scholarly journals Six- and seven-dimensional experiments by combination of sparse random sampling and projection spectroscopy dedicated for backbone resonance assignment of intrinsically disordered proteins

2015 ◽  
Vol 63 (3) ◽  
pp. 283-290 ◽  
Author(s):  
Szymon Żerko ◽  
Wiktor Koźmiński
Keyword(s):  
Resonance Assignment ◽  
Random Sampling ◽  
Intrinsically Disordered Proteins ◽  
Disordered Proteins ◽  
Backbone Resonance Assignment ◽  
Backbone Resonance ◽  
Intrinsically Disordered ◽  
Projection Spectroscopy

scholarly journals Dispersion from Cα or NH: 4D experiments for backbone resonance assignment of intrinsically disordered proteins

2020 ◽  
Vol 74 (2-3) ◽  
pp. 147-159
Author(s):  
Helena Tossavainen ◽  
Santeri Salovaara ◽  
Maarit Hellman ◽  
Riikka Ihalin ◽  
Perttu Permi
Keyword(s):  
Resonance Assignment ◽  
Intrinsically Disordered Proteins ◽  
Disordered Proteins ◽  
Backbone Resonance Assignment ◽  
Backbone Resonance ◽  
Intrinsically Disordered

scholarly journals Five and four dimensional experiments for robust backbone resonance assignment of large intrinsically disordered proteins: application to Tau3x protein

2016 ◽  
Vol 65 (3-4) ◽  
pp. 193-203 ◽  
Author(s):  
Szymon Żerko ◽  
Piotr Byrski ◽  
Paweł Włodarczyk-Pruszyński ◽  
Michał Górka ◽  
Karin Ledolter ◽  
...  
Keyword(s):  
Resonance Assignment ◽  
Intrinsically Disordered Proteins ◽  
Disordered Proteins ◽  
Backbone Resonance Assignment ◽  
Backbone Resonance ◽  
Intrinsically Disordered

1H, 13C and 15N backbone resonance assignment of the intrinsically disordered region of the nuclear envelope protein emerin

2016 ◽  
Vol 10 (1) ◽  
pp. 179-182 ◽  
Author(s):  
Camille Samson ◽  
Isaline Herrada ◽  
Florian Celli ◽  
Francois-Xavier Theillet ◽  
Sophie Zinn-Justin
Keyword(s):  
Nuclear Envelope ◽  
Resonance Assignment ◽  
Envelope Protein ◽  
Backbone Resonance Assignment ◽  
Backbone Resonance ◽  
Intrinsically Disordered ◽  
Intrinsically Disordered Region

scholarly journals Amino acid recognition for automatic resonance assignment of intrinsically disordered proteins

2016 ◽  
Vol 64 (3) ◽  
pp. 239-253 ◽  
Author(s):  
Alessandro Piai ◽  
Leonardo Gonnelli ◽  
Isabella C. Felli ◽  
Roberta Pierattelli ◽  
Krzysztof Kazimierczuk ◽  
...  
Keyword(s):  
Amino Acid ◽  
Resonance Assignment ◽  
Intrinsically Disordered Proteins ◽  
Disordered Proteins ◽  
Intrinsically Disordered ◽  
Amino Acid Recognition

Sequence Specificity Despite Intrinsic Disorder: How a Disease-Associated Val/Met Polymorphism Shifts Tertiary Interactions in a Long Disordered Protein

2019 ◽  
Author(s):  
Ruchi Lohia ◽  
Reza Salari ◽  
Grace Brannigan
Keyword(s):  
Secondary Structure ◽  
Electrostatic Interactions ◽  
Intrinsically Disordered Proteins ◽  
Disordered Proteins ◽  
Sequence Specificity ◽  
Intrinsically Disordered ◽  
Specific Effects ◽  
Heterogeneous Polymer ◽  
Non Local ◽  
Dynamics Simulations

<div>The role of electrostatic interactions and mutations that change charge states in intrinsically disordered proteins (IDPs) is well-established, but many disease-associated mutations in IDPs are charge-neutral. The Val66Met single nucleotide polymorphism (SNP) encodes a hydrophobic-to-hydrophobic mutation at the midpoint of the prodomain of precursor brain-derived neurotrophic factor (BDNF), one of the earliest SNPs to be associated with neuropsychiatric disorders, for which the underlying molecular mechanism is unknown. Here we report on over 250 μs of fully-atomistic, explicit solvent, temperature replica exchange molecular dynamics simulations of the 91 residue BDNF prodomain, for both the V66 and M66 sequence.</div><div>The simulations were able to correctly reproduce the location of both local and non-local secondary changes due to the Val66Met mutation when compared with NMR spectroscopy. We find that the local structure change is mediated via entropic and sequence specific effects. We show that the highly disordered prodomain can be meaningfully divided into domains based on sequence alone. Monte Carlo simulations of a self-excluding heterogeneous polymer, with monomers representing each domain, suggest the sequence would be effectively segmented by the long, highly disordered polyampholyte near the sequence midpoint. This is qualitatively consistent with observed interdomain contacts within the BDNF prodomain, although contacts between the two segments are enriched relative to the self-excluding polymer. The Val66Met mutation increases interactions across the boundary between the two segments, due in part to a specific Met-Met interaction with a Methionine in the other segment. This effect propagates to cause the non-local change in secondary structure around the second methionine, previously observed in NMR. The effect is not mediated simply via changes in inter-domain contacts but is also dependent on secondary structure formation around residue 66, indicating a mechanism for secondary structure coupling in disordered proteins. </div>

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