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derya vural

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New England Complex Systems Institute

Giancarlo Franzese

Universitat de Barcelona

Souleymane Diallo

Korea Advanced Institute of Science and Technology

Ursula Perez-salas

Boris Dzikovski

Michael Crawford

University of Delaware

Pamela Whitfield

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Papers by derya vural

Motional displacements in proteins incorporating dynamical diversity

Bulletin of the American Physical Society, 2016

The average mean square displacement (MSD), ⟨r 2 ⟩, of hydrogen H in proteins is measured using i... more The average mean square displacement (MSD), ⟨r 2 ⟩, of hydrogen H in proteins is measured using incoherent neutron scattering methods. The observed MSD shows a marked increase in magnitude at a temperature T D ≃ 240 K. This is widely interpreted as a dynamical transition to large MSDs which make function possible in proteins. However, when the data is interpreted in terms of a single averaged MSD, the extracted ⟨r 2 ⟩ depends on the neutron momentum transfer,hQ, used in the measurement. We have shown recently that this apparent dependence on Q arises because the dynamical diversity of the H in the protein is neglected[2]. We present models of the dynamical diversity of H in Lysosyme that when used in the analysis of simulated neutron data lead to consistent, Q independent values for the average MSD and for the diversity model.

Polymer principles behind solubilizing lignin with organic cosolvents for bioenergy

Green Chemistry, 2020

Polymer theory, developed for simple homopolymers, is applicable to the interaction of lignin wit... more

Impact of hydration and temperature history on the structure and dynamics of lignin

Green Chemistry, 2018

At a given temperature during a heating/cooling cycle, lignin is more dynamic upon cooling, which... more

Dynamics of the lignin glass transition

Physical chemistry chemical physics : PCCP, Jan 8, 2018

The dynamics of lignin, a complex and heterogeneous major plant cell-wall macromolecule, is of bo... more The dynamics of lignin, a complex and heterogeneous major plant cell-wall macromolecule, is of both fundamental and practical importance. Lignin is typically heated to temperatures above its glass transition to facilitate its industrial processing. We performed molecular dynamics simulations to investigate the segmental (α) relaxation of lignin, the dynamical process that gives rise to the glass transition. It is found that lignin dynamics involves mainly internal motions below Tg, while segmental inter-molecular motions are activated above Tg. The segments whose mobility is enhanced above Tg consist of 3-5 lignin monomeric units. The temperature dependence of the lignin segmental relaxation time changes from Arrhenius below Tg to Vogel-Fulcher-Tamman above Tg. This change in temperature dependence is determined by the underlying energy landscape being restricted below Tg but exhibiting multiple minima above Tg. The Q-dependence of the relaxation time is found to obey a power-law up...

Determination of Dynamical Heterogeneity from Dynamic Neutron-Scattering of Proteins

Biophysical journal, Jan 23, 2018

Motional displacements of hydrogen (H) in proteins can be measured using incoherent neutron-scatt... more Motional displacements of hydrogen (H) in proteins can be measured using incoherent neutron-scattering methods. These displacements can also be calculated numerically using data from molecular dynamics simulations. An enormous amount of data on the average mean-square motional displacement (MSD) of H as a function of protein temperature, hydration, and other conditions has been collected. H resides in a wide spectrum of sites in a protein. Some H are tightly bound to molecular chains, and the H motion is dictated by that of the chain. Other H are quite independent. As a result, there is a distribution of motions and MSDs of H within a protein that is denoted dynamical heterogeneity. The goal of this paper is to incorporate a distribution of MSDs into models of the H incoherent intermediate scattering function, I(Q,t), that is calculated and observed. The aim is to contribute information on the distribution as well as on the average MSD from comparison of the models with simulations ...

Quasielastic neutron scattering in biology: Theory and applications

Biochimica et biophysica acta, Jan 15, 2016

Neutrons scatter quasielastically from stochastic, diffusive processes, such as overdamped vibrat... more Neutrons scatter quasielastically from stochastic, diffusive processes, such as overdamped vibrations, localized diffusion and transitions between energy minima. In biological systems, such as proteins and membranes, these relaxation processes are of considerable physical interest. We review here recent methodological advances and applications of quasielastic neutron scattering (QENS) in biology, concentrating on the role of molecular dynamics simulation in generating data with which neutron profiles can be unambiguously interpreted. We examine the use of massively-parallel computers in calculating scattering functions, and the application of Markov state modeling. The decomposition of MD-derived neutron dynamic susceptibilities is described, and the use of this in combination with NMR spectroscopy. We discuss dynamics at very long times, including approximations to the infinite time mean-square displacement and nonequilibrium aspects of single-protein dynamics. Finally, we examine ...

Intrinsic Mean Square Displacement in Lysozyme

The internal dynamics of proteins is the essential interest of biophysics. The mean square displa... more The internal dynamics of proteins is the essential interest of biophysics. The mean square displacement (MSD) of hydrogen in proteins and its associated hydration water is obtained by molecular dynamic (MD) simulation. The MSD as currently determined depends on the time of the MD simulation. A method is proposed in this paper to obtain the intrinsic MSD ⟨r 2 ⟩ of hydrogen in the proteins. The intrinsic MSD is independent of the simulation time and defined as the infinite time value of calculated MSD that appears in the Debye-Waller factor. The method consists of fitting a model to the incoherent intermediate scattering function. The model contains the intrinsic MSD and a rate constant characterizing the motions of H in the protein. The method is illustrated by obtaining the intrinsic MSD ⟨r 2 ⟩ of lysozyme in 100 ns and 1 µs MD simulations.

Why the observed mean square motional displacement depends on wave vector Q

The motional mean square displacement (MSD) of hydrogen (H) in proteins is extensively measured u... more The motional mean square displacement (MSD) of hydrogen (H) in proteins is extensively measured using neutron scattering techniques. The MSD increases rapidly with temperature near room temperatures and a large MSD is often associated with protein function. One shortcoming of these measurements is that the observed MSD depends on the wave vector (Q) of the neutron data used to obtain the MSD. This dependence is often attributed to use of the Gaussian approximation made to the scattering function in the analysis of the data. To test this we have simulated the protein lysozyme and calculated the intermediate scattering function (ISF), both the full ISF and the ISF in the Gaussian approximation. We find that the MSD extracted in the usual way was the same and still Q dependent in both cases. Also, direct calculation of the terms beyond the Gaussian approximation shows these terms are small. Rather, we find that the apparent Q dependence of the MSD arises from the "dynamical diversity" of the H in lysozyme. Specifically, if the ISF of an individual H in the protein is calculated and the MSD extracted in the usual way, then the MSD is independent of Q. This Q dependence arises from ignoring the dynamical diversity in the data analysis.

Long-time mean-square displacements in proteins

Physical Review E, 2013

We propose a method for obtaining the intrinsic, long time mean square displacement (MSD) of atom... more We propose a method for obtaining the intrinsic, long time mean square displacement (MSD) of atoms and molecules in proteins from finite time molecular dynamics (MD) simulations. Typical data from simulations are limited to times of 1 to 10 ns and over this time period the calculated MSD continues to increase without a clear limiting value. The proposed method consists of fitting a model to MD simulation-derived values of the incoherent intermediate neutron scattering function, Iinc(Q, t), for finite times. The infinite time MSD, r 2 , appears as a parameter in the model and is determined by fits of the model to the finite time Iinc(Q, t). Specifically, the r 2 is defined in the usual way in terms of the Debye-Waller factor as I(Q, t = ∞) = exp(−Q 2 r 2 /3). The method is illustrated by obtaining the intrinsic MSD r 2 of hydrated lysozyme powder (h = 0.4 g water/g protein) over a wide temperature range. The intrinsic r 2 obtained from data out to 1 ns and to 10 ns is found to be the same. The intrinsic r 2 is approximately twice the value of the MSD that is reached in simulations after times of 1 ns which correspond to those observed using neutron instruments that have an energy resolution width of 1 µeV.

Vibrational dynamics of hydrogen in proteins

Physical Review E, 2011

Biological macromolecules expand with increasing temperature and this dynamic expansion is associ... more Biological macromolecules expand with increasing temperature and this dynamic expansion is associated with the onset of function. The expansion is typically characterized by the mean square vibrational displacement (MSD), u 2 , of specific constituents such as hydrogen within the macromolecules. The u 2 increases with increasing temperature and the slope of u 2 versus temperature can increase significantly at a temperature T D identified as a dynamical transition. We illustrate that the observed expansion and change in slope of u 2 with temperature at T D can be reproduced within a simple model of the vibration, an atom in an anharmonic potential, V (u). Given V (u), only the temperature is varied in the model. A simple Gaussian potential or a potential containing a hard wall is particularly effective is reproducing the observed change in the slope of u 2 with temperature around T D .

Motional displacements in proteins: The origin of wave-vector-dependent values

Physical review. E, Statistical, nonlinear, and soft matter physics, 2015

The average mean-square displacement, 〈r^{2}〉, of H atoms in a protein is frequently determined u... more The average mean-square displacement, 〈r^{2}〉, of H atoms in a protein is frequently determined using incoherent neutron-scattering experiments. 〈r^{2}〉 is obtained from the observed elastic incoherent dynamic structure factor, S_{i}(Q,ω=0), assuming the form S_{i}(Q,ω=0) =exp(-Q^{2}〈r^{2}〉/3). This is often referred to as the Gaussian approximation (GA) to S_{i}(Q,ω=0). 〈r^{2}〉 obtained in this way depends on the value of the wave vector, Q considered. Equivalently, the observed S_{i}(Q,ω=0) deviates from the GA. We investigate the origin of the Q dependence of 〈r^{2}〉 by evaluating the scattering functions in different approximations using molecular dynamics (MD) simulation of the protein lysozyme. We find that keeping only the Gaussian term in a cumulant expansion of S(Q,ω) is an accurate approximation and is not the origin of the Q dependence of 〈r^{2}〉. This is demonstrated by showing that the term beyond the Gaussian is negligible and that the GA is valid for an individual ato...

Motional displacements in proteins incorporating dynamical diversity

Bulletin of the American Physical Society, 2016

The average mean square displacement (MSD), ⟨r 2 ⟩, of hydrogen H in proteins is measured using i... more The average mean square displacement (MSD), ⟨r 2 ⟩, of hydrogen H in proteins is measured using incoherent neutron scattering methods. The observed MSD shows a marked increase in magnitude at a temperature T D ≃ 240 K. This is widely interpreted as a dynamical transition to large MSDs which make function possible in proteins. However, when the data is interpreted in terms of a single averaged MSD, the extracted ⟨r 2 ⟩ depends on the neutron momentum transfer,hQ, used in the measurement. We have shown recently that this apparent dependence on Q arises because the dynamical diversity of the H in the protein is neglected[2]. We present models of the dynamical diversity of H in Lysosyme that when used in the analysis of simulated neutron data lead to consistent, Q independent values for the average MSD and for the diversity model.

Polymer principles behind solubilizing lignin with organic cosolvents for bioenergy

Green Chemistry, 2020

Polymer theory, developed for simple homopolymers, is applicable to the interaction of lignin wit... more

Impact of hydration and temperature history on the structure and dynamics of lignin

Green Chemistry, 2018

At a given temperature during a heating/cooling cycle, lignin is more dynamic upon cooling, which... more

Dynamics of the lignin glass transition

Physical chemistry chemical physics : PCCP, Jan 8, 2018

The dynamics of lignin, a complex and heterogeneous major plant cell-wall macromolecule, is of bo... more The dynamics of lignin, a complex and heterogeneous major plant cell-wall macromolecule, is of both fundamental and practical importance. Lignin is typically heated to temperatures above its glass transition to facilitate its industrial processing. We performed molecular dynamics simulations to investigate the segmental (α) relaxation of lignin, the dynamical process that gives rise to the glass transition. It is found that lignin dynamics involves mainly internal motions below Tg, while segmental inter-molecular motions are activated above Tg. The segments whose mobility is enhanced above Tg consist of 3-5 lignin monomeric units. The temperature dependence of the lignin segmental relaxation time changes from Arrhenius below Tg to Vogel-Fulcher-Tamman above Tg. This change in temperature dependence is determined by the underlying energy landscape being restricted below Tg but exhibiting multiple minima above Tg. The Q-dependence of the relaxation time is found to obey a power-law up...

Determination of Dynamical Heterogeneity from Dynamic Neutron-Scattering of Proteins

Biophysical journal, Jan 23, 2018

Motional displacements of hydrogen (H) in proteins can be measured using incoherent neutron-scatt... more Motional displacements of hydrogen (H) in proteins can be measured using incoherent neutron-scattering methods. These displacements can also be calculated numerically using data from molecular dynamics simulations. An enormous amount of data on the average mean-square motional displacement (MSD) of H as a function of protein temperature, hydration, and other conditions has been collected. H resides in a wide spectrum of sites in a protein. Some H are tightly bound to molecular chains, and the H motion is dictated by that of the chain. Other H are quite independent. As a result, there is a distribution of motions and MSDs of H within a protein that is denoted dynamical heterogeneity. The goal of this paper is to incorporate a distribution of MSDs into models of the H incoherent intermediate scattering function, I(Q,t), that is calculated and observed. The aim is to contribute information on the distribution as well as on the average MSD from comparison of the models with simulations ...

Quasielastic neutron scattering in biology: Theory and applications

Biochimica et biophysica acta, Jan 15, 2016

Neutrons scatter quasielastically from stochastic, diffusive processes, such as overdamped vibrat... more Neutrons scatter quasielastically from stochastic, diffusive processes, such as overdamped vibrations, localized diffusion and transitions between energy minima. In biological systems, such as proteins and membranes, these relaxation processes are of considerable physical interest. We review here recent methodological advances and applications of quasielastic neutron scattering (QENS) in biology, concentrating on the role of molecular dynamics simulation in generating data with which neutron profiles can be unambiguously interpreted. We examine the use of massively-parallel computers in calculating scattering functions, and the application of Markov state modeling. The decomposition of MD-derived neutron dynamic susceptibilities is described, and the use of this in combination with NMR spectroscopy. We discuss dynamics at very long times, including approximations to the infinite time mean-square displacement and nonequilibrium aspects of single-protein dynamics. Finally, we examine ...

Intrinsic Mean Square Displacement in Lysozyme

The internal dynamics of proteins is the essential interest of biophysics. The mean square displa... more The internal dynamics of proteins is the essential interest of biophysics. The mean square displacement (MSD) of hydrogen in proteins and its associated hydration water is obtained by molecular dynamic (MD) simulation. The MSD as currently determined depends on the time of the MD simulation. A method is proposed in this paper to obtain the intrinsic MSD ⟨r 2 ⟩ of hydrogen in the proteins. The intrinsic MSD is independent of the simulation time and defined as the infinite time value of calculated MSD that appears in the Debye-Waller factor. The method consists of fitting a model to the incoherent intermediate scattering function. The model contains the intrinsic MSD and a rate constant characterizing the motions of H in the protein. The method is illustrated by obtaining the intrinsic MSD ⟨r 2 ⟩ of lysozyme in 100 ns and 1 µs MD simulations.

Why the observed mean square motional displacement depends on wave vector Q

The motional mean square displacement (MSD) of hydrogen (H) in proteins is extensively measured u... more The motional mean square displacement (MSD) of hydrogen (H) in proteins is extensively measured using neutron scattering techniques. The MSD increases rapidly with temperature near room temperatures and a large MSD is often associated with protein function. One shortcoming of these measurements is that the observed MSD depends on the wave vector (Q) of the neutron data used to obtain the MSD. This dependence is often attributed to use of the Gaussian approximation made to the scattering function in the analysis of the data. To test this we have simulated the protein lysozyme and calculated the intermediate scattering function (ISF), both the full ISF and the ISF in the Gaussian approximation. We find that the MSD extracted in the usual way was the same and still Q dependent in both cases. Also, direct calculation of the terms beyond the Gaussian approximation shows these terms are small. Rather, we find that the apparent Q dependence of the MSD arises from the "dynamical diversity" of the H in lysozyme. Specifically, if the ISF of an individual H in the protein is calculated and the MSD extracted in the usual way, then the MSD is independent of Q. This Q dependence arises from ignoring the dynamical diversity in the data analysis.

Long-time mean-square displacements in proteins

Physical Review E, 2013

We propose a method for obtaining the intrinsic, long time mean square displacement (MSD) of atom... more We propose a method for obtaining the intrinsic, long time mean square displacement (MSD) of atoms and molecules in proteins from finite time molecular dynamics (MD) simulations. Typical data from simulations are limited to times of 1 to 10 ns and over this time period the calculated MSD continues to increase without a clear limiting value. The proposed method consists of fitting a model to MD simulation-derived values of the incoherent intermediate neutron scattering function, Iinc(Q, t), for finite times. The infinite time MSD, r 2 , appears as a parameter in the model and is determined by fits of the model to the finite time Iinc(Q, t). Specifically, the r 2 is defined in the usual way in terms of the Debye-Waller factor as I(Q, t = ∞) = exp(−Q 2 r 2 /3). The method is illustrated by obtaining the intrinsic MSD r 2 of hydrated lysozyme powder (h = 0.4 g water/g protein) over a wide temperature range. The intrinsic r 2 obtained from data out to 1 ns and to 10 ns is found to be the same. The intrinsic r 2 is approximately twice the value of the MSD that is reached in simulations after times of 1 ns which correspond to those observed using neutron instruments that have an energy resolution width of 1 µeV.

Vibrational dynamics of hydrogen in proteins

Physical Review E, 2011

Biological macromolecules expand with increasing temperature and this dynamic expansion is associ... more Biological macromolecules expand with increasing temperature and this dynamic expansion is associated with the onset of function. The expansion is typically characterized by the mean square vibrational displacement (MSD), u 2 , of specific constituents such as hydrogen within the macromolecules. The u 2 increases with increasing temperature and the slope of u 2 versus temperature can increase significantly at a temperature T D identified as a dynamical transition. We illustrate that the observed expansion and change in slope of u 2 with temperature at T D can be reproduced within a simple model of the vibration, an atom in an anharmonic potential, V (u). Given V (u), only the temperature is varied in the model. A simple Gaussian potential or a potential containing a hard wall is particularly effective is reproducing the observed change in the slope of u 2 with temperature around T D .

Motional displacements in proteins: The origin of wave-vector-dependent values

Physical review. E, Statistical, nonlinear, and soft matter physics, 2015

The average mean-square displacement, 〈r^{2}〉, of H atoms in a protein is frequently determined u... more The average mean-square displacement, 〈r^{2}〉, of H atoms in a protein is frequently determined using incoherent neutron-scattering experiments. 〈r^{2}〉 is obtained from the observed elastic incoherent dynamic structure factor, S_{i}(Q,ω=0), assuming the form S_{i}(Q,ω=0) =exp(-Q^{2}〈r^{2}〉/3). This is often referred to as the Gaussian approximation (GA) to S_{i}(Q,ω=0). 〈r^{2}〉 obtained in this way depends on the value of the wave vector, Q considered. Equivalently, the observed S_{i}(Q,ω=0) deviates from the GA. We investigate the origin of the Q dependence of 〈r^{2}〉 by evaluating the scattering functions in different approximations using molecular dynamics (MD) simulation of the protein lysozyme. We find that keeping only the Gaussian term in a cumulant expansion of S(Q,ω) is an accurate approximation and is not the origin of the Q dependence of 〈r^{2}〉. This is demonstrated by showing that the term beyond the Gaussian is negligible and that the GA is valid for an individual ato...