Globular proteins often contain structurally well-resolved internal water molecules. Previously, we reported results from a molecular dynamics study that suggested that a buried water (Wat3) may play a role in modulating the structure of the FK506 binding protein-12 (FKBP12) 1. In particular, simulations suggested that disrupting a hydrogen bond to Wat3 by mutating E60 to either A or Q would cause a structural perturbation involving the distant W59 side chain, which rotates to a new conformation in response to the mutation. This effectively remodels the ligand binding pocket, as the side chain in the new conformation is likely to clash with bound FK506. To test if the protein structure is in effect modulated by the binding of a buried water in the distance, we determined high resolution (0.92 -1.29 Å) structures of wild type FKBP12 and its two mutants (E60A, E60Q) by x-ray crystallography. The structures of mutant FKBP12 show that the ligand-binding pocket is indeed remodeled as predicted by the substitution at position 60, even though the water molecule does not directly interact with any of the amino acids of the binding pocket. Thus, these structures support the view that buried water molecules constitute an integral, noncovalent component of the protein structure. Additionally, this study provides an example in which predictions from molecular dynamics simulations are experimentally validated with atomic precision, thus showing that the structural features of protein-water interactions can be reliably modeled at a molecular level.Keywords buried water; protein-water interaction; FKBP12; molecular dynamics simulation IntroductionWater is intimately involved in modulating protein stability, structure and function. The analysis of protein-water interaction is difficult as it must include the multiple roles of water as a bulk solvent as well as the possibility that it may contribute to the finer details in the makeup of protein molecules. While the principal outcome of protein folding is desolvation of hydrophobic surface and partitioning of hydrophobic residues in the core, folding to compact structures necessitates the burial of polar main chain nitrogens and oxygens in the core as well. To satisfy the hydrogen bonding needs of these polar atoms, proteins form extensive secondary structure, α-helices and β-sheets, in which most of the buried polar atoms participate in stable intramolecular hydrogen bonds. On the other hand, the hydrogen bonding needs of main chain polar atoms not involved in secondary structures, as well as those of buried polar side chain atoms, are often satisfied by buried water molecules 1 -5. As these water molecules provide energetically favorable interactions, they are usually structurally well-resolved 5 , 6. The details of the interaction between buried water molecules and protein atoms are important to model the protein core, and they have been examined using a variety of techniques, including mutational, biochemical, spectroscopic and structural studies as well as computer s...

Cystic fibrosis (CF) is a pleiotropic disease, originating from mutations in the CF transmembrane conductance regulator (CFTR). Lung injuries inflicted by recurring infection and excessive inflammation cause Ϸ90% of the morbidity and mortality of CF patients. It remains unclear how CFTR mutations lead to lung illness. Although commonly known as a Cl ؊ channel, CFTR also conducts thiocyanate (SCN ؊ ) ions, important because, in several ways, they can limit potentially harmful accumulations of hydrogen peroxide (H 2O2) and hypochlorite (OCl ؊ ). First, lactoperoxidase (LPO) in the airways catalyzes oxidation of SCN ؊ to tissue-innocuous hypothiocyanite (OSCN ؊ ), while consuming H2O2. Second, SCN ؊ even at low concentrations competes effectively with Cl ؊ for myeloperoxidase (MPO) (which is released by white blood cells), thus limiting OCl ؊ production by the enzyme. Third, SCN ؊ can rapidly reduce OCl ؊ without catalysis. Here, we show that SCN ؊ and LPO protect a lung cell line from injuries caused by H 2O2; and that SCN ؊ protects from OCl ؊ made by MPO. Of relevance to inflammation in other diseases, we find that in three other tested cell types (arterial endothelial cells, a neuronal cell line, and a pancreatic ␤ cell line) SCN ؊ at concentrations of >100 M greatly attenuates the cytotoxicity of MPO. Humans naturally derive SCN ؊ from edible plants, and plasma SCN ؊ levels of the general population vary from 10 to 140 M. Our findings raise the possibility that insufficient levels of antioxidant SCN ؊ provide inadequate protection from OCl ؊ , thus worsening inflammatory diseases, and predisposing humans to diseases linked to MPO activity, including atherosclerosis, neurodegeneration, and certain cancers.hydrogen peroxide ͉ hypochlorite ͉ hypothiocyanite ͉ lactoperoxidase ͉ myeloperoxidase

Assemblies of trans-bis(N-methylpyridinium-4-yl)diphenylporphine ions on the surface of calf thymus DNA have been studied using several spectroscopic techniques: absorbance, circular dichroism, and resonance light scattering. The aggregation equilibrium can be treated as a two-state system-monomer and assembly-each bound to the nucleic acid template. The aggregate absorption spectrum in the Soret region is resolved into two bands of Lorentzian line shape, while the DNA-bound monomer spectrum in this region is composed of two Gaussian bands. The Beer-Lambert law is obeyed by both porphyrin forms. The assembly is also characterized by an extremely large, bisignate induced circular dichroism (CD) profile and by enhanced resonance light scattering (RLS). Both the CD and RLS intensities depend linearly on aggregate concentration. The RLS result is consistent with a model for the aggregates as being either of a characteristic size or of a fixed distribution of sizes, independent of total porphyrin concentration or ionic strength. Above threshold values of concentration and ionic strength, the mass action expression for the equilibrium has a particularly simple form: K' = cac-1; where cac is defined as the "critical assembly concentration."offe dependence of the cac upon temperature and ionic strength (NaCl) has been investigated at a fixed DNA concentration. The value of the cac scales as the inverse square of the sodium chloride concentration and, from temperature dependence studies, the aggregation process is shown to be exothermic.