Biomedical subjects

R Parthasarathy

Publications and source records attributed to R Parthasarathy.

At least 19 recordsLinked to original sources

PubMed1992

Helix-forming tendencies of amino acids depend on the restrictions of side-chain rotamer conformations: crystal structure of the tripeptide GAI in two crystalline forms.

In our attempts to design crystalline alpha-helical peptides, we synthesized and crystallized GAI (C11H21N3O4) in two crystal forms, GAI1 and GAI2. Form 1 (GAI1) Gly-L-Ala-L-Ile (C11H21N3O4.3H2O) crystals are monoclinic, space group P2(1) with a = 8.171(2), b = 6.072(4), c = 16.443(4) A, beta = 101.24(2) degrees, V = 800 A3, Dc = 1.300 g cm-3 and Z = 2, R = 0.081 for 482 reflections. Form 2 (GAI2) Gly-L-Ala-L-Ile (C11H21N3O4.1/2H2O) is triclinic, space group P1 with a = 5.830(1), b = 8.832(2), c = 15.008(2) A, alpha = 102.88(1), beta = 101.16(2), gamma = 70.72(2) degrees, V = 705 A3, Z = 2, Dc = 1.264 g cm-3, R = 0.04 for 2582 reflections. GAI1 is isomorphous with GAV and forms a helix, whereas GAI2 does not. In GAI1, the tripeptide molecule is held in a near helical conformation by a water molecule that bridges the NH3+ and COO- groups, and acts as the fourth residue needed to complete the turn by forming two hydrogen bonds. Two other water molecules form intermolecular hydrogen bonds in stabilizing the helical structure so that the end result is a column of molecules that looks like an incipient alpha-helix. GAI2 imitates a cyclic peptide and traps a water molecule. The conformation angles chi 11 and chi 12 for the side chain are (-63.7 degrees, 171.1 degrees) for the helical GAI1, and (-65.1 degrees, 58.6 degrees) and (-65.0 degrees, 58.9 degrees) for the two independent nonhelical molecules in GAI2; in GAI1, both the C gamma atoms point away from the helix, whereas in GAI2 the C gamma atom with the g+ conformation points inward to the helix and causes sterical interaction with atoms in the adjacent peptide plane. From these results, it is clear that the helix-forming tendencies of amino acids correlate with the restrictions of side-chain rotamer conformations. Both the peptide units in GAI1 are trans and show significant deviation from planarity [omega 1 = -168(1) degrees; omega 2 = -171(1) degrees] whereas both the peptide units in both the molecules A and B in GAI2 do not show significant deviation from planarity [omega 1 = 179.3(3) degrees; omega 2 = -179.3(3) degrees for molecule A and omega 1 = 179.5(3) degrees; omega 2 = -179.4(3) degrees for molecule B], indicating that the peptide planes in these incipient alpha-helical peptides are considerably bent.

Amino Acid Sequence↗

PubMed1992

The effects of lithium isotopes on the myo-inositol 1-phosphatase reaction in rat brain, liver, and testes.

Enzyme inhibition studies were performed with several lithium isotopes in order to more precisely define how lithium inhibits the enzyme myo-inositol 1-phosphatase. This lithium-induced inhibition is thought to be central to the therapeutic effects of lithium in the treatment of manic-depressive disorder. Naturally occurring lithium (NLi) exists as a combination of isotopes: 6Li and 7Li. Lethality studies were performed comparing 6LiCl, 7LiCl, and NLiCl, did not demonstrate a differential effect as previous studies had suggested. Enzyme inhibition studies were performed with these individual lithium isotopes, and compared to the effects of the naturally occurring combination (NLi) on the inhibition of myo-inositol 1-phosphatase using a partially purified enzyme preparation from rat brain, liver and testes. Identical inhibition was observed with all lithium isotopes and their combinations. In addition, both D- and L-myo-inositol 1-phosphates were used as enzyme substrates and found to be equivalent. These experiments, along with previous work demonstrating lithium acting as an uncompetitive inhibitor in the reaction, and the lack of lithium binding sites on the enzyme, suggests the hypothesis that lithium is possibly inhibiting this reaction by interfering with the formation of a transition cyclic intermediate, myo-inositol 1,3-cyclic phosphate, which may be formed from either the D- or L-substrates. This proposal is in contrast to previous suggestions regarding the inhibitory mechanism of action of lithium on the myo-inositol 1-phosphatase reaction.

Analysis of Variance↗

PubMed1992

Acute renal failure following binge drinking and nonsteroidal antiinflammatory drugs.

Two college students who developed reversible acute deterioration in renal function following binge drinking of beer and the use of nonsteroidal antiinflammatory drugs (NSAIDs) are reported. Both patients presented with back and flank pain with muscle tenderness, but showed no evidence of overt rhabdomyolysis. The first case had marked renal failure, with a peak serum creatinine reaching 575 mumol/L (6.5 mg/dL), and acute tubular necrosis was documented by renal biopsy. The second case had only modest elevation in serum creatinine, and renal function rapidly improved on rehydration. The contribution of the potential muscle damage associated with alcohol ingestion to the changes in renal function in these two cases is not clear. However, the major mechanism for the acute renal failure was thought to be related to inhibition of renal prostaglandin synthesis in the face of compromised renal hemodynamics secondary to alcohol-induced volume depletion.

Acute Kidney Injury↗

PubMed1992

The identification of a membrane-bound myo-inositol 1-phosphatase in rat brain, liver, and testes.

A membrane-bound myo-inositol 1-phosphatase has been solubilized and partially purified from rat tissues. This particulate enzyme was detected in brain, liver and testis and certain physicochemical and enzymological properties were examined. Previously this major enzyme of the inositol signaling system was considered strictly cytosolic. The ratio of activity in the membrane form was approximately one-eighth of the activity found with the cytosolic fraction. The molecular weight of this phosphatase was found to be 59,000 by gel filtration chromatography and a subunit molecular weight of 29,000 by Western blot analysis, values comparable to the cytosolic form. This phosphatase cleaves both D- and L- myo-inositol 1-phosphates which originate from two different cellular pathways and is inhibited by lithium ions. Polyclonal antibodies were raised against homogeneous testicular cytosolic myo-inositol 1-phosphatase and cross-reacted with this membrane form as determined by western blot analysis showing immunological identity.

Animals↗

PubMed1991

Structure and conformation of 5-bromo-2',3'-dideoxyuridine.

C9H11BrN2O4, Mr = 291.11, monoclinic, P2(1), a = 11.307 (1), b = 5.954 (1), c = 15.829 (2) A, beta = 93.25 (1) degree, V = 1063.90 A3, Z = 4, Dx = 1.82 g cm-3, lambda(Cu K alpha) = 1.54184 A, mu = 53.58 cm-1, F(000) = 584, T = 295 K, R = 0.034 for 1927 observed reflections [I greater than 3 sigma(I)]. The crystal structure contains two independent molecules forming a dimer linked by a pair of N3--H...O2 hydrogen bonds; the crystal structure is stabilized by four additional hydrogen bonds. Two of these are internal C6--H6...O5' hydrogen bonds, one in molecule A and another in molecule B. These two molecules exhibit two different conformations; their sugar ring puckers are 2'-endo-3'-exo for molecule A and 3'-endo-2'-exo for molecule B. The Cl'--N1 distance, the chi CN torsion angle and the glycosidic conformation are 1.464 (8) A, -130.0 degrees and -anticlinal for molecule A and 1.506 (8) A, -168.9 degrees and -antiperiplanar for molecule B, respectively.

Antiviral Agents↗

PubMed1991

A sequence preference for nucleation of alpha-helix--crystal structure of Gly-L-Ala-L-Val and Gly-L-Ala-L-Leu: some comments on the geometry of leucine zippers.

The synthetic peptide Gly-L-Ala-L-Val (C10H19N3O4.3H2O; GAV) crystallizes in the monoclinic space group P21, with a = 8.052(2), b = 6.032(2), c = 15.779(7) A, beta = 98.520(1) degree, V = 757.8 A3, Dx = 1.312 g cm-3, and Z = 2. The peptide Gly-L-Ala-L-Leu (C11H21N3O4.3H2O; GAL) crystallizes in the orthorhombic space group P212121, with a = 6.024(1), b = 8.171(1), c = 32.791(1) A, V = 1614 A3, Dx = 1.289 g cm-3, and Z = 4. Their crystal structures were solved by direct methods using the program SHELXS-86, and refined to an R index of 0.05 for 1489 reflections for GAV and to an R index of 0.05 for 1563 reflections for GAL. The tripeptides exist as a zwitterion in the crystal and assume a near alpha-helical backbone conformation with the following torsion angles: psi 1 = -150.7 degrees; phi 2, psi 2 = -68.7 degrees, -38.1 degrees; phi 3, psi 32 = -74.8 degrees, -44.9 degrees, 135.9 degrees for GAV; psi 1 = -150.3 degrees; phi 2, psi 2 = -67.7 degrees, -38.9 degrees; phi 3, psi 31, psi 32 = -72.2 degrees, -45.3 degrees, 137.5 degrees for GAL. Both the peptide units in both of the tripeptides show significant deviation from planarity [omega 1 = -171.3(6) degrees and omega 2 = -172.0(6) degrees for GAV; omega 1 = -171.9(5) degrees and omega 2 = -173.2(6) degrees for GAL]. The side-chain conformational angles chi 21 and chi 22 are -61.7(5) degrees and 175.7(5) degrees, respectively, for valine, and the side-chain conformations chi 12 and chi 23's are -68.5(5) degrees and (-78.4(6) degrees, 159.10(5) degrees) respectively, for leucine. Each of the tripeptide molecule is held in a near helical conformation by a water molecule that bridges the NH3+ and COO- groups, and acts as the fourth residue needed to complete the turn by forming two hydrogen bonds. Two other water molecules form intermolecular hydrogen bonds in stabilizing the helical structure so that the end result is a column of molecules that looks like an alpha-helix.

Amino Acid Sequence↗

PubMed1991

Conformation and hydrogen bonding of N-formylpeptides: crystal and molecular structure of N-formyl-L-alanyl-L-aspartic acid.

Crystals of N-formyl-L-alanyl-L-aspartic acid (C8H11N2O6) grown from aqueous methanol solution are orthorhombic, space group, P2(1)2(1)2(1) with cell parameters at 294K of a = 13.619(2), b = 8.567(2), c = 9.583(3)A, V = 1118.1A3, M.W. = 232.2, Z = 4, Dm = 1.38 g/cm3 and Dx = 1.378 g/cm3. The crystal structure was solved by the application of direct methods and refined to an R value of 0.075 for 1244 reflections with I greater than or equal to 3 sigma collected on a CAD-4 diffractometer. The structure contains two short intermolecular hydrogen bonds: (i) between the C-terminal carboxyl OH and the N-acyl oxygen (2.624(3)A), a characteristic feature found in many N-acyl peptides and (ii) between the aspartic carboxyl OH. and the peptide oxygen OP1 (2.623(3)A). The peptide is nonplanar (omega = 165.5(6) degrees). The molecule takes up a folded conformation in contrast to N-formyl peptides which form extended beta-sheets; the values of phi 1, psi 1, phi 2, psi 2(1), and psi 2(2) are, respectively -65.7(6), 152.0(5), -107.2(5), 30.9(5), and -150.3(6). The aspartic acid side chain conformation is g- with chi 1 = 73.1(5). The formyl group, as expected, is transplanar [OF-CF-N1-CA1 = -4.0(8) degrees]. The presence of the short O-H ... O hydrogen bond emerges as a structural feature common to this peptide and several other N-formyl peptides. There are no C-H ... O hydrogen bonds in this structure.

Crystallography↗

PubMed1990

Structure of N-methylnicotinamide.

C7H8N2O, Mr = 136.2, monoclinic, P21/a, a = 7.055 (1), b = 9.849 (6), c = 10.066 (4) A, beta = 100.47 (2) degrees, V = 687.5 (5) A3, Z = 4, Dm = 1.32, Dx = 1.315 g cm-3, Cu K alpha, lambda = 1.5418 A, mu = 7.09 cm-1, F(000) = 288, T = 294 K, R = 0.048 for 1134 reflections [I greater than 3 sigma(I)]. The N-methylcarboxamide group is extended with the keto O(7) transoid to C(2) [C(2)--C(3)--C(7)--O(7) +/- 158.9 (3), C(3)--C(7)--N(7)--C(8) +/- 177.1 (3), C(2)--C(3)--C(7)--N(7) +/- 23.2 (3) and C(4)--C(3)--C(7)--N(7) +/- 158.2 (3) degrees]. The dihedral angle between the planes of the pyridine ring and the carboxamide plane is 22 degrees. The molecules are linked together by N--H...O hydrogen bonds involving the amino N(7) and the carbonyl O(7) atoms.

Molecular Conformation↗

PubMed1990

Design of crystalline helices of short oligopeptides as a possible model for nucleation of alpha-helix: role of water molecules in stabilizing helices.

We have designed, synthesized, crystallized, and performed x-ray analysis of several hydrophobic tripeptides that show an extended near alpha-helical structure in the crystalline state. All of the tripeptides that show this remarkably stable helix crystallize with two or three water molecules; they all have glycine at the N terminus and have increasing hydrophobicity as one moves from the N to C terminus. Even though three residues in the oligomer are not sufficient to complete a turn, one of the water molecules acts as an added residue and links up adjacent tripeptide segments along the helix axis so that in the crystal, the helix appears effectively as one long continuous helix. Two of these tripeptides are stabilized by two water molecules that enable the peptides to complete a turn of the helix and extend the helical structure throughout the crystal by linking translationally related peptides by hydrogen bonds. In two other peptides, these roles are played by three rather than two water molecules. Though these tripeptides have different crystal symmetry, they all show the basic pattern of hydrated helix and packing, indicating the strong conformational preference for a stable structure even for these tripeptides. Such conformationally stable hydrated structures for short specific related sequences illustrate their possible importance in nucleating protein folding and in the role water molecules play in such events.

Amino Acid Sequence↗

PubMed1989

The identification of a novel inositol lipid, phosphatidylinositol trisphosphate (PIP3), in rat cerebrum using in vivo techniques.

Rats received intraventricular injections of 20 uCi of [3H]-myo-inositol, and were sacrificed 24 hrs later by high-power head-focused microwave fixation. Two inositol lipid extraction methods were compared: The Hauser and Eichberg method yielded higher recovery of inositol lipids, but a lower inositol phosphate content. The Schacht method yielded reduced radiolabel in the lipid fractions, but increased water soluble phosphates. Both methods extracted a novel inositol lipid (PIP3) which contained inositol tetrakisphosphate (IP4) as its polar head group. This was determined by alkaline hydrolysis and analyzed by high performance liquid chromatography with authentic IP4 standard. Furthermore, preliminary studies of the fatty acid composition indicated a similarity with other inositol lipids. The radiolabel ratio of PIP2:PIP3 was 5:1. In summary, we have isolated a novel inositol phospholipid in rat brain, PIP3, the parent compound for inositol tetrakisphosphate (IP4).

Animals↗

PubMed1989

A model for hydropathy-based peptide interactions.

Two peptides are specified when the noncoding DNA strand is read in the 5' to 3', or the 3' to 5' direction, and both peptides form strong complexes with the natural peptide, as found by J. E. Blalock and K. L. Bost with ACTH [1986) Biochem. J. 234, 679-683). We report here that strong hydropathic complementarity (pairing of hydrophobic with hydrophilic residues), the assumed basis of these interactions, is obtained only if the peptide resulting from reading in the 3' to 5' direction is aligned parallel to the natural peptide, or if the peptide derived by opposite reading of the DNA is aligned antiparallel to it. Complementary is abolished in other alignments, including all staggered ones. In the appropriate alignments of the constructs the amino acid residues opposite one another are specified by a pair of complementary codons in the DNA; Blalock and Bost have indeed shown that complementary pairs of codons specify amino acids of opposite hydropathy. A model is proposed to explain how hydropathic complementarity can lead to interaction between peptides. We propose that in the interacting peptides hydrophilic residues of both chains are oriented toward the aqueous solvent, while the hydrophobic ones form the interphase between the two chains. Tight packing is made possible by the stipulation that whenever a hydrophilic residue turns toward the aqueous phase, a space is liberated which can accommodate a hydrophobic residue from the opposing chain. This entropy-driven configuration can lead to strong interactions between portions of peptides consisting of hydropathically complementary residues.

Adrenocorticotropic Hormone↗

PubMed1989

Short S...O contacts: structure of 2,5-bis(p-methoxyphenylhydroxymethyl)thiophene.

C20H20O4S, Mr = 356.4, monoclinic, P2(1)/c, a = 5.045 (3), b = 29.115 (7), c = 11.924 (2) A, beta = 94.82 (3) degrees, V = 1745.2 A3, Z = 4, Dx = 1.357 g cm-3, lambda(Cu K alpha) = 1.5418 A, mu = 17.86 cm-1, F(000) = 752, T = 298 K, R = 0.038, wR = 0.044 for 1212 reflections, I greater than 3 sigma(I). In the crystal, the molecule adopts a conformation in which one of the two hydroxymethyl fragments is synplanar to S and the other is anticlinal to S. Although the two fragments are otherwise equivalent, the C-C-O bond angles in the two hydroxymethyl fragments are significantly different from each other [106.7 (3) and 110.7 (3) degrees]. The decrease of 4 degrees in the bond angle is for the C-C-OH fragment that makes a short S...O contact and must indicate a non-bonded attractive interaction between the two atoms.

Chemical Phenomena↗

PubMed1989

Role of water molecules in the crystal structure of Gly-L-Ala-L-Phe: a possible sequence preference for nucleation of alpha-helix?

The synthetic peptide Gly-L-Ala-L-Phe (C14H19N3O4.2H2O; GAF) crystallizes in the monoclinic space group P2I1), with a = 5.879(1), b = 7.966(1), c = 17.754(2) A, beta = 95.14(2) degrees, Dx = 1.321 g cm-3, and Z = 2. The crystal structure was solved by direct methods using the program SHELXS-86 and refined to an R value of 0.031 for 1425 reflections (greater than 3 sigma). The tripeptide exists as a zwitterion in the crystal and assumes a near alpha-helical backbone conformation with the following torsion angles: psi 1 = -147.8 degrees; phi 2, psi 2 = -71.2 degrees, 33.4 degrees; phi 3, psi 3 = -78.3 degrees, -43.3 degrees. In this structure, one water molecule bridges the COO- and NH3+ terminii to complete a turn of an alpha-helix and another water molecule participates in head-to-tail intermolecular hydrogen bonding, so that the end result is a column of molecules that looks like an alpha-helix. Thus, the two water molecules of crystallization play a major role in stabilizing the near alpha-helical conformation of each tripeptide molecule and in elongating the helix throughout the crystal. An analysis of all protein sequences around regions containing a GAF fragment by Chou-Fasman's secondary structure prediction method showed that those regions are likely to assume an alpha-helical conformation with twice the probability they are likely to adopt a beta-sheet conformation. It is conceivable that a GAF fragment may be a good part of the nucleation site for forming alpha-helical fragments in a polypeptide, with the aqueous medium playing a crucial role in maintaining such transient species.

Amino Acid Sequence↗

PubMed1989

Crystal structure and conformation of L-pyroglutamyl-L-alanine.

Crystals of the dipeptide, pyroglutamyl-alanine (C8H12N2O4) grown from aqueous methanol are monoclinic, space group P2(1) with the following cell parameters: a = 4.863(2), b = 16.069(1), c = 6.534(2)A and beta = 109.9(2) degrees, V = 480.0A3, Mr = 200.2, Dc = 1.385 g cm-3, and Z = 2. The crystal structure was solved by the application of direct methods and refined to an R value of 0.044 for 699 reflections with I greater than 2 sigma. The amide of the pyroglutamyl side chain is cis, omega 1 = 2.6(7) degrees; the peptide unit is trans and appreciably non-planar (omega 2 = 167.4(5) degrees). The backbone torsional angles are: psi 1 = 166.1(5), phi 2 = -90.3(6), and psi 2 = -22.4(6) degrees. This structure contains a short (2.551(5)A) intermolecular hydrogen bond between the carboxyl OH and the N-acyl oxygen, a feature common to most acyl amino acids and acyl peptides.

Chemical Phenomena↗

PubMed1989

Crystal structure and conformation of glycyl-glycyl-sarcosine.

Crystals of the tripeptide, glycyl-glycyl-sarcosine (C7H13N3O4) from aqueous methanol are orthorhombic, space group Pbcn with cell parameters at 294 K of a = 8.279(1), b = 9.229(4), c = 24.447(5)A, V = 1868.0 A3, M.W. = 203.2, and Z = 8. The crystal structure was solved and refined using CAD-4 data (1171 reflections greater than or equal to 3 sigma) to a final R-value of 0.053. The first peptide linkage is trans and planar whereas the second peptide link between Gly and sarcosine is cis and appreciably non-planar (w = 7.4 degrees). The peptide backbone has an extended conformation at the N-terminal part but adopts a polyglycine-II type of conformation at the C-terminal part. The backbone torsion angles are: psi 1 = -173.9, w1 = -177.8, (phi 2, psi 2) = (-178.8, -170.8), w2 = 7.4, (phi 3, psi 3) = (-81.6, 165.6 degrees).

Crystallography↗

PubMed1989

Crystal structure of L-2-oxothiazolidine-4-carboxylic acid.

Crystals of the title compound, L-2-oxothiazolidine-4-carboxylic acid, OTC (C4H5NO3S), grown from an aqueous solution are orthorhombic, space group P2(1)2(1)2(1) with the following cell parameters at 22 +/- 3 degrees: a = 5.381(1), b = 5.961(1), c = 17.929(3)A, V = 575.1A(3), Mr = 146.2, Dc = 1.688 g.cm-3, mu = 43.9 cm-1 and Z = 4. The crystal structure was solved by the application of direct methods and refined to an R value of 0.032 for 596 reflections with I greater than 3 sigma(I). The thiazolidine ring adopts a "twist" conformation. This structure contains a short (2.619(3)A) intermolecular hydrogen bond between the carboxyl OH and the oxygen of the 2-oxo moiety, a feature common to most acyl amino acids and acyl peptides.

Crystallization↗

PubMed1989

Conformation and hydrogen bonding of N-formylmethionyl peptides. II. Crystal and molecular structure of N-formyl-L-methionyl-L-phenylalanine.

Crystals of N-formyl-L-methionyl-L-phenylalanine (C15H20N2O4S), grown from aqueous methanol solution are orthorhombic, space group, P2(1)2(1)2(1), with cell parameters at 294K of a = 4.900(2), b = 17.947(4), c = 18.726(4)A, V = 1646.8A3, M.W. = 324.4, Z = 4 and Dm = 1.308 g/cc, and as expected, all nearly identical to that of N-f-D-Met-D-Phe studied by Jeffs, Heald, Chodosh & Eggleston (Int. J. Peptide Protein Res. 24, 442-446, 1984). The crystal structure was solved and refined using CAD-4 data (1095 reflections greater than or equal to 3 sigma) to a final R value of 0.042. Molecules related by the alpha-translation form a parallel beta-sheet rather than anti-parallel sheet as stated in the earlier study of Jeffs et al. The formation of the parallel rather than the anti-parallel beta-sheet structure, the use of the C-H ...O hydrogen bonds to stabilize the beta-sheet and the very short O-H ...O hydrogen bond between the carboxyl OH and the N-acyl oxygen atom emerge as the main structural features of the chemotactic N-formyl methionyl peptides.

Chemotactic Factors↗

PubMed1988

Structure of adenosine-5'-mononicotinate (AMN) trihydrate: an analog of NAD for testing intramolecular stacking.

C16H16N6O5.3H2O, Mr = 426.4, monoclinic, P21, a = 9.535 (2), b = 13.932 (2), c = 7.138 (2) A, beta = 93.13 (2) degrees, V = 946.85 A3, Z = 2, Dx = 1.495 g cm-3, lambda (Cu K alpha) = 1.5418 A, mu = 9.93 cm-1, F(000) = 428, T = 294 K, R = 0.045 and wR = 0.059 for 1460 observed reflections [I greater than 3 sigma (I)]. The AMN molecules, unlike NAD or other model structures of NAD, are not charged and exhibit intra- as well as intermolecular stacking of pyridine ring over adenine ring. There is extensive hydrogen bonding in the crystal involving the pyridine and adenine rings and the three water molecules. Rather surprisingly, the ester carbonyl O atom is not involved in the hydrogen bonding.

Hydrogen Bonding↗