A graph theoretical approach for assessing bio-macromolecular complex structural stability.

Fast and proper assessment of bio macro-molecular complex structural rigidity as a measure of structural stability can be useful in systematic studies to predict molecular function, and can also enable the design of rapid scoring functions to rank automatically generated bio-molecular complexes. Based on the graph theoretical approach of Jacobs et al. [Jacobs DJ, Rader AJ, Kuhn LA, Thorpe MF (2001) Protein flexibility predictions using graph theory. Proteins: Struct Funct Genet 44:150-165] for expressing molecular flexibility, we propose a new scheme to analyze the structural stability of bio-molecular complexes. This analysis is performed in terms of the identification in interacting subunits of clusters of flappy amino acids (those constituting regions of potential internal motion) that undergo an increase in rigidity at complex formation. Gains in structural rigidity of the interacting subunits upon bio-molecular complex formation can be evaluated by expansion of the network of intra-molecular inter-atomic interactions to include inter-molecular inter-atomic interaction terms. We propose two indices for quantifying this change: one local, which can express localized (at the amino acid level) structural rigidity, the other global to express overall structural stability for the complex. The new system is validated with a series of protein complex structures reported in the protein data bank. Finally, the indices are used as scoring coefficients to rank automatically generated protein complex decoys.

In vitro hydrolysis of blends from enantiomeric poly(lactide)s. 3. Homocrystallized and amorphous blend films.

Homocrystallized and amorphous enantiomeric blend films were prepared from the melt of high molecular weight poly(L-lactide) (PLLA) and poly(D-lactide) (PDLA) (1:1) by crystallization and quenching, respectively. A phosphate-buffered solution was used to investigate effects of homocrystallinity via in vitro hydrolysis as well as crystallization process during the hydrolysis, which was performed for a period of 24 months at 37 degrees C and pH 7.4. Results derived from gravimetry, gel permeation chromatography, and tensile testing showed that hydrolyzability was higher for the homocrystallized film than for the amorphous film. Thus, probable mechanisms are proposed for the enhanced hydrolysis of the homocrystallized blend film compared with that of the amorphous blend film. The hydrolysis rate constant (k) values of the homocrystallized and amorphous films estimated from the changes in number-average molecular weight (M(n)) were 5.00 x 10(-3) and 3.32 x 10(-3) day(-1), respectively. Moreover, hydrolyzability of equimolar enantiomeric poly(lactic acid) blends can be altered in the k range of 0.73 x 10(-3) and 5.00 x 10(-3) day(-1) by varying their crystalline species, crystallinity, or molecular weights.