Biomedical subjects

M Sundaralingam

Publications and source records attributed to M Sundaralingam.

At least 91 records · Page 5Linked to original sources

PubMed1991

Phospholipase A2 engineering. X-ray structural and functional evidence for the interaction of lysine-56 with substrates.

Site-directed mutagenesis studies of bovine pancreatic phospholipase A2 (PLA2, overproduced in Escherichia coli) showed that replacement of surface residue Lys-56 by a neutral or hydrophobic amino acid residue resulted in an unexpected and significant change in the function of the enzyme. The kcat for phosphatidylcholine micelles increases 3-4-fold for K56M, K56I, and K56F and ca. 2-fold for K56N and K56T but does not change for K56R. These results suggest that the side chain of residue 56 has significant influence on the activity of PLA2. In order to probe the structural basis for the enhanced activity, the crystal structures of wild-type and K56M PLA2 were determined by X-ray crystallography to a resolution of 1.8 A. The results suggest that the mutation has not only perturbed the conformation of the side chain of Met-56 locally but also caused conformational changes in the neighboring loop (residues 60-70), resulting in the formation of a hydrophobic pocket by residues Met-56, Tyr-52, and Tyr-69. Docking of a phosphatidylcholine inhibitor analogue into the active site of K56M, according to the structure of the complex of cobra venom PLA2-phosphatidylethanolamine inhibitor analogue [White, S.P., Scott, D. L., Otwinowski, Z., Gleb, M. H., & Sigler, P. (1990) Science 250, 1560-1563], showed that the choline moiety [N(CH3)3]+ is readily accommodated into the newly formed hydrophobic pocket with a high degree of surface complementarity. This suggests a possible interaction between residue 56 and the head group of the phospholipid, explaining the enhanced activities observed when the positively charged Lys-56 is substituted by apolar residues, viz., K56M, K56I, and K56F. Further support for this interpretation comes from the 5-fold enhancement in kcat for the mutant K56E with a negatively charged side chain, where there would be an attractive electrostatic interaction between the side chain of Glu-56 and the positively charged choline moiety. Our results also refute a recent report [Tomasselli, A. G., Hui, J., Fisher, J., Zürcher-Neely, H., Reardon, I.M., Oriaku, E., Kézdy, F.J., & Heinrikson, R.L. (1989) J. Biol. Chem. 264, 10041-10047] that substrate-level acylation of Lys-56 is an obligatory step in the catalysis by PLA2.

Amino Acid Sequence↗

PubMed1991

Structure of the anti-cancer drug complex tetrakis (mu-acetato)-bis(1-methyladenosine)dirhodium(II) monohydrate.

[Rh2(C2H3O2)4(C11H16N5O4)2].H2O, Mr = 1024.6, triclinic, P1, a = 7.808 (3), b = 11.469 (4), c = 12.091 (2) A, alpha = 69.55 (2), beta = 79.46 (2), gamma = 76.61 (3) degrees, V = 980.7 (6) A3, Z = 1, Dx = 1.735 g cm-3, lambda (Cu K alpha) = 1.5418 A, mu = 77.6 cm-1, F(000) = 522, room temperature, R = 0.053 for 3638 unique reflections. Structure consists of two rhodium(II) ions in a metal--metal bond bridged by four acetate groups. The remaining axial coordination sites on the rhodium ions are coordinated to the N(7) positions of two 1-methyladenosine molecules.

Adenosine↗

PubMed1991

A highly propeller-twisted adenine-adenine base pair in 8-tert-butyladenine.

C9H13N5, Mr = 191.24, monoclinic, P2(1)/c, a = 7.562 (1), b = 6.825 (1), c = 20.905 (1) A, beta = 104.84 (1) degree, V = 1042.9 A3, Z = 4, room temperature, Dx = 1.218 g cm-3, lambda (Cu K alpha) = 1.5418 A, mu = 6.6 cm-1, F(000) = 408. The structure was solved by the multisolution technique and refined by the block-diagonal least-squares method to a final R index of 0.045 using 1970 intensities. The adenine bases form three pairs of hydrogen bonds to symmetry-related molecules in the crystal lattice. Two distinct modes of hydrogen bonding are observed. One mode involves a planar interaction between adjacent adenine bases while the second mode is characterized by an unusually high propeller twist angle of 79.3 degrees between the planes through the two participating adenine bases.

Adenine↗

PubMed1991

Hexagonal crystal structure of the A-DNA octamer d(GTGTACAC) and its comparison with the tetragonal structure: correlated variations in helical parameters.

The alternating DNA octamer d(GTGTACAC) has been grown in a novel hexagonal crystal form. The structure has been determined and refined to a 2-A resolution, with 51 water molecules. The A-DNA conformation is a variant of that observed for the tetragonal form of the same sequence (Jain et al., 1989) containing a bound spermine. The crystals belong to the space group P6(1)22, a = b = 32.40 A and c = 79.25 A, with one strand in the asymmetric unit. The new hexagonal structure was solved by rotation and translation searches in direct space and refined to a final R value of 12.7% by using 1561 unique reflections greater than 1.5 sigma (I). The electron density clearly shows that the penultimate A7 sugar had flipped into the alternative C2'-endo pucker. This dent in the molecule can be attributed to close intermolecular contacts. In contrast, in the tetragonal structure, the DNA is distorted in the central TA step, where the A5 backbone bonds C4'-C5' and O5'-P assume trans conformations. The hexagonal double helix more closely resembles the fiber diffraction A-DNA, compared to the tetragonal form. For instance, the tilt angle is higher (16 degrees vs 10 degrees), which is correlated with a larger displacement from the helix axis (3.5 vs 3.3), a lower rise per residue (2.9 vs 3.2), and a smaller major-groove width (6.1 vs 8.7), thus indicating that the variations in these global helical parameters are correlated. The propeller twist angles in both forms are higher for the G-C base pairs (15.3 degrees, 12.14 degrees) than for the A-T base pairs (10.8 degrees, 9.1 degrees), which is the reverse of the expected order. Unlike the tetragonal structure, the hexagonal crystal structure interestingly does not contain a bound spermine molecule. Our analysis reveals that the conformational differences between the tetragonal and hexagonal forms are not entirely due to the spermine binding, and crystal packing seems to play an important role.

Base Composition↗

PubMed1991

Structural comparison of the B-DNA dodecamers d(CGCGTTAACGCG) and d(CGCGAATTCGCG) with T2A2 and A2T2 tracts.

The x-ray structure of the deoxy oligonucleotide dodecamer d(CGCGTTAACGCG) recently determined in our laboratory shows that the helical parameters of the central TTAA segment are significantly different compared to the central AATT in d(CGCGAATTCGCG). The roll in the central TA step of the T2A2 dodecamer opens towards the minor groove while the AT step of the A2T2 dodecamer opens towards the major groove. Also, the roll angles at the steps 4 and 8 (GT and AC in T2A2) and (GA and TC in A2T2) are in opposite directions. The high cup and helical twist angles at the central base-pair of T2A2 decreases the base stacking interactions compared to A2T2. Tilt angles within the tetranucleotide segments TTAA and AATT have opposite signs. In spite of the local differences caused by the sequence inversion (TTAA----AATT), the two dodecamers exhibit similar overall bending. The top third is more bent than the bottom third relative to the central segment. This asymmetric bending in the two dodecamers is mainly due to crystal packing interactions.

Base Sequence↗

PubMed1990

Structures of the monohydrate and dihydrate of (bidentate pyrophosphato) trans-diammine cis-diaqua chromium (III).

(OC-6-32)-Diamminediaqua [pyrophosphato(3-)]chromium(III) monohydrate, [Cr(NH3)2-(H2O)2(HP2O7)]. H2O, Mr = 315.1, triclinic, P1, a = 7.127 (2), b = 8.390 (2), c = 9.619 (2) A, alpha = 72.14 (2), beta = 98.86 (2), gamma = 76.98 (3) degrees, V = 517.7 (3) A3, Z = 2, Dx = 2.02 g cm-3, lambda(Cu K alpha) = 1.5418 A, mu = 129 cm-1, F(000) = 322, T = 293 K. (OC-6-32)-Diamminediaqua[pyrophosphato(3-)]-chromium(III) dihydrate, 0.5( [Cr(NH3)2(H2O)2-(HP2O7)].2H2O), Mr = 0.5(333.1), monoclinic, C2/m, a = 13.118 (3), b = 12.101 (3), c = 7.436 (2) A, beta = 105.09 (2) degrees, V = 1139.7 (3) A3, Z = 8, Dx = 1.94 g cm-3, lambda(Cu K alpha) = 1.5418 A, mu = 118 cm-1, F(000) = 684, T = 293 K. The structures were solved by the multi-solution technique and refined by the method of least squares to yield a final R index of 0.057 for 986 reflections in the monohydrate and a final R index of 0.043 for 1030 reflections in the dihydrate. The six-membered chromium pyrophosphate chelate ring is in a boat conformation for the monohydrate with an intramolecular hydrogen bond between an ammonia proton and a pyrophosphate O atom. In the dihydrate, the chelate ring is bisected by the mirror plane resulting in an unusual planar chelate ring conformation which does not permit intramolecular hydrogen bonding.

Chromium↗

PubMed1990

Structures of the meridional and facial isomers of triamminechromium pyrophosphate dihydrate.

The meridional and facial isomers of triamminechromium pyrophosphate were separated by chromatography on Dowex-50-H+, and crystallized as isoionic species. The meridional isomer crystallized as a monomer [Cr(HP2O7)(NH3)3(H2O)].2H2O but the facial isomer crystallized as a centrosymmetric dimer of [Cr(HP2O7)(NH3)3]. 2H2O, in which the remaining water in the coordination sphere of each chromium is replaced by a phosphate oxygen from the other monomer unit. Meridional isomer: monoaquatriammine(pyrophosphato)chromium(III) dihydrate, Mr = 332.1, monoclinic, P21/c, a = 7.825 (2), b = 10.107 (3), c = 15.322 (5) A, beta = 103.92 (5) degrees, V = 1176 (1) A 3, Z = 4, Dx = 1.875 g cm-3 lambda(Mo K alpha) = 0.71073 A, mu = 12.6 cm-1, F(000) = 684, final R = 0.050 for 1828 reflections. The most notable difference between this compound and the corresponding tetraammine complex reported previously is a significant shortening of the metal-ligand bond lengths not only for the water ligand but also for the ammonia ligands. The dimer: mu-(pyrophosphato-O,O',O")-bis[triamminechromium(III)] dihydrate, Mr = 314.0, monoclinic, P21/c, a = 8.695 (2), b = 10.327 (3), c = 11.913 (4) A, beta = 97.81 (5) degrees, V = 1060 (1) A3, Z = 4, Dx = 1.969 g cm-3, lambda(Cu K alpha) = 1.5418 A, mu = 125.7 cm-1, F(000) = 644, final R = 0.047 for 1389 reflections. This structure, which sits on a center of inversion, forms a tricyclic complex involving two Cr atoms. The structure is characterized by reciprocal coordination between the metal ions and anionic O atoms of the pyrophosphate moieties.(ABSTRACT TRUNCATED AT 250 WORDS)

Molecular Structure↗

PubMed1989

Effect of crystal packing environment on conformation of the DNA duplex. Molecular structure of the A-DNA octamer d(G-T-G-T-A-C-A-C) in two crystal forms.

The structure of the octamer d(G-T-G-T-A-C-A-C) was determined in two different crystal forms, tetragonal P4(3)2(1)2 and hexagonal P6(1)22. Although in both forms the octamer adopts an A-DNA structure, there are significant conformational differences between them. In particular, the P-05' and the C5'-C4' bonds of the middle adenine (A5) residue exhibit a distorted trans-trans conformation in the tetragonal form, while they adopt the standard gauche-, gauche+ conformation in the hexagonal form. These differences can be correlated with certain features of the crystal packing interactions in the two forms. Furthermore, a comparison of the structures of various A-DNA octamers reveals that the A-form can be divided into two subclasses such that the hexagonal structures have helical and base pair parameters that fall closer to fiber A-DNA values, while in the tetragonal structures these parameters deviate more from fiber A-DNA. These results indicate that environment plays a major role in determining DNA conformation.

Base Composition↗

PubMed1989

Water-inserted alpha-helical segments implicate reverse turns as folding intermediates.

Information relevant to the folding and unfolding of alpha helices has been extracted from an analysis of protein structures. The alpha helices in protein crystal structures have been found to be hydrated, either externally by a water molecule hydrogen bonding to the backbone carbonyl oxygen atom, or internally by inserting into the helix hydrogen bond and forming a hydrogen-bonded bridge between the backbone carbonyl oxygen and the amide nitrogen atoms. The water-inserted alpha-helical segments display a variety of reverse-turn conformations, such as type III, type II, type I, and opened out, that can be considered as folding intermediates that are trapped in the folding-unfolding process of alpha helices. Since the alpha helix, most turns, and the extended beta strand occupy contiguous regions in the conformational space of phi, psi dihedral angles, a plausible pathway can be proposed for the folding-unfolding process of alpha helices in aqueous solution.

Hydrogen Bonding↗

PubMed1989

Base only binding of spermine in the deep groove of the A-DNA octamer d(GTGTACAC).

The crystal structure of a complex of spermine with the DNA octamer d(GTGTACAC) has been determined at 2.0-A resolution. The alternating sequence adopts an A-DNA conformation with a novel purine-purine extra-Watson-Crick hydrogen bond involving the central guanine G3 (G11) and adenine A13 (A5) in the deep groove. The oligocation spermine binds in the floor of the deep groove by interacting with the bases and assumes an S-shape. Its dyad is coincident with that of the DNA, reminiscent of repressor binding to B-DNA. The terminal and central ammonium groups of the top half of spermine form hydrogen-bonding interactions to the 5'-bases, GTG, of one strand; then the spermine winds across the groove to interact with the corresponding set of bases on the other strand. The methylene groups of spermine form a hydrophobic cluster with the methyl groups of the thymines and the O6 atoms of the guanines of the TGT sequences on either side of the dyad. The observed mode of binding of spermine to A-DNA can serve as a model for deep groove binding in RNA and DNA-RNA hybrids that show a propensity also for the A-conformation. It will be of interest to see if base binding of spermine to DNA is involved in the regulation of gene expression, since spermine and other oligocations are ubiquitous in cells and their concentration is coupled to stages in cell cycle.

DNA↗

PubMed1988

Nonintercalative binding of proflavin to Z-DNA: structure of a complex between d(5BrC-G-5BrC-G) and proflavin.

The crystal structure of a disordered 1:1 complex between the tetradeoxyoligomer d(5BrC-G-5BrC-G) and proflavin has been determined and refined to an R factor of 26.9% for 474 reflections initially in space group P6(5) and to an R factor of 22.2% for 475 reflections in space group P2(1), both at 2-A resolution with Fobsd greater than or equal to 4.0. The unit cell constants are a = b = 17.9 A, c = 44.5 A, and gamma = 120 degrees. The final models are essentially the same in the two space groups with greater disorder in space group P6(5). In space group P2(1), the asymmetric unit is a tetranucleotide duplex, two sandwiched proflavin molecules, and four "outside-bound" proflavins. The tetranucleotide duplex is in the Z conformation and is located at the origin of the unit cell with a pair of proflavins sandwiched between the tetranucleotides. Thus, the tetranucleotides and proflavin dimers stack alternatively forming a quasi-continuous helix with the helix axis coincident with the c axis. The structure analysis revealed the presence of outside-bound proflavins as well. It is interesting that one type of outside-bound proflavins occupies a similar environment as the cobalt hexaammines in their complex with the decadeoxyoligomer d(CGTACGTACG) [Brennan, R. G., Westhof, E., & Sundaralingam, M. (1986) J. Biomol. Struct. Dyn. 3, 649]. Crystals of the latter are isomorphous to the present complex. The outside-bound proflavins penetrate the deep minor groove, thereby closing it off, and provide a visualization of a quasi-internal mode of binding of proflavin to a nucleic acid.

Acridines↗

PubMed1988

Refined structure of chicken skeletal muscle troponin C in the two-calcium state at 2-A resolution.

The structure of troponin C has been refined at 2A resolution to an R value of 0.172 using a total of 8,100 reflections. Troponin C has an unusual dumbbell shape with only the two C-domain high affinity sites III and IV occupied with metals, while the pair of N-domain low affinity sites I and II are devoid of metals. The coordination of the Ca2+ approaches seven with the last glutamic acid residue in each site forming an asymmetric bidentate ligand. The flanking helices in the metal-bound EF hands are in similar orientation (both 113 degrees) while in the apo sites they are more obtuse (134 and 149 degrees). The EF hands of holo sites III and IV are similar while the apo sites I and II are less similar (rms for backbone atoms, 0.78 and 1.44). The half-loops of the 12-residue holo and apo sites show better agreement than the full loops themselves, suggesting a hinge motion at the midpoint of the loops. The long central helix is stabilized by electrostatic interactions and salt bridges between charged side chains spaced at 3 or 4 residues along the helix. A cluster of water molecules encircle the long helix and hydrogen bond to the backbone carbonyls. At the beginning of the B-helix, a water molecule is interposed at each of two consecutive backbone NH...OC hydrogen bonds. The terminal pair of helices A/D (apo) match with E/H (holo), and the internal pair of helices B/C (apo) match with F/G (holo). Thus, muscle contraction may be triggered by Ca2+ binding to loops I and II which results in a concerted rearrangement of residues in the loops, including the essential Gly at position 6 in each loop. This rearrangement than causes a reorientation of helices B and C along with the BC linker.

Animals↗

PubMed1988

A structure-function relationship for the calcium affinities of regulatory proteins containing 'EF-hand' pairs.

Using a series of homologous calcium-binding proteins, a quantitative structure-activity relationship (QSAR), log(1/Kd) = -18.986 - 1.6278(X1) + 0.7981(X2) + 0.2312(X3), has been established, which relates the calcium-binding affinities (1/Kd) of the regulatory proteins with (i) the net ligand charge (X1) of the two calcium binding loops, (ii) the hydrophobicity (X2) of the beta-sheet segment of the loops and (iii) the hydrophobicity (X3) of the four 'EF-hand' helices. It is found that the binding affinities are influenced by the 'EF-hand' pair rather than the individual 'EF-hands'. The QSAR, in addition to explaining satisfactorily the large variation in the observed calcium affinities, can predict the affinities of the 'EF-hand' pairs in other proteins from the amino acid sequence and can also account for the changes in the affinities caused by substitution in the hydrophobic and/or metal-coordinating residues. Thus, this relationship can be employed in protein design and engineering. The method is potentially useful in the development of similar relationships for the binding of other proteins to substrates, inhibitors, drugs and co-factors.

Amino Acid Sequence↗

PubMed1987

The crystal structure of diazomethyl beta-D-galactopyranosyl ketone.

The title compound (C8H12N2O6) crystallizes in the orthorhombic space group P2(1)2(1)2(1) (Z = 4), with a = 4.871(1), b = 11.136(2), c = 18.301(2) A. The structure was solved by the multi-solution technique and refined by full-matrix least-squares to a final R-index of 0.042. The compound adopts the 4C1(D) conformation. Bond lengths in the diazoacetyl group are consistent with the presence of a zwitterion.

Carbohydrate Conformation↗

PubMed1987

The potentially Z-DNA-forming sequence d(GTGTACAC) crystallizes as A-DNA.

(GT)n/(CA)n sequences have stimulated much interest because of their frequent occurrence in eukaryotic DNA and their potential for forming the left-handed Z-DNA structure. We here report the X-ray crystal structure of a self-complementary octadeoxynucleotide, d(GTGTACAC), at 2.5 A resolution. The molecule adopts a right-handed double-helical conformation belonging to the A-DNA family. In this alternating purine-pyrimidine DNA minihelix the roll and twist angles show alternations qualitatively consistent with Calladine's rules. The average tilt angle of 9.3 degrees is between the values found in A-DNA (19 degrees) and B-DNA (-6 degrees) fibers. It is envisaged that such intermediate conformations may render diversity to genomic DNA. The base-pair tilt angles and the base-pair displacements from the helix axis are found to be correlated for the known A-DNA double-helical fragments.

Base Sequence↗

PubMed1987

Structural and biochemical properties of bidentate tetraaquarhodium(III) complexes of inorganic pyrophosphate and adenosine 5'-diphosphate.

The structural and biochemical properties of the alpha,beta-bidentate tetraaquarhodium(III) complexes of inorganic pyrophosphate [Rh(H2O)4PP] and adenosine diphosphate [Rh(H2O)4ADP] are examined. These Rh(III) complexes are exchange-inert analogues of the corresponding physiologically important MgIIPP and MgIIADP complexes. The crystal structure of [Rh(H2O)4H2P2O7]+Cl- shows that the six-membered chelate ring adopts a twist-boat conformation with an unusually high puckering amplitude of 0.756 (3) A. The Rh coordination distances average 2.02 (1) A, while the bridge P-O bonds are virtually equal in length. All 10 protons of the complex participate in hydrogen bonding. There are two intramolecular hydrogen bonds between the phosphate oxygen atoms and the axially coordinated water molecules. The Rh(H2O)4PP complex was found to be a substrate for yeast inorganic pyrophosphatase, with Ki = 0.063 (7) mM and Vm = 500 (100) min-1. The two screw sense isomers of Rh(H2O)4ADP were prepared from (Rp)-[alpha-16O,18O]ADP and assigned configuration on the basis of the magnitude of their 31P NMR isotopic chemical shifts. The Rh(H2O)4ADP complex binds a number of kinases as tightly as MgADP. Arginine kinase and creatine kinase were shown to bind the delta Rh(H2O)4ADP isomer 7 and 45 times tighter, respectively, than the lambda isomer. The reactivity of Rh(H2O)4PP with pyrophosphatase is comparable to that of Cr(H2O)4PP, and the binding affinities of the Rh(H2O)4ADP screw sense isomers for kinases are also comparable to those observed for the corresponding Cr(H2O)4ADP screw sense isomers.

Adenosine Diphosphate↗

PubMed1987

Crystallographic analysis of the three-dimensional structure of baboon alpha-lactalbumin at low resolution. Homology with lysozyme.

The crystal structure of baboon alpha-lactalbumin has been determined at 6 A and at 4.5 A (0.6 nm and 0.45 nm) resolution by the method of isomorphous replacement. The principal derivative was prepared by reducing a disulphide bridge in the crystals and inserting a mercury atom. Detailed comparison of the electron-density maps with corresponding maps of hen egg-white lysozyme shows that they are closely similar, with correlation coefficients of 0.57 and 0.44 at 6 A and 4.5 A resolution respectively. This result, in accordance with earlier predictions based upon comparisons of amino-acid sequences, provides further evidence that class C lysozymes and alpha-lactalbumins are homologous proteins and it is in keeping with the hypothesis that the alpha-lactalbumins evolved from a lysozyme precursor.

Amino Acid Sequence↗

PubMed1987

Ion pairs in alpha helices.

A survey of 47 globular proteins was made to determine the probability of occurrence of ion pairs separated by 1,2,3,... and 8 residues in the alpha helices. As a control, the probability of occurrence of like charged pairs was also determined. The survey showed that ion pairs of the type i,i +/- 3 and i, i +/- 4 are the most predominant. Such a preference was not observed for like charged pairs. The observed frequency of ion pairs is significantly greater than their expected frequency. The normalized frequencies of occurrence of the ion pairs were also found to increase generally with the helix length. These results indicate that the ion pairs may contribute to the stability of solvent-exposed alpha helices. Since the stabilization of protein secondary structure enhances the stability of protein tertiary structure, these results may throw light on the mechanism of protein folding.

Amino Acids↗