B. P. Mukhopadhyay

Role of water molecules in protein-nucleic acid interactions: visualization of a model highly hydrated complex structure of Inosine 5′-monophosphate and L-Serine (2C10H13N4O8P·C3H7NO3·12H2O) at atomic resolution

The crystal structure of a dodecahydrated co-complex between two Inosine 5′-monophosphate (IMP) and one L-serine, the first of its kind reported, has been determined at atomic resolution by X-ray crystallographic methods. The crystal belongs to a monoclinic space group, P21, with the cell dimensionsa=8.695(7),b=21.898(6),c=12.374(3)Å, β=110.59(3)°. This structure reveals the recognition mechanism of serine to the nucleotides through direct and water-mediated hydrogen bonds. The phosphate oxygen (O22) seems to prefer the nonspecific interaction with the functional sites of serine (N...O22=2.735, OG...O22=2.970, O1...O22 =3.121 Å), whereas the bases prefer specific (N17...N=3.199, N23...O2=2.784 Å) bondings. The solvent-mediated hydrogen bonds N17...W3...N27 endow extra stabilization to the stacked bases. The presence of hydrogen-bonded water spines and their interplay in the specific and nonspecific bindings with potential ligands indicate the functional involvement of solvent molecules through cooperative donor-acceptor network and could act as viable centers of intricate interactions in protein-DNA complexation processes.

Recognition and Stabilization of A Unique CPRI—Structural Motif in Cucurbitaceae Family Trypsin Inhibitor Peptides: Molecular Dynamics Based Homology Modeling Using the X-ray Structure of MCTI-II

Abstract The high resolution crystallographic structure of MCTI-II complexed with beta trypsin (PDB entry 1MCT) was used to model the corresponding structures of the six inhibitor peptides belonging to Cucurbitaceae family (MCTI-I, LA-1, LA-2, CMTI-I, CMTI-III, CMTI- IV). Two model inhibitors, LA-1 and LA-2 were refined by molecular dynamics to estimate the average solution structure. The difference accessible surface area (DASA) study of the inhibitors with and without trypsin revealed the Arginine and other residues of the inhibitors which bind to trypsin. The hydration dynamics study of LA1 and LA2 also confirm the suitability of water molecules at the active Arg site. Moreover, the presence of a unique 3D-structural motif comprises with the four CPRI residues from the amino terminal is thought to be conserved in all the six studied inhibitors, which seems essential for the directional fixation for proper complexation of the Arg (5) residue towards the trypsin S1-binding pocket. The role of the disulphide linkage in the geometrical stabilization of CPRI (Cysteine, Proline, Arginine, Isoleucine) motif has also been envisaged from the comparative higher intra molecular Cys (3) -Cys (20) disulphide dihedral energies.

Regiospecificity of nucleotide-amino acid mating vs. water dynamics: a key to protein-nucleic acid assemblies: structure of unidecahydrated inosine-5'-monophosphate and L-glutamic acid (2C10H13N4O8P.C5H11NO4.11H2O) cocrystal at atomic resolution

The crystal structure of a unidecahydrated cocomplex between two Inosine-5′-monophosphates (IMP) and one L-glutamic acid has been determined by X-ray crystallographic methods. The crystal belongs to the monoclinic space group P21 with cell dimensions a = 8.650(1), b = 21.900(1), c = 12.370(1) Å, and β = 110.4°(9). This structure reveals extensive hydrogen bonding of glutamic acid to the nucleotide through direct and water-mediated interactions. The phosphate oxygens (O3B and O1B) seem to prefer nonspecific interaction with the functional sites of glutamic acid (OE2 ······O1B = 1.78 Å, NA······O3B = 2.73 Å, OH······O3B = 3.06 Å), whereas the bases prefer specific (O······N3B = 2.88 Å) binding. A solvent mediated N7A···W5···N7B hydrogen bond used for stabilization of the stacked purine bases has been observed as in other amino acid–nucleotide cocrystals. Glutamic acid occupies the same hydrophilic region in the nucleotide cocrystal as was found in glutamine–inosine monophosphate (Gln–IMP) and in serine–inosine monophosphate (Ser–IMP) complexes through substantial replacement of free and bound water molecules. This points to the dynamic hydrogen bonding nature of the water molecules and their stereochemical cooperation for the placement of amino acid through the polycoordination within the crystal.

Influences of cooperative hydrogen bonding economy on protein-nucleic acid complexation : Structure of unidecahydrated Inosine C5'-monophosphate and L-glutamine (2C10H13N4O8P.C5H10N2O3.11H2O) cocrystal at atomic resolution

The crystal structure of a unidecahydrated co-complex between two Inosine 5′-monophosphate (IMP) and one L-glutamine has been determined at atomic resolution by X-ray crystallographic methods. The crystal belongs to the monoclinic space group P21 with cell dimensions a = 8.690(2), b = 21.900(3), c = 12.370(1) Å, and β = 110.59(3)°. This structure reveals the recognition mechanism of glutamine to the nucleotide through direct and water-mediated hydrogen bonds. The phosphate oxygen (O23) seems to prefer the nonspecific interaction with the functional sites of glutamine (NA· · ·O23 = 2.672, OH· · ·O23 = 3.063, OE· · ·O23 = 3.104 Å), whereas the bases prefer specific (N23· · ·O = 2.874 Å) bindings. But here no specific interaction has been observed at N17 and N27, which were observed in serine—IMP complex. However, the solvent mediated N17· · ·OW3· · ·N27 hydrogen bonds for stabilization of the stacked purine bases have been observed as in other aminoacid-nucleotide cocrystals. The striking habit of glutamine to occupy the nearly same region of the nucleotide cocrystal as was found in the serine—IMP complex through substantial replacement of free and bound water molecules, shows certainly the cooperative hydrogen bonding economy of water molecules.

Hydrogen bonding cooperativity of water to nucleotide recognition : structure of octadecahydrated inosine 5'-monophosphate, 2(C10H12N4O8P).18H2O at atomic resolution

The crystal structure of an octadecahydrated complex between two inosine 5′-monophosphate (IMP) has been determined at atomic resolution, which reveals the hydrogen bonding and the coordination cooperativity of water molecules to nucleotide recognition. The crystal belongs to monoclinic space group P21 with cell dimensions a = 8.65(1), b = 21.90(1), c = 12.37(1)Å, and β = 110.38(9)°. The ribose hydroxyls, purine N7, keto(O6) bonded water molecules W1, W2, W5, W6, W8 and the phosphate bridge forming water oxygens of W4, W7, W11 appear to play an invariant role in their hydrogen bonding interactions with the IMPs. The synergistic role of the water molecules W5, W6, W8 in the purine staking domain N27⋯W5=2.583,O16⋯W8=2.759,O2627⋯W6=2.723 Åhave been clearly observed for the first time. The complexation of the water molecules through variable hydrogen bonding coordination indicate their functional involvement through extensive cooperative donor-acceptor network mechanism. The occurrence of hydrogen-bonded water spines, water bridges and their interplay in the structural association of IMPs could indicate the possible viability of those aquatic centers in the biological situation.

Crystal and molecular structure of di(2-methylbenzotriazole) sulfate, (C7N3H9)2SO4

AbstractThe structure of di(2-Methylbenzotriazole) sulphate, (C7N3H9)2SO4, has been solved by X-ray diffraction methods. The compound crystallises in triclinic space group P

The crystal and molecular structure of an epoxide, C30H50O

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Erratum: Structural and interactional homology of clinically potential typsin inhibitors: Molecular modelling of cucurbitaceae family peptides using the X-ray structure of MCTI-II (Protein Engineering (2000) 13 (551-555))

witha=6.986(1),b=18.914(1),c=6.990(1) Å, α=95.083 (1), β=115.56 (1) and γ=84.93(1)o, respectively.Mr=362.36,F(000)=380,Z=2,Dm=1.45 mg m−3, finalR=0.060,Rw=0.064. The structure was solved by direct methods (SHELXS86) and refined by least-squares methods. Dimers of planar 2-Methylbenzotriazole (MBT) molecules form stacks, one along thea-axis and the other parallel to thec-axis. The SO4−2 ions are confined by the two sets of stacks and are responsible for holding them together. The structure is mainly stabilized by the stacking forces. The average interplanar distances in any stack are 3.281 Å, within a dimer, and 3.361 Å, between the dimers.