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CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and widely used molecular simulation program. It has been developed over the last three decades with a primary focus on molecules of biological interest, including proteins, peptides, lipids, nucleic acids, carbohydrates, and small molecule ligands, as they occur in solution, crystals,(More)
Dengue virus is responsible for approximately 50-100 million infections, resulting in nearly 24,000 deaths annually. The capsid (C) protein of dengue virus is essential for specific encapsidation of the RNA genome, but little structural information on the C protein is available. We report the solution structure of the 200-residue homodimer of dengue 2 C(More)
The immunoreceptor tyrosine-based activation motif (ITAM) plays a central role in transmembrane signal transduction in hematopoietic cells by mediating responses leading to proliferation and differentiation. An initial signaling event following activation of the B cell antigen receptor is phosphorylation of the CD79a (Ig-alpha) ITAM by Lyn, a Src family(More)
The capsid proteins of two flaviviruses, yellow fever virus and dengue virus, were expressed in Escherichia coli and purified to near homogeneity suitable for biochemical characterization and structure determination by nuclear magnetic resonance. The oligomeric properties of the capsid protein in solution were investigated. In the absence of nucleic acid,(More)
Assembly of retrovirus particles is promoted by interaction of the Gag polyprotein with RNA. Nonspecific RNA association with the nucleocapsid domain (NC) of Gag induces the dimerization of Gag through protein-protein contacts in the capsid domain (CA), followed by higher order assembly to form the immature virus particle. NMR relaxation studies were(More)
It has been argued that a substrate-induced conformational change involving the orientation of catalytic groups cannot affect the specificity for two substrates in an enzymatic system where the chemical step is rate limiting, because such an induced fit would alter the catalytic efficiency for both to an equal extent. To the contrary, the generalized(More)
BACKGROUND The capsid protein (CA) of retroviruses, such as Rous sarcoma virus (RSV), consists of two independently folded domains. CA functions as part of a polyprotein during particle assembly and budding and, in addition, forms a shell encapsidating the genomic RNA in the mature, infectious virus. RESULTS The structures of the N- and C-terminal domains(More)
Picornaviruses are inactivated by a family of hydrophobic drugs that bind at an internal site in the viral capsid and inhibit viral uncoating. A basis for the capsid stabilization previously unrecognized is revealed by molecular dynamics simulations of the antiviral drug WIN52084s bound to a hydrophobic pocket of solvated human rhinovirus 14. Isothermal(More)
Quaternary structure polymorphism found in quasiequivalent virus capsids provides a static framework for studying the dynamics of protein interactions. The same protein subunits are found in different structural environments within these particles, and in some cases, the molecular switching required for the polymorphic quaternary interactions is obvious(More)