Conserved Water Mediated H-bonding Dynamics of Inhibitor, Cofactor, Asp 364 and Asn 303 in Human IMPDH II

The IMPDH (Inosine monophosphate dehydrogenase)-II is largely produced in cancer cells. Extensive MD-simulation (2 ns) of the 11330, 1NFB, 1NF7, 1LRT, and I MEW PDB-structures revealed the presence of a conserved water molecule, which is H-bonded and stabilized by the surrounding ribose hydroxyl (O2) of inhibitor, nitrogen (NN) of cofactor, carboxyl oxygen (OD2) and amide nitrogen atoms of the active site Asp 364 and Asn 303 of human. These water-mediated interaction are partially supported in the solvated and X-ray structures. The stereochemistry of the four- centered H-bonds around the conserved water center may be exploited to design a better model inhibitor for IMPDH-II

The putative role of some conserved water molecules in the structure and function of human transthyretin

Human transthyretin (hTTR) is a multifunctional protein that is involved in several neurodegenerative diseases. Besides the transportation of thyroxin and vitamin A, it is also involved in the proteolysis of apolipoprotein A1 and A beta peptide. Extensive analyses of 32 high-resolution X-ray and neutron diffraction structures of hTTR followed by molecular-dynamics simulation studies using a set of 15 selected structures affirmed the presence of 44 conserved water molecules in its dimeric structure. They are found to play several important roles in the structure and function of the protein. Eight water molecules stabilize the dimeric structure through an extensive hydrogen-bonding network. The absence of some of these water molecules in highly acidic conditions (pH <= 4.0) severely affects the interfacial hydrogen-bond network, which may destabilize the native tetrameric structure, leading to its dissociation. Three pairs of conserved water molecules contribute to maintaining the geometry of the ligand-binding cavities. Some other water molecules control the orientation and dynamics of different structural elements of hTTR. This systematic study of the location, absence, networking and interactions of the conserved water molecules may shed some light on various structural and functional aspects of the protein. The present study may also provide some rational clues about the conserved water-mediated architecture and stability of hTTR

Conserved water-mediated recognition and dynamics of NAD(+) (carboxamide group) to hIMPDH enzyme: water mimic approach toward the design of isoform-selective inhibitor

Inosine monophosphate dehydrogenase (IMPDH) enzyme involves in GMP biosynthesis pathway. Type I hIMPDH is expressed at lower levels in all cells, whereas type II is especially observed in acute myelogenous leukemia, chronic myelogenous leukemia cancer cells, and 10 ns simulation of the IMP-NAD(+) complex structures (PDB ID. 1B3O and 1JCN) have revealed the presence of a few conserved hydrophilic centers near carboxamide group of NAD(+). Three conserved water molecules (W1, W, and W1 `) in di-nucleotide binding pocket of enzyme have played a significant role in the recognition of carboxamide group (of NAD(+)) to D274 and H93 residues. Based on H-bonding interaction of conserved hydrophilic (water molecular) centers within IMP-NAD(+)-enzyme complexes and their recognition to NAD(+), some covalent modification at carboxamide group of di-nucleotide (NAD(+)) has been made by substituting the -CONH(2)group by -CONHNH2 (carboxyl hydrazide group) using water mimic inhibitor design protocol. The modeled structure of modified ligand may, though, be useful for the development of antileukemic agent or it could be act as better inhibitor for hIMPDH-II

Structural insight to mutated Y116S transthyretin by molecular dynamics simulation

197-202Familial amyloidotic polyneuropathy (FAP) is strictly associated with point mutations of transthyretin (TTR) protein. The Tyr116->Ser (Y116S) mutant TTR is an important amyloidogenic variant responsible for FAP. Structural dynamics of monomeric TTR and its mutant (Y116S) may give some clue relating to amyloid formation. In this study, molecular dynamic simulation at 310 K has been performed on wild-type and mutant (Y116S) TTR monomer, which can provide the molecular insight of structural transition in the inner and outer strand of the protein. Results show that mutation in the H-strand (Tyr116->Ser) leads to disruption of secondary structure and H-bonding pattern of some important parts of the inner DAGH-sheet of the protein. Especially, the residues T106, A108, L110 of G-strand, S117 and T119 of H-strand are affected, which are involved in the binding of thyroxin hormone. This unfolding of mutant structure during dynamics may cause instability in the protein and thus induce amyloidgenesis

Conserved water-mediated H-bonding dynamics of catalytic Asn 175 in plant thiol protease

The role of invariant water molecules in the activity of plant cysteine protease is ubiquitous in nature. On analysing the 11 different Protein DataBank (PDB) structures of plant thiol proteases, the two invariant water molecules W I and W2 (W220 and W222 in the template 1PPN structure) were observed to form H-bonds with the Ob atom of Asn 175. Extensive energy minimization and molecular dynamics simulation studies up to 2 ns on all the PDB and solvated structures clearly revealed the involvement of the H-bonding association of the two water molecules in fixing the orientation of the asparagine residue of the catalytic triad. From this study, it is suggested that H-bonding of the water molecule at the W1 invariant site better stabilizes the Asn residue at the active site of the catalytic triad

RT-PCR analysis for β-casein (I), κ-casein (II), Butyrophilin (III) and Lactoferrin (IV) in BuMECs.

<p>L: 100 bp ladder; A: BuMECs; B: Mammary Tissue (Positive control) and C: Skin fibroblasts (Negative control); Loading control represents the house keeping gene Glyceraldehyde 3–phosphate dehydrogenase (GAPDH). Results representative of minimum three independent experiments.</p

Immunostaining for cytoskeletal markers in BuMECs.

<p>A: Fluorescent image of BuMECs stained for Cytokeratin 18 showing intermediate filaments; B: Fluorescent image of BuMECs stained for Vimentin; C: Negative control with primary antibody replaced with a normal mouse IgG (Isotype control). The secondary antibodies were goat anti-mouse FITC conjugated antibody. Propidium iodide was used as a nuclear counter stain. Bars 100 µm. Results represent images from three independent experiments.</p

Immunostaining for casein in BuMECs

<p>A: Fluorecent image of casein producing BuMECs with relatively stronger signal from cells associated with domes (arrow); B: Light microscope image of same field as in A; C: Negative control experiments with rabbit IgG (Isotype control); D: Light microscope image of same field as in C. The secondary antibodies were rabbit anti-mouse FITC conjugated antibody. DAPI was used as nuclear counter stain. Bars 100 µm. Results represent minimum of three independent experiments.</p

Primer sequence and reaction conditions for PCR amplification.

<p>Primer sequence and reaction conditions for PCR amplification.</p