HYDRONMR: prediction of NMR relaxation of globular proteins from atomic-level structures and hydrodynamic calculations.

@article{GarcadelaTorre2000HYDRONMRPO,
  title={HYDRONMR: prediction of NMR relaxation of globular proteins from atomic-level structures and hydrodynamic calculations.},
  author={Jos{\'e} Garc{\'i}a de la Torre and M. L. Huertas and Beatriz Carrasco},
  journal={Journal of magnetic resonance},
  year={2000},
  volume={147 1},
  pages={
          138-46
        }
}
The heteronuclear NMR relaxation of globular proteins depends on the anisotropic rotational diffusion tensor. Using our previous developments for prediction of hydrodynamic properties of arbitrarily shaped particles, by means of bead models, we have constructed a computational procedure to calculate the rotational diffusion tensor and other properties of proteins from their detailed, atomic-level structure. From the atomic coordinates file used to build the bead model, the orientation of the… 

Figures and Tables from this paper

Interpretation of 15N NMR relaxation data of globular proteins using hydrodynamic calculations with HYDRONMR

Hydrodynamic modeling to calculate the spectral density functions for NH or Cα-H vectors in a rigid protein structure starting from an atomic level representation can be used to predict NMR relaxation times from a rigid model and to compare them with the experimental results.

HYDROMIC: prediction of hydrodynamic properties of rigid macromolecular structures obtained from electron microscopy images

A computer program is written, HYDROMIC, that implements all the stages of the calculation and is illustrated with a calculation of the solution properties of the volume of the cytosolic chaperonin CCT, obtained from cryoelectron microscopy images.

Calculation of hydrodynamic properties of small nucleic acids from their atomic structure.

If the hydrodynamic model for the short DNA is simply a cylindrical rod, the predictions for overall translation and rotation are slightly worse, but the NMR correlation times and the degree of hydration, which depend more on the cross-sectional structure, are more severely affected.

Prediction of Hydrodynamic and Other Solution Properties of Partially Disordered Proteins with a Simple, Coarse-Grained Model.

A very simple, coarse-grained, residue-level model, which is easily parametrized using available structural information, along with previously developed tools for the simulation of solution conformation and dynamics, allows the prediction of properties like sedimentation coefficients, relaxation times, and X-ray or neutron scattering.

Rotational Dynamics of Proteins from Spin Relaxation Times and Molecular Dynamics Simulations

Conformational fluctuations and rotational tumbling of proteins can be experimentally accessed with nuclear spin relaxation experiments. However, interpretation of molecular dynamics from the

A theory of protein dynamics to predict NMR relaxation.

We present a theoretical, site-specific, approach to predict protein subunit correlation times, as measured by NMR experiments of (1)H-(15)N nuclear Overhauser effect, spin-lattice relaxation, and

The HYDRO Software Suite for the Prediction of Solution Properties of Rigid and Flexible Macromolecules and Nanoparticles

With basis on the classical concept of bead modeling of polymer hydrodynamics, the HYDRO suite of computer programs allows the calculation of solution properties of macromolecules and nanoparticles

Characterization of the overall rotational diffusion of a protein from 15N relaxation measurements and hydrodynamic calculations.

Experimental and theoretical methods for characterizing the overall rotational diffusion of molecules in solution are discussed, and model-free characteristics of internal backbone motions in the protein are derived to show that different models for the overall motion can result in significantly different pictures of motion.
...

References

SHOWING 1-10 OF 52 REFERENCES

Prediction of the rotational diffusion behavior of biopolymers on the basis of their solution or crystal structure

The predicted harmonic mean of the rotational correlation times of compact globular macromolecules with molar masses of 14,000–65,000 g/mol agree with experimental results within the error limits.

Calculation of NMR relaxation, covolume, and scattering-related properties of bead models using the SOLPRO computer program

This work describes the calculation of relaxation rates in nuclear magnetic resonance (NMR) and devised and programmed a procedure to calculate the covolume of the bead model, related to the second virial coefficient and, in general, to the concentration dependence of solution properties.

Defining long range order in NMR structure determination from the dependence of heteronuclear relaxation times on rotational diffusion anisotropy

This paper shows how the dependence of heteronuclear longitudinal and transverse relaxation times on the rotational diffusion anisotropy of non-spherical molecules can be readily used to directly provide restraints for simulated annealing structure refinement that characterize long range order a priori.

SOLPRO: theory and computer program for the prediction of SOLution PROperties of rigid macromolecules and bioparticles

The hydrodynamic coefficients and solution properties can be combined to give universal, shape-dependent functions, which were initially intended for ellipsoidal particles, and are extended here for the most general case.

Hydrodynamic properties of macromolecular complexes. I. Translation

We have developed an improved theory for calculating the translational frictional coefficients of rigid macromolecular complexes composed of unequal spherical subunits. The Yamakawa hydrodynamic

Nuclear Magnetic Resonance Studies of Biopolymer Dynamics

This review describes NMR spectroscopic methods for investigation of conformational dynamics together with theoretical descriptions appropriate for interpretation and simulation of the techniques, surveys the range of results available from solution and solid state NMR studies of proteins and other biomolecules, and identifies opportunities for further individual and collaborative development of solution andSolid State NMR techniques for characterizing the dynamical properties of biological macromolecules.

Improved hydrodynamic interaction in macromolecular bead models

The calculation of hydrodynamic properties of macromolecules in terms of bead models requires an adequate description of the hydrodynamic interaction between the spherical elements. For this purpose,

Rotational diffusion anisotropy of proteins from simultaneous analysis of 15N and 13Cα nuclear spin relaxation

Theoretical and experimental results for calbindin D9k,granulocyte colony stimulating factor, and ubiquitin, three proteins with different distributions of N-H and Cα-Hα bond vectors, are used to illustrate the advantages of theultaneous utilization of 13Cα and 15N relaxation data.
...