The ruggedness of protein-protein energy landscape and the cutoff for 1/r(n) potentials

Interfacial adhesive properties between a rigid-rod pyromellitimide molecular layer and a covalent semiconductor via atomistic simulations

We conducted a comprehensive atomistic simulation study of the adhesive properties of aromatic rigid-rod poly-[(4,4'diphenylene) pyromellitimide] on a dimer-reconstructed silicon surface. We describe the structural developments within the adherent's interfacial region at the atomistic scale, and evaluate the energetics of the adhesive interactions between bimaterial constituents. In particular, we observe a transition between noncontact and contact adhesion regimes as a function of the interfacial bonding strength between the polyimide repeat units and the silicon substrate. This transition is manifest by a three- to four-fold increase in adhesive energy, which is entirely attributable to structural relaxation in the organic layer near the interface, revealing the importance of accurately describing structural details at interfaces for reliable interfacial strength predictions. The underlying molecular reconfigurations in the pyromellitimide layer include preferred orientation of the rigid-rod molecules, molecular stacking, ordering, and the local densification. The role of each of these factors in the adhesive behavior is analyzed and conclusively described. Where possible, simulation results are compared with theoretical model predictions or experimental data.

Sequence composition and environment effects on residue fluctuations in protein structures

Structure fluctuations in proteins affect a broad range of cell phenomena, including stability of proteins and their fragments, allosteric transitions, and energy transfer. This study presents a statistical-thermodynamic analysis of relationship between the sequence composition and the distribution of residue fluctuations in protein-protein complexes. A one-node-per-residue elastic network model accounting for the nonhomogeneous protein mass distribution and the interatomic interactions through the renormalized inter-residue potential is developed. Two factors, a protein mass distribution and a residue environment, were found to determine the scale of residue fluctuations. Surface residues undergo larger fluctuations than core residues in agreement with experimental observations. Ranking residues over the normalized scale of fluctuations yields a distinct classification of amino acids into three groups: (i) highly fluctuating-Gly, Ala, Ser, Pro, and Asp, (ii) moderately fluctuating-Thr, Asn, Gln, Lys, Glu, Arg, Val, and Cys, and (iii) weakly fluctuating-Ile, Leu, Met, Phe, Tyr, Trp, and His. The structural instability in proteins possibly relates to the high content of the highly fluctuating residues and a deficiency of the weakly fluctuating residues in irregular secondary structure elements (loops), chameleon sequences, and disordered proteins. Strong correlation between residue fluctuations and the sequence composition of protein loops supports this hypothesis. Comparing fluctuations of binding site residues (interface residues) with other surface residues shows that, on average, the interface is more rigid than the rest of the protein surface and Gly, Ala, Ser, Cys, Leu, and Trp have a propensity to form more stable docking patches on the interface. The findings have broad implications for understanding mechanisms of protein association and stability of protein structures.