Coherent Neutron Scattering and Collective Dynamics in the Protein, GFP

Nickels, Jonathan D.; Perticaroli, Stefania; O’Neill, Hugh; Zhang, Qiu; Ehlers, Georg; Sokolov, Alexei P.

doi:10.1016/j.bpj.2013.09.029

Cited by 26 publications

(46 citation statements)

References 54 publications

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“…The rigidity as measured over a few nanometers was investigated through the analysis of the low frequency collective vibrations, known as the boson peak (BP). This feature occurs on a sub‐picosecond time scale and appears in both neutron and LS spectra of proteins, polymers, and glass forming systems below ∼5 meV . Interpretation of these data is that the higher the frequency of the BP, the stiffer is the material.…”

Section: Resultsmentioning

confidence: 96%

Rigidity of poly‐L‐glutamic acid scaffolds: Influence of secondary and supramolecular structure

Nickels

Perticaroli

Ehlers

et al. 2015

J Biomedical Materials Res

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Poly-l-glutamic acid (PGA) is a widely used biomaterial, with applications ranging from drug delivery and biological glues to food products and as a tissue engineering scaffold. A biodegradable material with flexible conjugation functional groups, tunable secondary structure, and mechanical properties, PGA has potential as a tunable matrix material in mechanobiology. Recent studies in proteins connecting dynamics, nanometer length scale rigidity, and secondary structure suggest a new point of view from which to analyze and develop this promising material. We have characterized the structure, topology, and rigidity properties of PGA prepared with different molecular weights and secondary structures through various techniques including scanning electron microscopy, FTIR, light, and neutron scattering spectroscopy. On the length scale of a few nanometers, rigidity is determined by hydrogen bonding interactions in the presence of neutral species and by electrostatic interactions when the polypeptide is negatively charged. When probed over hundreds of nanometers, the rigidity of these materials is modified by long range intermolecular interactions that are introduced by the supramolecular structure.

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Section: Resultsmentioning

confidence: 96%

Rigidity of poly‐L‐glutamic acid scaffolds: Influence of secondary and supramolecular structure

Nickels

Perticaroli

Ehlers

et al. 2015

J Biomedical Materials Res

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“…6). 6,10,18,19,28,29,38,41,101,125,136 Thus the nanosecond relaxation process should be attributed to the internal protein dynamics. 41 Such a behavior of hydration water contradicts current neutron scattering, NMR and simulations studies.…”

Section: Iii4 Nanosecond Dynamics: Conformational Jumpsmentioning

confidence: 99%

“…41 The characteristic activation energy barrier for hydration water motion is B15-18 kJ mol À1 , but it increases with a decrease in temperature, leading to the VFT-like temperature dependence of the characteristic relaxation time (Fig. [37][38][39]48,90,91,101,102,107,130 Its characteristic time scale and temperature dependence are dictated by the behavior of hydration water that together with internal rigidity/flexibility of the biomacromolecules control the friction of the sub-nanosecond process. The VFT-like behavior is typical for Soft Matter and is usually ascribed to the cooperative nature of the relaxation process that involves several molecular units in a single relaxation event.…”

Section: General Picture Of Protein Dynamicsmentioning

confidence: 99%

“…[1][2][3][4][5][6][7][8][9][10][11] Currently we have reasonable knowledge of the structure of many proteins, and a clear understanding of the importance of protein dynamics and conformational fluctuations to their function. 11,[27][28][29][30][31][32][33][34][35][36][37][38][39] The high contrast between neutron scattering of hydrogen and deuterium atoms provides additional advantage for this technique in studies of biological molecules. The same is true for dynamics of RNA and DNA.…”

Section: Introductionmentioning

confidence: 99%

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Protein dynamics: from rattling in a cage to structural relaxation

2015

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We present an overview of protein dynamics based mostly on results of neutron scattering, dielectric relaxation spectroscopy and molecular dynamics simulations. We identify several major classes of protein motions on the time scale from faster than picoseconds to several microseconds, and discuss the coupling of these processes to solvent dynamics. Our analysis suggests that the microsecond backbone relaxation process might be the main structural relaxation of the protein that defines its glass transition temperature, while faster processes present some localized secondary relaxations. Based on the overview, we formulate a general picture of protein dynamics and discuss the challenges in this field.

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“…Moreover, there are phenomena that can only be probed by TAS due to the unique characteristics of neutron during interaction especially with magnetic materials. Recent research on phenomena such as quantum magnetism [2,3], high-T c superconductor materials [4,5], frustrated magnets [6], energy/hydrogen storage [7][8][9][10], multiferroics [11], and protein dynamics [12,13] are some examples among other topics that apply inelastic neutron scattering to investigate many novel and interesting properties. As a national research institution, BATAN should also be involved in research activities on advanced materials that apply nuclearbased technique for their characterizations.…”

mentioning

confidence: 99%

First Magnon of BATAN’s Neutron Triple-Axis Spectrometer

Sumirat

2016

Atom Indo.

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The National Nuclear Energy Agency of Indonesia (BATAN) has one dedicated spectrometer for inelastic neutron scattering experiments. The instrument is a thermal neutron triple-axis spectrometer known as SN1. SN1 was installed in 1992 in the experimental hall of G. A. Siwabessy Research Reactor, Serpong, Banten. Malfunctions of the hardware and software have prevented the instrument from performing inelastic scattering measurements since 1996. The 2011-2015 five years project has been initiated to revitalize and optimize the SN1. The project serves as a preparation for the utilization of SN1 for the investigation of lattice dynamics, spin wave and magnetic excitations in condensed matters that will be started in 2016. In 2013, SN1 has successfully been repaired and was able to measure phonon dispersion relation of available single crystals, i.e., Cu, pyrolytic graphite (PG), Ge, and Al. In 2015, the first experiment on magnetic excitation to investigate magnon dispersion relation of a known Fe single crystal has been carried out. Standard methods of inelastic scattering measurements, i.e., a constant-energy transfer ħ with either fixed final neutron energy E f = 14.7 meV or fixed incoming neutron energy E i = 30.59 meV, and a constant momentum transfer Q with fixed incoming neutron energy E i = 30.59 meV, were applied to measure the low-energy magnetic excitations. For fixed E f measurement, a 5-cm thick PG filter was set between the sample and the analyzer to eliminate /n harmonics. To limit the energy and momentum spreads of the beam, collimations of 40 minutes were applied before and after the sample. The spin waves were measured along the three principal symmetry directions of [00], [0], and []. The measured magnons were compared to values in reference and were found to be in a good agreement with them. With such accomplishments, we are convinced that SN1 is now ready for its inelastic scattering application and will become one of BATAN's neutron instrument which is routinely utilized for materials characterization on lattice dynamics and magnetic excitations by local and foreign scientists. Besides reporting the SN1 first measured magnon, the current status of SN1 instrument development will also be presented briefly.

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Coherent Neutron Scattering and Collective Dynamics in the Protein, GFP

Cited by 26 publications

References 54 publications

Rigidity of poly‐L‐glutamic acid scaffolds: Influence of secondary and supramolecular structure

Rigidity of poly‐L‐glutamic acid scaffolds: Influence of secondary and supramolecular structure

Protein dynamics: from rattling in a cage to structural relaxation

First Magnon of BATAN’s Neutron Triple-Axis Spectrometer

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