to aggregate at higher concentration. These alterations remained almost constant and no significant changes were observed on increasing concentration further. Also, crotonic acid is more noxious, as it instigates conformational alterations at lower concentration than citric acid.

Archives of Biochemistry and Biophysics, Aug 1, 2016

Fib having intrinsically disordered αC domains is involved in coagulation cascade and thrombosis.... more Fib having intrinsically disordered αC domains is involved in coagulation cascade and thrombosis. Fib molecules forms prefibrillar oligomers at 30%, and associate in 40% and 50% TFE to proceed α to β transition, suggesting the formation of an intermolecular βstructure. AFM images confirmed the nature of Fib aggregates at 40% and 50% TFE to be prefibrillar and fibrillar respectively. These aggregates possess high thioflavin T fluorescence with a shifted Congo red absorbance. Kinetics of Fib aggregation data at 50% TFE supports nucleation-dependent polymerization mechanism. At 60 and 70% TFE, no aggregation was observed. The inhibition of protein aggregation appears due to weakening of the hydrophobic interactions that were initially stabilizing the intermolecular β-sheet structure in the protein aggregation. The loss of hydrophobic contacts seems to favor the formation of intramolecular hydrogen bonds over intermolecular hydrogen bonds leads to helix formation. To conclude, protein aggregation is accompanied by the formation of β-sheet conformation, and induction of non-native helical segments in the protein inhibits aggregation. The discrepancy of the secondary structures on aggregation is proposed to stem from the disparity in the nature of the hydrogen bonds and packing of hydrophobic residues of the side chains in the βsheet and α-helix conformation.

Journal of Applied Microbiology, May 1, 2009

Dental caries is caused by the disturbance in oral homeostasis, marked by a notable increase in t... more Dental caries is caused by the disturbance in oral homeostasis, marked by a notable increase in the population of Streptococcus mutans. Lectins are a group of plant proteins that are capable of recognizing the glycoconjugates present on the bacterial surface. The aim of this study was to evaluate the effect of seven plant lectins on the growth and initial adhesion of S. mutans. Lectins of different carbohydrate specificities were isolated from plant sources by conventional methods of protein purification. The effect on growth of S. mutans was evaluated following CLSI guidelines. None of the lectins used in this study inhibited the bacterial growth and multiplication. The adherence and biofilm formation of bacteria to saliva-coated polystyrene plates was tested in the presence of plant lectins. All the plant lectins tested, inhibited both the adherence and biofilm in a concentration dependent manner. Confocal microscopy and scanning electron microscopy were employed to assess the biofilm formation in the presence of plant lectin (glucose/mannose-specific) at sub-minimal inhibitory concentrations. These evaluations revealed that lectins inhibited the clumping and attachment of S. mutans. Lectins tested here inhibited initial biofilm formation by S. mutans. Glucose/Mannose-specific lectin altered the adhesion arrangement of the bacteria on the saliva-coated surfaces. The plant lectins used in this study may offer a novel strategy to reduce development of dental caries by inhibiting the initial adhesion and subsequent biofilm formation of S. mutans.

Process Biochemistry, Nov 1, 2013

Folding and unfolding are crucial ways of modulating biological activity and targeting proteins t... more Folding and unfolding are crucial ways of modulating biological activity and targeting proteins to different cellular locations. In the living system, protein folding occurs in a very crowded environment, often assisted with helper proteins. In some cases this pathway can go off beam and the protein can either misfold or aggregate or form structures of elongated-unbranched morphology known as amyloid fibrils. Protein folding is not just an academic matter. Recombinant biotechnology and pharmaceutical industries are some of the fields where both theoretical and practical knowledge of protein folding is required. Misfolded protein and amyloid fibrils that escape the cellular quality control check are the basic reason of a number of increasingly widespread neurodegenerative diseases such as Alzheimer's and variant Creutzfeldt-Jakob etc. Thus, protein folding study also emerges as an interesting area in the field of biomedical research. This review deals with basic concepts related to protein folding and misfolding forming toxic aggregates and amyloid fibrils as well as disease associated with them. A more practical approach will be revealed to the early diagnosis of aggregation-prone diseases and amyloid states and their balanced therapeutics.

International Journal of Biological Macromolecules, Jul 1, 2011

A sequential addition of acetonitrile to human and bovine immunoglobulin G induces molten globule... more A sequential addition of acetonitrile to human and bovine immunoglobulin G induces molten globulelike state at 50% (v/v) and 60% (v/v) respectively having secondary structure similar to native protein as evident from far-UV circular dichroism and Fourier transform infra red spectroscopy. Further addition of acetonitrile up to 80% forms aggregate of IgG as confirmed by increase in thioflavin T, loss of signals in near-UV CD spectra, decrease in ANS and tryptophan fluorescence. Thus at high acetonitrile concentration, a relatively large amount of partially unfolded intermediates of IgG are present which result in aggregates formation.

Protein Journal, May 19, 2007

A lectin present in seeds of Clitoria ternatea agglutinated trypsin-treated human B erythrocytes.... more A lectin present in seeds of Clitoria ternatea agglutinated trypsin-treated human B erythrocytes. The sugar specificity assay indicated that lectin belongs to Gal/Gal NAc-specific group. Hence the lectin, designated C. ternatea agglutinin (CTA), was purified by the combination of acetic acid precipitation, salt fractionation and affinity chromatography. HPLC gel filtration, SDS-polyacrylamide gel electrophoresis and mass spectrometry indicated that the native lectin is composed of two identical subunits of molecular weight 34.7 kDa associated by non covalent bonds. The N-terminal sequence of CTA shared homology with Glycine max and Pisum sativum. Complete sequence was also found to be homologous to S-64 protein of Glycine max, suggesting that CTA probably exhibits both hemagglutination and probably sugar uptake activity. The carbohydrate binding specificity of the lectin was investigated by quantitative turbidity measurements, and percent inhibition assays. Based on these assays, we conclude that CTA binds b-D-galactosides, and also may has an extended specificity towards non-reducing terminal Neu5Aca2,6Gal.