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Powerful first-order analysis of intraprotein electron transfer is developed from electron-transfer measurements both in biological and in chemical systems. A variation of 20 A in the distance between donors and acceptors in protein changes the electron-transfer rate by 10(12)-fold. Protein presents a uniform electronic barrier to electron tunnelling and a(More)
We present a novel protein-ligand docking method that accurately accounts for both ligand and receptor flexibility by iteratively combining rigid receptor docking (Glide) with protein structure prediction (Prime) techniques. While traditional rigid-receptor docking methods are useful when the receptor structure does not change substantially upon ligand(More)
Tropomyosins (TMs) are highly conserved, coiled-coil, actin binding regulatory proteins found in most eukaryotic cells. The amino-terminal domain of 284-residue TMs is among the most conserved and functionally important regions. The first nine residues are proposed to bind to the carboxyl-terminal nine residues to form the "overlap" region between(More)
Understanding the underlying physics of the binding of small-molecule ligands to protein active sites is a key objective of computational chemistry and biology. It is widely believed that displacement of water molecules from the active site by the ligand is a principal (if not the dominant) source of binding free energy. Although continuum theories of(More)
A water-soluble, 62-residue, di-alpha-helical peptide has been synthesized which accommodates two bis-histidyl haem groups. The peptide assembles into a four-helix dimer with 2-fold symmetry and four parallel haems that closely resemble native haems in their spectral and electrochemical properties, including haem-haem redox interaction. This protein is an(More)
We provide an overview of the IMPACT molecular mechanics program with an emphasis on recent developments and a description of its current functionality. With respect to core molecular mechanics technologies we include a status report for the fixed charge and polarizable force fields that can be used with the program and illustrate how the force fields, when(More)
The function of G-protein-coupled receptors is tightly modulated by the lipid environment. Long-timescale molecular dynamics simulations (totaling approximately 3 mus) of the A(2A) receptor in cholesterol-free bilayers, with and without the antagonist ZM241385 bound, demonstrate the instability of helix II in the apo receptor in cholesterol-poor membrane(More)
Many oxidoreductases are constructed from (a) local sites of strongly coupled substrate-redox cofactor partners participating in exchange of electron pairs, (b) electron pair/single electron transducing redox centers, and (c) nonadiabatic, long-distance, single-electron tunneling between weakly coupled redox centers. The latter is the subject of an(More)
Structured-based drug design has traditionally relied on a single receptor structure as a target for docking and screening studies. However, it has become increasingly clear that in many cases where protein flexibility is an issue, it is critical to accurately model ligand-induced receptor movement in order to obtain high enrichment factors. We present a(More)
We created a homology model of the homo-tetrameric pore domain of HERG using the crystal structure of the bacterial potassium channel, KvAP, as a template. We docked a set of known blockers with well-characterized effects on channel function into the lumen of the pore between the selectivity filter and extracellular entrance using a novel docking and(More)