Biomedical subjects

D Velmurugan

Publications and source records attributed to D Velmurugan.

At least 19 recordsLinked to original sources

PubMed2006

Suggestive evidence for the involvement of the second calcium and surface loop in interfacial binding: monoclinic and trigonal crystal structures of a quadruple mutant of phospholipase A2.

The crystal structures of the monoclinic and trigonal forms of the quadruple mutant K53,56,120,121M of recombinant bovine pancreatic phospholipase A2 (PLA2) have been solved and refined at 1.9 and 1.1 A resolution, respectively. Interestingly, the monoclinic form reveals the presence of the second calcium ion. Furthermore, the surface-loop residues are ordered and the conformation of residues 62-66 is similar to that observed in other structures containing the second calcium ion. On the other hand, in the trigonal form the surface loop is disordered and the second calcium is absent. Docking studies suggest that the second calcium and residues Lys62 and Asp66 from the surface loop could be involved in the interaction with the polar head group of the membrane phospholipid. It is hypothesized that the two structures of the quadruple mutant, monoclinic and trigonal, represent the conformations of PLA2 at the lipid interface and in solution, respectively. A docked structure with a phospholipid molecule and with a transition-state analogue bound, one at the active site coordinating to the catalytic calcium and the other at the second calcium site, but both at the i-face, is presented.

Animals↗

PubMed2006

Third calcium ion found in an inhibitor-bound phospholipase A2.

The lipolytic enzyme phospholipase A2 plays a crucial role in lipid metabolism and catalyzes hydrolysis of the fatty-acid ester bond at the sn-2 position of phospholipids. Here, the crystal structure (1.7 A resolution) of the triple mutant (K53,56,121M) of bovine pancreatic phospholipase A2 complexed with an organic molecule, p-methoxybenzoic acid (anisic acid), is reported. Residues 60-70 (the surface-loop residues) are ordered and adopt conformations which are different from those normally found in structures in which a second calcium ion is present. It is interesting to note that for the first time a third calcium ion has been identified. In addition, four Tris (2-amino-2-hydroxymethyl-1,3-propanediol) molecules were located. It is believed that one of the Tris molecules plays a role in clamping the third calcium ion and that another is involved in controlling the dynamics of the surface loop through hydrogen bonds.

Animals↗

PubMed2006

Quantitative structure-activity relationship (QSAR) analysis of a series of indole analogues as inhibitor for human group V secretory phospholipase A2.

Phospholipase A2s (PLA2) are a class of enzymes, which catalyze the hydrolysis of membrane phospholipids at the sn-2 position to release fatty acids and lysophospholipids. When the fatty acid is arachidonic acid (AA), a complementary metabolism leads to pro-inflammatory mediators collectively known as eicosanoids. Thus, inhibiting PLA2 activity remains a prime target for the development of new drugs for the treatment of inflammation-related diseases. More than one type of PLA2s plays a major role in inflammatory disease conditions. In the present study, quantitative structure-activity relationship (QSAR) study was performed for a series of 48 Me-indoxam derivatives as human group V PLA, (hVPLA2) inhibitors, using molecular operating environment (MOE) software. The hVPLA2 is a secretory PLA2 (sPLA2), involved in eicosanoid formation in inflammatory cells such as macrophages and mast cells. These studies have come out with three good predictive models (r = 0.82-0.84), which are cross-validated (rcv = 0.68-0.70) by leave-out-one method (Loo). The positive correlation of spatial descriptor Pmiz with inhibitory activity shows that proper orientation of the substitution at R position towards Z-axis is necessary to facilitate the possible interactions of the indole core with active site residues of the PLA2 enzyme. The negative contribution of b_rotN (atom and bond count-type descriptor) suggests that increasing flexibility conferred by the R substitution is detrimental for the activity. In addition to the hVPLA2 inhibitory activity is found to be highly influenced by molecular size, energy and polarity of the Me-indoxam derivatives.

Catalytic Domain↗

PubMed2006

Iterative ACORN as a high throughput tool in structural genomics.

High throughput macromolecular structure determination is very essential in structural genomics as the available number of sequence information far exceeds the number of available 3D structures. ACORN, a freely available resource in the CCP4 suite of programs is a comprehensive and efficient program for phasing in the determination of protein structures, when atomic resolution data are available. ACORN with the automatic model-building program ARP/wARP and refinement program REFMAC is a suitable combination for the high throughput structural genomics. ACORN can also be run with secondary structural elements like helices and sheets as inputs with high resolution data. In situations, where ACORN phasing is not sufficient for building the protein model, the fragments (incomplete model/dummy atoms) can again be used as a starting input. Iterative ACORN is proved to work efficiently in the subsequent model building stages in congerin (PDB-ID: lis3) and catalase (PDB-ID: 1gwe) for which models are available.

Animals↗

PubMed2005

Atomic resolution structure of the double mutant (K53,56M) of bovine pancreatic phospholipase A2.

The structure of the double mutant K53,56M has previously been refined at 1.9 A resolution using room-temperature data. The present paper reports the crystal structure of the same mutant K53,56M refined against 1.1 A data collected using synchrotron radiation. A total of 116 main-chain atoms from 29 residues and 44 side chains are modelled in alternate conformations. Most of the interfacial binding residues are found to be disordered and alternate conformations could be recognized. The second calcium ion-binding site residue Glu92 adopts two alternate conformations. The minor and major conformations of Glu92 correspond to the second calcium ion bound and unbound states.

Animals↗

PubMed2005

1,2,3-Trimethoxy-5,11-dihydroindolo[1,2-b]isoquinoline-5,11-dione.

The title compound, C15H19NO5, crystallizes in the monoclinic space group P2(1)/c with four molecules in the asymmetric unit, which differ from each other in the orientation of their methoxy groups. Of the three methoxy groups in each molecule, one lies close to the plane of the molecule and the other two have an out-of-plane conformation where they point in opposite directions. In the crystal structure, four different types of pi-stacks are observed and the molecules pack in two different types of stacking sheets, with alternating molecules A and B in one ribbon and alternating molecules C and D in the other. The supramolecular structure is supported by C-H...O and pi-pi interactions.

Journal Article↗

PubMed2004

Atomic resolution (0.97 A) structure of the triple mutant (K53,56,121M) of bovine pancreatic phospholipase A2.

The enzyme phospholipase A2 catalyzes the hydrolysis of the sn-2 acyl chain of phospholipids, forming fatty acids and lysophospholipids. The crystal structure of a triple mutant (K53,56,121M) of bovine pancreatic phospholipase A2 in which the lysine residues at positions 53, 56 and 121 are replaced recombinantly by methionines has been determined at atomic resolution (0.97 A). The crystal is monoclinic (space group P2), with unit-cell parameters a = 36.934, b = 23.863, c = 65.931 A, beta = 101.47 degrees. The structure was solved by molecular replacement and has been refined to a final R factor of 10.6% (Rfree = 13.4%) using 63,926 unique reflections. The final protein model consists of 123 amino-acid residues, two calcium ions, one chloride ion, 243 water molecules and six 2-methyl-2,4-pentanediol molecules. The surface-loop residues 60-70 are ordered and have clear electron density.

Animals↗

PubMed2004

A redetermination of the structure of the triple mutant (K53,56,120M) of phospholipase A2 at 1.6 A resolution using sulfur-SAS at 1.54 A wavelength.

The crystal structure of the triple mutant K53,56,120M of bovine pancreatic phospholipase A(2) has been redetermined using sulfur single-wavelength anomalous scattering. The synchrotron data were collected at lambda = 1.54 A and the crystal diffracted to 1.6 A resolution. The program SOLVE was used to locate the heavy atoms and to estimate the initial phases and the resulting map was then subjected to RESOLVE. The output of 455 non-H atoms, including 12 S atoms, one calcium ion and one chloride ion, were then subjected to ARP/wARP followed by REFMAC. With the improved phases, the automatic model building successfully built more than 85% of the 123 residues, excluding the N- and C-terminal residues. The final crystallographic R factor is 17.7% (R(free) = 21.7%). The refined model consists of 954 non-H protein atoms, 165 water O atoms, three 2-methyl-2,4-pentanediol (MPD) molecules, one calcium ion and one chloride ion. The present work is yet another example that shows the utility of single-wavelength anomalous scattering data for solving a protein structure.

Animals↗

PubMed2004

The use of ACORN in solving a 39.5 kDa macromolecule with 1.9 A resolution laboratory source data.

Data from the alkaline cellulase apo form were collected at a resolution of 1.9 A using an in-house X-ray source (Cu K alpha). By using different fragments of helices from the model solved by macromolecular crystallographic means, the direct-methods program ACORN was used to arrive at the complete model. Attempts have been made to use various percentages of input phasing information from these helices. The minimum input phasing required in feeding the fragments was about 14% of the whole structure. The phases obtained from ACORN were of superb quality, allowing automated model building to be carried out using ARP/wARP. Minimal manual model building was required and the structure determination was completed using the maximum-likelihood refinement program REFMAC. The whole process, starting from the running of ACORN and ending with the refined model, took nearly 15 h of CPU time using a Pentium III PC.

Algorithms↗

PubMed2003

Applications of ACORN to data at 1.45 A resolution.

One of the main interests in the molecular biosciences is in understanding structure-function relations and X-ray crystallography plays a major role in this. ACORN can be used as a comprehensive and efficient phasing procedure for the determination of protein structures when atomic resolution data are available. An initial model can automatically be built by ARP/wARP followed by REFMAC for refinement. The alpha helices and beta sheets occurring in many protein structures can be taken as starting fragments for structure solution in ACORN. ACORN, along with ARP/wARP followed by REFMAC, can be an ab initio method for solving protein structure for which data are better than 1.2 A (atomic resolution). Attempts are here made in extending its applications to real data at 1.45 A resolution and also to truncated data at 1.6 A resolution. Two previously known structures, congerin II and alkaline cellulase N257, were resolved using the above approach. Automatic structure solution, phasing and refinement for real data at still lower resolutions for proteins of various complexities are being carried out. Data mining of the secondary structural features using PDB is being carried out for this new approach for 'seed-phasing' to ACORN.

Algorithms↗

PubMed2003

Crystal structures of the free and anisic acid bound triple mutant of phospholipase A2.

Phospholipase A2 catalyses the hydrolysis of the ester bond of 3-sn-phosphoglycerides. Here, we report the crystal structures of the free and anisic acid-bound triple mutant (K53,56,120M) of bovine pancreatic phospholipase A2. In the bound triple mutant structure, the small organic molecule p-anisic acid is found in the active site, and one of the carboxylate oxygen atoms is coordinated to the functionally important primary calcium ion. The other carboxylate oxygen atom is hydrogen bonded to the phenolic hydroxyl group of Tyr69. In addition, the bound anisic acid molecule replaces one of the functionally important water molecules in the active site. The residues 60-70, which are in a loop (surface loop), are disordered in most of the bovine pancreatic phospholipase A2 structures. It is interesting to note that these residues are ordered in the bound triple mutant structure but are disordered in the free triple mutant structure. The organic crystallization ingredient 2-methyl-2,4-pentanediol is found near the active site of the free triple mutant structure. The overall tertiary folding and stereochemical parameters for the final models of the free and anisic acid-bound triple mutant are virtually identical.

Allosteric Site↗

PubMed2003

Supramolecular structures of 2-cyano-3-dimethylamino-N-(4-methylphenyl)acrylamide and 2-cyano-3-dimethylamino-N-(2-methoxyphenyl)acrylamide.

In the title compounds, C(13)H(15)N(3)O, (I), and C(13)H(15)N(3)O(2), (II), the dihedral angles between the planes of the phenyl ring and the amide group are 4.1 (1) and 20.7 (1) degrees, respectively. The molecules adopt a fully extended conformation, aided by intramolecular interactions. The molecular structures of (I) and (II) display different crystal packing and hydrogen-bonding networks.

Journal Article↗

PubMed2003

1-(2-Hydroxy-4-methoxyphenyl)-3-(2,3,4-trimethoxyphenyl)prop-2-en-1-one.

The title compound, C(19)H(20)O(6), crystallizes in the centrosymmetric space group P2(1)/c with one molecule in the asymmetric unit. The molecule is approximately planar and the dihedral angle between the phenyl rings is 11.0 (1) degrees. The H atoms of the central propenone group are trans. There is an intramolecular O-H.O hydrogen bond and the molecules are crosslinked by four intermolecular C-H.O hydrogen bonds, producing a three-dimensional network.

Journal Article↗

PubMed2003

3,3'-[o-Phenylenebis(methyleneoxy)]bis(6-chloroflavone) and 3,3'-propylenedioxybis[6-chloro-2-(2-furyl)-4H-1-benzopyran-4-one].

The title compound 3,3'-[o-phenylenebis(methyleneoxy)]bis(6-chloroflavone), C(38)H(24)Cl(2)O(6), (I), crystallizes in the monoclinic space group C2/c, with the molecules lying across twofold rotation axes so that there is half a molecule in the asymmetric unit, while the other title compound, 3,3'-propylenedioxybis[6-chloro-2-(2-furyl)-4H-1-benzopyran-4-one], C(29)H(18)Cl(2)O(8), (II), crystallizes in monoclinic space group P2(1)/n with one molecule in the asymmetric unit. In both compounds, the benzopyran moiety is nearly planar, with dihedral angles between the two fused rings of 1.43 (8) degrees in (I), and 2.54 (7) and 3.00 (6) degrees with respect to the benzopyran moieties in the two halves of (II). The furan rings are twisted by 8.3 (1) and 8.4 (1) degrees in the two halves of (II). In both compounds, the molecular structure is stabilized by intramolecular C-H.O hydrogen bonds, while the crystal packing is stabilized by C-H.Cl and C-H.O intermolecular hydrogen bonds in (I) and (II), respectively.

Journal Article↗

PubMed2003

2-nitroso-1,3-diphenyl-1,2,3,4-tetrahydrobenzo[b][1,6]naphthyridine.

The title compound, C(24)H(19)N(3)O, crystallizes in the centrosymmetric space group P2(1)/a with one molecule in the asymmetric unit. The tetrahydropyridine ring has a boat conformation. The dihedral angle between the fused pyridine rings is 16.2 (1) degrees. The equatorial and axial orientations of the two phenyl groups with respect to the tetrahydropyridine ring are confirmed. The nitroso group is coplanar with the attached C-N-C group. The interplanar angle formed between the fused tetrahydropyridine and benzene planes is 13.4 (1) degrees. The crystal packing is stabilized by an intermolecular C-H.O hydrogen bond, which forms a C(9) graph-set chain running along the [001] direction.

Crystallography, X-Ray↗

PubMed2003

A cis-stilbene derivative.

The title compound, 4'-methoxy-alpha,2,3',4-tetranitrostilbene, C(15)H(10)N(4)O(9), crystallizes in the centrosymmetric space group P2(1)/c with one molecule in the asymmetric unit. The phenyl rings are inclined to one another and form a dihedral angle of 57.4 (1) degrees. The size of this angle is a result of intermolecular C-H...O interactions involving the phenyl H atoms. The torsion angle between the phenyl rings, -7.5 (3) degrees, indicates a cis geometry between them. The methoxy group is almost coplanar with the phenyl ring, and the nitro groups are twisted with respect to the phenyl rings because of the short H...O contacts. The crystal packing is stabilized by C-H...O hydrogen bonds, and the intermolecular hydrogen bonds form a C(12) graph-set chain running along the [010] direction.

Journal Article↗

PubMed2003

Side-chain conformation angles of amino acids: effect of temperature factor cut-off.

The paper presents the analysis of the side-chain conformation angles of amino acids in 90% non-identical protein structures. The analysis has been carried out using 113,699 residues, which is higher compared to the previous studies. In the present study, one more quality check, namely, temperature factor cut-off, has been introduced in addition to resolution and R-factor cut-offs. Due to this, the present calculation reveals the approximate values for the minimum and the maximum of the three-rotameric states of chi1. In addition, the conformation angles chi2 and chi3 have been addressed with the improved data set. The results reported here could be of use in protein modeling.

Amino Acids↗

PubMed2002

Observation of additional calcium ion in the crystal structure of the triple mutant K56,120,121M of bovine pancreatic phospholipase A2.

Phospholipase A(2) catalyses hydrolysis of the ester bond at the C2 position of 3-sn-phosphoglycerides. Here we report the 1.9A resolution crystal structure of the triple mutant K56,120,121M of bovine pancreatic phospholipase A(2). The structure was solved by molecular replacement method using the orthorhombic form of the recombinant phospholipase A(2). The final protein model contains all the 123 amino acid residues, two calcium ions, 125 water molecules and one 2-methyl-2-4-pentanediol molecule. The model has been refined to a crystallographic R-factor of 19.6% (R(free) of 25.9%) for all data between 14.2A and 1.9A. The residues 62-66, which are in a surface loop, are always disordered in the structures of bovine pancreatic phospholipase A(2) and its mutants. It is interesting to note that the residues 62-66 in the present structure is ordered and the conformation varies substantially from those in the previously published structures of this enzyme. An unexpected and interesting observation in the present structure is that, in addition to the functionally important calcium ion in the active site, one more calcium ion is found near the N terminus. Detailed structural analyses suggest that binding of the second calcium ion could be responsible for the conformational change and the ordering of the surface loop. Furthermore, the results suggest a structural reciprocity between the k(cat)(*) allosteric site and surface loop at the i-face, which represents a newly identified structural property of secreted phospholipase A(2).

Allosteric Site↗