NMR paper NMR Characterization of Conformational Fluctuations and Non-covalent Interactions of SUMO protein from Drosophila melanogaster (dSmt3).

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[NMR paper] NMR Characterization of Conformational Fluctuations and Non-covalent Interactions of SUMO protein from Drosophila melanogaster (dSmt3).

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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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04-09-2019, 11:33 PM

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NMR Characterization of Conformational Fluctuations and Non-covalent Interactions of SUMO protein from Drosophila melanogaster (dSmt3).

Related Articles NMR Characterization of Conformational Fluctuations and Non-covalent Interactions of SUMO protein from Drosophila melanogaster (dSmt3).

Proteins. 2019 Apr 08;:

Authors: Kaur A, Gourav, Kumar S, Jaiswal N, Vashisht A, Kumar D, Gahlay GK, Mithu VS

Abstract
Structural heterogeneity in the native-state ensemble of dSmt3, the only Small Ubiquitin like MOdifier (SUMO) in Drosophila melanogaster, was investigated and compared with its human homologue SUMO1. Temperature dependence of amide proton's chemical shift was studied to identify amino acids possessing alternative structural conformations in the native state. Effect of small concentration of denaturant (1M urea) on this population was also monitored to assess the ruggedness of near-native energy landscape. Owing to presence of many such amino acids, especially in the ?2 -loop-? region, the native state of dSmt3 seems more flexible in comparison to SUMO1. Information about backbone dynamics in ns-ps timescale was quantified from the measurement of 15 N-relaxation experiments. Furthermore, the non-covalent interaction of dSmt3 and SUMO1 with Daxx12 (Daxx729 DPEEIIVLSDSD740 ), a [V/I]-X-[V/I]-[V/I] based SUMO interaction motif (SIMs), was characterized using Bio-layer Interferometery and NMR spectroscopy. Daxx12 fits itself in the groove formed by ?2 -loop-? structural region in both dSmt3 and SUMO1, but the binding is stronger with the former. Flexibility of ?2 -loop-? region in dSmt3 is suspected to assist its interaction with Daxx12. Our results highlight the role of native-state flexibility in assisting non-covalent interactions of SUMO proteins especially in organisms where a single SUMO isoform has to tackle multiple substrates single handedly. This article is protected by copyright. All rights reserved.

PMID: 30958586 [PubMed - as supplied by publisher]

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