@article { ISI:000232157000036, title = {Cloning, preparation and preliminary crystallographic studies of penicillin V acylase autoproteolytic processing mutants}, journal = {Acta Crystallographica Section F-Structural Biology and Crystallization Communications}, volume = {61}, number = {1}, year = {2005}, month = {JAN}, pages = {124-127}, publisher = {BLACKWELL PUBLISHING}, type = {Article}, address = {9600 GARSINGTON RD, OXFORD OX4 2DQ, OXON, ENGLAND}, issn = {1744-3091}, doi = {10.1107/S1744309104031227}, author = {Chandra, P. M. and Brannigan, James A. and Prabhune, Asmita and Pundle, A. and Turkenburg, J. P. and Dodson, Guy G. and Suresh, C. G.} } @article { ISI:000232320400015, title = {Cloning, purification, crystallization and preliminary structural studies of penicillin V acylase from Bacillus subtilis}, journal = {Acta Crystallographica Section F-Structural Biology Communications}, volume = {61}, number = {7}, year = {2005}, month = {JUL}, pages = {680-683}, publisher = {INT UNION CRYSTALLOGRAPHY}, type = {Article}, address = {2 ABBEY SQ, CHESTER, CH1 2HU, ENGLAND}, abstract = {

{Penicillin acylase proteins are amidohydrolase enzymes that cleave penicillins at the amide bond connecting the side chain to their beta-lactam nucleus. An unannotated protein from Bacillus subtilis has been expressed in Escherichia coli, purified and confirmed to possess penicillin V acylase activity. The protein was crystallized using the hanging-drop vapour-diffusion method from a solution containing 4 M sodium formate in 100 mM Tris-HCl buffer pH 8.2. Diffraction data were collected under cryogenic conditions to a spacing of 2.5 A. The crystals belonged to the orthorhombic space group C222(1), with unit-cell parameters a = 111.0

}, issn = {2053-230X}, author = {Rathinaswamy, P. and Pundle, A. V. and Prabhune, Asmita and SivaRaman, H. and Brannigan, James A. and Dodson, Guy G. and Suresh, C. G.} } @article { ISI:000232157000041, title = {Crystallization and preliminary x-ray characterization of a lectin from Cicer arietinum (chickpea)}, journal = {Acta Crystallographica Section F-Structural Biology and Crystallization Communications}, volume = {61}, number = {1}, year = {2005}, month = {JAN}, pages = {141-143}, publisher = {BLACKWELL PUBLISHING}, type = {Article}, address = {9600 GARSINGTON RD, OXFORD OX4 2DQ, OXON, ENGLAND}, issn = {1744-3091}, doi = {10.1107/S1744309104032166}, author = {Katre, Uma V. and Gaikwad, S. M. and Bhagyawant, S. S. and Deshpande, U. D. and Khan, Mohammad Islam and Suresh, C. G.} } @article { ISI:000258819000009, title = {Characterization of smallest active monomeric penicillin V acylase from new source: a yeast, rhodotorula aurantiaca (NCIM 3425)}, journal = {Process Biochemistry}, volume = {43}, number = {9}, year = {2008}, month = {SEP}, pages = {961-967}, publisher = {ELSEVIER SCI LTD}, type = {Article}, address = {THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, OXON, ENGLAND}, abstract = {

An intracellular monomeric penicillin V acylase (PVA) of 36,000 Da exhibiting pI of 4.19, purified from newly identified yeast source, Rhodotorula aurantiaca (NCIM 3425). The enzyme was purified by hydrophobic interaction chromatography. The enzyme showed optimal activity at 45 degrees C and retained 80\% activity after incubation at 45 degrees C and pH 5.5 for I h. The enzyme showed maximum activity at pH 5.5 and was very stable between pH 5.5-6.5 with optimum stability at pH 6.0. It exhibited 50\% of its original activity after 30 min incubation at 60 degrees C. Enzyme hydrolyzed substrates with benzyl side chain but preferred penicillin V as primary substrate. N-terminally located serine supports the fact that it belongs to Ntn (N-terminal nucleophile)-hydrolase superfamily. The initial ten amino acid residues of R. aurantiaca PVA were identical to the initial sequence of NADH dehydrogenase (EC 1.6.99.3): however the enzyme lacks dehydrogenase activity. EGTA, EDTA, hexane and ethyl acetate stabilized the activity where as small chain alcohols inhibited it. 1,4-Dioxane, THF (tetrahydrofurane), phenol and benzyl alcohol severely inhibited enzyme activity while BME and DTT increased it. Tween 80 and Tween 20 highly enhanced the activity where as SIDS and Triton X-100 inhibited it. (C) 2008 Elsevier Ltd. All rights reserved.

}, keywords = {Intracellular enzyme, N-terminal sequencing, Penicillin V acylase, Purification, Rhodotorula aurantiaca, Substrate specificity}, issn = {1359-5113}, doi = {10.1016/j.procbio.2008.04.024}, author = {Kumar, Atul and Prabhune, Asmita and Suresh, C. G. and Pundle, Archana} } @article { ISI:000264484400007, title = {Comparative studies of two araceous lectins by steady state and time-resolved fluorescence and CD spectroscopy}, journal = {Journal of Fluorescence}, volume = {19}, number = {2}, year = {2009}, month = {MAR}, pages = {239-248}, publisher = {SPRINGER/PLENUM PUBLISHERS}, address = {233 SPRING ST, NEW YORK, NY 10013 USA}, abstract = {

Transitions in the tryptophan microenvironment and secondary structure of two monocot lectins from Sauromatum guttatum and Arisaema tortuosum under different denaturing conditions were studied by steady state and time resolved fluorescence and CD spectroscopy. The lectins exist as tetramers with a single tryptophan residue estimated per monomer, present in a polar environment. Quenching with ionic quenchers showed predominantly electropositive environment for tryptophan residues. Acrylamide had maximum quenching effect. A decrease in KI quenching due to lectin denaturation indicated redistribution of charges as a result of possible conformational change. The two values for lifetimes of tryptophanyl population (1.2-1.4 and 6.3-6.4 ns) reduced substantially on quenching or denaturation. Similarly, both the lectins showed a drastic loss of secondary structure in 5 M Gdn-HCl or 6 M Urea or at pH 2.0 and below. For the first time araceous lectins, like legume lectins are shown to bind adenine. The presence of a compact structure at alkaline pH 10.0-12.0 was observed in CD spectra.

}, keywords = {Araceae lectins, Denaturation, fluorescence, Lifetime spectroscopy, Secondary structure}, issn = {1053-0509}, doi = {10.1007/s10895-008-0409-z}, author = {Dharker, Poorva N. and Gaikwad, Sushama M. and Suresh, C. G. and Dhuna, Vikram and Khan, Mohammad Islam and Singh, Jatinder and Kamboj, Sukhdev Singh} } @article { ISI:000271552400019, title = {Conformational characterization of human eukaryotic initiation factor 2 alpha: a single tryptophan protein}, journal = {Biochemical and Biophysical Research Communications}, volume = {390}, number = {2}, year = {2009}, month = {DEC}, pages = {273-279}, publisher = {ACADEMIC PRESS INC ELSEVIER SCIENCE}, address = {525 B ST, STE 1900, SAN DIEGO, CA 92101-4495 USA}, abstract = {

The alpha-subunit of the human eukaryotic initiation factor 2 (heIF2 alpha), a GTP binding protein, plays a major role in the initiation of protein synthesis. During various cytoplasmic stresses, eIF2 alpha gets phosphorylated by eIF2 alpha-specific kinases resulting in inhibition of protein synthesis. The cloned and over expressed heIF2 alpha, a protein with a single tryptophan (trp) residue was examined for its conformational characteristics using steady-state and time-resolved tryptophan fluorescence, circular dichroism (CD) and hydrophobic dye binding. The steady-state fluorescence spectrum, fluorescence lifetimes (tau(1) = 1.13 ns and tau(2) = 4.74 ns) and solute quenching studies revealed the presence of trp conformers in hydrophobic and differential polar environment at any given time. Estimation of the alpha-helix and beta-sheet content showed: (i) more compact structure at pH 2.0, (ii) distorted alpha-helix and rearranged beta-sheet in presence of 4 M guanidine hydrochloride and (iii) retention of more than 50\% ordered structure at 95 degrees C. Hydrophobic dye binding to the protein with loosened tertiary structure was observed at pH 2.0 indicating the existence of a molten globule-like structure. These observations indicate the inherent structural stability of the protein under various denaturing conditions. (C) 2009 Elsevier Inc. All rights reserved.

}, keywords = {Circular dichroism, heIF2 alpha, K562 cells, Molten globule, Steady-state and time-resolved fluorescence}, issn = {0006-291X}, doi = {10.1016/j.bbrc.2009.09.106}, author = {Sreejith, R. K. and Yadav, Viveka Nand and Varshney, Nishant K. and Berwal, Sunil K. and Suresh, C. G. and Gaikwad, Sushama M. and Pal, Jayanta K.} } @article { ISI:000291061500032, title = {Conformational transitions in ariesaema curvatum lectin: characterization of an acid induced active molten globule}, journal = {Journal of Fluorescence}, volume = {21}, number = {2}, year = {2011}, month = {MAR}, pages = {753-763}, publisher = {SPRINGER/PLENUM PUBLISHERS}, address = {233 SPRING ST, NEW YORK, NY 10013 USA}, abstract = {

Biophysical characterization of a lectin from Ariesaema curvatum (ACL) was carried out using steady state as well as time resolved fluorescence and CD spectroscopy under various denaturing conditions. An intermediate with altered tryptophan microenvironment was detected in the phase diagram, which exibited pronounced secondary structure and hemagglutinating activity in presence of 0.25 M Gdn-HCl. An acid induced molten- globule like structure possessing activity and higher thermostability was detected. Transition to the molten globule state was reversible in nature. The lectin retained hemagglutinating activity even after incubation at 95 A degrees C. Both chemical and thermal unfolding of the lectin were found to consist of multistate processes. Fluorescence quenching of ACL was strong with acrylamide and KI. The single tryptophan was found to be surrounded by high density of the positively charged amino acid residues as shown by a ten fold higher K(sv) for KI compared to that for CsCl. The average lifetime of tryptophan fluorescence increased from 1.24 ns in the native state to 1.72 ns in the denatured state.

}, keywords = {Araceae, Fluorescence lifetime, Hemagglutinin, Molten globule, Secondary structure, Thermostability, Unfolding}, issn = {1053-0509}, doi = {10.1007/s10895-010-0766-2}, author = {Sharma, Urvashi and Gaikwad, Sushama M. and Suresh, C. G. and Dhuna, Vikram and Singh, Jatinder and Kamboj, Sukhdev Singh} } @article {Dutta Chowdhury, title = {Conformational transitions of the catalytic domain of heme-regulated eukaryotic initiation factor 2 alpha kinase, a key translational regulatory molecule}, journal = {Journal of Fluorescence}, volume = {22}, number = {1}, year = {2012}, month = {JAN}, pages = {431-441}, publisher = {SPRINGER/PLENUM PUBLISHERS}, address = {233 SPRING ST, NEW YORK, NY 10013 USA}, abstract = {

In mammalian cells, the heme-regulated inhibitor (HRI) plays a critical role in the regulation of protein synthesis at the initiation step through phosphorylation of a-subunit of the eukaryotic initiation factor 2 (eIF2). In this study we have cloned and performed biophysical characterization of the kinase catalytic domain (KD) of rabbit HRI. The KD described here comprises kinase 1, the kinase insertion domain (KI) and kinase 2. We report here the existence of an active and stable monomer of HRI (KD). The HRI (KD) containing three tryptophan residues was examined for its conformational transitions occurring under various denaturing conditions using steady-state and time-resolved tryptophan fluorescence, circular dichroism (CD) and hydrophobic dye binding. The parameter A and phase diagram analysis revealed multi-state unfolding and existence of three stable intermediates during guanidine hydrochloride (Gdn-HCl) induced unfolding of HRI (KD). The protein treated with 6 M Gdn-HCl showed collisional and static mechanism of acrylamide quenching and the constants (K-sv=3.08 M-1 and K-s=5.62 M-1) were resolved using time resolved fluorescence titration. Based on pH, guanidine hydrochloride and temperature mediated transitions, HRI (KD) appears to exemplify a rigid molten globule-like intermediate with compact secondary structure, altered tertiary structure and exposed hydrophobic patches at pH 3.0. The results indicate the inherent structural stability of HRI (KD), a member of the class of stress response proteins.

}, keywords = {Circular dichroism (CD), eIF2 alpha kinase, Heme-regulated inhibitor, Molten globule, Steady-state and time-resolved fluorescence}, issn = {1053-0509}, doi = {10.1007/s10895-011-0976-2}, author = {Sreejith, R. K. and Suresh, C. G. and Bhosale, Siddharth H. and Bhavnani, Varsha and Kumar, Avinash and Gaikwad, Sushama M. and Pal, Jayanta K.} } @article { ISI:000301921300006, title = {Crystallization and X-ray structure analysis of a thermostable penicillin G acylase from alcaligenes faecalis}, journal = {Acta Crystallographica Section F-Structural Biology and Crystallization Communications}, volume = {68}, number = {3}, year = {2012}, month = {MAR}, pages = {273-277}, publisher = {WILEY-BLACKWELL}, address = {COMMERCE PLACE, 350 MAIN ST, MALDEN 02148, MA USA}, abstract = {

{The enzyme penicillin G acylase (EC 3.5.1.11) catalyzes amide-bond cleavage in benzylpenicillin (penicillin G) to yield 6-aminopenicillanic acid, an intermediate chemical used in the production of semisynthetic penicillins. A thermostable penicillin G acylase from Alcaligenes faecalis (AfPGA) has been crystallized using the hanging-drop vapour-diffusion method in two different space groups: C2221, with unit-cell parameters a = 72.9

}, keywords = {calcium binding, disulfide bridges, Ntn hydrolases, orthorhombic form, tetragonal form, Thermostability}, issn = {1744-3091}, doi = {10.1107/S1744309111053930}, author = {Varshney, Nishant Kumar and Kumar, R. Suresh and Ignatova, Zoya and Prabhune, Asmita and Pundle, Archana and Dodson, Eleanor J. and Suresh, C. G.} } @article { ISI:000322512300025, title = {Cloning, overexpression, crystallization and preliminary X-ray crystallographic analysis of a slow-processing mutant of penicillin G acylase from Kluyvera citrophila}, journal = {Acta Crystallographica Section F-Structural Biology and Crystallization Communications}, volume = {69}, number = {8}, year = {2013}, month = {AUG}, pages = {925-929}, publisher = {WILEY-BLACKWELL}, address = {111 RIVER ST, HOBOKEN 07030-5774, NJ USA}, abstract = {

{Kluyvera citrophila penicillin G acylase (KcPGA) has recently attracted increased attention relative to the well studied and commonly used Escherichia coli PGA (EcPGA) because KcPGA is more resilient to harsh conditions and is easier to immobilize for the industrial hydrolysis of natural penicillins to generate the 6-aminopenicillin (6-APA) nucleus, which is the starting material for semi-synthetic antibiotic production. Like other penicillin acylases, KcPGA is synthesized as a single-chain inactive pro-PGA, which upon autocatalytic processing becomes an active heterodimer of alpha and beta chains. Here, the cloning of the pac gene encoding KcPGA and the preparation of a slow-processing mutant precursor are reported. The purification, crystallization and preliminary X-ray analysis of crystals of this precursor protein are described. The protein crystallized in two different space groups, P1, with unit-cell parameters a = 54.0

}, issn = {1744-3091}, doi = {10.1107/S174430911301943X}, author = {Varshney, Nishant Kumar and Ramasamy, Sureshkumar and Brannigan, James A. and Wilkinson, Anthony J. and Suresh, C. G.} } @article { ISI:000326207600012, title = {Complementation of intramolecular interactions for structural-functional stability of plant serine proteinase inhibitors}, journal = {Biochimica Et Biophysica Acta-General Subjects}, volume = {1830}, number = {11}, year = {2013}, month = {NOV}, pages = {5087-5094}, publisher = {ELSEVIER SCIENCE BV}, address = {PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS}, abstract = {

Background: Plant protease inhibitors (PIs) constitute a diverse group of proteins capable of inhibiting proteases. Among Pls, serine Pls (SPIs) display stability and conformational restrictions of the reactive site loop by virtue of their compact size, and by the presence of disulfide bonds, hydrogen bonds, and other weak interactions. Scope of review: The significance of various intramolecular interactions contributing to protein folding mechanism and their role in overall stability and activity of SPIs is discussed here. Furthermore, we have reviewed the effect of variation or manipulation of these interactions on the activity/stability of SPIs. Major conclusions: The selective gain or loss of disulfide bond(s) in SPIs can be associated with their functional differentiation, which is likely to be compensated by non-covalent interactions (hydrogen bonding or electrostatic interactions). Thus, these intramolecular interactions are collectively responsible for the functional activity of SPIs, through the maintenance of scaffold framework, conformational rigidity and shape complementarities of reactive site loop. General significance: Structural insight of these interactions will provide an in-depth understanding of kinetic and thermodynamic parameters involved in the folding and stability mechanisms of SPIs. These features can be explored for engineering canonical SPIs for optimizing their overall stability and functionality for various applications. (C) 2013 Elsevier B.V. All rights reserved.

}, keywords = {Disulfide bond, hydrogen bonding, Intramolecular weak interaction, Protease, Reactive site loop, Serine proteinase inhibitor}, issn = {0304-4165}, doi = {10.1016/j.bbagen.2013.07.019}, author = {Joshi, Rakesh S. and Mishra, Manasi and Suresh, C. G. and Gupta, Vidya S. and Giri, Ashok P.} } @article { ISI:000316859400002, title = {Crystal structure and fluorescence analysis of alkaline thermostable xylanase from bacillus sp (NCL 87-6-10)}, journal = {Protein and Peptide Letters}, volume = {20}, number = {2}, year = {2013}, month = {FEB}, pages = {125-132}, publisher = {BENTHAM SCIENCE PUBL LTD}, address = {EXECUTIVE STE Y-2, PO BOX 7917, SAIF ZONE, 1200 BR SHARJAH, U ARAB EMIRATES}, abstract = {

Structural information deduced from the new crystal form of xylanase from Bacillus sp (NCL 87-6-10) (ATBXYL-C) helped us to identify the active site and interpret the stability of the enzyme. The analysis of the tetragonal crystal structure of ATBXYL-C with a bound and cleaved xylotriose revealed the two glutamic acid residues in the structure that could act as nucleophile (Glu94) and base (Glu184) in the enzyme activity and also the tryptophan residues interacting with the substrate. The cleavage of xylotriose in the crystal showed xylobiose to be the major product. Intrinsic fluorescence of the enzyme showed the presence of tryptophans in partially exposed to the solvent at the active site and surface tryptophans in electropositive environment. The titration experiments with xylobiose and xylotriose revealed slightly enhanced preference for longer chain X3 compared with X2. The crystal structure also account for some of the factors, such as increased number of ionic interactions and additional interactions at the N-terminus, which contributed to increased alkalophilicity and thermostability of the enzyme.

}, keywords = {active site residues, Alkaline thermophile Bacillus xylanase (ATBXYL-C), fluorescence studies, three-dimensional structure}, issn = {0929-8665}, doi = {10.2174/092986613804725271}, author = {Satyanarayana, L. and Gaikwad, Sushama M. and Balkrishnan, H. and Suresh, C. G.} } @article {46374, title = {Chickpea Kunitz Inhibitor: a mechanistic basis for trypsin inhibition}, journal = {Acta Crystallographica A-Foundation and Advances}, volume = {70}, year = {2014}, month = {MAR}, pages = {C271}, type = {Meeting Abstract}, keywords = {Chickpea, Kunitz Inhibitor, Protease}, issn = {2053-2733}, author = {Bendre, Ameya Dipak and Ramasamy, Sureshkumar and Suresh, C. G.} } @article { ISI:000353218500003, title = {Crystal structure of a plant albumin from cicer arietinum (chickpea) possessing hemopexin fold and hemagglutination activity}, journal = {Planta}, volume = {241}, number = {5}, year = {2015}, month = {MAY}, pages = {1061-1073}, publisher = {SPRINGER}, address = {233 SPRING ST, NEW YORK, NY 10013 USA}, abstract = {

Crystal structure of a reported PA2 albumin from Cicer arietinum shows that it belongs to hemopexin fold family, has four beta-propeller motifs and possesses hemagglutination activity, making it different from known legume lectins. A plant albumin (PA2) from Cicer arietinum, presumably a lectin (CAL) owing to its hemagglutination activity which is inhibited by complex sugars as well as glycoproteins such as fetuin, desialylated fetuin and fibrinogen. The three-dimensional structure of this homodimeric protein has been determined using X-ray crystallography at 2.2 in two crystal forms: orthorhombic (P2(1)2(1)2) and trigonal (P3). The structure determined using molecular replacement method and refined in orthorhombic crystal form reached R-factors R (free) 22.6 \% and R (work) 18.2 \% and in trigonal form had 22.3 and 17.9 \% in the resolution range of 20.0-2.2 and 35.3-2.2 , respectively. Interestingly, unlike the known legume lectin fold, the structure of this homodimeric hemagglutinin belonged to hemopexin fold that consisted of four-bladed beta-propeller architecture. Each subunit has a central cavity forming a channel, inside of which is lined with hydrophobic residues. The channel also bears binding sites for ligands such as calcium, sodium and chloride ions, iodine atom in the case of iodine derivative and water molecules. However, none of these ligands seem important for the sugar recognition. No monosaccharide sugar specificity could be detected using hemagglutination inhibition. Chemical modification studies identified a potential sugar-binding site per subunit molecule. Comparison of C-alpha atom positions in subunit structures showed that the deviations between the two crystal forms were more with respect to blades I and IV. Differences also existed between subunits in two forms in terms of type and site of ligand binding.

}, keywords = {Beta-propeller fold, Chemical modification, Chickpea lectin, Complex sugars, PA2 albumin, Sugar binding}, issn = {0032-0935}, doi = {10.1007/s00425-014-2236-6}, author = {Sharma, Urvashi and Katre, Uma V. and Suresh, C. G.} }