Coupling between lysozyme and glycerol dynamics: Microscopic insights from molecular-dynamics simulations

Dirama, Taner E.; Carri, Gustavo A.; Sokolov, Alexei P.

doi:10.1063/1.1938191

Cited by 46 publications

(79 citation statements)

References 53 publications

(64 reference statements)

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“…This has been shown to be true in ref. [19] for the case of Ribonuclease A in pure water and by Dirama et al [57] for the case of Lysozyme in glycerol or in trehalose [18]. Thus, the effect of an increase in trehalose concentration is very similar to that of a decrease in temperature.…”

Section: H(t)supporting

confidence: 53%

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The effect of complex solvents on the structure and dynamics of protein solutions: The case of Lysozyme in trehalose/water mixtures

GhattyVenkataKrishna

Carri

2013

Eur. Phys. J. E

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Abstract. We present a Molecular Dynamics simulation study of the effect of trehalose concentration on the structure and dynamics of individual proteins immersed in trehalose/water mixtures. Hen egg-white Lysozyme is used in this study and trehalose concentrations of 0%, 10%, 20%, 30% and 100% by weight are explored. Surprisingly, we have found that changes in trehalose concentration do not change the global structural characteristics of the protein as measured by standard quantities like the mean square deviation, radius of gyration, solvent accessible surface area, inertia tensor and asphericity. Only in the limit of pure trehalose these metrics change significantly. Specifically, we found that the protein is compressed by 2% when immersed in pure trehalose. At the amino acid level there is noticeable rearrangement of the surface residues due to the change in polarity of the surrounding environment with the addition of trehalose. From a dynamic perspective, our computation of the Incoherent Intermediate Scattering Function shows that the protein slows down with increasing trehalose concentration; however, this slowdown is not monotonic. Finally, we also report in-depth results for the hydration layer around the protein including its structure, hydrogen-bonding characteristics and dynamic behavior at different length scales.

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Section: H(t)supporting

confidence: 53%

“…The behavior of proteins in pure water [19, and pure trehalose [18,57] has been studied extensively using computer simulation methods. In the particular case of globular proteins immersed in trehalose-water binary mixtures Lins et al [58] and Lebret et al [56] have reported studies of Lysozyme in various trehalose-water mixtures.…”

Section: Introductionmentioning

confidence: 99%

The effect of complex solvents on the structure and dynamics of protein solutions: The case of Lysozyme in trehalose/water mixtures

GhattyVenkataKrishna

Carri

2013

Eur. Phys. J. E

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“…No dependence on NADPH concentration was observed although we noted that in these laser photoexcitation experiments the initial concentration of NADPH was relatively high to ensure that prior to catalysis all of the Pchlide substrate was in the ternary substrate complex form. As the enzyme also has a high affinity for NADPH (18,19) it is perhaps not surprising that a dependence on the NADPH concentration is not observed.…”

Section: Figure 4 the Effects Of Nadpmentioning

confidence: 99%

Laser Excitation Studies of the Product Release Steps in the Catalytic Cycle of the Light-driven Enzyme, Protochlorophyllide Oxidoreductase

Heyes

Sakuma

Scrutton³

2007

Journal of Biological Chemistry

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The latter stages of the catalytic cycle of the light-driven enzyme, protochlorophyllide oxidoreductase, have been investigated using novel laser photoexcitation methods. The formation of the ternary product complex was initiated with a 6-ns laser pulse, which allowed the product release steps to be kinetically accessed for the first time. Subsequent absorbance changes associated with the release of the NADP ؉ and chlorophyllide products from the enzyme could be followed on a millisecond timescale. This has facilitated a detailed kinetic and thermodynamic characterization for the interconversion of all the various bound and unbound product species. Initially, NADP ؉ is released from the enzyme in a biphasic process with rate constants of 1210 and 237 s ؊1 . The rates of both phases show a significant dependence on the viscosity of the solvent and become considerably slower at higher glycerol concentrations. The fast phase of this process exhibits no dependence on NADP ؉ concentration, suggesting that conformational changes are required prior to NADP ؉ release. Following NADP ؉ release, the NADPH rebinds to the enzyme with a maximum rate constant of ϳ72 s ؊1 . At elevated temperatures (>298 K) chlorophyllide is released from the enzyme to yield the free product with a maximum rate constant of 20 s ؊1 . The temperature dependencies of the rates of each of these steps were measured, and enthalpies and entropies of activation were calculated using the Eyring equation. A comprehensive kinetic and thermodynamic scheme for these final stages of the reaction mechanism is presented.

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“…[14] Most neutron and MD studies to date have investigated the MSD on a picosecond-nanosecond (ps-ns) timescale. [1,5,[15][16][17][18][19][20][21][22][23][24][25][26][27][28] At low temperatures (T < 100 K), a protein is essentially harmonic. As the temperature is increased beyond the harmonic regime, proline puckering transitions and methyl rotations are activated.…”

Section: Introductionmentioning

confidence: 99%

“…Similar simulation systems are discussed in the literature. [8,26,[41][42][43][44] The system was simulated using GROMACS 4.5.1.…”

Section: Introductionmentioning

confidence: 99%

Long-time mean-square displacements in proteins

et al. 2013

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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.

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Coupling between lysozyme and glycerol dynamics: Microscopic insights from molecular-dynamics simulations

Cited by 46 publications

References 53 publications

The effect of complex solvents on the structure and dynamics of protein solutions: The case of Lysozyme in trehalose/water mixtures

The effect of complex solvents on the structure and dynamics of protein solutions: The case of Lysozyme in trehalose/water mixtures

Laser Excitation Studies of the Product Release Steps in the Catalytic Cycle of the Light-driven Enzyme, Protochlorophyllide Oxidoreductase

Long-time mean-square displacements in proteins

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