CHARMM force field parameterization protocol for self-assembling peptide amphiphiles : the Fmoc moiety

Aromatic peptide amphiphiles are known to self-assemble into nanostructures but the molecular level structure and the mechanism of formation of these nanostructures is not yet understood in detail. Molecular dynamic simulations using the CHARMM force field have been applied to a wide variety of peptide-based systems to obtain molecular level details of processes that are inaccessible with experimental techniques. However, this force field does not include parameters for the aromatic moieties which dictate the self-assembly of these systems. The standard CHARMM force field parameterization protocol uses hydrophilic interactions for the non-bonding parameters evaluation. However, to effectively reproduce the self-assembling behaviour of these molecules, the balance between the hydrophilic and hydrophobic nature of the molecule is essential. In this work, a modified parameterization protocol for the CHARMM force field for these aromatic moieties is presented. This protocol is applied for the specific case of the Fmoc moiety. The resulting set of parameters satisfies the conformational and interactions analysis and is able to reproduce experimental results such as the Fmoc-S-OMe water/octanol partition free energy and the self-assembly of Fmoc-S-OH and Fmoc-Y-OH into spherical micelles and fibres, respectively, while also providing detailed information on the mechanism of these processes. The effectiveness of the parameters for the Fmoc moiety validates the protocol as a robust approach to paramterise this class of compounds

Molecular dynamics simulations reveal disruptive self-assembly in dynamic peptide libraries

There is a significant interest in the use of unmodified self-assembling peptides as building blocks for functional, supramolecular biomaterials. Recently, dynamic peptide libraries (DPLs) have been proposed to select self-assembling materials from dynamically exchanging mixture of dipeptide inputs in the presence of a nonspecific protease enzyme, where peptide sequences are selected and amplified based on their self-assembling tendencies. It was shown that the results of DPL of mixed sequences (e.g. starting from a mixture of dileucine, L2 and diphenylalanine, F2) did not give the same outcome as the separate L2 and F2 libraries (which give rise to formation of F6 and L6), implying that interaction between these sequences could disrupt the self-assembly. In this study, coarse grained molecular dynamic (CG-MD) simulations are used to understand the DPL results for F2, L2 and mixed libraries. CG-MD simulations demonstrate that interactions between precursors can cause the low formation yield of hexapeptides in mixtures of dipeptides and show that this ability to disrupt is influenced by the concentration of the different species in the DPL. The disrupting self-assembly effect between the species in DPL is an important effect to take into account in dynamic combinatorial chemistry as it affects the possible discovery of new materials. The work shows that combined computational and experimental screening can be used complementary and in combination provide a powerful means to discover new supramolecular peptide nanostructures

Guiding principles for peptide nanotechnology through directed discovery

Life's diverse molecular functions are largely based on only a small number of highly conserved building blocks-the twenty canonical amino acids. These building blocks are chemically simple, but when they are organized in three-dimensional structures of tremendous complexity, new properties emerge. This review explores recent efforts in the directed discovery of functional nanoscale systems and materials based on these same amino acids, but that are not guided by copying or editing biological systems. The review summarises insights obtained using three complementary approaches of searching the sequence space to explore sequence-structure relationships for assembly, reactivity and complexation, namely: (i) strategic editing of short peptide sequences; (ii) computational approaches to predicting and comparing assembly behaviours; (iii) dynamic peptide libraries that explore the free energy landscape. These approaches give rise to guiding principles on controlling order/disorder, complexation and reactivity by peptide sequence design

Fishery dynamics of the California market squid (Loligo opalescens), as measured by satellite remote sensing

Novel data on the spatial and temporal distribution of fishing effort and population abundance are presented for the market squid fishery (Loligo opalescens) in the Southern California Bight, 1992−2000. Fishing effort was measured by the detection of boat lights by the Defense Meteorological Satellite Program (DMSP) Operational Linescan System (OLS). Visual confirmation of fishing vessels by nocturnal aerial surveys indicated that lights detected by satellites are reliable indicators of fishing effort. Overall, fishing activity was concentrated off the following Channel Islands: Santa Rosa, Santa Cruz, Anacapa, and Santa Catalina. Fishing activity occurred at depths of 100 m or less. Landings, effort, and squid abundance (measured as landings per unit of effort, LPUE) markedly declined during the 1997−98 El Niño; landings and LPUE increased afterwards. Within a fishing season, the location of fishing activity shifted from the northern shores of Santa Rosa and Santa Cruz Islands in October, the typical starting date for squid fishing in the Bight, to the southern shores by March, the typical end of the squid season. Light detection by satellites offers a source of fine-scale spatial and temporal data on fishing effort for the market squid fishery off California, and these data can be integrated with environmental data and fishing logbook data in the development of a management plan

Effect of hydrogen on ground state structures of small silicon clusters

We present results for ground state structures of small Si$_{n}$H (2 \leq \emph{n} \leq 10) clusters using the Car-Parrinello molecular dynamics. In particular, we focus on how the addition of a hydrogen atom affects the ground state geometry, total energy and the first excited electronic level gap of an Si$_{n}$ cluster. We discuss the nature of bonding of hydrogen in these clusters. We find that hydrogen bonds with two silicon atoms only in Si$_{2}$H, Si$_{3}$H and Si$_{5}$H clusters, while in other clusters (i.e. Si$_{4}$H, Si$_{6}$H, Si$_{7}$H, Si$_{8}$H, Si$_{9}$H and Si$_{10}$H) hydrogen is bonded to only one silicon atom. Also in the case of a compact and closed silicon cluster hydrogen bonds to the cluster from outside. We find that the first excited electronic level gap of Si$_{n}$ and Si$_{n}$H fluctuates as a function of size and this may provide a first principles basis for the short-range potential fluctuations in hydrogenated amorphous silicon. Our results show that the addition of a single hydrogen can cause large changes in the electronic structure of a silicon cluster, though the geometry is not much affected. Our calculation of the lowest energy fragmentation products of Si$_{n}$H clusters shows that hydrogen is easily removed from Si$_{n}$H clusters.Comment: one latex file named script.tex including table and figure caption. Six postscript figure files. figure_1a.ps and figure_1b.ps are files representing Fig. 1 in the main tex

Organ Donation and Utilization in the United States, 1997–2006

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/75743/1/j.1600-6143.2008.02171.x.pd

Two-Neutron Sequential Decay of 24^{24}O

A two-neutron unbound excited state of $^{24}$O was populated through a (d,d') reaction at 83.4 MeV/nucleon. A state at $E = 715 \pm 110$ (stat) $\pm 45$ (sys) keV with a width of $\Gamma < 2$ MeV was observed above the two-neutron separation energy placing it at 7.65 $\pm$ 0.2 MeV with respect to the ground state. Three-body correlations for the decay of $^{24}$O $\rightarrow$ $^{22}$O + $2n$ show clear evidence for a sequential decay through an intermediate state in $^{23}$O. Neither a di-neutron nor phase-space model for the three-body breakup were able to describe these correlations

Neutron-Unbound Excited States of 23N

Neutron unbound states in 23N were populated via proton knockout from an 83.4 MeV/nucleon 24O beam on a liquid deuterium target. The two-body decay energy displays two peaks at E1∼100keV and E2∼1MeV with respect to the neutron separation energy. The data are consistent with shell model calculations predicting resonances at excitation energies of ∼3.6MeV and ∼4.5MeV. The selectivity of the reaction implies that these states correspond to the first and second 3/2− states. The energy of the first state is about 1.3 MeV lower than the first excited 2+ in 24O. This decrease is largely due to coupling with the πp−13/2 hole along with a small reduction of the N=16 shell gap in 23N