The kinetics of aggregation of poly-glutamic acid based polypeptides.

Department of Chemical Engineering, University of California Berkeley, Berkeley, CA 94720, United States.
Biophysical Chemistry (Impact Factor: 2.32). 09/2008; 136(2-3):74-86. DOI: 10.1016/j.bpc.2008.04.008
Source: PubMed

ABSTRACT The aggregation of two negatively-charged polypeptides, poly-L-glutamic acid (PE) and a copolymer of poly-glutamic acid and poly-alanine (PEA), has been studied at different peptide and salt concentrations and solution pH conditions. The kinetics of aggregation were based on Thioflavin T (ThT) fluorescence measurements. The observed lag phase shortened and the aggregation was faster as the pH approached the polypeptides' isoelectric points. While the initial polypeptide structures of PE and PEA appeared identical as determined from circular dichroism spectroscopy, the final aggregate morphology differed; PE assumed large twisted lamellar structures and the PEA formed typical amyloid-like fibrils, although both contained extensive beta-sheet structure. Differences in aggregation behavior were observed for the two polypeptides as a function of salt concentration; aggregation progressed more slowly for PE and more quickly for PEA with increasing salt concentration. Several models of aggregation kinetics were fit to the data. No model yielded consistent rate constants or a critical nucleus size. A modified nucleated polymerization model was developed based on that of Powers and Powers [E.T. Powers, D.L. Powers, The kinetics of nucleated polymerizations at high concentrations: Amyloid fibril formation near and above the "supercritical concentration", Biophys. J. 91 (2006) 122-132], which incorporated the ability of oligomeric species to interact. This provided a best fit to the experimental data.

1 Bookmark
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Abnormal protein aggregates, so called amyloid fibrils, are mainly known as pathological hallmarks of a wide range of diseases, but in addition these robust well-ordered self-assembled natural nanostructures can also be utilized for creating distinct nanomaterials for bioelectronic devices. However, current methods for producing amyloid fibrils in vitro offer no spatial control. Herein, we demonstrate a new way to produce and spatially control the assembly of amyloid-like structures using an organic electronic ion pump (OEIP) to pump distinct cations to a reservoir containing a negatively charged polypeptide. The morphology and kinetics of the created proteinaceous nanomaterials depends on the ion and current used, which we leveraged to create layers incorporating different conjugated thiophene derivatives, one fluorescent (p-FTAA) and one conducting (PEDOT-S). We anticipate that this new application for the OEIP will be useful for both biological studies of amyloid assembly and fibrillogenesis as well as for creating new bioelectronic nanomaterials and devices.
    Small 10/2010; 6(19):2153-61. · 7.51 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: Transmission electron microscopy (TEM) is the standard procedure for qualitatively confirming the presence of amyloid fibers in a protein aggregation reaction product. However, extracting quantitative information about the amyloid size distribution from the electron micrographs is a nontrivial problem. Here we describe methods for (i) the simulation of pseudo-TEM images of amyloid fiber distributions having known characteristic properties and (ii) the semi-automated processing of experimental TEM images of amyloid fibers to produce two-dimensional histogram plots reflecting either the distribution of amyloid length and width or, alternatively, the distribution of width and fiber rigidity/persistence. The processing method is fully automatic when the density of fibers on the grid is sufficiently low (such that the adsorbed fibers do not touch) and is semi-automatic (requiring some user decision making) when the fibers are overlapping. Termed "ADM" (for Amyloid Distribution Measurement), the program suite is written in MATLAB code and is available on request from the author.
    Analytical Biochemistry 10/2011; 421(1):262-77. · 2.31 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: The influence of the salts KCl, NaCl, and NaI at molar concentrations on the α-helical folding kinetics of the alanine-based oligopeptide Ace-AEAAAKEAAAKA-Nme is investigated by means of (explicit-water) molecular dynamics simulations and a diffusional analysis. The mean first passage times for folding and unfolding are found to be highly salt-specific. In particular, the folding times increase about 1 order of magnitude for the sodium salts. The drastic slowing can be traced to long-lived, compact configurations of the partially folded peptide, in which sodium ions are tightly bound by several carbonyl and carboxylate groups. This multiple trapping leads to a nonexponential residence time distribution of the cations in the first solvation shell of the peptide. The analysis of α-helical folding in the framework of diffusion in a reduced (one-dimensional) free energy landscape further shows that the salt not only specifically modifies equilibrium properties but also induces kinetic barriers due to individual ion binding. In the sodium salts, for instance, the peptide's configurational mobility (or "diffusivity") can decrease about 1 order of magnitude. This study demonstrates the highly specific action of ions and highlights the intimate coupling of intramolecular friction and solvent effects in protein folding.
    The Journal of Physical Chemistry B 10/2010; 114(43):13815-22. · 3.38 Impact Factor


1 Download
Available from