Molecular Dynamics as a pattern recognition tool: an automated process detects peptides that preserve the 3D arrangement of Trypsin's Active Site.

Recently, the synthesis of a molecule has been reported that belongs to a Lysine based, branched cyclic peptide class. This work explores the ability of such molecules to preserve the 3D geometry of the Trypsin's Active Site (TAS) by applying an integrated framework of automated computer procedures. The following four factors a) D/L chirality, b) different amino acids at different positions of the molecular scaffold's cyclic part, c) the application of AMBER and CHARMM force fields and d) different implicit solvation models were evaluated against TAS similarity. It was found that a number of molecules exhibit satisfactory geometric affinity to the TAS during extended Molecular Dynamics runs. We estimated that more than 2000 molecules (belonging to this class) could retain good similarity to the TAS arrangement.

C22H46: the smallest open 3(1)-knotted alkane by computer-aided design.

The program MolKnot [Chem. Phys. Lett. 433 (2007) 422-426] has been used in order to detect the smallest ever-reported alkane configured to an open-knotted shape with three crossings (3(1)). High level ab initio calculations support our findings that 22 carbon atoms are enough to create a knotted polyethylene strand with open ends. These tight open molecular knots exhibit unusually distorted geometric characteristics as multiple extended CC bonds (maximum bond length approximately 1.70A) and several large CCC bond angles (maximum bond angle approximately 145 degrees ). The energy decomposition shows that the strain mainly affects the valence angles of the entangled structure. We observed that this 22-knotted carbon atoms' region remained almost intact as a part of alkanes with longer chain lengths.

Computational screening of branched cyclic peptide motifs as potential enzyme mimetics.

In a previous work we described the design, synthesis and catalytic activity of a branched cyclic peptide as a serine protease mimic. To maximize its catalytic activity we present now a systematic search of a large number of homologous peptides for potential enzyme activity as revealed by the topological arrangement of the catalytic triad residues. This process is accomplished by applying a combined molecular mechanics and molecular dynamics conformational search of about 200 molecules. Starting from a previously synthesized compound that showed some hydrolytic activity several analogues were modelled by aminoacid substitutions in the main molecular framework using the Insight II molecular modelling environment with some script automation. Also presented is an algorithm that: (a) generates all possible combinations of residue substitutions, (b) scans the conformational space for each molecule via high temperature molecular dynamics, (c) picks the set of molecules the trajectories of which retained, to a considerable degree, the catalytic triad molecular arrangement, (d) subjects the selected molecules to layer solvation and energy minimization and chooses the molecules, the conformations of which could preserve the catalytic triad arrangement. Finally, a modelling with periodic boundary conditions, was performed to further support the reported algorithm. We found that at least one of the analogues could be a potential serine protease mimic, as revealed by the root-mean-square comparison between the catalytic triad in two molecular dynamics trajectories of the peptide and the corresponding residues in the crystal structure of trypsin. The most promising model candidate was synthesized and tested for its catalytic activity.