Santanu Deb-choudhury | AgResearch Limited (original) (raw)

Papers by Santanu Deb-choudhury

PloS one, 2015

Thaumatin-like proteins (TLPs) and chitinases are the main constituents of so-called protein haze... more Thaumatin-like proteins (TLPs) and chitinases are the main constituents of so-called protein hazes which can form in finished white wine and which is a great concern of winemakers. These soluble pathogenesis-related (PR) proteins are extracted from grape berries. However, their distribution in different grape tissues is not well documented. In this study, proteins were first separately extracted from the skin, pulp and seed of Sauvignon Blanc grapes, followed by trypsin digestion and analysis by liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS). Proteins identified included 75 proteins from Sauvignon Blanc grape skin, 63 from grape pulp and 35 from grape seed, mostly functionally classified as associated with metabolism and energy. Some were present exclusively in specific grape tissues; for example, proteins involved in photosynthesis were only detected in grape skin and proteins found in alcoholic fermentation were only detected in grape pulp. M...

Molecular and cellular biochemistry, 1997

Characterization of cathepsin B from buffalo kidney and goat spleen showed the presence of isozym... more Characterization of cathepsin B from buffalo kidney and goat spleen showed the presence of isozymes in case of the goat spleen (GSCB-I and GSCB-II) whereas cathepsin B from buffalo kidney exhibited only one form (BKCB). The molecular weights determined by SDS-PAGE for GSCB-I, GSCB-II, and BKCB were 25.7, 26.6 and 25.5 kDa respectively. The kinetic parameters (Km and Vmax) of GSCB-I showed close similarities with BKCB against alpha-N-benzoyl-DL-arginine-2-napthylamide whereas GSCB-II was closer to the buffalo enzyme with regards to its activity against Z-Arg-Arg-MCA and Z-Phe-Arg-MCA. All the three enzymes had similar sensitivities towards urea, antipain and leupeptin. However, clear differences were observed in the inhibition patterns of the enzyme with iodoacetic acid and iodoacetamide. Differences in the kinetic, immunogenic and some catalytic properties of GSCB-I and II, which had similarities with regard to most of their physico-chemical properties, were considered to be due to ...

Journal of cosmetic science

There is increasing awareness of the importance of reductive and oxidative (redox) protein damage... more There is increasing awareness of the importance of reductive and oxidative (redox) protein damage in protein-based materials including, hair, wool, nails, and skin. Light-induced damage to protein-based materials is of particular concern because of its impact on age-related degradation and product life spans. Consequently, cosmetic applications frequently target hair and skin restoration, where the integrity of the constituent filamentous proteins is essential to a healthy appearance. The keratins constitute an important subset of the structural proteins within skin, hair, and wool. We will introduce a means to assess damage to this important group of proteins at the molecular level, utilizing proteomic techniques to track the formation or degradation of sensitive peptides within intermediate filament proteins. The degradation of three molecular markers of redox damage, the peptides SFGYR, LASDDFR, and DVEEWYIR, along with the formation of their oxidized products, is demonstrated af...

Indian journal of biochemistry & biophysics, 1997

A simple purification scheme was developed for isolation and purification of cathepsin B from buf... more A simple purification scheme was developed for isolation and purification of cathepsin B from buffalo kidney. The use of CM-Sephadex and chromatofocusing helped in better and simultaneous separation of cathepsin B, H and L. As judged by PAGE and SDS-PAGE studies, the enzyme was found to be pure on the basis of charge and had a molecular mass of 25.5 kDa. The amino acid composition, number of free sulfhydryl groups and other major physico-chemical properties of the purified enzyme were similar to the properties reported for cathepsin B from other sources/tissues. However, the NH2-terminal amino acid residue of the enzyme was found to be Ala as against Leu reported from other tissues/species. The total carbohydrate content was also found to be significantly lower (3.6%) as compared to 7.0-7.6% reported for the enzyme from other sources. Thiol reducing compounds activated the enzyme whereas thiol blocking compounds inhibited it. The buffalo kidney enzyme hydrolyzed Z-Phe-Arg-MCA (Vmax/...

Journal of Food Composition and Analysis, 2015

ABSTRACT In this work egg white was used to study the effect of common food processing conditions... more ABSTRACT In this work egg white was used to study the effect of common food processing conditions on in vitro protein digestibility and on the modification of amino acid residues. Egg white was treated at 20 °C and 100 °C, varying pH (2-12), and zero and high-salt concentrations (0 mM, 200 mM). The digestibility assays confirmed previous findings that exposure of egg white to high temperatures increased digestibility markedly. However, the effects of pH and salt concentrations were found to be minimal. Proteomic analysis was utilised to map amino acid modifications, revealing that increased digestibility in heated egg white comes at the cost of a higher degree of amino acid residue-level modification. The predominant modifications were found to be dehydration and deamidation reactions that increased with increasing heat exposure time. The effects of the Maillard reaction on digestibility and amino acid modification were also determined for egg white in the presence of glucose and methylglyoxal. Proteomic assessment clearly revealed a high degree of modification of up to 38% of available arginine residues in the presence of methylglyoxal. An important correlation was therefore established between increased levels of Maillard reaction products and a decrease in the nutritional value of egg white.

Fibers and Polymers, 2014

Methods in Molecular Biology, 2013

One of the promising new techniques in the production of biomaterials is the electrospinning proc... more One of the promising new techniques in the production of biomaterials is the electrospinning process, whereby fibers of uniform thickness down to the nanoscale can be produced from solutions of polymeric material in a high electric field. At the same time there has been increasing interest in the manufacture of biodegradable nanomaterials from nonfood sources and this has led to investigations into the use of proteins such as collagen, keratin, and fibroin. Explorations into the use of these proteins in the generation of mats suitable for filtration purposes or scaffolds with applications for tissue engineering form the subject of this review.

Polymer Degradation and Stability, 2014

ABSTRACT Keratins derived from wool and feathers are a source of raw materials for biomaterial us... more ABSTRACT Keratins derived from wool and feathers are a source of raw materials for biomaterial use. Such biomaterials are essentially biodegradable polyamides, and offer many favourable features such as biocompatibility in contrast with petro-derived synthetic materials. In the present study, raw wool samples were dissolved in hot ionic liquid (1-butyl-3-methylimidazolium chloride) at temperatures ranging from 120 to 180 °C, resulting in regenerated keratins after coagulation with water. The physicochemical characteristics of the regenerated keratins were evaluated with respect to their protein profile, thermal stability, mechanical performance and SEM morphology, and contrasted with those of raw wool. Cysteine content reduced significantly on increasing temperature of ionic liquid and some disordering of protein secondary structures occurred in regenerated keratins. Keratin regenerated from a solution prepared with ionic liquid at 180 °C showed improved thermal processing properties, and it revealed dense fibrous network morphology of the film's cross-sectional surface produced under compression moulding. This in-depth study on regenerated keratins demonstrates a potential new route for the conversion of keratinous materials into bio-resin for industrial applications. However, further development is required to create keratinous materials that are melt-processable like classical synthetic polymers.

Journal of Agricultural and Food Chemistry, 2014

Thermal treatment of meat proteins induces a range of observable and molecular-level changes. In ... more Thermal treatment of meat proteins induces a range of observable and molecular-level changes. In order to understand and track these heat-induced modifications at the amino acid level, various analytical techniques were used. Changes were observed both in the soluble and in the insoluble fractions after hydrothermal treatment of minced beef samples. Redox proteomics clearly indicated increasing oxidative modification of proteins with increased heat exposure. Collagens in the soluble fraction and myosin in the insoluble fraction were found to be highly susceptible to such modifications. Maillard reaction products in the insoluble and pyrrolidone formation in the soluble fraction steadily increased with increased heat exposure. Fluorescence studies indicated a rapid increase in fluorescence with heat, suggesting the formation of advanced glycation end products. Overall these results provide a deeper understanding of the effect of cooking on meat proteins and the possible relationship to processing conditions in meat-derived food.

Proteins: Structure, Function, and Bioinformatics, 2014

The disulfide bond network within the cortex of mammalian hair has a critical influence on the ph... more The disulfide bond network within the cortex of mammalian hair has a critical influence on the physical and mechanical characteristics of the fiber. The location, pattern, and accessibility of free and crosslinked cysteines underpin the properties of this network, but have been very difficult to map and understand, because traditional protein extraction techniques require the disruption of these disulfide bonds. Cysteine accessibility in both trichocyte keratins and keratin associated proteins (KAPs) of wool was investigated using staged labeling, where reductants and chaotropic agents were used to expose cysteines in a stepwise fashion according to their accessibility. Cysteines thus exposed were labeled with distinguishable alkylation agents. Proteomic profiling was used to map peptide modifications and thereby explore the role of KAPs in crosslinking keratins. Labeled cysteines from KAPs were detected when wool was extracted with reductant only. Among them were sequences from the end domains of KAPs, indicating that those cysteines were easily accessible in the fiber and could be involved in forming interdisulfide linkages with keratins or with other KAPs. Some of the identified peptides were from the rod domains of Types I and II keratins, with their cysteines positioned on the exposed surface of the α-helix. Peptides were also identified from keratin head and tail domains, demonstrating that they are not buried within the filament structure and, hence, have a possible role in forming disulfide linkages. From this study, a deeper understanding of the accessibility and potential reactivity of cysteine residues in the wool fiber cortex was obtained. Proteins 2015; 83:224-234. © 2014 Wiley Periodicals, Inc.

The separation of the upper dermal of the skin (the papillary layer or grain) from the lower derm... more The separation of the upper dermal of the skin (the papillary layer or grain) from the lower dermis (corium) is regarded as a defect in leather making. It is difficult to detect pelts at an early processing stage and it only becomes really apparent once the skin is made into leather. There would be great advantages in detecting the problem

Photochemical & Photobiological Sciences, 2013

The effect of reactive oxidation species (ROS) on tryptophan or tyrosine was investigated by qual... more The effect of reactive oxidation species (ROS) on tryptophan or tyrosine was investigated by qualitatively determining the major detectable oxidation products generated by hydroxyl radicals, produced by the Fenton process, or singlet oxygen, generated by exposure to green light in the presence of Rose Bengal, on these photosensitive amino acids in synthetic pentapeptides. Based on mass spectrometric analysis it would appear that the hydroxyl radical favours a pathway leading to the formation of tryptophandione-based products from tryptophan. In contrast singlet oxygen attack appears to favour the formation of kynurenine-type products from tryptophan. Specific oxidative products observed proteomically are therefore potentially able to discriminate between predominant ROS-mediated pathways. To validate these findings, a keratin-enriched extract was exposed to UVB light under aqueous conditions. The observation of the conversion of tryptophan to hydroxytryptophan in marker peptides, and the absence of singlet-oxygen specific modifications, suggested that under these conditions oxidative degradation occurred primarily via hydroxyl radical attack. These observations provide the first direct proteomic evidence of the dominant photodegradation pathways in wet wool.

Journal of Proteomics, 2010

The wool proteome has been largely uncharted due to a lack of database coverage, poor protein ext... more The wool proteome has been largely uncharted due to a lack of database coverage, poor protein extractability and dynamic range issues. Yet, investigating correlations between wool physical properties and protein content, or characterising UV-, heat-or processinginduced protein damage requires the availability of an identifiable and identified proteome.

Journal of Proteomics, 2009

Keratin-associated proteins (KAPs) are important constituents of the wool cuticle, comprised of t... more Keratin-associated proteins (KAPs) are important constituents of the wool cuticle, comprised of the endo-, exocuticle and a-layers, which contribute significantly to the fibre's molecular and mechanical characteristics. Relatively little is known about the distribution of specific KAPs across these layers, and correct protein identification of individual KAPs is difficult due to extensive homology and identity among individual KAPs.

Journal of Proteomics, 2012

With ongoing efforts to make wool more competitive alongside other fibres, notably synthetics, th... more With ongoing efforts to make wool more competitive alongside other fibres, notably synthetics, there is a need to obtain a better understanding of the relationship between protein composition and characteristic wool properties to assist sheep breeding programmes. Before this can be achieved, the wool proteome needs to be mapped, by gel and non-gel techniques, and methods developed to reliably quantitate protein expression. Nevertheless, in setting out to achieve this, there are numerous challenges to be faced in the application of proteomics to wool, including the relative lack of wool protein sequence information in the publically accessible databases, the wide variety of proteins in the wool fibre, the high homology within the Type I and Type II keratins, the high degree of homology and polymorphism within individual keratin associated protein families, the dominance of the keratin proteins over others in wool and the peculiar chemistries found in keratins and their associated proteins. This review will discuss the various strategies that have been developed to both identify these proteins in the wool protein map and quantify them with the view to their application to the identification of markers for wool quality traits.

Journal of Biochemical and Biophysical Methods, 2008

Excessive removal of structural material from skin during leather processing results in unattract... more Excessive removal of structural material from skin during leather processing results in unattractive crease formation in leather. It is difficult to detect this in pelts at an early processing stage as it only becomes really apparent once the skin is made into leather. There would be great advantages in detecting the problem at the pickled pelt stage (skins treated with sodium sulphide and lime, bated with enzymes, and then preserved in NaCl and sulphuric acid) so that adjustments to the processing could be made to mitigate the effect. A novel bio-sensor for inspection of pickled lamb pelts has been fabricated and developed. The sensor has the planar Interdigital structure. The experimental results show that the sensor has a great potential to predict the quality of leather in a non-invasive and non-destructive way.

Journal of Proteome Research, 2010

The cuticle is responsible for important wool fiber characteristics such as handle and abrasion r... more The cuticle is responsible for important wool fiber characteristics such as handle and abrasion resistance, which impact on the fiber's performance in both interior and apparel textiles. The cuticle proteome, however, is not well understood due to the difficulty in isolating pure wool cuticle and its significant resistance to protein extraction, which is attributed to the presence of extensive disulfide and isopeptide cross-linking. We investigated the proteome of highly pure Merino wool cuticle using a combined strategy of chemical and enzymatic digestion and identified 108 proteins, including proteins responsible for a variety of cellular processes. The majority of identified proteins belonged to keratin and nonkeratin protein families known to play an important role in molecular assembly and cellular structure. Keratinassociated, intermediate filament and cytoskeletal keratin proteins were identified as the most prominent keratinous cuticular constituents, while histones, tubulins, and desmosomes were the key nonkeratin structural proteins. We conclude that a variety of proteins contribute to cuticle structure and fiber characteristics, and that the keratinous protein families of IFPs and KAPs represent the most important cuticular constituents.

Journal of Photochemistry and Photobiology B: Biology, 2010

Photo-oxidation of proteinaceous fibres correlates directly to lowered appearance retention and p... more Photo-oxidation of proteinaceous fibres correlates directly to lowered appearance retention and performance, with particular commercial significance for wool and human hair. We here outline the first detailed proteomic evaluation of differential photo-oxidation occurring in the cuticle and cortex of wool fibres.

Journal of Food Composition and Analysis, 2014

ABSTRACT Lipid oxidation plays a critical role in the quality of meat and meat products; however,... more ABSTRACT Lipid oxidation plays a critical role in the quality of meat and meat products; however, lipid degradation is generally evaluated at a holistic level, without attention to spatial distribution. Marker lipids were selected based on their relative abundance and characteristic MS fragmentation patterns (10 phospholipids, 2 triglycerides, and cholesterol). These markers were subsequently utilised for temporal and spatial profiling of lipid degradation in bovine M. longissimus dorsi lumborum steaks subjected to high (packaged in 80% O2/20% CO2 modified atmosphere), atmospheric (oxygen permeable film) and ultra-low (vacuum-packaged) oxygen packaging during storage through matrix-assisted laser desorption/ionization time-of-flight/time-of-flight (MALDI-TOF/TOF) mass spectrometric imaging. Interestingly, markers showed highly contrasting effects in terms of their oxidative stability over time. The relative abundance of phophatidylcholines generally declined rapidly under high oxygen conditions. In contrast, PC 18:1/18:0 showed high relatively stability to oxidation. Cholesterol also displayed high relative stability. Overall, high oxygen packing was found to result in rapid lipid degradation, while vacuum-packaging significantly mitigated lipid degradation. Oxidative degradation profiles were spatially heterogeneous across meat sub-samples and differences were also observed from the centre and edge of the steaks. This new approach to tracking lipid degradation directly from meat samples offers increasingly precise tracking of modification in meat and other foods.

Journal of Applied Polymer Science, 2013

ABSTRACT Wool surface and interior modification can impart favorable properties, such as felting/... more ABSTRACT Wool surface and interior modification can impart favorable properties, such as felting/shrink resistance, settability, or improved affinity for dyes. However, in principle such modification may have an either beneficial or adverse effect on the subsequent photostability of the modified wool. In this study, a range of representative physical and chemical modification approaches including the use of helium gas plasma, papain, acylation with acid anhydride, and permanganate oxidation were applied to wool fabrics, and the subsequent effects characterized using scanning electron microscopy, FTIR‐ATR, contact angle goniometry, fluorescence spectrophotometry, and tensile strength test. The relative photostability of control and treated wool were evaluated in terms of coloration changes under UVA, UVB, and blue light irradiation. We have shown that the subsequent photostability of modified wool fabrics is highly dependent on the modification type, and this factor should be carefully considered in the design and application of wool treatments. © 2012 Wiley Periodicals, Inc. J. Appl. Polym. Sci., 2013