Thursday 11 July 2013, Strathblane & Cromdale Halls, 16:30-18:30
Poster Session C - Biological dynamics and kinetics
P.001 The interactions of water with biological molecules
S Busch1, C D Bruce2, C Redfield1, C D Lorenz3 and S E McLain1
1
University of Oxford, UK, 2John Carroll University, USA, 3King's College London, UK
Water is of fundamental importance for biological molecules to assemble and function. The folding of proteins or
formation of cell membranes are driven by bio-molecular association which necessarily takes place in solution. We
have investigated solutions in the presence of water of both, the peptide Gly-Pro-Gly-NH2 (gpg-NH2), an amino acid
sequence which is thought to induce beta-hairpin folding in natural proteins; and the lipid ceramide which is a
major component of e.g. the skin or blood-brain barrier.
gpg-NH2 was measured in aqueous solution with Cl- counterions in order to ascertain the role water plays in its
ability to fold. Evidence was found that water molecules mediate an intramolecular hydrogen bond which increases
the stability of a turn-like formation of the peptide.
Ceramide on the other hand was measured in water/choloroform solutions, where the chloroform mimics the
hydrophobic environment of the lipid bilayer in cell membranes -- in order to find out more about lipid hydration
which is fundamental to understand how water interacts with cellullar membranes.
Both these systems were studied using a combination of neutron diffraction, nuclear magnetic resonance (NMR)
measurements and molecular dynamics (MD) computer simulation. The neutron scattering experiments were
performed at the SANDALS diffractometer at ISIS and evaluated using the empirical structure refinement (EPSR)
program.
P.002 EINS wavevector and thermal analysis on homologous disaccharides
M T Caccamo, S Magazù and F Migliardo
Università of Messina, Italy
A wavevector analysis, performed by wavelet transform, of Elastic Incoherent Neutron Scattering (EINS) intensity
data collected, as a function of temperature, on three glass forming systems, i.e. on the homologous disaccharides
trehalose, maltose and sucrose, is presented.
The wavelet analysis allows to explore the wavevector behavior of the scattered intensity at several scales, namely
at different scales for each wavevector value, in order to highlight the correlation between the signal and the set of
the scaled and translated wavelet functions.
The analysis performed in the wavevector range of Q = 0.28Å-1 ÷4.28Å-1, reveals, as a function of temperature, the
existence of different kinds of protons dynamics which interest different spatial scales. It emerges that, differently
from previous analyses, for trehalose the intensity data at all the investigated temperature values, are constantly
lower and sharper in respect to maltose and sucrose, giving rise to a global spectral density along the wavevector
range markedly less extended.
Furthermore the application of an interpretative model for the partial and global EINS intensity temperature behavior
allows to put into evidence for the disaccharides both the different wavevector dependence of the system relaxation
times extracted from the intensity vs temperature inflection point and the higher thermal restrain of trehalose in
respect to the other two homologous disaccharides.
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P.003 Inhebriated: partitioning of ethanol into lipid membranes
V Garcia Sakai1, L Toppozini2, C L Armstrong2, M A Barrett2, S Zheng2, L Luo2, H Nanda3 and M Rheinstadter2
1
ISIS Facility, UK, 2McMaster University, Canada, 3NIST Center for Neutron Research, USA
Short-chain alcohols are known to increase fluidity, membrane disorder and thus its permeability. This alcoholinduced permeability can drastically alter the efficacy of a prescribed drug. There is strong effort to better
understand the molecular interactions between ethanol and membranes, specifically the influence of ethanol on
lipid membrane structure and dynamics. Earlier neutron scattering (NS) experiments show an additional low-energy
mode of the membrane in the presence of ethanol, which originates from a vertical perturbation traversing the
membrane[1]. These fluctuations may enable active transport through bilayers by creating a series of travelling
voids from kinks wiggling along tails to act as molecular elevators for small molecules, allowing for easier cell entry.
Here we present combined x-ray and dynamical NS to determine the precise location of ethanol molecules in a lipid
bilayer and the impact on membrane dynamics[2]. Lipids hydrated with a 5% w/w ethanol solution were used in
NS experiments on HFBS at the NCNR-NIST, and x-ray diffraction experiments on BLADE at McMaster Univ. We find
that the ethanol molecules reside amongst the lipids in the head group region. Lipid-ethanol binding slows lipid
diffusion, while nano-scale lipid tail dynamics is drastically enhanced. These results will be crucial in developing a
molecular mechanism for membrane-driven permeability and may be helpful in the development of drug enhancers.
[1]
[2]
M. D. Kaye, K. Schmalzl, V. Conti Nibali, M. Tarek, M. C. Rheinstädter, Phys. Rev. E 83, 050907(R) (2011).
L. Toppozini, C.L. Armstrong, M.A. Barrett, S. Zheng, L. Luo, H. Nanda, V. Garcia Sakai, M.C. Rheinstädter,
Soft Matter, 2012, 8 (47), 11839.
P.004 Hemoglobin diffusion in red blood cells: a physiological application
S Longeville
CEA, France
Hemoglobin and myoglobin are oxygen storage molecules in blood and muscles, respectively. Their diffusion is
since a long time supposed to facilitate oxygen transport. We have studied by neutron spin echo the protein
diffusion at intermolecular scale, in vitro [1] and in vivo [2]. We have shown that theories developed for colloid
diffusion can be applied understand long and short time protein diffusion if one includes the water shell in the
hydrodynamic volume of the molecules, which is usually assumed to be of the order of 0.35 g of water per gram of
protein. The more hemoglobin in the red blood cells the more oxygen can be transported but the strong reduction of
the protein diffusion lower kinetics of oxygen capture. However, this process must be completed in the limited time
spend by the red blood cells in the capillaries near the. The characteristic time scales of oxygen capture and release
were given by Clark et al[3]. Using the concentration dependence of the transport diffusion coefficient of the
hemoglobin we are able to show that the concentration in the red blood cells correspond to an optimum in oxygen
transport for individuals sustaining strong physical activity [4].
[1]
[2]
[3]
[4]
C. Le Coeur & S. Longeville, Chem. Phys. 345 (2008) 298.
W. Doster & S. Longeville, Biophys. J. 93 (2007) 1360.
A. Clark, W. J. Federspiel P. A. Clark and G. R Cokelet, Biophys. J. 47 (1985) 171.
S. Longeville, Submitted to Biophys. J.
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P.005 An inelastic neutron scattering study of dietary phenolic compounds
M P Marques1, L Batista de Carvalho1, R Valero1, N Machado1 and S Parker2
1
University of Coimbra, Portugal, 2ISIS Facility, STFC Rutherford Appleton Laboratory, UK
Phenolic acid derivatives constitute one of the most ubiquitous groups of plant metabolites, present in the human
diet in significant amounts and long known to display antioxidant properties. Since oxidative damage to vital
biomolecules is responsible for numerous pathological processes including inflammation, atherosclerosis, cancer
and neurodegenerative disorders, these dietary phytochemicals have been the object of intense research in
Medicinal Chemistry. Accordingly, they have been shown to be promising preventive agents against oxidative stressinduced diseases, apart from being widely exploited as model systems for drug development.
The conformational preferences and H-bonding motifs of several hydroxycinnamic derivatives were determined by
inelastic neutron scattering (INS) spectroscopy, with a view to understand their recognised beneficial activity and
establish reliable structure-activity relationships. A series of phenolic acids with different hydroxyl/methoxyl ring
substitution patterns was studied: trans-cinnamic, m- and p -coumaric, caffeic and ferulic acids. The low energy
vibrational region was accessed and assigned in the light of theoretical calculations performed at the Density
Functional Theory (DFT) level, allowing the identification of some particular modes associated with H-bonding
interactions (intra- and intermolecular) that are the determinant of the main conformational preferences and
antioxidant capacity in these systems.
P.006 20,000 leagues under the sea: Molecular adaptation of organisms to high pressure environments
N Martinez1, G Michoud2, A Cario3, M Jebbar2, P Oger3, B Franzetti4 and J Peters5
1
UJF - IBS, France, 2Laboratoire de microbiologie des environments extremes UMR 6197 CNRS-Ifremer-UBO,
Laboratoire de Géologie de Lyon, 4Institut de Biologie Structurale CEA-CNRS-UJF, 5Instrument CRG-IN13 c/o
Institut Laue Langevin, France
3
More than 80% of the oceans volume is considered as a high hydrostatic pressure environment. It is known to
harbor a variety of prokaryotes which, according to certain studies, represent up to 70% of the Earth's biomass.
Many of these organisms are living near hot vents, at very high temperatures and in anaerobic environments
experiencing conditions that are very different to what we can observe on the surface of Earth.
Despite being widely studied, the molecular mechanism underlying their adaptation to these extreme conditions is
poorly understood.
Incoherent Neutron Scattering is an ideal tool to characterize in vivo dynamics as it can probe dynamics in a nondestructive fashion.
Our work focuses on three different micro-organisms: E. coli which natural habitat is the human gut, T. kodakarensis
that can be found in hot sulfur springs at the surface of the Earth and finally T. barophilus that lives in the bottom of
the oceans near hot vents. In vivo whole proteome dynamics measurements under pressure show striking
differences between these organisms and could help us to explain how these bacteria cope with extreme conditions.
Another part of our project is dedicated to measure the influence of pressure on the phase transitions of natural
membranes extracted from these organisms. Pressure has a rigidifying effect on membranes, and it has been
hypothesized that cells have the capacity to adapt the lipidic composition of their membrane by a metabolic
response to compensate it. Our objective is to precisely map the membrane phase transitions as a function of
pressure to see how we can link lipid composition to adaptation to high pressure.
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P.007 Monte Carlo simulation for experimental system of attenuation of gamma radiation in biological interest
materials
R A Medeiros, E M Bruder, J Mesa, V E Costa and M A Rezende
Universidade Estadual Paulista, Brazil
The study of biological systems as structures is dated to the early 20th century. There are several tests to determine
physical and structural of biological interest material, as destructive and non-destructive. The project goal is to
establish a set of routines and algorithms for simulation by the Monte Carlo method using the code MCNPX, that
can reproduce an experimental system for the attenuation of gamma radiation that has been tested successfully in
determining the mass attenuation coefficient in materials of biological interest to investigate possible physical and
chemical variations in these materials. The work will be divided in two stages, where the first is the development of
the simulation and the second one is its application in biological materials. In the first stage will be obtained a set
of routines and algorithms for simulation by Monte Carlo method using the code MCNPX, which will reproduce the
existing experimental system for the attenuation of gamma radiation from 241Am with energy of 60 keV installed in
the laboratory. In the second stage the simulation will be validated by comparing the attenuation coefficient
obtained by gamma radiation in the experimental system, the simulation by the Monte Carlo method and the XCOM
program, using samples of bone from mongrel dogs and wood species Eucalyptus grandis. The concentration of
calcium in bone from mongrel dogs will be change in the simulation in order to determine the variations of the
attenuation coefficient. In case of wood, the water content will be change in the simulation also for checking the
variation of the attenuation coefficient. These results will be analyzed quantitatively.
P.008 Anomalous water diffusion in malignant glioma tumor tissue
F Natali1, J Peters1, G Leduc2, C Dolce3 and E Barbier4
1
Institut Laue-Langevin, France, 2European Synchrotron Radiation Facility, France, 3University of Palermo, Italy and
Institut Laue-Langevin, France 4GIN/Centre de Recherche U836 INSERM UJF CHU CEA, France
Brain tissues from the Central Nervous System are heterogeneous systems containing glia cells, neurons, myelin
sheaths and extracellular space, separated by impermeable and semipermeable membranes. The major tissue
constituent is the water (> 70%). Interacting with cell membranes during their random motion, water molecules can
be used as a tool to probe tissue structure at microscopic scale. Nowadays, diffusion magnetic resonance imaging
technique (DMRI), based on water diffusion, is widely used to detect variation at the micron scale in the tissue
contrast induced by brain diseases such as ischemia, tumors etc. [1]. However, at micron scale, the cellular
contributions are averaged hiding a correct interpretation of the diagnostic images. Using neutron scattering
techniques, the measuring distance is reduced to the scale of the macromolecular separation. This allows having
access to so far unexplored atomic and picosecond distance-time scales [2-4]. We report here results aimed at
determining if neutrons reveal changes at atomic scale in water diffusion in tissues affected by brain pathologies
such as the aggressive primary malignant tumor glioma, as seen by DMRI at lower spatial resolution.
[1]
[2]
[3]
[4]
C.F. Hazlewood, H.E. Rorschach, C. Lin, Magn. Reson. Med. 19(2)(1991) 214.
G. Schiro, C. Caronna, F. Natali, A. Cupane, J. Am. Chem. Soc. 132 (2010) 1371.
M. Jasnin, M. Moulin, M. Haertlein, G. Zaccai, M. Tehei, EMBO Rep. 9 (2008) 543.
A.M. Stadler, J.P. Embs, I. Digel, G.M. Artmann, T. Unruh, J. Am. Chem. Soc. 130 (2008) 16852.
ICNS 2013 International Conference on Neutron Scattering
P.009 Dynamics of proteins at thermal melting
A Paciaroni1, S Capaccioli2 and K Ngai2
1
University of Perugia, Italy 2University of Pisa, Italy
Neutron scattering experiments have been made to investigate the extent of protein atomic thermal fluctuations in a
wide temperature range till thermal unfolding. Proteins are simply hydrated or embedded in glycerol, glucose and
glucose-water glassy environments, so as to suitably vary their melting temperature. The measured elastic
intensities indicate that the protein thermal fluctuations at the different unfolding temperatures are very similar, this
result being reminiscent of the well-known Lindemann criterion for melting. Dielectric spectroscopy data on the
same systems are exploited to interpret these findings and the role of structural relaxation is addressed.
P.010 Effects of high pressure on the dynamics of biological systems
J Peters1, M Trapp2, N Martinez1, J Marion3 and M Trovaslet4
1
Institut de Biologie Structurale, France, 2Helmholtz Zentrum Berlin, Germany, 3Université Joseph Fourier Grenoble I,
France, 4Institut de Recherche Biomédicale des Armées, France
Pressure is a thermodynamic variable that has been under-used to probe biological molecules so far. It is supposed
to open access to intermediate molecular states, which cannot be reached by temperature variation only. The lack
of research in the domain is due to technical challenges, especially in combination with neutron scattering.
Pressure is a macroscopic variable, whose effects are based on statistical observations, accessible by experiments
with a huge number of particles in a given volume. Elastic incoherent neutron scattering on the other hand is an
adequate method to probe an average over the motions of a great number of atoms, the so-called “mean square
displacement”. The combination of pressure perturbation and neutron scattering permits to relate a macroscopic
variable with an average over microscopic quantities, in order to yield a complete picture of molecular motions.
Recent developments of high pressure cells adapted to neutron scattering experiments, in-situ tests with these cells,
and first results of this approach applied to biological systems will be presented. Studying the enzyme human
acetylcholinesterase, which plays a crucial role in neurotransmission, up to pressure values of 6 kbar, provided
evidence for a pressure-induced stable intermediate state. Furthermore we will report our investigations on multi
lamellar lipid membranes. The applied pressure induces an ordering of the acyl chains and therefore a shift of the
main phase transition with consequences for the local dynamics of the system. Other recent investigations on betalactoglobulin, lysozyme and molecular adaptation of deep sea microbes will also be shown.
P.011 From whole cells towards photosynthetic reaction centres: dynamics properties for biotechnological
applications
D Russo1, G Campi2, G Rea2 and M Lambreva2
1
CNR-IOM, Italy, 2CNR-IC, France
Photosynthesis gain renewed interest due to the possibility to integrate photosynthetic sub-components into
optoelectronic devices such as biosensors for environmental monitoring.In this context, it is of great relevance to
study the function/dynamics relationships of genetically modified photosynthetic organisms, in order to identify the
parameters underlying an increased performance in terms of charge separation, protein stability and functional
reliability.Here, we address the question if there is a “functional” dynamics in addition to the intrinsic dynamical
behaviour common to all proteins and how do they couple. In particular, understanding if “rigidity” is essential for
the charge transfer process and if this property is shared by all the photosynthetic systems and how this information
can be apply to design high performant bio-sensors.To this end a comparison between Chlamydomonas cells
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carrying both native and mutated D1 protein ( hosted in the PSII of the cell) has been undertaken using neutron
scattering experiment.Some of these mutants displayed improved sensitivity and selectivity for different classes of
herbicides.Results show that point genetic mutations may notably affect not only the biochemical proterties but
also the T dependence of the whole complex dynamics describing a wild type system always more rigid than the les
performant mutants.In addition, a complementary hydration water collective dynamics investigation reveal with a
distinct sound propagation speed not only a more rigidstructure of hydration water than intracellular water but also
of the native compare to the mutatant.Our results suggest a new direction of investigation and improvement of
engeneering bio-sensor.
P.012 Combining structure and dynamics: high pressure effect on the protein solution
D Russo1, Alessandro Paciaroni2, Alessandra Filabozzi3, Maria Grazia Ortore4 and Francesco Spinozzi4
1
CNR-IOM, Italy 2University of Perugi, Italy 3University of Roma II, Italy, 4University of Ancora, Italy
Unfolding processes are induced by pressures larger than 2Kbar, while non-denaturing pressures may modify
protein interactions and affect the solvent arrangement around a protein surface. On these grounds, some new
insights into the relationship between the protein dynamics and the properties of the hydration shell can be
obtainedCombining small angle and inelastic neutron scattering experiments we have investigated the impact of
high hydrostatic pressure on the structure and dynamics following particle-particle interactions, low-resolution
structure and overall and local dynamics of protein solutions. At non denaturanting pressure the protein changes
the protein-protein attractive interactions and the hydration water density. Theinternal dynamics shows a clear
evolution from diffusing to more localized motions suggesting a correlation to the new first hydration properties. At
unfolding pressure a slowing down of the relaxation time is accompanied by an increase of the protein dynamics
contribution to picoseconds timescale. The increased solvent packaging around the protein percolates in the
hydrophobic core promoting the protein unfolding. Hydration water collective dynamics investigations reveal a shift
of the excitation of the low energy mode, whilst the position of the high energy excitation is not modified. A strong
modulation of both modes is found. We support the hypothesis that not only the amount of water but also the
structure of hydrogen bond network has a key role in the protein fluctuationsand transport properties.
P.013 Nano-confinement tuning of biomolecules for bio-technological interest
D Russo1, B Aoun2, M Gonzales2 and S Pechevloska2
1
CNR-IOM, Italy, 2Institut Laue-Langevin, France
Individual biomolecules can be encapsulated, preventing possible self-aggregation, isolate some allosteric
conformational states, protecting them from microbial degradation, and somewhere for drug preservation and
delivery. Confinement can be achieved by the presence of other stable macromolecules or by the wall of a cage as
silica matrix, pores or nanotubes. Molecular dynamics simulations have been used to study the confinement
packing characteristics of small hydrophilic and hydrophobic bio-molecules [1] in carbon nanotubes (CNT). The
self-diffusion coefficients and radial densities of confined peptides and water molecules were calculated. The results
shown that in CNT with a diameter smaller than 15 Å, biomolecules can hardly penetrate. With a diameter of 20 Å,
hydrophilic peptides fill the CNT quick and easily, and organize themselves in geometrical configurations which
remind the confined water structural organization [2]. The hydrophilic peptides adopts a corona like structural
organization with a thickness of 3 Å and a minimal distance from the CNT walls equal to 2Å. In this geometry all
water molecules are segregated in the central part of the nanotube. The hydrophobic molecules converge slower
into the CNT acquiring a different configuration always accompanied by water segregation. New opportunities for
interesting applications such as intelligent drug delivery can be envisaged.
[1]
[2]
D. Russo et al , JACS 133(13) 4882-4888 (2011), Chem Phys Letters, 517(1-3) 80-85 (2011).
Kolesnikov A. et al. (2004). Physical Review Letters, 93(3), 035503.
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P.014 (invited) The spin-echo spectroscopy suite at the ESS
M Sharp1, M Monkenbusch2, S Pasini2, R Georgii3, W Haussler3 and G Brandl3
1
ESS, Sweden, 2Forschungszentrum Jülich - JCNS Institute, Germany, 3Technical University of Munich, Germany
Neutron spin-echo spectroscopy is the technique with the highest energy resolution for probing the dynamics of
materials. It is used to study the slow dynamics in a variety of materials including soft matter, polymers,
biomolecules, energy materials and magnetism. Typically the timescale is from picoseconds to several hundreds of
nanoseconds over a broad Q-range.
The European Spallation Source will be a long pulse source and aims to become a world leading neutron source by
2025. Work is underway to optimise the instrumentation for this new facility, including 3 potential concepts for
neutron spin-echo spectroscopy. Here an overview of this instrument class and the scientific opportunities it will
provide will be given.
P.015 Structure and dynamics of myelin basic protein as a model system for intrinsically disordered proteins
A Stadler1, L Stingaciu1, O Holderer1, A Radulescu1, C Blanchet3, R Biehl1 and D Richter1
1
FZ Jülich, Germany, 2Research Center Juelich, Germany, 3EMBL c/o DESY, Germany
Myelin basic protein (MBP) is a major component of the myelin sheath in the central nervous system. MBP is
primarily unstructured in aqueous solution and is considered as an intrinsically disordered protein under those
conditions. From a biophysical point of view, the disordered protein can serve as a model system to study the
physical properties of intrinsically disordered or partially folded proteins using scattering methods.
Small angle X-ray and neutron scattering was measured of the protein in solution. For data analysis a large pool of
coarse grained disordered structures was generated and a representative ensemble of structures could be selected.
Dynamics of MBP in solution was measured using neutron spin echo spectroscopy up to 140ns. Rigid body
diffusion and internal protein dynamics could be separated from the spin echo data. The disordered protein was
found to be very flexible with relaxation rates of internal dynamics between 7 and 8 ns. Internal protein dynamics
were interpreted using normal mode analysis. The observed dynamics could be related to collective bending and
stretching modes with amplitudes of motion of a few Ångstrom.
P.016 Influence of blocking agent on the structure and dynamics of ImmunoglobulinG
L R Stingaciu1, R Biehl2, D Richter2 and M Ohl2
1
Research Center Juelich, Germany, 2Forschungszentrum Juelich GmbH, Germany
Antibodies are major components of the immune system. Representing approximately 75% of serum
immunoglobulins in humans, ImmunoglobulinG (IgG) is the most abundant antibody isotype found in the
circulation. It binds many kinds of pathogen including viruses, bacteria, and fungi, and protects the body against
them. IgG antibody is a large molecule of about 150 kDa composed of four peptide chains. It contains two identical
heavy chains of about 50 kDa and two identical light chains of about 25 kDa arranged in a typical Y-shape. The
relative arrangement of the domains can be influenced by addition of ArgCl [1].Here we examine the structural
changes and dynamics variations of IgG in a native state and under the influence of ArgCl.The low-resolution shape
of the protein with respect to the configuration of the arms will be measured by Small Angle Neutron Scattering,
Dynamic Light Scattering and Circular Dichroism spectroscopy as a prerequisite for later neutron spin echo
measurements to observe the domain dynamics of the protein and the interplay with structural changes.
[1]
W.G. Lilyestrom, S.J. Shire and T.M. Scherer, J. Phys. Chem. B (2012), 116, 9611−9618.
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P.017 Dynamics of intrinsically disordered proteins probed with neutron spin-echo spectroscopy
L R Stingaciu1, A Stadler2, R Biehl2, C Do3, D Richter2 and M Ohl2
1
Research Center Juelich, Germany, 2Forschungszentrum Juelich GmbH, Germany, 3Oak Ridge National Laboratory,
USA
Intrinsically disordered proteins are proteins characterized by lack of stable tertiary and metastable secondary
structure. Under physiological conditions these proteins can exist as isolated polypeptide chains or in partial
disordered proteins disordered regions connect structured domains allowing a great flexibility. The metastable
structure and accompanied dynamics is a key to understand structural transitions during binding to target, which
can involve some residues or complete domains. The disordered protein Myelin Basic Protein can serve as a
prototype to study the dynamics inside more complex disordered proteins and to understand their functionality.
Here we examine the structure and dynamics of the completely unfolded Myelin Basic Protein in different denaturing
environmental conditions. Neutron Spin-Echo spectroscopy has proven to be an excellent method to study domain
motions of proteins up to 100ns [1, 2]. The unfolded chain dynamics (approaching the Zimm dynamics of polymer
chains) can be accessed and identified. Residual order and correlations in the unfolded protein chain shall be
investigated and quantified by measuring the deviations from the free polymer chains behavior.
[1]
[2]
R. Biehl, M. Monkenbusch and D. Richter, Soft Matter (2011), 7, 1299–1307.
R. Inoue, R. Biehl, T. Rosenkranz, J. Fitter, M. Monkenbusch, A. Radulescu, B. Farago, D. Richter,
Biophysical J. (2010), 99, 2309–2317.
P.018 Intrinsic mean square displacements in proteins
D Vural1, H Glyde1 and L Hong2
1
University of Delaware, USA, 2Oak Ridge National Laboratory, USA
The incoherent intermediate scattering function (ISF) and the mean square displacement (MSD) <Δ2(t)> of
hydrated lysozyme (h = 0.4 g water/ g protein) are calculated from MD simulation of length 100 ns and 1000 ns.
From the simulations, the simulated MSD <Δ2(t)> can be calculated out to t = 1 and 10 ns, respectively. The
simulated MSD <Δ2(t)> remains a function of simulation time and does not reach a converged value at 10 ns. An
intrinsic, infinite time MSD <r2> can be defined in terms of the ISF I(Q,t) as I(Q,∞) = exp[-Q2<r2>/3]. By fitting a
model to simulated ISF, we obtain the intrinsic MSD. The intrinsic value obtained from the fit is the same for both
simulation times. The intrinsic <r2> = <Δ2(t→∞)>/2 is typically 30 percent larger than the simulated MSD
<Δ2(t)>/2 at t = 10 ns. The simulations of I(Q,t) and the above definition of < r2> provide a method of obtaining
the long time value of <r2> from simulations.
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