(i) Optical studies on the structures of amyloid peptides and proteins are continuing.We are particularly interested in origin of the very intense CD spectrum which has been associated with the cross-beta structure of amyloid fibrils. This phenomenon is shown by peptides which have been shown to form amyloid with both parallel and anti-parallel beta sheet structure. (ii) In collaboration with the group of T. K. Dayie and B. Chen (Univ. of MD), we have investigated the effect of a small inert cosolute, trimethylamine oxide (TMAO), on the conformational changes of the SAM II riboswitch in the presence of increasing concentrations of the metabolite S-adenosyl-methionine (SAM) and Mg++. The free riboswitch was thought to be in an open or semi-random conformation in the absence of SAM and Mg++ and to become more folded and compact upon binding SAM and/or Mg++. Extensive measurements of the dependence of circular dichroism spectra of the riboswitch upon the concentrations of these small ligands may be quantitatively accounted for by a model, according to which SAM binds exclusively to a compact conformation. In the absence of SAM, the riboswitch seems to be a mixture of open and compact states. Low concentrations of Mg++ or TMAO bind to the open form(s), inhibiting the binding of SAM. At higher concentrations, cooperative binding of Mg++ or molecular crowding by TMAO, transform the riboswitch into the compact form, facilitating the binding of SAM. Further binding of Mg++ increases the affinity of the compact form of the riboswitch for SAM. Hydrodynamic measurements show that the riboswitch is compacted by concentrated TMAO.

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McPhie, Peter; Brown, Patrick; Chen, Bin et al. (2016) Modulation of Conformational Equilibria in the S-Adenosylmethionine (SAM) II Riboswitch by SAM, Mg(2+), and Trimethylamine N-Oxide. Biochemistry 55:5010-20
Zhang, Min; Khripin, Constantine Y; Fagan, Jeffrey A et al. (2014) Single-step total fractionation of single-wall carbon nanotubes by countercurrent chromatography. Anal Chem 86:3980-4
Chagas, Andrezza C; McPhie, Peter; San, Hong et al. (2014) Simplagrin, a platelet aggregation inhibitor from Simulium nigrimanum salivary glands specifically binds to the Von Willebrand factor receptor in collagen and inhibits carotid thrombus formation in vivo. PLoS Negl Trop Dis 8:e2947
Backus, Keriann M; Dolan, Michael A; Barry, Conor S et al. (2014) The three Mycobacterium tuberculosis antigen 85 isoforms have unique substrates and activities determined by non-active site regions. J Biol Chem 289:25041-53
Chattopadhyay, Manas K; Fernandez, Cristina; Sharma, Deepak et al. (2011) Yeast ornithine decarboxylase and antizyme form a 1:1 complex in vitro: purification and characterization of the inhibitory complex. Biochem Biophys Res Commun 406:177-82
McGlinchey, Ryan P; Shewmaker, Frank; Hu, Kan-nian et al. (2011) Repeat domains of melanosome matrix protein Pmel17 orthologs form amyloid fibrils at the acidic melanosomal pH. J Biol Chem 286:8385-93
Phillips, Robert S; Miles, Edith W; McPhie, Peter et al. (2010) Effects of hydrostatic pressure on the conformational equilibrium of tryptophan synthase from Salmonella typhimurium. Ann N Y Acad Sci 1189:95-103
Calvo, Eric; Tokumasu, Fuyuki; Mizurini, Daniella M et al. (2010) Aegyptin displays high-affinity for the von Willebrand factor binding site (RGQOGVMGF) in collagen and inhibits carotid thrombus formation in vivo. FEBS J 277:413-27
McGlinchey, Ryan P; Shewmaker, Frank; McPhie, Peter et al. (2009) The repeat domain of the melanosome fibril protein Pmel17 forms the amyloid core promoting melanin synthesis. Proc Natl Acad Sci U S A 106:13731-6
Fernandez, Cristina; Minton, Allen P (2009) Static light scattering from concentrated protein solutions II: experimental test of theory for protein mixtures and weakly self-associating proteins. Biophys J 96:1992-8

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