NMR paper Molecular dynamics simulation of E. coli ribonuclease H1 in solution: correlation wit

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[NMR paper] Molecular dynamics simulation of E. coli ribonuclease H1 in solution: correlation wit

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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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08-22-2010, 03:50 AM

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Molecular dynamics simulation of E. coli ribonuclease H1 in solution: correlation wit

Molecular dynamics simulation of E. coli ribonuclease H1 in solution: correlation with NMR and X-ray data and insights into biological function.

Related Articles Molecular dynamics simulation of E. coli ribonuclease H1 in solution: correlation with NMR and X-ray data and insights into biological function.

J Mol Biol. 1995 Dec 8;254(4):771-92

Authors: Philippopoulos M, Lim C

A 500 ps molecular dynamics simulation of Escherichia coli RNase H1 in the presence of explicit water molecules has been carried out to aid in the interpretation of NMR N-H backbone model free parameters and X-ray B-factor values of the free enzyme. Both experimental techniques have revealed unusual structural and dynamic features of the protein. Atomic fluctuations (B-factors) and re-orientational motions of the backbone heteronuclear bonds (order parameters) computed from the simulation are compared with results obtained from experiments. Qualitative agreement is obtained between the computed and X-ray B-factors, whereas the agreement between the computed and NMR generalized order parameters is as good as quantitative for most residues. Reasons for significant discrepancies, the physical basis and the plausible biological consequences of the observed protein dynamics are discussed.

PMID: 7500349 [PubMed - indexed for MEDLINE]

Source: PubMed

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