The 40-42 residue amyloid beta-protein (Abeta) plays a central role in the pathogenesis of Alzheimer's disease (AD). Of the two main alloforms, Abeta40 and Abeta42, the longer Abeta42 is linked particularly strongly to AD. Despite the relatively small two amino acid length difference in primary structure, in vitro studies demonstrate that Abeta40 and Abeta42 oligomerize through distinct pathways. Recently, a discrete molecular dynamics (DMD) approach combined with a four-bead protein model recapitulated the differences in Abeta40 and Abeta42 oligomerization and led to structural predictions amenable to in vitro testing. Here, the same DMD approach is applied to elucidate folding of Abeta40, Abeta42, and two mutants, [G22]Abeta40 and [G22]Abeta42, which cause a familial ("Arctic") form of AD. The implicit solvent in the DMD approach is modeled by amino acid-specific hydropathic and electrostatic interactions. The strengths of these effective interactions are chosen to best fit the temperature dependence of the average beta-strand content in Abeta42 monomer, as determined using circular dichroism (CD) spectroscopy. In agreement with these CD data, we show that at physiological temperatures, the average beta-strand content in both alloforms increases with temperature. Our results predict that the average beta-strand propensity should decrease in both alloforms at temperatures higher than approximately 370 K. At physiological temperatures, both Abeta40 and Abeta42 adopt a collapsed-coil conformation with several short beta-strands and a small (<1%) amount of alpha-helical structure. At slightly above physiological temperature, folded Abeta42 monomers display larger amounts of beta-strand than do Abeta40 monomers. At increased temperatures, more extended conformations with a higher amount of beta-strand (approximately < 30%) structure are observed. In both alloforms, a beta-hairpin at A21-A30 is a central folding region. We observe three additional folded regions: structure 1, a beta-hairpin at V36-A42 that exists in Abeta42 but not in Abeta40; structure 2, a beta-hairpin at R5-H13 in Abeta42 but not in Abeta40; and structure 3, a beta-strand A2-F4 in Abeta40 but not Abeta42. At physiological temperatures, the Arctic mutation, E22G, disrupts contacts in the A21-A30 region of both [G22]Abeta peptides, resulting in a less stable main folding region relative to the wild type peptides. The Arctic mutation induces a significant structural change at the N-terminus of [G22]Abeta40 by preventing the formation of structure 3 observed in Abeta40 but not Abeta42, thereby reducing the structural differences between [G22]Abeta40 and [G22]Abeta42 at the N-terminus. [G22]Abeta40 is characterized by a significantly increased amount of average beta-strand relative to the other three peptides due to an induced beta-hairpin structure at R5-H13, similar to structure 2. Consequently, the N-terminal folded structure of the Arctic mutants closely resembles the N-terminal structure of Abeta42, suggesting that both Arctic Abeta peptides might...

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We have elucidated the binding sites of four moncyclam and one bicyclam antagonist AMD3100, in the human chemokine receptor CXCR4. Using the predicted structural models of CXCR4, we have further predicted the binding sites of these cyclam compounds. We used the computational method LITiCon to map the differences in receptor structure stabilized by the mono and bicyclam compounds. Accounting for the receptor flexibility lead to a single binding mode for the cyclam compounds, that has not been possible previously using a single receptor structural model and fixed receptor docking algorithms. There are several notable differences in the receptor conformations stabilized by monocyclam antagonist compared to a bicylam antagonist. The loading of the Cu(2+) ions in the cyclam compounds, shrinks the size of the cyclam rings and the residue D262(6.58) plays an important role in bonding to the copper ion in the monocylam compounds while residue E288(7.39) is important for the bicyclam compound.

We present a critical assessment of the performance of our homology model refinement method for G-protein coupled receptors (GPCRs), called LITICon, that led to top ranking structures in a recent structure prediction assessment GPCRDOCK2010. GPCRs form the largest class of drug targets for which only a few crystal structures are currently available. Therefore accurate homology models are essential for drug design in these receptors. We submitted five models each for human chemokine CXCR4 (bound to small molecule IT1t and peptide CVX15) and dopamine D3DR (bound to small molecule eticlopride) before the crystal structures were published. Our models in both CXCR4/IT1t and D3/eticlopride assessments were ranked first and second respectively by ligand RMSD to the crystal structures. For both receptors, we developed two types of protein models: homology models based on known GPCR crystal structures, and ab initio models based on the prediction method MembStruk. The homology based models compared better to the crystal structures than the ab initio models. However a robust refinement procedure for obtaining high accuracy structures is needed. We demonstrate that optimization of the helical tilt, rotation and translation are vital for GPCR homology model refinement. As a proof of concept, our in-house refinement program LITiCon captured the distinct orientation of TM2 in CXCR4, which differs from that of adrenoreceptors. These findings would be critical for refining GPCR homology models in future.

Cataracts is a misfolding protein disease in which one of its major components is the γD-crystallin protein. The conformational structure of the aggregated γD-crystallin and the interactions that cause aggregation are largely unknown. A recent experimental two-dimensional infrared (2DIR) spectroscopy study determined that the C-terminal domain has a high propensity to form β-sheets whereas the N-terminal domain forms a disordered structure in the fiber state. We present a combined computational molecular dynamics (MD) and infrared spectroscopy study of the local dynamics of these domains. The computed 2DIR signals agree remarkably well with experiment. We show that both domains having a Greek key structural fold experience different electrostatic environments, which may be related to the fact that the C-terminal domain is more structurally stable than the N-terminal domain. We correlate the vibrational couplings to known energy dissipation mechanisms and reveal their origin.