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NMR processing:
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PINE
Side-chains:
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UNIO Candid
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Ab initio:
GeNMR
Cyana
XPLOR-NIH
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UNIO ATNOS-Candid
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Fragment-based:
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Template-based:
GeNMR
I-TASSER
Refinement:
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Structure from chemical shifts:
Fragment-based:
WeNMR CS-Rosetta
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Homology-based:
CS23D
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Torsion angles from chemical shifts:
Preditor
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Secondary structure from chemical shifts:
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MICS caps, β-turns
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Flexibility from chemical shifts:
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Interactions from chemical shifts:
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Chemical shifts re-referencing:
Shiftcor
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RDCs:
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Flexibility from structure:
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Methyl S2
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Molecular dynamics:
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Chemical shifts prediction:
From structure:
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ArShift- Aromatic
ShiftS
Proshift
PPM
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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:
camLILA
ccSOL
Camfold
camGroEL
Zyggregator
Isotope labeling:
UPLABEL
Solid-state NMR:
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Old 05-27-2015, 10:39 AM
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Default An integrative approach combining ion mobility mass spectrometry, X-ray crystallography and NMR spectroscopy to study the conformational dynamics of ?1 -antitrypsin upon ligand binding.

An integrative approach combining ion mobility mass spectrometry, X-ray crystallography and NMR spectroscopy to study the conformational dynamics of ?1 -antitrypsin upon ligand binding.

An integrative approach combining ion mobility mass spectrometry, X-ray crystallography and NMR spectroscopy to study the conformational dynamics of ?1 -antitrypsin upon ligand binding.

Protein Sci. 2015 May 26;

Authors: Nyon MP, Prentice T, Day J, Kirkpatrick J, Sivalingam GN, Levy G, Haq I, Irving JA, Lomas DA, Christodoulou J, Gooptu B, Thalassinos K

Abstract
Native mass spectrometry (MS) methods permit the study of multiple protein species within solution equilibria, whilst ion mobility (IM)-MS can report on conformational behaviour of specific states. We used IM-MS to study a conformationally labile protein (?1 -antitrypsin) that undergoes pathological polymerisation in the context of point mutations. The folded, native state of the Z variant remains highly polymerogenic in physiological conditions, despite only minor thermodynamic destabilisation relative to the wild-type variant. Various data implicate kinetic instability (conformational lability within a native state ensemble) as the basis of Z ?1 -antitrypsin polymerogenicity. We show the ability of IM-MS to track such disease-relevant conformational behaviour in detail by studying the effects of peptide binding on ?1 -antitrypsin conformation and dynamics. IM-MS is therefore an ideal platform for the screening of compounds that result in therapeutically-beneficial kinetic stabilisation of native ?1 -antitrypsin. Our findings are confirmed with high resolution X-ray crystallographic and NMR spectroscopic studies of the same event, which together dissect structural changes from dynamic effects caused by peptide binding at a residue specific level. IM-MS methods therefore have great potential for further study of biologically-relevant thermodynamic and kinetic instability of proteins and provide rapid and multidimensional characterisation of ligand interactions of therapeutic interest. This article is protected by copyright. All rights reserved.


PMID: 26011795 [PubMed - as supplied by publisher]



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