Water is an essential component of all living cells and their extracellular surroundings. Transport of water in and out of cells occurs during a variety of important cellular functions such as regulation of body temperature, elimination of toxins, digestion, respiration, circulation, and neural homeostasis. Aquaporin-1 (AQP1) is an integral membrane protein that functions as a specific and constitutively active water conducting channel [92, 93]. We are attempting to predict the structure of AQP1 from human erythrocyte membranes [94] by means of a hierarchical structure prediction approach. In this approach molecular dynamics simulations and energy minimization are combined with conventional structure prediction methods under experimental constraints derived from biochemical and spectroscopical data. AQP1 from human erythrocyte is composed of 269 residues [94] that form six transmembrane helices. Hydropathy analysis was performed to identify the putative transmembrane segments, which were then independently verified by multiple sequence alignment propensity analyses and homology modeling. A consensus assignment for secondary structure was derived from combination of all the prediction methods used. Three dimensional structures for transmembrane helical segments were built by comparative modeling. The resulting tertiary structures were then aggregated into a quaternary structure through molecular dynamics simulations followed by energy minimization under constraints provided by a low resolution three dimensional electron density map measured by electron microscopy [95], site directed mutagenesis and FT Resonance Raman spectra, as well as conservation of residues.
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