Pradeep Mandal

Publications (13) View all

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  Available from: Pradeep Mandal

  Article: Expression, purification, crystallization and preliminary X-ray diffraction analysis of carbonyl reductase from Candida parapsilosis ATCC 7330.

  Nidhi Aggarwal, P K Mandal, Namasivayam Gautham, Anju Chadha
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  ABSTRACT: The NAD(P)H-dependent carbonyl reductase from Candida parapsilosis ATCC 7330 catalyses the asymmetric reduction of ethyl 4-phenyl-2-oxobutanoate to ethyl (R)-4-phenyl-2-hydroxybutanoate, a precursor of angiotensin-converting enzyme inhibitors such as Cilazapril and Benazepril. The carbonyl reductase was expressed in Escherichia coli and purified by GST-affinity and size-exclusion chromatography. Crystals were obtained by the hanging-drop vapour-diffusion method and diffracted to 1.86 Å resolution. The asymmetric unit contained two molecules of carbonyl reductase, with a solvent content of 48%. The structure was solved by molecular replacement using cinnamyl alcohol dehydrogenase from Saccharomyces cerevisiae as a search model.
  Acta Crystallographica Section F Structural Biology and Crystallization Communications 03/2013; 69(Pt 3):313-5. · 0.51 Impact Factor
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  Article: Interactions of Mn 2+ with a non-self-complementary Z-type DNA duplex

  P K Mandal, S Venkadesh, N Gautham
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  ABSTRACT: Crystal structures of the hexanucleotide d(CACGCG)Ád(CGCGTG) were determined in two crystal lattices when different concentrations of the counterion Mn 2+ were used in crystallization. The availability of Mn 2+ during the crystallization process appears to play an important role in inducing different crystal packings that lead to crystals belonging to the two space groups P2 1 and P6 5 . Analysis of the molecular interactions of Mn 2+ with the Z-form duplexes shows direct coordination to the purine residues G and A.
  Acta Crystallographica Section F Structural Biology and Crystallization Communications 12/2012; 68. · 0.51 Impact Factor
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  Article: Anti-inflammatory property of n-hexadecanoic acid: structural evidence and kinetic assessment.

  Vasudevan Aparna, Kalarickal V Dileep, Pradeep K Mandal, Ponnuraj Karthe, Chittalakkottu Sadasivan, Madathilkovilakathu Haridas
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  ABSTRACT: Ester bond hydrolysis of membrane phospholipids by Phospholipase A(2) and consequent release of fatty acids are the initiating steps of inflammation. It is proposed in this study that the inhibition of phospholipase A(2) is one of the ways to control inflammation. Investigations are carried out to identify the mode of inhibition of phospholipase A(2) by the n-hexadecanoic acid. It may help in designing of specific inhibitors of phospholipase A(2) as anti-inflammatory agents. The enzyme kinetics study proved that n-hexadecanoic acid inhibits phospholipase A(2) in a competitive manner. It was identified from the crystal structure at 2.5 Å resolution that the position of n-hexadecanoic acid is in the active site of the phospholipase A(2). The binding constant and binding energy have also been calculated using Isothermal Titration Calorimetry. Also, the binding energy of n-hexadecanoic acid to phospholipase A(2) was calculated by in silico method and compared with known inhibitors. It may be concluded from the structural and kinetics studies that the fatty acid, n-hexadecanoic acid, is an inhibitor of phospholipase A(2), hence, an anti-inflammatory compound. The inferences from the present study validate the rigorous use of medicated oils rich in n-hexadecanoic acid for the treatment of rheumatic symptoms in the traditional medical system of India, Ayurveda.
  Chemical Biology &amp Drug Design 05/2012; 80(3):434-9. · 2.28 Impact Factor
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  Article: Structure of the tetradecanucleotide d(CCCCGGTACCGGGG)2 as an A-DNA duplex.

  Pradeep Kumar Mandal, Sarkarai Venkadesh, Namasivayam Gautham
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  ABSTRACT: The crystal structure of the tetradecanucleotide sequence d(CCCCGGTACCGGGG)(2) has been determined at 2.5 Å resolution in the tetragonal space group P4(1). This sequence was designed with the expectation of a four-way junction. However, the sequence crystallized as an A-DNA duplex and represents more than one full turn of the A-helix. The crystallographic asymmetric unit consists of one tetradecanucleotide duplex. The structural parameters of the A-type DNA duplex structure and the crystal-packing arrangement are described. One Mn(2+) ion was identified with direct coordination to the N7 position of G(13) and a water molecule at the major-groove side of the C(2)·G(13) base pair.
  Acta Crystallographica Section F Structural Biology and Crystallization Communications 04/2012; 68(Pt 4):393-9. · 0.51 Impact Factor
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  Article: Crystallographic and spectroscopic studies of d(CCGGTACCGG).

  S Venkadesh, P K Mandal, N Gautham
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  ABSTRACT: The decanucleotide sequence d(CCGGTACCGG) crystallizes as a four-way junction at low cobalt ion concentrations (i.e., 1 mM). When the cobalt concentration in the crystallization solution is increased to 5 mM, the sequence crystallizes as resolved B-DNA duplexes. Gel retardation studies of the decamer show both a faint slow-moving band and a much thicker fast-moving band at low cobalt ion concentrations, and only the intense fast-moving band at higher ion concentration. Circular dichroism (CD) spectroscopy of the decamer indicates a structural transition as the cobalt ion concentration in the solution is increased, probably from B-type to A-type DNA. These studies revealed that the oligomer sequence has several conformations and structures accessible to it, in a manner dependent on sequence, ion concentration, and DNA concentration. [Supplementary materials are available for this article. Go to the publisher's online edition of Nucleosides, Nucleotides & Nucleic Acids for the following free supplemental resources(s): Supplementary Figures 1, 2, and 3.].
  Nucleosides Nucleotides &amp Nucleic Acids 03/2012; 31(3):184-96. · 0.90 Impact Factor