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  1. How modification of accessible lysines to phenylalanine modulates the structural and functional properties of horseradish peroxidase: a simu...

    PLoS ONE 9(10):e109062 (2014) PMID 25313804 PMCID PMC4196758

    We altered these lysines to phenylalanine residues to model those chemical modifications or genetic manipulations in which these positively charged lysines are converted to aromatic hydrophobic residues. Simulation results implied that upon these substitutions, the protein structure becomes less fle...
  2. Structural Stabilization and Functional Improvement of Horseradish Peroxidase upon Modification of Accessible Lysines: Experiments and Simul...

    Biophysical Journal 92(4):1192 (2007) PMID 17114227 PMCID PMC1783884

    We previously reported that covalent attachment of an electron relay (anthraquinone 2-carboxylic acid) to the surface-exposed Lys residues successfully improves electron transfer properties of HRP. Here we investigated structural and functional consequences of this modification, which alters three a...
  3. Fibrillation of alpha-lactalbumin: effect of crocin and safranal, two natural small molecules from Crocus sativus.

    Biopolymers 93(10):854 (2010) PMID 20564050

    We investigated the inhibitory effect of crocin and safranal, two principal components of saffron, on fibrillation of apo-alpha-lactalbumin (a-alpha-LA), used as a model protein, under amyloidogenic conditions. In the absence of any ligand, formation of soluble oligomers became evident after 18 hour...
  4. Molecular Dynamics Simulation of Interaction of a Cytotoxin with a Lipid Bilayer: A Multiscale Modeling

    Biophysical Journal 102(3):452a (2012)

  5. Structural and functional characterization of a mutant of Pseudocerastes persicus natriuretic peptide.

    Protein & Peptide Letters 13(3):295 (2006) PMID 16515458

    We hereby report on a mutational analysis of a novel natriuretic peptide (PNP), recently isolated by us from the Iranian snake venom. The PNP variant (mutPNP) with four substitutions (G16T, K18S, R21S, G23R) and a disulfide bonded ring shortened by 3 residues. mutPNP peptide was expressed in pET32 a...
  6. Nanomechanical properties of lipid bilayer: asymmetric modulation of lateral pressure and surface tension due to protein insertion in one le...

    The Journal of Chemical Physics 138(6):065101 (2013) PMID 23425492

    Our simulations reveal that the insertion of CTX A3 into one monolayer results in an asymmetrical change in the lateral pressure and corresponding spatial distribution of surface tension of the individual bilayer leaflets. The relative variation in the surface tension of the two monolayers as a resu...
  7. Turn plasticity distinguishes different modes of amyloid-β aggregation.

    Journal of the American Chemical Society 136(13):4913 (2014) PMID 24617810

    We demonstrate that phosphorylation at serine 26 (S26) impairs Aβ fibrillization while stabilizing its monomers and nontoxic soluble assemblies of nonfibrillar morphology. NMR spectroscopy and replica-exchange molecular dynamics indicate that introduction of a phosphate group or phosphomimetic at po...
  8. A molecular dynamics simulation study of nanomechanical properties of asymmetric lipid bilayer.

    Journal of Membrane Biology 246(1):67 (2013) PMID 23073731

    Our simulations indicate that adding more phospholipids into one monolayer results in asymmetrical changes in the lateral pressure of the individual bilayer leaflets. Interestingly, it has been observed that a change in phospholipid density in one leaflet affects the physical properties of unperturb...
  9. Functional and structural characterization of a novel member of the natriuretic family of peptides from the venom ofPseudocerastes persicus

    FEBS Letters 557(1):104 (2004) PMID 14741349

    We conclude that PNP binds to the NPR-A receptor. The solution conformation of PNP was characterized using 1H nuclear magnetic resonance spectroscopy and indicates a high degree of conformational flexibility....
  10. Conformational Changes ofα-Chymotrypsin in a Fibrillation-Promoting Condition: A Molecular Dynamics Study

    Biophysical Journal 95(9):4139 (2008) PMID 18658209 PMCID PMC2567952

    We employed a molecular dynamics simulation to investigate the early events in TFE-induced conformational changes of aCT that precede amyloid formation, and compared the results of the simulation with previous experiments. TFE molecules were found to rapidly replace the water molecules closely assoc...