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Research Publications (Applied Sciences)

Permanent URI for this collectionhttp://ir-dev.dut.ac.za/handle/10321/213

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Author: search.filters.author.Bisetty, KrishnaEnd date: 2019

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    Molecular dynamics simulation of chitinase I from Thermomyces lanuginosus SSBP to ensure optimal activity
    (Taylor and Fancis Online, 2016-09-22) Khan, Faez Iqbal; Bisetty, Krishna; Gu, Ke-Ren; Singh, Suren; Permaul, Kugen; Hassan, Md. Imtaiyaz; Wei, Dong-Qing
    The fungal chitinase I obtained from Thermomyces lanuginosus SSBP, a thermophilic deuteromycete, has an optimum growth temperature and pH of 323.15 K and 6.5, respectively. This enzyme plays an important task in the defence mechanism of organisms against chitin-containing parasites by hydrolysing β-1, 4-linkages in chitin. It acts as both anti-fungal and biofouling agents, with some being thermostable and suitable for the industrial applications. Three-dimensional model of chitinase I enzyme was predicted and analysed using various bioinformatics tools. The structure of chitinase I exhibited a well-defined TIM barrel topology with an eight-stranded α/β domain. Structural analysis and folding studies at temperatures ranging from 300 to 375 K using 10 ns molecular dynamics simulations clearly showed the stability of the protein was evenly distributed even at higher temperatures, in accordance with the experimental results. We also carried out a number of 20 ns constant pH molecular dynamics simulations of chitinase I at a pH range 2–6 in a solvent. This work was aimed at establishing the optimum activity and stability profiles of chitinase I. We observed a strong conformational pH dependence of chitinase I and the enzyme retained their characteristic TIM barrel topology at low pH.
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    Chitinase from Thermomyces lanuginosus SSBP and its biotechnological applications
    (Springerlink, 2015) Khan, Faez Iqbal; Bisetty, Krishna; Singh, Suren; Permaul, Kugen; Hassan, Md. Imtaiyaz
    Chitinases are ubiquitous class of extracellu-lar enzymes, which have gained attention in the past few years due to their wide biotechnological applications. The effectiveness of conventional insecticides is increasingly compromised by the occurrence of resistance; thus, chi-tinase offers a potential alternative to the use of chemical fungicides. The thermostable enzymes from thermophilic microorganisms have numerous industrial, medical, envi-ronmental and biotechnological applications due to their high stability for temperature and pH. Thermomyces lanug-inosus produced a large number of chitinases, of which chi-tinase I and II are successfully cloned and purified recently. Molecular dynamic simulations revealed that the stability of these enzymes are maintained even at higher tempera-ture. In this review article we have focused on chitinases from different sources, mainly fungal chitinase of T. lanug-inosus and its industrial application.
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    Theoretical principles and applications of high performance capillary electrophoresis
    (Nova Science Publishers, 2015) Bathinapatla, Ayyappa; Kanchi, Suvardhan; Sabela, Myalowenkosi I.; Bisetty, Krishna
    This book chapter is aimed at addressing the theoretical principles and applications of capillary electrophoresis (CE) for the separation of high intensity artificial sweeteners. Electrophoresis is a technique in which solutes are separated by their movement with different rates of migration in the presence of an electric field. Capillary electrophoresis emerged as a combination of the separation mechanism of electrophoresis and instrumental automation concepts in chromatography. Its separation mainly depends on the difference in the solutes migration in an electric field caused by the application of relatively high voltages, thus generating an electro-osmotic flow (EOF) within the narrow-bore capillaries filled with the background electrolyte. Currently capillary electrophoresis is a very powerful analytical technique with a major and outstanding importance in separations of compounds such as amino acids, chiral drugs, vitamins, pesticides etc., because of simpler method development, minimal sample volume requirements and lack of organic waste. The main advantage of capillary electrophoresis over conventional techniques is the availability of the number of modes with different operating and separation characteristics include free zone electrophoresis and molecular weight based separations (capillary zone electrophoresis), micellar based separations (micellar electrokinetic chromatography), chiral separations (electrokinetic chromatography), isotachophoresis and isoelectrofocusing makes it a more versatile technique being able to analyse a wide range of analytes. The ultimate goal of the analytical separations is to achieve low detection limits and CE is compatible with different external and internal detectors such as UV or photodiode array detector (DAD) similar to HPLC. CE also provides an indirect UV detection for analytes that do not absorb in the UV region. Besides the UV detection, CE provides five types of detection modes with special instrumental fittings such as Fluorescence, Laserinduced Fluorescence, Amperometry, Conductivity and Mass spectrometry. Infact, the lowest detection limits attained in the whole field of separations are for CE with laser induced fluorescence detection. Regarding the applications of CE, the separation and determination of high intensity sweeteners were discussed in this chapter. The materials which show sweetness are divided into two types (i) nutritive sweeteners and (ii) non-nutritive sweeteners. The main nutritive sweeteners include glucose, crystalline fructose, dextrose, corn sweeteners, honey, lactose, maltose, invert sugars, concentrated fruit juice, refined sugars, high fructose corn syrup and various syrups. Non-nutritive sweeteners are sub-divided into two groups of artificial sweeteners and reduced polyols. On the other hand, based on their generation; artificial sweeteners can further be divided into three types as (a) first generation artificial sweeteners which includes saccharin, cyclamate and glycyrrhizin (b) second generation artificial sweeteners are aspartame, acesulfame K, thaumatin and neohesperidinedihydrochalcone (c) neotame, sucralose, alitame and steviol glycosides falls under third generation artificial sweeteners. Artificial sweeteners are also classified into three types based on their synthesis and extraction: (i) synthetic (saccharin, cyclamate, aspartame, acesulfame K, neotame, sucralose, alitame) (ii) semi-synthetic (neohesperidinedihydrochalcone) and (iii) natural sweeteners (steviol glycosides, mogrosides and brazzein protein). Polyols are other groups of reduced-calorie sweeteners which provide bulk of the sweetness, but with fewer calories than sugars. The commonly used polyols are: erythritol, mannitol, isomalt, lactitol, maltitol, xylitol, sorbitol and hydrogenated starch hydrolysates (HSH). The studies revealed that capillary electrophoresis was successfully used for the separation of high intensity artificial sweeteners such as neotame, sucralose and steviol glycosides. Additionally, the available methods for the other artificial sweeteners using capillary electrophoresis were reviewed besides the above indicated sweeteners.
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    Biosynthesis of ZnO nanoparticles using Jacaranda mimosifolia flowers extract: Synergistic antibacterial activity and molecular simulated facet specific adsorption studies
    (Elsevier, 2016) Sharma, Deepali; Sabela, Myalowenkosi Innocent; Kanchi, Suvardhan; Mdluli, Phumlani Selby; Singh, Gulshan; Stenström, Thor-Axel; Bisetty, Krishna
    The naturally occurring biomolecules present in the plant extracts have been identified to play an active role in the single step formation of nanoparticles with varied morphologies and sizes which is greener and environmen-tally benign. In the present work, spherical zinc oxide nanoparticles (ZnO NPs) of 2–4 nm size were synthesized using aqueous extract of fallen Jacaranda mimosifolia flowers (JMFs), treated as waste. The microwave assisted synthesis was completed successfully within 5 min. Thereafter, phase identification, morphology and optical band gap of the synthesized ZnO NPs were done using X-ray diffraction (XRD), high resolution transmission elec-tron microscopy (HRTEM) and UV–Visible spectroscopy techniques. The composition of JMFs extract was ana-lyzed by gas chromatography–mass spectrometry (GC–MS) and the ZnO NPs confirmation was further explored with fourier transform infrared spectroscopy (FTIR). The GC–MS results confirmed the presence of oleic acid which has high propensity of acting as a reducing and capping agent. The UV–Visible data suggested an optical band gap of 4.03 eV for ZnO NPs indicating their small size due to quantum confinement. Further, facet specific adsorption of oleic acid on the surface of ZnO NPs was studied computationally to find out the im-pact of biomolecules in defining the shape and size of NPs. The viability of gram negative Escherichia coli and gram positive Enterococcus faecium bacteria was found to be 48% and 43%, respectively at high concentration of NPs.
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    Thermostable chitinase II from Thermomyces lanuginosus SSBP: Cloning, structure prediction and molecular dynamics simulations
    (Elsevier, 2015) Khan, Faez Iqbal; Govender, Algasan; Permaul, Kugen; Singh, Suren; Bisetty, Krishna
    Thermomyces lanuginosus is a thermophilic fungus that produces large number of industrially-significant enzymes owing to their inherent stability at high temperatures and wide range of pH optima, including thermostable chitinases that have not been fully characterized. Here, we report cloning, characterization and structure prediction of a gene encoding thermostable chitinase II. Sequence analysis revealed that chitinase II gene encodes a 343 amino acid protein of molecular weight 36.65 kDa. Our study reports thatchitinase II exhibits a well-defined TIM-barrel topology with an eight-stranded α/β domain. Structural analysis and molecular docking studies suggested that Glu176 is essential for enzyme activity. Folding studies of chitinase II using molecular dynamics simulations clearly demonstrated that the stability of the protein was evenly distributed at 350 K.
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    Cloning, expression, and molecular dynamics simulations of a xylosidase obtained from Thermomyces lanuginosus
    (Taylor and Francis Online, 2015-10-19) Gramany, Vashni; Khan, Faez Iqbal; Govender, Algasan; Bisetty, Krishna; Singh, Suren; Permaul, Kugenthiren
    The aim of this study was to clone, express, and characterize a β-xylosidase (Tlxyn1) from the thermophilic fungus Thermomyces lanuginosus SSBP in Pichia pastoris GS115 as well as analyze optimal activity and stability using computational and experimental methods. The enzyme was constitutively expressed using the GAP promoter and secreted into the medium due to the alpha-mating factor secretion signal present on the expression vector pBGPI. The 1276 bp gene consists of an open reading frame that does not contain introns. A 12% SDS–PAGE gel revealed a major protein band at an estimated molecular mass of 50 kDa which corresponded to zymogram analysis. The three-dimensional structure of β-xylosidase was predicted, and molecular dynamics simulations at different ranges of temperature and pH were performed in order to predict optimal activity and folding energy. The results suggested a strong conformational temperature and pH dependence. The recombinant enzyme exhibited optimal activity at pH 7 and 50°C and retained 80% activity at 50°C, pH 7 for about 45 min. This is the first report of the cloning, functional expression, and simulations study of a β-xylosidase from Thermomyces species in a fungal host.
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    Functional insight into Putative Conserved Proteins of Rickettsia rickettsii and their Virulence characterization
    (Bentham Science Publishers, 2015) Shahbaaz, Mohd; Bisetty, Krishna; Ahmad, Faizan
    Abstract: Rickettsia rickettsii is an aerobic, Gram-negative and non-motile coccobacillus known to cause Rocky Mountain spotted fever. The sequenced genome of its 'Sheila Smith' strain contains 1,343 protein-coding genes, 3 rRNA genes and 33 transfer RNA genes. There are 680 hypothetical proteins (HPs) present in the genome of R. rickettsii. Since functions of these proteins are not validated ex-perimentally, characterization of these HPs may play a significant role in understanding the patho-genic mechanisms of R. rickettsii. Hence, functions of these HPs were annotated by in silico methods based on sequence similarity, protein clustering and protein-protein interactions. We have successfully predicted functions of 214 proteins among 680 HPs present in R. rickettsii. These annotated proteins were further classified into 88 enzymes, 59 transport and membrane proteins, 35 binding proteins, 12 structural motifs and the rest of the protein families. Moreo-ver, we identified HPs involved in virulence among 214 functionally annotated proteins. 15 HPs were classified as viru-lence factors and two proteins with the highest scores were selected for further analyses. Additionally, molecular dynam-ics simulations were performed on these selected virulent HPs in order to observe their conformational behaviors. These analyses can further be utilized in the identification of new drug targets for development of better therapeutic agents against the infections caused by R. rickettsii.
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    PKR-inhibitor binds efficiently with human microtubule affinity-regulating kinase 4
    (Elsevier, 2015) Naz, Farha; Shahbaaz, Mohd; Khan, Shama; Bisetty, Krishna; Islam, Asimul; Ahmad, Faizan; Hassan, Md. Imtaiyaz
    MAP/microtubule affinity-regulating kinase 4 (MARK4) plays a central role in the cellular physiology, and it is inseparably linked with many human diseases including cancer, diet induced obesity, type2 diabetes and neurodegenerative disorders. Here, we studied the interaction of PKR-inhibitor with two variants of human MARK4. One variant is named as MARK4-F1 which has 59 N-terminal residues along with kinase domain while another variant is MARK4-F2 which has kinase domain only. Molecular-docking, molecular dynamics (MD) simulation and fluorescence-binding studies were undertaken to understand the role of N-terminal 59-residues in the binding of substrate/inhibitors. Molecular docking studies revealed that the PKR-inhibitor binds in the large hydrophobic cavity of the kinase domain of MARK4 through several hydrophobic and hydrogen-bonded interactions. Furthermore, MD simulation showed a stable param-eters for the complexes of both MARK4-F1 and MARK4-F2 to PKR-inhibitor with marginal difference in their binding affinities. A significant decrease in the fluorescence intensity of MARK4 was observed on successive addition of the PKR-inhibitor. Using fluorescence data we have calculated the binding-affinity and the number of binding site of PKR-inhibitor to the MARK4. A significantly high binding affinity was observed for the PKR-inhibitor to the MARK4 variants. However, there is no any significant difference in the binding affinity of PKR-inhibitor to the MARK4 variants was observed, indicating that 59 N-terminal residues of MARK4-F1 are not playing a crucial role in the ligand binding. The present study will pro-vide an insights into designing of new PKR-inhibitor derivative as potent and selective therapeutic agent against many life threatening diseases which are associated with MARK4.
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    Designing new kinase inhibitor derivatives as therapeutics against common complex diseases : structural basis of microtubule affinity-regulating kinase 4 (MARK4) inhibition
    (Mary Ann Liebert, Inc., 2015) Naz, Farha; Shahbaaz, Mohd; Bisetty, Krishna; Islam, Asimul; Ahmad, Faizan; Hassan, Md. Imtaiyaz
    Drug development for common complex diseases is in need of new molecular entities and actionable drug targets. MAP/microtubule affinity-regulating kinase 4 (MARK4) is associated with numerous diseases such as neurodegenerative disorders, obesity, cancer, and type 2 diabetes. Understanding the structural basis of ligands’ (inhibitors) and substrates’ binding to MARK4 is crucial to design new kinase inhibitors for therapeutic pur-poses. This study reports new observations on docking three well-known kinase inhibitors in the kinase domain of MARK4 variants and the calculated binding affinity. These variants of MARK4 are named as MARK4-F1 (59 N-terminal residues along with kinase domain) and MARK4-F2 (kinase domain of MARK4). We addi-tionally performed molecular dynamics (MD) simulation and fluorescence binding studies to calculate the actual binding affinity of kinase inhibitors, BX-912, BX-795, and OTSSP167 (hydrochloride) for the MARK4. Docking analyses revealed that ligands bind in the large hydrophobic cavity of the kinase domain of MARK4 through several hydrophobic and hydrogen-bonded interactions. Simulations suggested that OTSSP167 (hy-drochloride) is forming a stable complex, and hence the best inhibitor of MARK4. Intrinsic fluorescence of MARK4 was significantly quenched by addition of ligands, indicating their potential binding to MARK4. A lower KD value of MARK4 with OTSSP167 (hydrochloride) suggested that it is a better interacting partner than BX-912 and BX-795. These data form a basis for designing novel and potent OTSSP167 (hydrochloride) derivatives as therapeutic candidates against common complex diseases. The inhibitors designed as such might possibly suppress the growth of tumor-forming cells and be potentially applied for treatment of a wide range of human cancers as well.
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    Thermostable chitinase II from Thermomyces lanuginosus SSBP : Cloning, structure prediction and molecular dynamics simulations
    (Elsevier, 2015-04-08) Khan, Faez Iqbal; Govender, Algasan; Permaul, Kugen; Singh, Suren; Bisetty, Krishna
    Thermomyces lanuginosus is a thermophilic fungus that produces large number of industrially-significant enzymes owing to their inherent stability at high temperatures and wide range of pH optima, including thermostable chitinases that have not been fully characterized. Here, we report cloning, characterization and structure prediction of a gene encoding thermostable chitinase II. Sequence analysis revealed that chitinase II gene encodes a 343 amino acid protein of molecular weight 36.65 kDa. Our study reports that chitinase II exhibits a well-defined TIM-barrel topology with an eight-stranded α/β domain. Structural analysis and molecular docking studies suggested that Glu176 is essential for enzyme activity. Folding studies of chitinase II using molecular dynamics simulations clearly demonstrated that the stability of the protein was evenly distributed at 350 K.