Polarization Force Fields for Peptides Implemented in ECEPP2 and MM2

A comparative study of O2, CO and CN binding to heme IX protein models

Parametrization of a molecular-mechanics program to include terms specific for five- and six-coordinate transition metal complexes results in computer-simulated structures of heme complexes. The principal new feature peculiar to five and six coordination is a term that measures the effect of electron-pair repulsion modified by the ligand electronegativity and takes into account the different structural possibilities. The model system takes into account the structural differences of the fixing centre in the haemoglobin subunits. The customary proximal histidine is added. The prosthetic group heme IX is wholly considered in our model. The calculations show clearly that certain conformations are much more favourable that others for fixing O2. From the O2 binding in haemoglobin, myoglobin and simple Fe porphyrin models it is concluded that the bent O2 ligand is best viewed as bound superoxide O2-. Axial ligands are practically free-rotating. A small modification of the model in both crystal and protein matrix affects the orientation of the ligands in experimental systems.

Thermodynamic assessment of the stability of thrombin receptor antagonistic peptides in hydrophobic environments

In this paper, a general procedure is described to determine thermodynamic parameters associated with the interaction of thrombin receptor antagonistic peptides (TRAPs) with immobilized nonpolar ligands. The results show that these interactions were associated with nonlinear van't Hoff dependencies over a wide temperature range. Moreover, changes in relevant thermodynamic parameters, namely the changes in Gibbs free energy of interaction, DeltaG(0)assoc, enthalpy of interaction, DeltaH(0)assoc, entropy of interaction, DeltaS(0)assoc, and heat capacity, DeltaC(0)p, have been related to the structural properties of these TRAP analogs. The implications of these investigations for the design of thrombin receptor agonists/antagonists with structures stabilized by intramolecular hydrophobic interactions are discussed.

Molecular Polarizability of Sc and C (Fullerene and Graphite) Clusters

A method (POLAR) for the calculation of the molecular polarizability <α> is presented. It uses the interacting induced dipoles polarization model. As an example, the method is applied to Sc_n and C_n (fullerene and one-shell graphite) model clusters. On varying the number of atoms, the clusters show numbers indicative of particularly polarizable structures. The <α> are compared with reference calculations (PAPID). In general, the Sc_n calculated (POLAR) and C_n computed (POLAR and PAPID) are less polarizable than what is inferred from the bulk. However, the Sc_n calculated (PAPID) are more polarizable than what is inferred. Moreover, previous theoretical work yielded the same trend for Si_n, Ge_n and Ga_nAs_m small clusters. The high polarizability of the Sc_n clusters (PAPID) is attributed to arise from dangling bonds at the surface of the cluster.