NMR paper Interpretation of 15N NMR relaxation data of globular proteins using hydrodynamic cal

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[NMR paper] Interpretation of 15N NMR relaxation data of globular proteins using hydrodynamic cal

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NMR processing:

MDD

NMR assignment:

Backbone:

Side-chains:

NOEs:

Structure from NMR restraints:

Ab initio:

Fragment-based:

Rosetta-NMR (Robetta)

Template-based:

GeNMR

I-TASSER

Refinement:

Amber

Structure from chemical shifts:

Fragment-based:

Homology-based:

Torsion angles from chemical shifts:

Preditor

TALOS

Promega- Proline

Secondary structure from chemical shifts:

CSI (via RCI server)

TALOS

MICS caps, β-turns

d2D

PECAN

Flexibility from chemical shifts:

RCI

Interactions from chemical shifts:

HADDOCK

Chemical shifts re-referencing:

NMR model quality:

NOEs, other restraints:

Chemical shifts:

RDCs:

Pseudocontact shifts:

Protein geomtery:

SAVES2 or SAVES4

Quality Control Check

NMR spectrum prediction:

FANDAS

MestReS

V-NMR

Flexibility from structure:

Backbone S2

Methyl S2

B-factor

Molecular dynamics:

Gromacs

Amber

Antechamber

Chemical shifts prediction:

From structure:

Shiftx2

Sparta+

Camshift

CH3shift- Methyl

ArShift- Aromatic

ShiftS

Proshift

PPM

CheShift-2- Cα

From sequence:

Shifty

Camcoil

Poulsen_rc_CS

Disordered proteins:

MAXOCC

Format conversion & validation:

CCPN

From NMR-STAR 3.1

Validate NMR-STAR 3.1

NMR sample preparation:

Protein disorder:

DisMeta

Protein solubility:

Isotope labeling:

Solid-state NMR:

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11-24-2010, 08:49 PM

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Interpretation of 15N NMR relaxation data of globular proteins using hydrodynamic cal

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

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

J Biomol NMR. 2002 Jun;23(2):139-50

Authors: Bernadó P, García de la Torre J, Pons M

HYDRONMR is an implementation of state of the art hydrodynamic modeling to calculate the spectral density functions for NH or C(alpha)-H vectors in a rigid protein structure starting from an atomic level representation. Thus HYDRONMR can be used to predict NMR relaxation times from a rigid model and to compare them with the experimental results. HYDRONMR contains a single adjustable parameter, the atomic element radius. A protocol to determine the value that gives the best agreement between calculated and experimental T1/T2 values is described. For most proteins, the value of the atomic element radius ranges between 2.8 A and 3.8 A with a distribution centered at 3.3 A. Deviations from the usual range towards larger values are associated to aggregation in several proteins. Deviations to lower values may be related to large-scale motions or inappropriate model structures. If the average structure is correct, deviations between experimental T1/T2 values and those calculated with HYDRONMR can be used to distinguish residues affected by anisotropic motion from those that are involved in chemical exchange.

PMID: 12153039 [PubMed - indexed for MEDLINE]

Source: PubMed

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