The covalent complex of Jo-In results from a long-lived, non-covalent intermediate state with near-native structure.

Covalent protein complexes have been used to assemble enzymes in large scaffolds for biotechnology purposes. Although the catalytic mechanism of the covalent linking of such proteins is well known, the recognition and overall structural mechanisms driving the association are far less understood but could help further functional engineering of these complexes. Here, we study the Jo-In complex by NMR spectroscopy and molecular modelling. We characterize a transient non-covalent complex, with structural elements close to those in the final covalent complex. Using site specific mutagenesis, we further show that this non-covalent association is essential for the covalent complex to form.

Theoretical studies on the transport mechanism of 5-fluorouracil through cyclic peptide based nanotubes.

Cyclic peptide nanotubes (CPNTs) formed by the self-assembly of cyclic peptides (CPs) with an even number of alternate l/d amino acids are typically used in the field of the transport of ions and drug molecules across the lipid bilayer. This study investigates the transport mechanism of the antitumor drug molecule, 5-fluorouracil (5FU), through the CPNT using classical and steered molecular dynamics simulations combined with umbrella sampling. During the transport of 5FU through the CPNT, 5FU is partially desolvated because the lumen of the CPNT is too small to allow for water molecules solvating it. 5FU forms H-bonding interactions with the backbones of the CPNT and at the same time, also forms hydrophobic contacts with the backbone Cα and C atoms of the CPNT. The cooperative breaking of the H-bond and hydrophobic interactions between the CPNT and 5FU increases the pulling force to transport the 5FU from the mid-Cα region to the Cα one. The calculated free energies of binding reveal that the energy barriers for the transport of 5FU are ∼-6.0 and ∼-2.0 kcal mol(-1) in the mid-Cα and Cα plane regions, respectively.

Structure and stability of cyclic peptide based nanotubes: a molecular dynamics study of the influence of amino acid composition.

The stability of self-assembling cyclic peptides (CPs) is attained by the intermolecular backbone-backbone hydrogen bonding (H-bonding) interactions. In addition to these H-bonding interactions, the self-assembled CPs are further stabilized by various intermolecular side chain-side chain interactions. This study investigates the role of amino acids on the structure and stability of self-assembled CPs using classical molecular dynamics (MD) simulations and molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA) method. The amino acids considered for the construction of model structures of cyclic peptide nanotubes (CPNTs) are Ala, Leu, Phe, Gln, Glu, and Trp. The calculated structural parameters from classical MD simulations reveal that the backbone flexibility of CPNTs composed of non-Ala residues results from an intrinsic property of the amino acids. The presence of an Ala residue at the alternate position increases the solvation of side chains of Gln residue. The occurrence of Glu residue does not favour the formation of intermolecular side chain-side chain H-bonding interactions in aqueous medium. It is evident from the calculated free energy of binding that CPNTs composed of non-polar residues are highly stable in aqueous medium. At the same time, CPNTs with polar side chains are less stable in aqueous medium. Results obtained from this study demonstrate the role played by amino acid side chains on the structure and stability of CPNTs and provide valuable suggestions for the design of CPNTs with moderate stability in various solvent environments.

Bonding, aromaticity, and structure of trigonal dianion metal clusters.

Various isomers of the trigonal dianion metal clusters, X(3)(2-), X = Be, Mg, Ca, and their mono- and disodium complexes are optimized at the B3LYP/6-311+G(d) level. Different conceptual density functional theory based reactivity descriptors as well as the induced magnetic field values are calculated to understand the stability and aromaticity of these systems. Possibility of bond stretch isomerism is explored. Genetic algorithm results lend additional insights into the structures of these isomers.

In silico study of amphiphilic nanotubes based on cyclic peptides in polar and non-polar solvent.

The stability of cyclic peptide assemblies (CPs) forming a macromolecular nanotube structure was investigated in solvents of different polarity using computational methods. The stability and structure of the complexes were studied using traditional molecular dynamics (MD). Energy of dissociation was estimated from steered MD in combination with umbrella sampling simulations. A cyclic peptide nanotube (CPNT) was constructed by stacking of eight cyclo[(D-Trp-L-Gln-D-Trp-L-Glu)2], and hereafter is referred to as (WQWE)8. Its dissociation was studied by pulling 1, 2, or 3 subunits from the nanotube. The crucial point in the dissociation event of the CP subunit(s) is the breaking of backbone-backbone hydrogen bonds and consecutive annihilation of side chain interactions. Gibbs free energy calculations to estimate the binding affinity of CP subunit(s) reveal that the (WQWE)8 nanotube is significantly more stable in non-polar environments than in polar environments. The presently investigated nanotube, (WQWE)8, displays a higher stability in polar solvent than the previously studied nanotube, (QAEA)8. It appears that tryptophan contributes favorable to the improved stability by forming side chain-side chain hydrogen bonds.

3D-QSAR studies on the inhibitory activity of trimethoprim analogues against Escherichia coli dihydrofolate reductase.

Three-dimensional quantitative structure activity relationship (3D-QSAR) study has been carried out on the Escherichia coli DHFR inhibitors 2,4-diamino-5-(substituted-benzyl)pyrimidine derivatives to understand the structural features responsible for the improved potency. To construct highly predictive 3D-QSAR models, comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) methods were used. The predicted models show statistically significant cross-validated and non-cross-validated correlation coefficient of r2 CV and r2 nCV, respectively. The final 3D-QSAR models were validated using structurally diverse test set compounds. Analysis of the contour maps generated from CoMFA and CoMSIA methods reveals that the substitution of electronegative groups at the first and second position along with electropositive group at the third position of R2 substitution significantly increases the potency of the derivatives. The results obtained from the CoMFA and CoMSIA study delineate the substituents on the trimethoprim analogues responsible for the enhanced potency and also provide valuable directions for the design of new trimethoprim analogues with improved affinity.

3D-QSAR and docking studies on the HEPT derivatives of HIV-1 reverse transcriptase.

Three-dimensional Quantitative Structure Activity Relationship (3D-QSAR) has been derived for a set of HEPT derivatives of HIV-1 reverse transcriptase (RT) using Comparative Molecular Field Analysis (CoMFA). The CoMFA models have been developed using two different alignment procedures such as common substructure and bioactive conformation. The CoMFA model I is derived from a common substructure procedure that includes steric and electrostatic fields with the cross-validated q(2) and the non-cross-validated r(2) value of 0.86 and 0.97, respectively. The same for the CoMFA model II that is derived based on the bioactive conformation are 0.19 and 0.77, respectively. It is evident from the results that the common substructure-based alignment model has good statistical significance when compared with that of bioactive conformation for the selected systems in this study. The docking study revealed that the conformational flexibility observed at the R3 position favors different orientations of the substitution at the active site of HIV-1 RT and thereby leads to inconsistency in the CoMFA alignment based on bioactive conformation.