The NMR structure of the autophagy-related protein Atg8

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The NMR structure of the autophagy-related protein Atg8

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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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08-14-2010, 04:19 AM

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The NMR structure of the autophagy-related protein Atg8

The NMR structure of the autophagy-related protein Atg8

Content Type Journal Article
DOI 10.1007/s10858-010-9420-1
Authors
- Hiroyuki Kumeta, Hokkaido University Laboratory of Structural Biology, Graduate School of Pharmaceutical Sciences Kita 12 Nishi 6 Kita-ku Sapporo 060-0812 Japan
- Masahiro Watanabe, Hokkaido University Laboratory of Structural Biology, Graduate School of Pharmaceutical Sciences Kita 12 Nishi 6 Kita-ku Sapporo 060-0812 Japan
- Hitoshi Nakatogawa, Tokyo Institute of Technology Integrated Research Institute Yokohama 226-8503 Japan
- Masaya Yamaguchi, Hokkaido University Laboratory of Structural Biology, Graduate School of Pharmaceutical Sciences Kita 12 Nishi 6 Kita-ku Sapporo 060-0812 Japan
- Kenji Ogura, Hokkaido University Laboratory of Structural Biology, Graduate School of Pharmaceutical Sciences Kita 12 Nishi 6 Kita-ku Sapporo 060-0812 Japan
- Wakana Adachi, Hokkaido University Laboratory of Structural Biology, Graduate School of Pharmaceutical Sciences Kita 12 Nishi 6 Kita-ku Sapporo 060-0812 Japan
- Yuko Fujioka, Hokkaido University Laboratory of Structural Biology, Graduate School of Pharmaceutical Sciences Kita 12 Nishi 6 Kita-ku Sapporo 060-0812 Japan
- Nobuo N. Noda, Hokkaido University Laboratory of Structural Biology, Graduate School of Pharmaceutical Sciences Kita 12 Nishi 6 Kita-ku Sapporo 060-0812 Japan
- Yoshinori Ohsumi, Tokyo Institute of Technology Integrated Research Institute Yokohama 226-8503 Japan
- Fuyuhiko Inagaki, Hokkaido University Laboratory of Structural Biology, Graduate School of Pharmaceutical Sciences Kita 12 Nishi 6 Kita-ku Sapporo 060-0812 Japan

- Journal Journal of Biomolecular NMR
- Online ISSN 1573-5001
- Print ISSN 0925-2738
- Journal Volume Volume 47
- Journal Issue Volume 47, Number 3

Source: Journal of Biomolecular NMR

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