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Simultaneous Identification of Spectral Properties and Sizes of Multiple Particles in Solution with Subnanometer Resolution

We report an unsurpassed solution characterization technique based on analytical ultracentrifugation, which demonstrates exceptional potential for resolving particle sizes in solution with sub‐nm resolution. We achieve this improvement in resolution by simultaneously measuring UV/Vis spectra while hydrodynamically separating individual components in the mixture. By equipping an analytical ultracentrifuge with a novel multi‐wavelength detector, we are adding a new spectral discovery dimension to traditional hydrodynamic characterization, and amplify the information obtained by orders of magnitude. We demonstrate the power of this technique by characterizing unpurified CdTe nanoparticle samples, avoiding tedious and often impossible purification and fractionation of nanoparticles into apparently monodisperse fractions. With this approach, we have for the first time identified the pure spectral properties and band‐gap positions of discrete species present in the CdTe mixture.     

Macrocyclic beta-sheet peptides that mimic protein quaternary structure through intermolecular beta-sheet interactions

This paper reports the design, synthesis, and characterization of a family of cyclic peptides that mimic protein quaternary structure through beta-sheet interactions. These peptides are 54-membered-ring macrocycles comprising an extended heptapeptide beta-strand, two Hao beta-strand mimics [JACS 2000, 122, 7654] joined by one additional alpha-amino acid, and two delta-linked ornithine beta-turn mimics [JACS 2003, 125, 876]. Peptide 3a, as the representative of these cyclic peptides, contains a heptapeptide sequence (TSFTYTS) adapted from the dimerization interface of protein NuG2 [PDB ID: 1mio]. 1H NMR studies of aqueous solutions of peptide 3a show a partially folded monomer in slow exchange with a strongly folded oligomer. NOE studies clearly show that the peptide self-associates through edge-to-edge beta-sheet dimerization. Pulsed-field gradient (PFG) NMR diffusion coefficient measurements and analytical ultracentrifugation (AUC) studies establish that the oligomer is a tetramer. Collectively, these experiments suggest a model in which cyclic peptide 3a oligomerizes to form a dimer of beta-sheet dimers. In this tetrameric beta-sheet sandwich, the macrocyclic peptide 3a is folded to form a beta-sheet, the beta-sheet is dimerized through edge-to-edge interactions, and this dimer is further dimerized through hydrophobic face-to-face interactions involving the Phe and Tyr groups. Further studies of peptides 3b-3n, which are homologues of peptide 3a with 1-6 variations in the heptapeptide sequence, elucidate the importance of the heptapeptide sequence in the folding and oligomerization of this family of cyclic peptides. Studies of peptides 3b-3g show that aromatic residues across from Hao improve folding of the peptide, while studies of peptides 3h-3n indicate that hydrophobic residues at positions R3 and R5 of the heptapeptide sequence are important in oligomerization.     

Parallel computational techniques for the analysis of sedimentation velocity experiments in UltraScan

The advent of parallel computing technology and low-cost computing hardware has facilitated the adoption of high-performance computing tools for the analysis of sedimentation data. Over the past 15 years, we have developed the UltraScan software (Demeler et al., ) to support sedimentation analysis, experimental design, and data management. We describe here recent extensions and advances in methodology that have been adapted in UltraScan. High-performance computing methods implemented on parallel supercomputers utilizing grid computing technology are used to analyze sedimentation experiments at much higher resolution than was previously possible. We discuss the implementation of parallel computing in three novel algorithms used in UltraScan for modeling of sedimentation velocity experiments and provide guidelines for effective data analysis.