Co-operative intra-protein structural response due to protein–protein complexation revealed through thermodynamic quantification: study of MDM2-p53 binding

The p53 protein activation protects the organism from propagation of cells with damaged DNA having oncogenic mutations. In normal cells, activity of p53 is controlled by interaction with MDM2. The well understood p53-MDM2 interaction facilitates design of ligands that could potentially disrupt or prevent the complexation owing to its emergence as an important objective for cancer therapy. However, thermodynamic quantification of the p53-peptide induced structural changes of the MDM2-protein remains an area to be explored. This study attempts to understand the conformational free energy and entropy costs due to this complex formation from the histograms of dihedral angles generated from molecular dynamics simulations. Residue-specific quantification illustrates that, hydrophobic residues of the protein contribute maximum to the conformational thermodynamic changes. Thermodynamic quantification of structural changes of the protein unfold the fact that, p53 binding provides a source of inter-element cooperativity among the protein secondary structural elements, where the highest affected structural elements (α2 and α4) found at the binding site of the protein affects faraway structural elements (β1 and Loop1) of the protein. The communication perhaps involves water mediated hydrogen bonded network formation. Further, we infer that in inhibitory F19A mutation of P53, though Phe19 is important in the recognition process, it has less prominent contribution in the stability of the complex. Collectively, this study provides vivid microscopic understanding of the interaction within the protein complex along with exploring mutation sites, which will contribute further to engineer the protein function and binding affinity.     

Facile synthesis of substituted pyrrole-fused isocoumarins from ninhydrin

A simple and efficient procedure has been developed for the synthesis of substituted pyrrole-fused isocoumarins from easily available ninhydrin. The cyclic hemiaminal dihydroxy-indenopyrroles, the adducts of ninhydrin with enamines of acetylacetone, give pyrrole-fused isocoumarins upon heating in acidic medium. The process constitutes an interesting acid-catalyzed rearrangement to eight-membered lactams followed by intramolecular cyclization involving the amino and keto groups.     

In vitro evolution of ligands to the membrane protein caveolin

Membrane proteins comprise a third of the human genome, yet present challenging targets for reverse chemical genetics. For example, although implicated in numerous diseases including multiple myeloma, the membrane protein caveolin-1 appears to offer a poor target for the discovery of synthetic ligands due to its largely unknown structure and insolubility. To break this impasse and identify new classes of caveolae controlling lead compounds, we applied phage-based, reverse chemical genetics for the discovery of caveolin-1 ligands derived from the anti-HIV therapeutic T20. Substitution of homologous residues into the T20 sequence used a process analogous to medicinal chemistry for the affinity maturation to bind caveolin. The resultant caveolin-1 ligands bound with >1000-fold higher affinity than wild-type T20. Two types of ELISAs and isothermal titration calorimetry (ITC) measurements demonstrated high affinity binding to caveolin by the T20 variants with K(d) values in the 150 nM range. Microscopy experiments with the highest affinity caveolin ligands confirmed colocalization of the ligands with endogenous caveolin in NIH 3T3 cells. The results establish the foundation for targeting caveolin and caveolae formation in living cells.     

Conformational fluctuations of a protein-DNA complex and the structure and ordering of water around it

Protein-DNA binding is an important process responsible for the regulation of genetic activities in living organisms. The most crucial issue in this problem is how the protein recognizes the DNA and identifies its target base sequences. Water molecules present around the protein and DNA are also expected to play an important role in mediating the recognition process and controlling the structure of the complex. We have performed atomistic molecular dynamics simulations of an aqueous solution of the protein-DNA complex formed between the DNA binding domain of human TRF1 protein and a telomeric DNA. The conformational fluctuations of the protein and DNA and the microscopic structure and ordering of water around them in the complex have been explored. In agreement with experimental studies, the calculations reveal conformational immobilization of the terminal segments of the protein on complexation. Importantly, it is discovered that both structural adaptations of the protein and DNA, and the subsequent correlation between them to bind, contribute to the net entropy loss associated with the complex formation. Further, it is found that water molecules around the DNA are more structured with significantly higher density and ordering than that around the protein in the complex.     

2-(2-Pyridyl) benzimidazole based Co(II) complex as an efficient fluorescent probe for trace level determination of aspartic and glutamic acid in aqueous solution: a displacement approach

A weakly fluorescent cobalt(II) complex is synthesized using 2-(2-pyridyl)-benzimidazole (PBI) as a chelating fluorescent ligand and characterized by single crystal X-ray structure. This complex serves as an efficient fluorescent probe for trace level determination of aspartic acid (AspA) and glutamic acid (GluA) in aqueous solution. Rest of the naturally occurring amino acids did not interfere. Both aspartic acid and glutamic acid replaces PBI from the coordination sphere of Co(II)-PBI complex resulting appearance of strong fluorescence signal for the released free PBI. The signal response is very fast and the interaction of both the AspA and GluA with the Co(II) is strong enough as evident from their displacement equilibrium constant values, viz. 4357.8 M(-1) and 8333.33 M(-1) respectively.     

Surfactant mediated oxygen reuptake in water for green aerobic oxidation: mass-spectrometric determination of discrete intermediates to correlate oxygen uptake with oxidation efficiency

A novel strategy of catalytic green aerobic oxidation by surfactant-mediated oxygen reuptake in water offers a new dimension to the applications of surfactants to look beyond as solubility aids and a conceptual advancement in understanding the role of surfactants in aquatic organic reactions through mass spectrometry guided identification of discrete intermediates.     

PEGylated inorganic nanoparticles

Application of inorganic nanoparticles in diagnosis and therapy has become a critical component in the targeted treatment of diseases. The surface modification of inorganic oxides is important for providing diversity in size, shape, solubility, long-term stability, and attachment of selective functional groups. This Minireview describes the role of polyethylene glycol (PEG) in the surface modification of oxides and focuses on their biomedical applications. Such a PEGylation of surfaces provides "stealth" characteristics to nanomaterials otherwise identified as foreign materials by human body. The role of PEG as structure-directing agent in synthesis of oxides is also presented.     

Dynamic properties of water around a protein-DNA complex from molecular dynamics simulations

Formation of protein-DNA complex is an important step in regulation of genes in living organisms. One important issue in this problem is the role played by water in mediating the protein-DNA interactions. In this work, we have carried out atomistic molecular dynamics simulations to explore the heterogeneous dynamics of water molecules present in different regions around a complex formed between the DNA binding domain of human TRF1 protein and a telomeric DNA. It is demonstrated that such heterogeneous water motions around the complex are correlated with the relaxation time scales of hydrogen bonds formed by those water molecules with the protein and DNA. The calculations reveal the existence of a fraction of extraordinarily restricted water molecules forming a highly rigid thin layer in between the binding motifs of the protein and DNA. It is further proved that higher rigidity of water layers around the complex originates from more frequent reformations of broken water-water hydrogen bonds. Importantly, it is found that the formation of the complex affects the transverse and longitudinal degrees of freedom of surrounding water molecules in a nonuniform manner.     

A new analytic approximation method for the non-zero angular momentum states of the Hulthén potential

We propose a new approximation scheme to obtain analytic expressions for the bond-state energies and eigenfunctions for any arbitrary bound nl-state of the Hulthén potential. The predicted energies E_nl are in excellent agreement with the perturbative results of Lai and Lin. The scope for an extension of the method to the continuum states is also discussed.