Interpretation of biomolecular NMR spin relaxation parametersThis paper is one of a selection of papers published in this special issue entitled “Canadian Society of Biochemistry, Molecular &amp; Cellular Biology 52nd Annual Meeting — Protein Folding: Principles and Diseases” and has undergone the Journal's usual peer review process.

Reddy, Tyler; Rainey, Jan K.

doi:10.1139/o09-152

Cited by 17 publications

(3 citation statements)

References 85 publications

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“…However, for SutA, the results of these analyses lend credence to the bioinformatics predictions and suggest that much of the protein outside a central α-helix is disordered. Residues 56-76 show the positive Cα and CO and negative Hα secondary chemical shifts associated with an α-helix structure (Wishart et al, 1991) and also show fast R 2 relaxation rates and positive ( 1 H-15 N) NOE, suggesting that they are not disordered (Reddy and Rainey, 2010). RDCs for the helix region are also positive, as has been observed for α-helical regions of a partially denatured protein (Mohana-Borges et al, 2004).…”

Section: Suta Consists Of a Conserved α Helix Flanked By Flexible Tailsmentioning

confidence: 67%

The dormancy‐specific regulator, SutA, is intrinsically disordered and modulates transcription initiation in Pseudomonas aeruginosa

Bergkessel

Babin

VanderVelde

et al. 2019

Molecular Microbiology

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Summary Though most bacteria in nature are nutritionally limited and grow slowly, our understanding of core processes like transcription comes largely from studies in model organisms doubling rapidly. We previously identified a small protein of unknown function, SutA, in a screen of proteins synthesized in Pseudomonas aeruginosa during dormancy. SutA binds RNA polymerase (RNAP), causing widespread changes in gene expression, including upregulation of the ribosomal RNA genes. Here, using biochemical and structural methods, we examine how SutA interacts with RNAP and the functional consequences of these interactions. We show that SutA comprises a central α‐helix with unstructured N‐ and C‐terminal tails, and binds to the β1 domain of RNAP. It activates transcription from the rrn promoter by both the housekeeping sigma factor holoenzyme (Eσ70) and the stress sigma factor holoenzyme (EσS) in vitro, but has a greater impact on EσS. In both cases, SutA appears to affect intermediates in the open complex formation and its N‐terminal tail is required for activation. The small magnitudes of in vitro effects are consistent with a role in maintaining activity required for homeostasis during dormancy. Our results add SutA to a growing list of transcription regulators that use their intrinsically disordered regions to remodel transcription complexes.

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Section: Suta Consists Of a Conserved α Helix Flanked By Flexible Tailsmentioning

confidence: 67%

The dormancy‐specific regulator, SutA, is intrinsically disordered and modulates transcription initiation in Pseudomonas aeruginosa

Bergkessel

Babin

VanderVelde

et al. 2019

Molecular Microbiology

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“…4.1 ns for human ubiquitin which is a 76 residue protein 10 and 8.57 ns for MUP-I which contains 157 amino acids 11 ; and conforms to the general rule of 0.5 ns overall correlation time per 1 kD of molecular weight. 12 …”

Section: Resultsmentioning

confidence: 99%

Increased Hydrophobicity and Decreased Backbone Flexibility Explain the Lower Solubility of a Cataract-Linked Mutant of γD-Crystallin

Banerjee

Puttamadappa

Pande

et al. 2011

Journal of Molecular Biology

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A number of point mutations in γD-crystallin are associated with human cataract. The Pro23Thr (P23T) mutation is perhaps the most common, geographically-widespread, and presents itself in a variety of phenotypes. It is therefore important to understand the molecular basis of lens opacity due to this mutation. In our earlier studies we noted that P23T shows retrograde and sharply lowered solubility, possibly due to the emergence of hydrophobic patches involved in protein aggregation. Binding of Bis-ANS dye, a commonly used probe of surfacehydrophobicity, competed with aggregation, suggesting that the residues involved in Bis-ANS binding are also involved in protein aggregation. Here, using NMR spectroscopy in conjunction with Bis-ANS binding, we identify three residues, Y16, D21 and Y50 in P23T, involved in binding the dye. Furthermore, using 15N NMR-relaxation experiments, we show that in the mutant protein, backbone fluctuations are restricted in picosecond to nanosecond and microsecond time-scales, relative to the wild type. Our present studies identify the residues involved in these two pivotal characteristics of the mutant protein, namely increased surface hydrophobicity and restricted mobility of the protein backbone, which can explain the nucleation and further propagation of protein aggregates. Thus we have now identified the residues in the P23T mutant that give rise to novel hydrophobic surfaces, as well as those regions of the protein backbone where fluctuations in different time-scales are restricted, providing a comprehensive understanding of how lens opacity could result from this mutation.

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“…The most frequently measured protein relaxation parameters are the longitudinal, R 1 , and transverse, R 2 , relaxation rates of backbone amide 15 N nuclei complemented with 15 N-{ 1 H} NOE s (Palmer 2004 ; Reddy and Rainey 2010 ). Nuclear magnetic relaxation measurements are long lasting, their data reduction is demanding, and interpretation of the results complex (Zhukov and Ejchart 1999 ; Pawley et al 2006 ; Jaremko et al 2015 ).…”

Section: Introductionmentioning

confidence: 99%

Fast evaluation of protein dynamics from deficient 15N relaxation data

Jaremko

Ejchart

et al. 2018

J Biomol NMR

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Simple and convenient method of protein dynamics evaluation from the insufficient experimental 15N relaxation data is presented basing on the ratios, products, and differences of longitudinal and transverse 15N relaxation rates obtained at a single magnetic field. Firstly, the proposed approach allows evaluating overall tumbling correlation time (nanosecond time scale). Next, local parameters of the model-free approach characterizing local mobility of backbone amide N–H vectors on two different time scales, S2 and Rex, can be elucidated. The generalized order parameter, S2, describes motions on the time scale faster than the overall tumbling correlation time (pico- to nanoseconds), while the chemical exchange term, Rex, identifies processes slower than the overall tumbling correlation time (micro- to milliseconds). Advantages and disadvantages of different methods of data handling are thoroughly discussed.Electronic supplementary materialThe online version of this article (10.1007/s10858-018-0176-3) contains supplementary material, which is available to authorized users.

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Cited by 17 publications

References 85 publications

The dormancy‐specific regulator, SutA, is intrinsically disordered and modulates transcription initiation in Pseudomonas aeruginosa

The dormancy‐specific regulator, SutA, is intrinsically disordered and modulates transcription initiation in Pseudomonas aeruginosa

Increased Hydrophobicity and Decreased Backbone Flexibility Explain the Lower Solubility of a Cataract-Linked Mutant of γD-Crystallin

Fast evaluation of protein dynamics from deficient 15N relaxation data

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