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See detailDNA partitions into triplets under tension in the presence of organic cations, with sequence evolutionary age predicting the stability of the triplet phase
Taghavi, Amirhossein UL; van der Schoot, Paul; Berryman, Josh UL

in Quarterly Reviews of Biophysics (2017), 50

Using atomistic simulations, we show the formation of stable triplet structure when particular GC-rich DNA duplexes are extended in solution over a timescale of hundreds of nanoseconds, in the presence of ... [more ▼]

Using atomistic simulations, we show the formation of stable triplet structure when particular GC-rich DNA duplexes are extended in solution over a timescale of hundreds of nanoseconds, in the presence of organic salt. We present planar-stacked triplet disproportionated DNA (Σ DNA) as a possible solution phase of the double helix under tension, subject to sequence and the presence of stabilising co-factors. Considering the partitioning of the duplexes into triplets of base pairs as the first step of operation of recombinase enzymes like RecA, we emphasise the structure–function relationship in Σ DNA. We supplement atomistic calculations with thermodynamic arguments to show that codons for ‘phase 1’ amino acids (those appearing early in evolution) are more likely than a lower entropy GC-rich sequence to form triplets under tension. We further observe that the four amino acids supposed (in the ‘GADV world’ hypothesis) to constitute the minimal set to produce functional globular proteins have the strongest triplet-forming propensity within the phase 1 set, showing a series of decreasing triplet propensity with evolutionary newness. The weak form of our observation provides a physical mechanism to minimise read frame and recombination alignment errors in the early evolution of the genetic code. [less ▲]

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See detailCompetition between crystal and fibril formation in molecular mutations of amyloidogenic peptides
Reynolds, Nicholas; Adamcik, Jozef; Berryman, Josh UL et al

in Nature Communications (2017), 8

Amyloidogenic model peptides are invaluable for investigating assembly mechanisms in disease related amyloids and in protein folding. During aggregation, such peptides can undergo bifurcation leading to ... [more ▼]

Amyloidogenic model peptides are invaluable for investigating assembly mechanisms in disease related amyloids and in protein folding. During aggregation, such peptides can undergo bifurcation leading to fibrils or crystals, however the mechanisms of fibril-to-crystal conversion are unclear. We navigate herein the energy landscape of amyloidogenic peptides by studying a homologous series of hexapeptides found in animal, human and disease related proteins. We observe fibril-to-crystal conversion occurring within single aggregates via untwisting of twisted ribbon fibrils possessing saddle-like curvature and cross-sectional aspect ratios approaching unity. Changing sequence, pH or concentration shifts the growth towards larger aspect ratio species assembling into stable helical ribbons possessing mean-curvature. By comparing atomistic calculations of desolvation energies for association of peptides we parameterise a kinetic model, providing a physical explanation of fibril-to-crystal interconversion. These results shed light on the self-assembly of amyloidogenic peptides, suggesting amyloid crystals, not fibrils, represent the ground state of the protein folding energy landscape. [less ▲]

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See detailThe early crystal nucleation process in hard spheres shows synchronised ordering and densification
Berryman, Josh UL; Anwar, Muhammad UL; Dorosz, Sven UL et al

in Journal of Chemical Physics (2016), 145

We investigate the early part of the crystal nucleation process in the hard sphere fluid using data produced by computer simulation. We find that hexagonal order manifests continuously in the ... [more ▼]

We investigate the early part of the crystal nucleation process in the hard sphere fluid using data produced by computer simulation. We find that hexagonal order manifests continuously in the overcompressed liquid, beginning approximately one diffusion time before the appearance of the first “solid-like” particle of the nucleating cluster, and that a collective influx of particles towards the nucleation site occurs simultaneously to the ordering process: the density increases leading to nucleation are generated by the same individual particle displacements as the increases in order. We rule out the presence of qualitative differences in the early nucleation process between medium and low overcompressions and also provide evidence against any separation of translational and orientational order on the relevant lengthscales. [less ▲]

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See detailAbsolute Free Energies for Biomolecules in Implicit or Explicit Solvent
Berryman, Josh UL; Schilling, Tanja UL

in Physics Procedia (2014), 57

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See detailILQINS hexapeptide, identified in lysozyme left-handed helical ribbons and nanotubes, forms right-handed helical ribbons and crystals.
Lara, Cecile; Reynolds, Nicholas; Berryman, Josh UL et al

in Journal of the American Chemical Society (2014), 136(12), 4732-4739

Amyloid fibrils are implicated in over 20 neurodegenerative diseases. The mechanisms of fibril structuring and formation are not only of medical and biological importance but are also relevant for ... [more ▼]

Amyloid fibrils are implicated in over 20 neurodegenerative diseases. The mechanisms of fibril structuring and formation are not only of medical and biological importance but are also relevant for material science and nanotechnologies due to the unique structural and physical properties of amyloids. We previously found that hen egg white lysozyme, homologous to the disease-related human lysozyme, can form left-handed giant ribbons, closing into nanotubes. By using matrix-assisted laser desorption ionization mass spectrometry analysis, we here identify a key component of such structures: the ILQINS hexapeptide. By combining atomic force microscopy and circular dichorism, we find that this fragment, synthesized by solid-phase peptide synthesis, also forms fibrillar structures in water at pH 2. However, all fibrillar structures formed possess an unexpected right-handed twist, a rare chirality within the corpus of amyloid experimental observations. We confirm by small- and wide-angle X-ray scattering and molecular dynamics simulations that these fibrils are composed of conventional left-handed β-sheets, but that packing stresses between adjacent sheets create this twist of unusual handedness. We also show that the right-handed fibrils represent a metastable state toward β-sheet-based microcrystals formation. [less ▲]

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See detailCrystal nucleation mechanism in melts of short polymer chains under quiescent conditions and under shear flow
Anwar, Muhammad UL; Berryman, Josh UL; Schilling, Tanja UL

in Journal of Chemical Physics (2014), (141), 124910

We present a molecular dynamics simulation study of crystal nucleation from undercooled melts of n-alkanes, and we identify the molecular mechanism of homogeneous crystal nucleation under quiescent ... [more ▼]

We present a molecular dynamics simulation study of crystal nucleation from undercooled melts of n-alkanes, and we identify the molecular mechanism of homogeneous crystal nucleation under quiescent conditions and under shear flow. We compare results for n-eicosane (C20) and npentacontahectane (C150), i.e., one system below the entanglement length and one above, at 20%– 30% undercooling. Under quiescent conditions, we observe that entanglement does not have an effect on the nucleation mechanism. For both chain lengths, the chains first align and then straighten locally, then the local density increases and finally positional ordering sets in. At low shear rates the nucleation mechanism is the same as under quiescent conditions, while at high shear rates the chains align and straighten at the same time. We report on the effects of shear rate and temperature on the nucleation rates and estimate the critical shear rates, beyond which the nucleation rates increase with the shear rate. In agreement with previous experimental observation and theoretical work, we find that the critical shear rate corresponds to a Weissenberg number of order 1. Finally, we show that the viscosity of the system is not affected by the crystalline nuclei. [less ▲]

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See detailThe Flexible Rare Event Sampling Harness System (FRESHS)
Kratzer, Kai; Berryman, Josh UL; Taudt, Aaron et al

in Computer Physics Communications (2014)

We present the software package FRESHS (http://www.freshs.org) for parallel simulation of rare events using sampling techniques from the ‘splitting’ family of methods. Initially, Forward Flux Sampling ... [more ▼]

We present the software package FRESHS (http://www.freshs.org) for parallel simulation of rare events using sampling techniques from the ‘splitting’ family of methods. Initially, Forward Flux Sampling (FFS) and Stochastic Process Rare Event Sampling (SPRES) have been implemented. These two methods together make rare event sampling available for both quasi-static and full non-equilibrium regimes. Our framework provides a plugin system for software implementing the underlying physics of the system of interest. At present, example plugins exist for our framework to steer the popular MD packages GROMACS, LAMMPS and ESPResSo, but due to the simple interface of our plugin system, it is also easy to attach other simulation software or self-written code. Use of our framework does not require recompilation of the simulation program. The modular structure allows the flexible implementation of further sampling methods or physics engines and creates a basis for objective comparison of different sampling algorithms. Our code is designed to make optimal use of available compute resources. System states are managed using standard database technology so as to allow checkpointing, scaling and flexible analysis. The communication within the framework uses plain TCP/IP networking and is therefore suited to high-performance parallel hardware as well as to distributed or even heterogeneous networks of inexpensive machines. For FFS we implemented an automatic interface placement that ensures optimal, nearly constant flux through the interfaces. We introduce ‘ghost’ (or ‘look-ahead’) runs that remedy the bottleneck which occurs when progressing to the next interface. FRESHS is open-source, providing a publicly available parallelized rare event sampling system. [less ▲]

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See detailAmber 14
Case, D. A.; Babin, V.; Berryman, Josh UL et al

Book published by University of California (2014)

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See detailSystematic examination of polymorphism in amyloid fibrils by molecular-dynamics simulation.
Berryman, Josh UL; Radford, Sheena E.; Harris, Sarah A.

in Biophysical Journal (2011), 100(9), 2234-2242

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See detailA general algorithm for sampling rare events in non-equilibrium and non-stationary systems
Berryman, Josh UL; Schilling, Tanja UL

in Journal of Chemical Physics (2010), 133

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See detailConsiderations in experimental and theoretical collision cross-section measurements of small molecules using travelling wave ion mobility spectrometry-mass spectrometry
Knapman, Tom W.; Berryman, Josh UL; Campuzano, Iain et al

in International Journal of Mass Spectrometry (2010), 298(1-3), 17-23

Travelling wave ion mobility spectrometry-mass spectrometry (TWIMS-MS) has the capability to separate ions based on their mobility through a gas-filled travelling wave (T-wave) device in the presence of a ... [more ▼]

Travelling wave ion mobility spectrometry-mass spectrometry (TWIMS-MS) has the capability to separate ions based on their mobility through a gas-filled travelling wave (T-wave) device in the presence of a train of transient voltage pulses. By calibration of this device using analytes of previously determined cross-sectional area (from conventional IMS experiments), collision cross-sections of ions can be determined based on their drift time through the T-wave device. Comparison of experimentally determined cross-sections with theoretical calculations from structural models has the potential to provide methodology which can be applied to analytes of previously uncharacterised structure; however, this comparison relies on a high degree of confidence in both experimental and theoretical methods. Focussing on small (≤200 Da) molecules, collision cross-sections have been measured by TWIMS-MS employing a calibration procedure that uses both oligo-glycine peptides and human haemoglobin-derived tryptic peptides in order to extend the calibration range for the measurement of high mobility ions. The effect of TWIMS wave height parameters on the calibration is addressed. Theoretical TWIMS cross-section calculations have been performed using a rapid, Windows-based, in-house developed projection approximation algorithm. These estimates were optimised by comparison with experimental values for a series of small molecules with rigid core structures by systematic variation of the interaction radii of the atoms comprising these species until theoretical measurements were in agreement with experimentally derived TWIMS cross-sections. The effect of varying the interaction radius for the buffer gas was subsequently studied by comparison of theoretical collision cross-sections calculated using helium and nitrogen radii with TWIMS-MS cross-section measurements determined in either helium or nitrogen buffer gases. It was found that the buffer gas used in theoretical calculations should ideally match the buffer gas in which the cross-sections of the calibrants were originally determined by conventional IMS. The resolving potential of the experimental methodology was demonstrated by separation of two isomeric amino acids, leucine and isoleucine, which showed <3% difference in cross-sectional areas. Furthermore, the application of both experimental and theoretical methods to compare the gas phase and solution conformations of seven amino acids was demonstrated. This study describes important considerations for the comparison of TWIMS-MS collision cross-sections with those obtained by theoretical methods, and also demonstrates that TWIMS-MS could be applied specifically to study a range of small molecules including those of pharmaceutical interest, in particular structural isomers and diastereoisomers that may not be distinguishable by mass spectrometry alone. [less ▲]

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See detailThermodynamic Description of Polymorphism in Q- and N-Rich Peptide Aggregates Revealed by Atomistic Simulation
Berryman, Josh UL; Radford, Sheena E.; Harris, Sarah A.

in Biophysical Journal (2009), 97(1), 1-11

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See detailDeciphering drift time measurements from travelling wave ion mobility spectrometry-mass spectrometry studies
Smith, David P.; Knapman, Tom W.; Campuzano, Iain et al

in European Journal of Mass Spectrometry (Chichester, England) (2009), 15(2), 113-130

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See detailPrediction of Twist of Amyloid Fibrils Using Molecular Dynamics
Berryman, Josh UL; Radford, S.; Harris, S.

in Proceedings of the NIC Workshop 2008 (2008)

Detailed reference viewed: 22 (4 UL)