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Several techniques are simultaneously employed to explain the structures and equilibrium of the hypoxia-inducible factor, HIF2[alpha] PAS-B with different artificial ligands. The various phenomenon involved in the binding of ligands in these factors are also explained.

Multiple molecular dynamics simulations of the single amino-acid substitutions R46Q, R131Q and R154H human Ogg1 are performed to predict the structural and dynamic effects of the substitutions throughout the protein and within the active site and substrate recognition site. These substitutions have not induced any unfolding or global structural changes instead their effects are confined to the active and recognition sites.

The thermodynamics of interaction between trimethylamine n-oxide (TMAO) and protein functional groups are studied. The findings suggest that TMAO stabilizes proteins through enhancement of water structure, such that interactions with the amide unit are discouraged.

Molecular dynamics simulations with explicit waters are employed to investigate the dominant source of elastin's elasticity. The results support the hydrophobic mechanism of elasticity and provide a framework for description of the molecular basis of the phenomenon.

The atomic interactions resulting from the addition of trans-sodium crocetinate (TSC) were analyzed to explain the diffusion of oxygen through aqueous solutions. The diffusivity levels of oxygen which were recorded at 3-5 Angstrom from TSC within the shell were larger than the bulk value. Moreover, hydrophobic hydration established an orderly channel which facilitated the efficient diffusion of oxygen in aqueous solutions.

Molecular dynamics simulations of thermal denaturation of wild-type and two mutant forms of barnase are employed in the comparison of the phi-value analysis of the folding/unfolding pathway of barnase with an explicit structural analysis of the transition state. Results of experiment and simulation were searched for similarities, finding excellent agreement. THe key difference between simulation and experiment is the presence of alpha2 in the simulated transition state, although phi-values indicate that it is unstructured.

Analyzes the folding and unfolding pathway of barnase using a method similar to the classical Bronsted-beta approach. Description of the unfolding of wild-type barnase and the Y17G and 188V mutants; Characterization of the transition state of unfolding; Effect of mutations on the unfolding pathway; Effect of mutations on the transition state of unfolding.

Examines the molecular mechanism of stabilization of proteins by trimethylamine n-oxide (TMAO). Solubilities of a homologous series of cyclic dipeptides; Interaction between TMAO solution and the amide unit; Increase of the number of hydrogen bond.