Assembly of normally soluble proteins into amyloid fibrils is a cause or associated symptom of numerous human disorders, including Alzheimer's and the prion diseases. We report molecularlevel simulation of spontaneous fibril formation. Systems containing 12-96 model polyalanine peptides form fibrils at temperatures greater than a critical temperature that decreases with peptide concentration and exceeds the peptide's folding temperature, consistent with experimental findings. Formation of small amorphous aggregates precedes ordered nucleus formation and subsequent rapid fibril growth through addition of ␤-sheets laterally and monomeric peptides at fibril ends. The fibril's structure is similar to that observed experimentally.amyloid ͉ protein aggregation T he pathological manifestation of the so-called amyloid diseases, including Alzheimer's, Parkinson's, and the prion diseases, is the slow coming together of specific proteins to form fibrillar plaques or tangles rich in ␤-sheet structure (1-3) within a specific organ in the body. Although progress toward understanding the molecular-level mechanisms driving protein fibrillization has been made through in vitro studies of particular proteins, concomitant atomic-resolution computer simulation studies have been impossible due to the large system sizes required and the long timescales involved. As a consequence, to date, most atomic-resolution simulation studies of spontaneous fibril formation (4-8) have been limited to consideration of small model systems containing only a few peptides, too small to model the nucleation and subsequent growth of the large ␤-sheet complexes that are observed in experiments. Recent suggestions (1, 9, 10), however, that fibrils are stabilized by forces common to all proteins, hydrophobic interactions and backbone hydrogen bonding, and not by forces particular to a specific sequence imply that: (i) progress toward understanding the etiology of the various amyloid diseases can be made by examining the fibrillization of systems containing model proteins that are less complex than the specific amyloidogenic protein, and (ii) in silico examination of fibril formation is possible using low-tointermediate-resolution protein models provided that such models faithfully capture the essential features of protein geometry, hydrophobicity, and hydrogen bonding. We have developed an intermediate-resolution protein model to meet the latter requirements.In this work, we simulate the formation of fibrils using an intermediate-resolution protein model originally introduced by Smith and Hall (11), which we now call PRIME (Protein Intermediate-Resolution Model). PRIME is simple enough to allow the simulation of multiprotein systems over relatively long timescales yet contains sufficient detail to mirror real protein dynamics when used with discontinuous molecular dynamics (DMD), a fast alternative to conventional molecular dynamics. We are able to simulate the spontaneous formation of fibrils in systems containing up to 96 16-residue alanine-based peptide...

Self-assembly of viral proteins into icosahedral capsids is an interesting yet poorly understood phenomenon of which elucidation may aid the exploration of beneficial applications of capsids in materials science and medicine. Using molecular dynamics simulations of coarse-grained models for capsid proteins, we show that the competition between the formation of full capsids and nonidealized structures is strongly dependent upon the protein concentration and temperature, occurring kinetically as a cascade of elementary reactions in which free monomers are added to the growing oligomers on a downhill free-energy landscape. However, the insertion of the final subunits is the rate-limiting, energetically unfavorable step in viral capsid assembly. A phase diagram has been constructed to show the regions where capsids or nonidealized structures are stable at each concentration and temperature. We anticipate that our findings will provide guidance in identifying suitable conditions required for in vitro viral capsid assembly experiments.

Directed self-assembly of designed viral capsids holds significant potential for applications in materials science and engineering. However, the complexity of preparing these systems for assembly and the difficulty of quantitative experimental measurements on the assembly process has limited access to critical mechanistic questions that dictate the final product yields and isomorphic forms. Molecular simulations provide a means of elucidating self-assembly of viral proteins into icosahedral capsids and are the focus of the present study. Using geometrically realistic coarse-grained models with specialized molecular dynamics methods, we delineate conditions of temperature and coat protein concentration that lead to the spontaneous self-assembly of T=1 and T=3 icosahedral capsids. In addition to the primary product of icosahedral capsids, we observe a ubiquitous presence of non-icosahedral yet highly symmetric and enclosed aberrant capsules in both T=1 and T=3 systems. This polymorphism in assembly products recapitulates the scope and morphology of particle types that have been observed in mis-assembly experiments of virus capsids. Moreover, we find that this structural polymorphism in the endpoint structures is an inherent property of the coat proteins and arises from condition-dependent kinetic mechanisms that are independent of the elemental mechanisms of capsid growth (as long as the building blocks of the coat proteins are all either monomeric, dimeric or trimeric) and the capsid T number. The kinetic mechanisms responsible for self-assembly of icosahedral capsids and aberrant capsules are deciphered; the self-assembly of icosahedral capsids requires a high level of assembly fidelity whereas self-assembly of non-icosahedral capsules is a consequence of an off-pathway mechanism that is prevalent under non-optimal conditions of temperature or protein concentration during assembly. The latter case involves kinetically trapped dislocations of pentamer-templated proteins with hexameric organization. These findings provide insights into the complex processes that govern viral capsid assembly suggest some features of the assembly process that can be exploited to control the assembly of icosahedral capsids and non-icosahedral capsules.

The limitation of pH inside electrode-respiring biofilms is a well-known concept. However, little is known about how pH and redox potential are affected by increasing current inside biofilms respiring on electrodes. Quantifying the variations in pH and redox potential with increasing current is needed to determine how electron transfer is tied to proton transfer within the biofilm. In this research, we quantified pH and redox potential variations in electrode-respiring Geobacter sulfurreducens biofilms as a function of respiration rates, measured as current. We also characterized pH and redox potential at the counter electrode. We concluded that (1) pH continued to decrease in the biofilm through different growth phases, showing that the pH is not always a limiting factor in a biofilm and (2) decreasing pH and increasing redox potential at the biofilm electrode were associated only with the biofilm, demonstrating that G. sulfurreducens biofilms respire in a unique internal environment. Redox potential inside the biofilm was also compared to the local biofilm potential measured by a graphite microelectrode, where the tip of the micro-electrode was allowed to acclimatize inside the biofilm.