# 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…

## 483 Citations

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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.

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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.

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- Materials ScienceJournal of chemical theory and computation
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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

- PhysicsThe journal of physical chemistry. B
- 2018

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.

- PhysicsBiophysical journal
- 2007

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…

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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.

- BiologyMethods in molecular biology
- 2004

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.

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