TGQR 2010Q4 Report.pdf - Teragridforum.org

416. Armstrong, B. D.; Soto, P.; Shea, J.-E.; Han, S. Overhauser dynamic nuclear polarization and
molecular dynamics simulations using pyrroline and piperidine ring nitroxide radicals. J. Magn. Reson. 2009,
200, 137-141.
417. Penev, E. S.; Lampoudi, S.; Shea, J.-E. TiReX: Replica-exchange molecular dynamics using
TINKER. Comput. Phys. Commun. 2009, 180, 2013-2019.
418. Wu, C.; Biancalana, M.; Koide, S.; Shea, J.-E. Binding modes of thioflavin-T to the single-layer -
sheet of the peptide self-assembly mimics. J. Mol. Biol. 2009, 394, 627-633.
419. Dupuis, N. F.; Wu, C.; Shea, J.-E.; Bowers, M. T. Human islet amyloid polypeptide monomers form
ordered -hairpins: A possible direct amyloidogenic precursor. J. Am. Chem. Soc. 2009, 191, 18283–18292.
420. Grabenauer, M.; Wu, C.; Soto, P.; Shea, J.-E.; Bowers, M. T. Oligomers of the prion protein
fragment 106-126 are likely assembled from -hairpins in solution and methionine oxidation inhibits
assembly without altering the peptide's monomeric conformation. J. Am. Chem. Soc. 2010, 132, 532-539.
421. Wei, G. H.; Jewett, A. I.; Shea, J.-E. Structural diversity of the dimer of the Alzheimer amyloid-
(25-35) peptide and polymorphism of the resulting fibrils. Phys. Chem. Chem. Phys. 2010, 12, 3622-3629.
422. Wu, C.; Bowers, M. T.; Shea, J.-E. Molecular structures of quiescently-grown and brain-derived
polymorphic fibrils of the Alzheimer amyloid Aβ9-40 peptide: A comparison to agitated fibrils. PLoS Comp.
Biol. 2010, 6, e1000693.
423. Wu, C.; Bowers, M. T.; Shea, J.-E. The binding of thioflavin T and of PIB to the cross-β subunit of
the Alzheimer Aβ9-40 protofibril. 2010, submitted.
424. Wu, C.; Shea, J.-E. On the origins of the weak folding cooperativity of a designed ultrafast
protein. 2010, submitted.
MCA06N060
425. G. Enkavi and E. Tajkhorshid. Dynamics of Spontaneous Substrate Binding and Identi fication of the
Binding Site in GlpT. Biochemistry., 49:1105–1114, 2010.
426. J. Diao, A. J. Maniotis, R. Follberg and E. Tajkhorshid. Interplay of mechanical and binding
properties of type I fibronectin. Theoret. Chem. Acc., 125:397–405, 2010.
427. Y. Wang, S. A. Shaikh and E. Tajkhorshid. Exploring transmembrane diffusion pathways with
molecular dynamics. Physiology, 25: 142-145, 2010.
428. Y. Z. Ohkubo, J. H. Morrissey, and E. Tajkhorshid. Dynamical view of membrane binding and
complex formation of human factor VIIa and tissue factor. J. Thromb. Haemost., 8:1044, 2010
429. Y. Wang and E. Tajkhorshid. Exploring the Permeability of Aquaporin AQP4 to Signaling
Gas Molecule NO with Molecular Dynamics. PROTEINS, 78(3): 661-670, 2010. 6. J. H. Morrissey, R. L.
Davis-Harrison, N. Tavoosi, K. Ke, V. Pureza, J. M. Boettcher, M. C. Clay, C. M. Rienstra, Y. Z. Ohkubo, T.
V. Pogorelov, and Emad Tajkhorshid. Protein-Phospholipid interactions in blood clotting. Thromb. Research,
125 (Suppl. 1):S23, 2010 Saher Shaikh, Po-Chao Wen, Giray Enkavi, Zhijian Huang, and Emad
Tajkhorshid. Capturing Functional Motions of Membrane Channels and Transporters with Molecular
Dynamics Simulation. J. Comput. Theor. Nanosci., 7:1-10, 2010 8. J. Feng, E. Lucchinetti, G. Enkavi, Y.
Wang, P. Gehrig, B. Roschitzki, M. Schaub, E. Tajkhorshid, K. Zaugg and M. Zaugg. Phosphorylation of the
conserved aromatic ladder (Y194/Y190) in adenine nucleotide translocase 1 (ANT1, AAC1) is Src-family
kinase-mediated and regulates ADP/ATP exchange in mitochondria: a downstream mechanism of
cardioprotection. Am. J. Physiol. Cell Physiol.,298:C740C748, 2010.
430. F. Khalili-Araghi, V. Jogini, V. Yarov-Yarovoy, E. Tajkhorshid, B. Roux, and K. Schulten.
Calculation of the gating charge for the Kv1.2 voltageactivated potassium channel. Biophys. J., 98:2189–
2198, 2010.
431. X.-D. Yang, E. Tajkhorshid, and L.-F. Chen Functional Interplay between Acetylation and
Methylation of the RelA Subunit of NF-kappaB. Mol. Cell. Biol., 30:2170–2180, 2010.
432. Z. Huang and E. Tajkhorshid. Identification of the Third Na + Site and the Sequence of Extracellular
Binding Events in the Glutamate Transporter. Biophys. J., In press.