Accurate measurement of dipole/dipole transverse cross-correlated relaxation $$\varGamma _2$$ in methylenes and primary amines of uniformly $${}^{13}\text {C}/{}^{15}\text {N}$$-labeled proteins

Lesovoy, Dmitry M.; Dubinnyi, Maxim A.; Nolde, Svetlana B.; Bocharov, Eduard V.; Arseniev, Alexander S.

doi:10.1007/s10858-019-00252-6

Cited by 6 publications

(8 citation statements)

References 56 publications

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“…The residues from the disordered C -terminal fragments of Lypd6 and Lypd6b, which did not satisfactorily fit into any model of intramolecular mobility, are shown in red. Structural data for Lynx1, SLURP-2, WTX-P33A, and NTII were taken from previous publications [ 11 , 32 , 43 , 44 ]; other data are from the present work. PDB codes: WTX-P33A—2MJ0, SLURP-1—6ZZE/6ZZF, SLURP-2—2N99, Lynx1—2L03, Lynx2—6ZSS, Lypd6—6IB6, Lypd6B—6ZSO.…”

Section: Figurementioning

confidence: 99%

“…Structures of the SLURP-1, Lypd6, Lypd6b, and Lynx2 LU-domains were compared with the previously published structures of human neuromodulator Lynx1 [11], human epithelial protein SLURP-2 [32], Pro33Ala mutant of 'weak' toxin from Naja kaouthia venom (WTX-P33A) [43], and short α-neurotoxin II from Naja oxiana venom (NTII) [44]. 15 N relaxation data describing backbone dynamics are available for these proteins.…”

Section: Lynx1 Slurp-2 and Snake Toxinsmentioning

confidence: 99%

“…To investigate conformational plasticity of TFPs, we measured relaxation parameters of backbone 15 N nuclei for SLURP-1, Lypd6, Lypd6b, and Lynx2, and used the published data about Lynx1, SLURP-2, WTX-P33A, and NTII [32,43,44]. To provide an unified view on the protein dynamics, the relaxation measurements were carried out under identical experimental conditions ( 1 H spectrometer frequency 800 MHz and temperature 37 • C).…”

Section: Backbone Dynamics Of Tfps In Solutionmentioning

confidence: 99%

“…To estimate experimental uncertainty, the additional 2D plans with 34 and 136 ms CPMG sequence lengths were measured. The values of 15 N relaxation parameters for Lynx1, SLURP-2, WTX, and NTII were taken from the previous reports [11,32,43,44] and from the Biological Magnetic Resonance Data Bank (BMRB ID 19704 for NTII).…”

Section: J H N Hmentioning

confidence: 99%

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Structural Diversity and Dynamics of Human Three-Finger Proteins Acting on Nicotinic Acetylcholine Receptors

Paramonov

Kocharovskaya

Tsarev

et al. 2020

IJMS

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Ly-6/uPAR or three-finger proteins (TFPs) contain a disulfide-stabilized β-structural core and three protruding loops (fingers). In mammals, TFPs have been found in epithelium and the nervous, endocrine, reproductive, and immune systems. Here, using heteronuclear NMR, we determined the three-dimensional (3D) structure and backbone dynamics of the epithelial secreted protein SLURP-1 and soluble domains of GPI-anchored TFPs from the brain (Lynx2, Lypd6, Lypd6b) acting on nicotinic acetylcholine receptors (nAChRs). Results were compared with the data about human TFPs Lynx1 and SLURP-2 and snake α-neurotoxins WTX and NTII. Two different topologies of the β-structure were revealed: one large antiparallel β-sheet in Lypd6 and Lypd6b, and two β-sheets in other proteins. α-Helical segments were found in the loops I/III of Lynx2, Lypd6, and Lypd6b. Differences in the surface distribution of charged and hydrophobic groups indicated significant differences in a mode of TFPs/nAChR interactions. TFPs showed significant conformational plasticity: the loops were highly mobile at picosecond-nanosecond timescale, while the β-structural regions demonstrated microsecond-millisecond motions. SLURP-1 had the largest plasticity and characterized by the unordered loops II/III and cis-trans isomerization of the Tyr39-Pro40 bond. In conclusion, plasticity could be an important feature of TFPs adapting their structures for optimal interaction with the different conformational states of nAChRs.

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Section: Figurementioning

confidence: 99%

Section: Lynx1 Slurp-2 and Snake Toxinsmentioning

confidence: 99%

Section: Backbone Dynamics Of Tfps In Solutionmentioning

confidence: 99%

Section: J H N Hmentioning

confidence: 99%

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Structural Diversity and Dynamics of Human Three-Finger Proteins Acting on Nicotinic Acetylcholine Receptors

Paramonov

Kocharovskaya

Tsarev

et al. 2020

IJMS

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“…calculated based on the deviation of the triplet intensities from 1:2:1 using the equation below (Yang et al 1998;Zheng and Yang 2004;Yang 2011;Lesovoy et al 2019).…”

Section: Methodsmentioning

confidence: 99%

Proton TOCSY NMR relaxation rates quantitate protein side chain mobility in the Pin1 WW domain

Danmaliki

Hwang

2022

J Biomol NMR

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Protein side chain dynamics play a vital role in many biological processes, but differentiating mobile from rigid side chains remains a technical challenge in structural biology. Solution NMR spectroscopy is ideally suited for this but suffers from limited signal-to-noise, signal overlap, and a need for fractional 13C or 2H labeling. Here we introduce a simple strategy measuring initial 1H relaxation rates during a 1H TOCSY sequence like DIPSI-2, which can be appended to the beginning of any multi-dimensional NMR sequence that begins on 1H. The TOCSY RF field compels all 1H atoms to behave similarly under the influence of strong coupling and rotating frame cross-relaxation, so that differences in relaxation rates are due primarily to side chain mobility. We apply the scheme to a thermostable mutant Pin1 WW domain and demonstrate that the observed 1H relaxation rates correlate well with two independent NMR measures of side-chain dynamics, cross-correlated 13C relaxation rates in 13CβH2 methylene groups and maximum observable 3J couplings sensitive to the χ1 side chain dihedral angle (3JHα,Hβ, 3JN,Hβ, and 3JCO,Hβ). The most restricted side chains belong to Trp26 and Asn40, which are closely packed to constitute the folding center of the WW domain. None of the other conserved aromatic residues is as immobile as the first tryptophan side chain of the WW domain. The proposed 1H relaxation methodology should make it relatively easy to measure side chain dynamics on uniformly 15N- or 13C-labeled proteins, so long as chemical shift assignments are obtainable.

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Combined NMR and molecular dynamics conformational filter identifies unambiguously dynamic ensembles of Dengue protease NS2B/NS3pro

Agback,

Lesovoy,

Han

et al. 2023

Commun Biol

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The dengue protease NS2B/NS3pro has been reported to adopt either an ‘open’ or a ‘closed’ conformation. We have developed a conformational filter that combines NMR with MD simulations to identify conformational ensembles that dominate in solution. Experimental values derived from relaxation parameters for the backbone and methyl side chains were compared with the corresponding back-calculated relaxation parameters of different conformational ensembles obtained from free MD simulations. Our results demonstrate a high prevalence for the ‘closed’ conformational ensemble while the ‘open’ conformation is absent, indicating that the latter conformation is most probably due to crystal contacts. Conversely, conformational ensembles in which the positioning of the co-factor NS2B results in a ‘partially’ open conformation, previously described in both MD simulations and X-ray studies, were identified by our conformational filter. Altogether, we believe that our approach allows for unambiguous identification of true conformational ensembles, an essential step for reliable drug discovery.

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Accurate measurement of dipole/dipole transverse cross-correlated relaxation $$\varGamma _2$$ in methylenes and primary amines of uniformly $${}^{13}\text {C}/{}^{15}\text {N}$$-labeled proteins

Cited by 6 publications

References 56 publications

Structural Diversity and Dynamics of Human Three-Finger Proteins Acting on Nicotinic Acetylcholine Receptors

Structural Diversity and Dynamics of Human Three-Finger Proteins Acting on Nicotinic Acetylcholine Receptors

Proton TOCSY NMR relaxation rates quantitate protein side chain mobility in the Pin1 WW domain

Combined NMR and molecular dynamics conformational filter identifies unambiguously dynamic ensembles of Dengue protease NS2B/NS3pro

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