Hydrodynamic properties of complex, rigid, biological macromolecules: theory and applications

Torre, José Garcı́a de la; Bloomfield, Victor A.

doi:10.1017/s0033583500002080

Cited by 640 publications

(500 citation statements)

References 99 publications

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“…This value is close to the value of 1.69 ns calculated using the hydro program [43,44]. J(v c ) and J(1.56 Â v H ) are plotted as a function of J(0) in Fig.…”

Section: Analysis Of the Chimeric Protein Relaxation Datasupporting

confidence: 82%

“…Indeed, we have calculated the diffusion tensors of both proteins using the hydro program [43] and a protocol similar to that proposed by Tjandra et al [44]. Both tensors were found to be poorly anisotropic (1.18 and 1.19 for charybdotoxin and the chimeric protein, respectively), and not asymmetric at all (1.00 and 1.03 for charybdotoxin and the chimeric protein, respectively).…”

Section: Nmr Experimental Conditionsmentioning

confidence: 96%

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Characterization of the internal motions of a chimeric protein by ¹³C NMR highlights the important dynamic consequences of the engineering on a millisecond time scale

Wolff¹,

Guenneugues²,

Gilquin³

et al. 2000

European Journal of Biochemistry

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By transferring the central curaremimetic b hairpin of the snake toxin a into the scaffold of the scorpion charybdotoxin, a chimeric protein was constructed that reproduced the three-dimensional structure and partially reproduced the function of the parent b hairpin, without perturbing the three-dimensional structure of the scaffold [1]. Picosecond to hour time scale motions of charybdotoxin and the engineered protein were observed, in order to evaluate the dynamic consequences of the six deletions and eight mutations differentiating the two molecules. The chimeric protein dynamics were also compared to that of toxin a, in order to examine the b hairpin motions in both structural contexts. Thus, 13 C R 1 , R 1r and 1 H3 13 C nOe were measured for all the C a H a and threonine C b H b vectors. As the proteins were not labeled, accordion techniques combined to coherence selection by pulsed field gradients and preservation of magnetization following equivalent pathways were used to considerably reduce the spectrometer time needed. On one hand, we observed that the chimeric protein and charybdotoxin are subjected to similar picosecond to nanosecond time scale motions except around the modified b sheet region. The chimeric protein also exhibits an additional millisecond time scale motion on its whole sequence, and its b structure is less stable on a minute to hour time scale. On the other hand, when the b hairpin dynamics is compared in two different structural contexts, i.e. in the chimeric protein and the curaremimetic toxin a, the picosecond to nanosecond time scale motions are fairly conserved. However, the microsecond to millisecond time scale motions are different on most of the b hairpin sequence, and the b sheet seems more stable in toxin a than in the chimera. The slower microsecond to hour time scale motions seem to be extremely sensitive to the structural context, and thus poorly transferred from one protein to another.

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“…This value is close to the value of 1.69 ns calculated using the hydro program [43,44]. J(v c ) and J(1.56 Â v H ) are plotted as a function of J(0) in Fig.…”

Section: Analysis Of the Chimeric Protein Relaxation Datasupporting

confidence: 82%

Section: Nmr Experimental Conditionsmentioning

confidence: 96%

Characterization of the internal motions of a chimeric protein by ¹³C NMR highlights the important dynamic consequences of the engineering on a millisecond time scale

Wolff¹,

Guenneugues²,

Gilquin³

et al. 2000

European Journal of Biochemistry

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show abstract

“…For these applications, it is surely better to include most of the effects of hydrodynamics without slowing down the simulation too much than to either have no HI at all or the correct HI at a prohibitive computational cost. Other applications could be to describe the behavior of non-spherical particles by assembling them from smaller spheres 19,31 . Here the quality of the model increases with the number of spheres used to build the non-spherical particles.…”

Section: Discussionmentioning

confidence: 99%

An O(N2) approximation for hydrodynamic interactions in Brownian dynamics simulations

Geyer

Winter²

2009

The Journal of Chemical Physics

102

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In the Ermak-McCammon algorithm for Brownian Dynamics, the hydrodynamic interactions (HI) between N spherical particles are described by a 3N ×3N diffusion tensor. This tensor has to be factorized at each timestep with a runtime of O(N 3 ), making the calculation of the correlated random displacements the bottleneck for many-particle simulations. Here we present a faster algorithm for this step, which is based on a truncated expansion of the hydrodynamic multi-particle correlations as two-body contributions. The comparison to the exact algorithm and to the Chebyshev approximation of Fixman verifies that for bead-spring polymers this approximation yields about 95% of the hydrodynamic correlations at an improved runtime scaling of O(N 2 ) and a reduced memory footprint. The approximation is independent of the actual form of the hydrodynamic tensor and can be applied to arbitrary particle configurations. This now allows to include HI into large manyparticle Brownian dynamics simulations, where until now the runtime scaling of the correlated random motion was prohibitive.

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“…More recently numerical results for arbitrary shapes have also been obtained. [25][26][27][28][29] Another path involves extracting diffusion coefficients from experimental observables, such as fluorescence depolarization, 30,31 light scattering, 32,33 forced Rayleigh scattering, 34 electric birefringence 35 and nuclear magnetic resonance ͑NMR͒ spectral parameters. 5,[36][37][38] Finally, the advent of computer simulations has opened the door to direct simulations of diffusion, which enable both validation of theoretical models and insight into atomic-level phenomena responsible for experimentally observed effects.…”

Section: Introductionmentioning

confidence: 99%

Influence of temperature and viscosity on anthracene rotational diffusion in organic solvents: Molecular dynamics simulations and fluorescence anisotropy study

Jas

Wang

Pauls

et al. 1997

The Journal of Chemical Physics

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Molecular dynamics simulations and fluorescence anisotropy decay measurements are used to investigate the rotational diffusion of anthracene in two organic solvents-cyclohexane and 2-propanol-at several temperatures. Molecular dynamics simulations of 1 ns length were performed for anthracene in cyclohexane ͑at 280, 296, and 310 K͒ and in 2-propanol ͑at 296 K͒. The calculated time constants for reorientation of the short in-plane axis were 7-9 and 11-16 ps at 296 K in cyclohexane and 2-propanol, respectively, in excellent agreement with corresponding fluorescence depolarization measurements of 8 and 14 ps. The measured rotational reorientation times and the calculated average rotational diffusion coefficients varied in accord with DebyeStokes-Einstein theory. Their magnitudes were close to values predicted for an ellipsoid of shape and size equivalent to an anthracene molecule, and exhibited predictable variation with external conditions-increasing with temperature and decreasing with solvent viscosity. However, analysis of the calculated rotational diffusion coefficients for the individual molecular axes gave a more complex picture. The diffusion was highly anisotropic and changes in temperature and solvent type led to nonuniform variation of the diffusion coefficients. The nature of these changes was rationalized based on analysis of variation of solvation patterns with temperature and solvent.

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Hydrodynamic properties of complex, rigid, biological macromolecules: theory and applications

Cited by 640 publications

References 99 publications

Characterization of the internal motions of a chimeric protein by ¹³C NMR highlights the important dynamic consequences of the engineering on a millisecond time scale

Characterization of the internal motions of a chimeric protein by ¹³C NMR highlights the important dynamic consequences of the engineering on a millisecond time scale

An O(N2) approximation for hydrodynamic interactions in Brownian dynamics simulations

Influence of temperature and viscosity on anthracene rotational diffusion in organic solvents: Molecular dynamics simulations and fluorescence anisotropy study

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Hydrodynamic properties of complex, rigid, biological macromolecules: theory and applications

Cited by 640 publications

References 99 publications

Characterization of the internal motions of a chimeric protein by 13C NMR highlights the important dynamic consequences of the engineering on a millisecond time scale

Characterization of the internal motions of a chimeric protein by 13C NMR highlights the important dynamic consequences of the engineering on a millisecond time scale

An O(N2) approximation for hydrodynamic interactions in Brownian dynamics simulations

Influence of temperature and viscosity on anthracene rotational diffusion in organic solvents: Molecular dynamics simulations and fluorescence anisotropy study

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Characterization of the internal motions of a chimeric protein by ¹³C NMR highlights the important dynamic consequences of the engineering on a millisecond time scale

Characterization of the internal motions of a chimeric protein by ¹³C NMR highlights the important dynamic consequences of the engineering on a millisecond time scale