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Thioflavin T (ThT) is a fluorescent dye commonly used to stain amyloid plaques, but the binding sites of this dye onto fibrils are poorly characterized. We present molecular dynamics simulations of the binding of ThT and its neutral analog BTA-1 [2-(4'-methylaminophenyl)benzothiazole] to model protofibrils of the Alzheimer's disease Abeta(16-22) (amyloid beta) peptide. Our simulations reveal two binding modes located at the grooves of the beta-sheet surfaces and at the ends of the beta-sheet. These simulations provide new insight into recent experimental work and allow us to characterize the high-capacity, micromolar-affinity site seen in experiment as binding to the beta-sheet surface grooves and the low-capacity, nanomolar-affinity site seen as binding to the beta-sheet extremities of the fibril. The structure-activity relationship upon mutating charged ThT to neutral BTA-1 in terms of increased lipophilicity and binding affinity was studied, with calculated solvation free energies and binding energies found to be in qualitative agreement with the experimental measurements.

Aggregation of alpha-synuclein (alpha-syn), a protein implicated in Parkinson's disease (PD), is believed to progress through formation of a partially folded intermediate. Using nanoelectrospray ionization (nano-ESI) mass spectrometry combined with ion mobility measurements we found evidence for a highly compact partially folded family of structures for alpha-syn and its disease-related A53T mutant with net charges of -6, -7, and -8. For the other early onset PD mutant, A30P, this highly compact population was only evident when the protein had a net charge of -6. When bound to spermine near physiologic pH, all three proteins underwent a charge reduction from the favored solution charge state of -10 to a net charge of -6. This charge reduction is accompanied by a dramatic size reduction of about a factor of 2 (cross section of 2600 A2 (-10 charge state) down to 1430 A2 (-6 charge state)). We conclude that spermine increases the aggregation rate of alpha-syn by inducing a collapsed conformation, which then proceeds to form aggregates.

Evidence from cross section data indicates that ubiquitin +13 ions lose their secondary and tertiary structure in mass spectrometric experiments. These transitions from the folded state into the near linear final structure occur at the experimental temperatures on time scales that are far too long for conventional molecular dynamics simulations. In this study, an approach to mass spectrometric unfolding processes is developed and a detailed application to an ubiquitin +13 ion system is presented. The approach involves a sequence of molecular dynamics simulations at gradually increasing temperatures leading to identification of major intermediate states, and the unfolding pathway. The unfolding rate at any temperature can then be calculated by a Rice-Ramsperger-Kassel (RRK) approach. For ubiquitin +13, three interesting intermediate states were found and the final near linear geometry was computed. The several relevant energy barriers calculated for the process are in the range of 7 to 15 kcal mol(-1). The unfolding time scale at 300 K was computed to be 2 ms. Cross section calculations using a hard sphere scattering model were carried out for the final structure and found to be in good accord with the results of electrospray experiments supporting the theoretical model used. The approach employed here should be applicable to any other solvent-free protein system.

Oligomeric, neurotoxic amyloid protein assemblies are thought to be causative agents in Alzheimer's and other neurodegenerative diseases. Development of oligomer-specific therapeutic agents requires a mechanistic understanding of the oligomerization process. This is a daunting task because amyloidogenic protein oligomers often are metastable and comprise structurally heterogeneous populations in equilibrium with monomers and fibrils. A single methodological approach cannot elucidate the entire protein assembly process. An integrated multidisciplinary program is required. We discuss here the synergistic application of in hydro, in vacuo, and in silico methods to the study of the amyloid beta-protein, the key pathogenetic agent in Alzheimer's disease.

Folding and self-assembly of the 42-residue amyloid beta-protein (Abeta) are linked to Alzheimer's disease (AD). The 21-30 region of Abeta, Abeta(21-30), is resistant to proteolysis and is believed to nucleate the folding of full-length Abeta. The conformational space accessible to the Abeta(21-30) peptide is investigated by using replica exchange molecular dynamics simulations in explicit solvent. Conformations belonging to the global free energy minimum (the "native" state) from simulation are in good agreement with reported NMR structures. These conformations possess a bend motif spanning the central residues V24-K28. This bend is stabilized by a network of hydrogen bonds involving the side chain of residue D23 and the amide hydrogens of adjacent residues G25, S26, N27, and K28, as well as by a salt bridge formed between side chains of K28 and E22. The non-native states of this peptide are compact and retain a native-like bend topology. The persistence of structure in the denatured state may account for the resistance of this peptide to protease degradation and aggregation, even at elevated temperatures.

The structural properties of the Abeta42 peptide, a main constituent of the amyloid plaques formed in Alzheimer's disease, were investigated through a combination of ion-mobility mass spectrometry and theoretical modeling. Replica exchange molecular dynamics simulations using a fully atomic description of the peptide and implicit water solvent were performed on the -3 charge state of the peptide, its preferred state under experimental conditions. Equilibrated structures at 300 K were clustered into three distinct families with similar structural features within a family and with significant root mean square deviations between families. An analysis of secondary structure indicates the Abeta42 peptide conformations are dominated by loops and turns but show some helical structure in the C-terminal hydrophobic tail. A second calculation on Abeta42 in a solvent-free environment yields compact structures turned "inside out" from the solution structures (hydrophobic parts on the outside, polar parts on the inside). Ion mobility experiments on the Abeta42 -3 charge state electrosprayed from solution yield a bimodal arrival time distribution. This distribution can be quantitatively fit using cross-sections from dehydrated forms of the three families of calculated solution structures and the calculated solvent-free family of structures. Implications of the calculations on the early stages of aggregation of Abeta42 are discussed.

We have deposited Au atoms on the surface of titania without sintering or surface damage. Mass-selected Au+ atoms were deposited from the gas phase at room temperature with kinetic energies from <3 to 190+/-3.5 eV. Scanning tunneling microscopy reveals island formation following deposition at <3 eV, while mainly atomic features are observed for energies between approximately 35 and approximately 190 eV. A mixture of islands and atomic features is observed at a landing energy of 20+/-3.5 eV, suggesting a critical energy above which pinning occurs. Cluster size is also probed as a function of coverage in the deposition of Au+ with 100 eV of energy, revealing that sintering begins at a coverage of only 0.06 ML. These observations suggest a mechanism in which high-energy collision leads to the annealing of any impact-created surface damage and the pinning of Au atoms to the surface. We provide a new method of preparing isolated Au atoms on an oxide surface, which can serve as a platform for catalytic studies.

We present the first scanning tunneling microscopy (STM) study of the deposition of mass-selected silver clusters (Ag(n),n=1, 2, 3) on a rutile TiO(2)(110)-1x1 surface at room temperature under hard-landing conditions. Under hard-landing conditions, only small features are observed on the surface in all cases without sintering or surface damage. This suggests that the high impact energy of the clusters mainly dissipates as thermal energy in the substrate, resulting in the recovery of any initial impact-induced surface damage and the formation of bound clusters on the surface near the impact point. STM images indicate that Ag(1) binds on the bridging oxygen rows twice as often as on the Ti rows. Density-functional Theory (DFT) calculations are consistent with Ag(1) binding at either bridging oxygen vacancies or with two adjacent bridging oxygen atoms in the same bridging oxygen row. STM images of Ag(2) and Ag(3) depositions indicate almost exclusive binding centered on the Ti-atom rows. DFT calculations suggest that the Ag(2) and Ag(3) clusters are bound between two bridging oxygen rows, which is consistent with the STM observations.

Experiments in which mass-selected gold clusters were deposited on a surface have found that the catalytic properties depend strongly on cluster size. However, these experiments have not established definitively that the clusters maintain their size after deposition. We report here work in which we deposit low kinetic energy, mass-selected Aun+ (n = 1-8) clusters on a rutile TiO2(1 x 1) surface and use ultrahigh vacuum scanning tunneling microscopy (UHV-STM) to determine their size and shape.

A new method that utilizes ligation to probe geometries of clusters in the gas-phase has been developed. This technique bases structural assignments on thermodynamic quantities obtained for sequential ligand additions to a bare cluster. The information is obtained from temperature-dependent equilibrium data. This method is also sensitive to changes in bare cluster conformations that occur as a result of ligand addition, and the results can be fine-tuned by choosing ligands that appropriately adjust cluster-ligand binding energies.

Biologists have observed that the presence of divalent metal is essential for the binding of the hormone oxytocin (OT) to its cellular receptor. However, this interaction is not understood on the molecular level. Because conformation is a key factor controlling ligand binding in biomolecule systems, we have used ion mobility experiments and molecular modeling to probe the conformation of the oxytocin-zinc complex. Results show that Zn2+ occupies an octahedral site in the interior of the OT peptide that frees the N-terminus and creates a structured hydrophobic binding site on the peptide exterior; both factors are conducive to binding oxytocin to its receptor.

Mass-selected Ag(n) (+) (n=1,2,3) clusters with impact energy less than 2 eV per atom were deposited from the gas phase onto rutile titania (110)-(1x1) single crystal surfaces at room temperature and imaged using ultra-high vacuum scanning tunneling microscopy. Upon reaching the surface, Ag monomers sintered to form three-dimensional islands of approximately 50 atoms in size, with an average measured height of 7.5 A and diameter of 42 A. This suggests that the monomers are highly mobile on the titania surface at room temperature. Dimers also sintered to form large clusters upon deposition, approximately 30 atoms in size, with an average height of 6.2 A and diameter of 33 A. Clusters formed from monomer deposition appeared approximately three times more frequently at step edges than clusters formed from dimer deposition, indicating that the surface mobility of deposited monomers is higher than that of deposited dimers. In sharp contrast to the deposition of monomers and dimers, the deposition of trimers resulted in a high density of very small clusters on the order of a few atoms in size, indicative of intact trimers on the surface, implying that deposited trimers have very limited mobility on the surface at room temperature.

The gas-phase conformations of a series of cytosine/guanine DNA duplexes were examined by ion mobility and molecular dynamics methods. Deprotonated duplex ions were formed by electrospray ionization, and their collision cross sections measured in helium were compared to calculated cross sections of theoretical models generated by molecular dynamics. The 4-mer (dCGCG) and 6-mer (dCGCGCG) duplexes were found to have globular conformations. Globular and helical structures were observed for the 8-mer (dCGCGCGCG) duplex, with the globular form being the more favored conformer. For the 10-mer (dCGCGCGCGCG), 14-mer (dCGCGCGCGCGCGCG), and 18-mer (dCGCGCGCGCGCGCGCGCG) duplexes, only helical structures were observed in the ion mobility measurements. Theory predicts that the helical structures are less stable than the globular forms in the gas phase and should collapse into the globular form given enough time. However, molecular dynamics simulations at 300 K indicate the helical structures are stable in aqueous solution and will retain their conformations for a limited time in the gas phase. The presence of helical structures in the ion mobility experiments indicates that the duplexes retain "solution structures" in the gas phase on the millisecond time scale.

The protein alpha-synuclein, implicated in Parkinson's disease, was studied by combining nano-electrospray ionization (N-ESI) mass spectrometry and ion mobility. It was found that both the charge-state distribution in the mass spectra and the average protein shape deduced from ion mobility data, depend on the pH of the spray solution. Negative-ion N-ESI of pH 7 solutions yielded a broad charge-state distribution from -6 to -16, centered at -11, and ion mobility data consistent with extended protein structures. Data obtained for pH 2.5 solutions, on the other hand, showed a narrow charge-state distribution from -6 to -11, centered at -8, and ion mobilities in agreement with compact alpha-synuclein structures. The data indicated that there are two distinct families of structures: one consisting of relatively compact proteins with eight or less negative charges and one consisting of relatively extended structures with nine or more charges. The average cross section of a-synuclein at pH 2.5 is 33% smaller than for the extended protein sprayed from pH 7 solution. Significant dimer formation was observed when sprayed from pH 7 solution but no dimers were observed from the low pH solution. A plausible mechanism for aggregate formation in solution is proposed.

The sequential addition of water molecules to a series of small protonated peptides was studied by equilibrium experiments using electrospray ionization combined with drift cell techniques. The experimental data were compared to theoretical structures of selected hydrated species obtained by molecular mechanics simulations. The sequential water binding energies were measured to be of the order of 7-15 kcal/mol, with the largest values for the first water molecule adding to either a small nonarginine containing peptide (e.g., protonated dialanine) or to a larger peptide in a high charge state (e.g., triply protonated neurotensin). General trends are (a) that the first water molecules are more strongly bound than the following water molecules, (b) that very small peptides (2-3 residues) bind the first few water molecules more strongly than larger peptides, (c) that the first few water molecules bind more strongly to higher charge states than to lower charge states, and (d) that water binds less strongly to a protonated guanidino group (arginine containing peptides) than to a protonated amino group. Experimental differential entropies of hydration were found to be of the order of -20 cal/mol/K although values vary from system to system. At constant experimental conditions the number of water molecules adding to any peptide ion is strongly dependent on the peptide charge state (with higher charge states adding proportionally more water molecules) and only weakly dependent on the choice of peptide. For small peptides molecular mechanics calculations indicate that the first few water molecules add preferentially to the site of protonation until a complete solvation shell is formed around the charge. Subsequent water molecules add either to water molecules of the first solvation shell or add to charge remote functional groups of the peptide. In larger peptides, charge remote sites generally compete more effectively with charge proximate sites even for the first few water molecules.

The sequential association energies for one through six water molecules clustering to Na(2)I(+), as well as one and two water molecules clustering to Na(3)I(2)(+), are measured. The association energies show a pairwise behavior, indicating a symmetric association of water molecules to the linear Na(2)I(+) and Na(3)I(2)(+) ions. This pairwise behavior is well reproduced by Density Functional Theory (DFT) calculations. DFT calculations also suggest that a significant separation of charge for the Na-I ion pair occurs when four or more water molecules cluster to a single sodium center. Two different solvent-separated ion pairs have been identified with the DFT calculations. Experiments also show that the dissolution processes, loss of a neutral NaI unit, occurs when six or more water molecules have been added to Na(2)I(+) cluster. However, one or two water molecules are able to detach an NaI unit from the Na(3)I(2)(+) cluster. The difference in solubility of the Na(2)I(+) and Na(3)I(2)(+) ions is due to the difference in the energies required to lose an NaI unit from these two species. The experiment also confirms that the loss of a neutral NaI unit, instead of an Na(+) ion, occurs during the dissolution processes of Na(3)I(2)(+). The microsolvation schemes proposed to explain our experimental observations are supported by DFT and phase space theory (PST) calculations.