Summary: This thesis is mainly concerned with dewetting transitions in the confined regions of protein complexes. To identify the protein complexes capable of displaying dewetting transitions at the end stage of folding, we performed a search of the protein oligomers database using a scoring function based on aligned hydrophobic surface areas. A few candidates on the list indeed display the drying transition, which is fairly robust. The distribution of hydrophobic and hydrophilic sites plays an important role in determining the surface hydrophobicity and nanoscopic hydrophobic interactions. It is manifested by the existence or absence of a dewetting transition as well as by attractive or repulsive solvent induced interactions. We investigated the role of water in the assembly of Alzheimer Abeta16-22 Protofilaments. Our simulations reveal a subtle interplay between a water mediated assembly and one driven by favorable energetic interactions between specific residues forming the interior of the protofilaments. It is found that the existence of a dewetting transition in simulation might be sensitive to the details of the force field parameterization. We studied the dynamics of water confined in the inter-domain region of a two-domain protein, BphC enzyme, and found it is slower than water at a single protein surface and in the bulk. The local surface curvature and hydrophobicity can have significant influence on the dynamics of confined water. In this thesis, the molecular mechanism of chemical denaturing was probed by a case study of lysozyme in 8 M urea. We find little change in the structure of water in 8 M urea except that a very small fraction of the water molecules which engage in two simultaneous hydrogen bonds with the same urea slow down the reorientational dynamics. The direct interaction of urea with protein is responsible for the denaturation of lysozyme by the favorable dispersion interaction of urea, relative to water, with the protein atoms and by the preferential hydrogen bond formation between urea and protein backbone.