Protein and solvent dynamics: How strongly are they coupled?

Caliskan, Gokhan; Mechtani, D; Roh, Joon Ho; Kisliuk, A.; Sokolov, Alexei P.; Azzam, Sausan; Cicerone, Marcus T.; Lin‐Gibson, Sheng; Peral, Inma

doi:10.1063/1.1764491

Cited by 139 publications

(175 citation statements)

References 34 publications

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“…Indeed, it was previously shown that the ATP hydrolysis of several NBDs, e.g., HisP (33) and Mdl1 (C. van der Does and R. Tampé, unpublished data), is inhibited by glycerol. Moreover, studies on protein and solvent dynamics suggest that compounds such as glycerol can control the solvent dynamics of proteins and affect their activity by forming rigid structures that increase the energy barriers for conformational fluctuations of proteins (34). We also noticed that the E166A mutant is not completely arrested in ATP hydrolysis, but that its activity is decreased 100-fold as compared to that of wt GlcV.…”

Section: Discussionmentioning

confidence: 66%

Thermodynamics of the ATPase Cycle of GlcV, the Nucleotide-Binding Domain of the Glucose ABC Transporter of Sulfolobus solfataricus

et al. 2006

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ATP-binding cassette transporters drive the transport of substrates across the membrane by the hydrolysis of ATP. They typically have a conserved domain structure with two membrane-spanning domains that form the transport channel and two cytosolic nucleotide-binding domains (NBDs) that energize the transport reaction. Binding of ATP to the NBD monomer results in formation of a NBD dimer. Hydrolysis of the ATP drives the dissociation of the dimer. The thermodynamics of distinct steps in the ATPase cycle of GlcV, the NBD of the glucose ABC transporter of the extreme thermoacidophile Sulfolobus solfataricus, were studied by isothermal titration calorimetry using the wild-type protein and two mutants, which are arrested at different steps in the ATP hydrolytic cycle. The G144A mutant is unable to dimerize, while the E166A mutant is defective in dimer dissociation. The ATP, ADP, and AMP-PNP binding affinities, stoichiometries, and enthalpies of binding were determined at different temperatures. From these data, the thermodynamic parameters of nucleotide binding, NBD dimerization, and ATP hydrolysis were calculated. The data demonstrate that the ATP hydrolysis cycle of isolated NBDs consists of consecutive steps where only the final step of ADP release is energetically unfavorable.

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Section: Discussionmentioning

confidence: 66%

Thermodynamics of the ATPase Cycle of GlcV, the Nucleotide-Binding Domain of the Glucose ABC Transporter of Sulfolobus solfataricus

et al. 2006

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“…In this case, understanding the structure and dynamics of the protein-solvent interface is critical for a comprehensive understanding of the dynamic behavior of proteins. Indeed, it is well known that the dynamics of proteins is slaved to the one of the surrounding solvents [13][14][15][16][17]. In the case of pure trehalose, the dynamic coupling between the protein and the solvent has been studied by Dirama et al [18].…”

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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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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“…Especially, conformational changes, low-energy vibrational excitations and the corresponding temperature dependences turn out to be very sensitive to the solvents dynamics. [295] We will thus consider the vibrational degrees of freedom of counterions and hydration shells of the solvent as a dynamical bath able to break the electronic phase coherence and additionally to act as a dissipative environment. We do not consider specific features of the environment but represent it in a generic way by a bosonic bath of M harmonic oscillators.…”

Section: 1 the Model Hamiltonianmentioning

confidence: 99%

Green Function Techniques in the Treatment of Quantum Transport at the Molecular Scale

Ryndyk

Gutiérrez²,

Song

2009

Springer Series in Chemical Physics

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The theoretical investigation of charge (and spin) transport at nanometer length scales requires the use of advanced and powerful techniques able to deal with the dynamical properties of the relevant physical systems, to explicitly include out-of-equilibrium situations typical for electrical/heat transport as well as to take into account interaction effects in a systematic way. Equilibrium Green function techniques and their extension to non-equilibrium situations via the Keldysh formalism build one of the pillars of current state-of-the-art approaches to quantum transport which have been implemented in both model Hamiltonian formulations and first-principle methodologies. In this chapter we offer a tutorial overview of the applications of Green functions to deal with some fundamental aspects of charge transport at the nanoscale, mainly focusing on applications to model Hamiltonian formulations.

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Protein and solvent dynamics: How strongly are they coupled?

Cited by 139 publications

References 34 publications

Thermodynamics of the ATPase Cycle of GlcV, the Nucleotide-Binding Domain of the Glucose ABC Transporter of Sulfolobus solfataricus

Thermodynamics of the ATPase Cycle of GlcV, the Nucleotide-Binding Domain of the Glucose ABC Transporter of Sulfolobus solfataricus

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

Green Function Techniques in the Treatment of Quantum Transport at the Molecular Scale

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