Pub Date : 2021-02-24DOI: 10.1007/s10858-021-00359-9
C. Ashley Barnes, Mary R. Starich, Nico Tjandra, Pushpa Mishra
Paramagnetic relaxation enhancements (PREs) are routinely used to provide long-range distance restraints for the determination of protein structures, to resolve protein dynamics, ligand–protein binding sites, and lowly populated species, using Nuclear Magnetic Resonance Spectroscopy (NMR). Here, we propose a simultaneous 1H-15?N, 1H-13C SESAME based pulse scheme for the rapid acquisition of 1HC/N-R2 relaxation rates for the determination of backbone and sidechain PREs of proteins. The 1HN-R2 rates from the traditional and our approach on Ubiquitin (UBQ) are well correlated (R2?=?0.99), revealing their potential to be used quantitatively. Comparison of the S57C UBQ calculated and experimental PREs provided backbone and side chain Q factors of 0.23 and 0.24, respectively, well-fitted to the UBQ NMR structure, showing that our approach can be used to acquire accurate PRE rates from the functionally important sites of proteins but in at least half the time as traditional methods.
{"title":"Simultaneous measurement of 1HC/N-R2′s for rapid acquisition of backbone and sidechain paramagnetic relaxation enhancements (PREs) in proteins","authors":"C. Ashley Barnes, Mary R. Starich, Nico Tjandra, Pushpa Mishra","doi":"10.1007/s10858-021-00359-9","DOIUrl":"https://doi.org/10.1007/s10858-021-00359-9","url":null,"abstract":"<p>Paramagnetic relaxation enhancements (PREs) are routinely used to provide long-range distance restraints for the determination of protein structures, to resolve protein dynamics, ligand–protein binding sites, and lowly populated species, using Nuclear Magnetic Resonance Spectroscopy (NMR). Here, we propose a simultaneous <sup>1</sup>H-<sup>15</sup>?N, <sup>1</sup>H-<sup>13</sup>C SESAME based pulse scheme for the rapid acquisition of <sup>1</sup>H<sup>C/N</sup>-R<sub>2</sub> relaxation rates for the determination of backbone and sidechain PREs of proteins. The <sup>1</sup>H<sup>N</sup>-R<sub>2</sub> rates from the traditional and our approach on Ubiquitin (UBQ) are well correlated (R<sup>2</sup>?=?0.99), revealing their potential to be used quantitatively. Comparison of the S57C UBQ calculated and experimental PREs provided backbone and side chain Q factors of 0.23 and 0.24, respectively, well-fitted to the UBQ NMR structure, showing that our approach can be used to acquire accurate PRE rates from the functionally important sites of proteins but in at least half the time as traditional methods.</p>","PeriodicalId":613,"journal":{"name":"Journal of Biomolecular NMR","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2021-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10858-021-00359-9","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4928532","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
In-cell NMR spectroscopy provides precious structural and functional information on biological macromolecules in their native cellular environment at atomic resolution. However, the intrinsic low sensitivity of NMR imposes a big limitation in the applicability of the methodology. In this respect, the recently developed commercial 1.2?GHz NMR spectrometer is expected to introduce significant benefits. However, cell samples may suffer from detrimental effects at ultrahigh fields, that must be carefully evaluated. Here we show the first in-cell NMR spectra recorded at 1.2?GHz on human cells, and we compare resolution and sensitivity against those obtained at 900 and 950?MHz. To evaluate the effects of different spin relaxation rates, SOFAST-HMQC and BEST-TROSY spectra were recorded on intracellular α-synuclein and carbonic anhydrase. Major improvements are observed at 1.2?GHz when analyzing unfolded proteins, such as α-synuclein, while the TROSY scheme improves the resolution for both globular and unfolded proteins.
{"title":"Protein in-cell NMR spectroscopy at 1.2 GHz","authors":"Enrico Luchinat, Letizia Barbieri, Matteo Cremonini, Lucia Banci","doi":"10.1007/s10858-021-00358-w","DOIUrl":"https://doi.org/10.1007/s10858-021-00358-w","url":null,"abstract":"<p>In-cell NMR spectroscopy provides precious structural and functional information on biological macromolecules in their native cellular environment at atomic resolution. However, the intrinsic low sensitivity of NMR imposes a big limitation in the applicability of the methodology. In this respect, the recently developed commercial 1.2?GHz NMR spectrometer is expected to introduce significant benefits. However, cell samples may suffer from detrimental effects at ultrahigh fields, that must be carefully evaluated. Here we show the first in-cell NMR spectra recorded at 1.2?GHz on human cells, and we compare resolution and sensitivity against those obtained at 900 and 950?MHz. To evaluate the effects of different spin relaxation rates, SOFAST-HMQC and BEST-TROSY spectra were recorded on intracellular α-synuclein and carbonic anhydrase. Major improvements are observed at 1.2?GHz when analyzing unfolded proteins, such as α-synuclein, while the TROSY scheme improves the resolution for both globular and unfolded proteins.</p>","PeriodicalId":613,"journal":{"name":"Journal of Biomolecular NMR","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2021-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10858-021-00358-w","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4493247","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-02-04DOI: 10.1007/s10858-021-00357-x
Mengli Cai, Ying Huang, John Lloyd, Robert Craigie, G. Marius Clore
A simple and cost-effective protocol is presented for expression of perdeuterated, Ile/Leu/Val 1H/13C methyl protonated proteins from 100?ml cultures in M9?++?/D2O medium induced at high (OD600?~?10) cell density in shaker flasks. This protocol, which is an extension of our previous protocols for expression of 2H/15N/13C and 1H/13C labeled proteins, yields comparable quantities of protein from 100?ml cell culture to those obtained using a conventional 1 L culture with M9/D2O medium, while using three-fold less α-ketoisovaleric (1,2,3,4-13C4; 3,4′,4′,4′-d4) and α-ketobutyric (13C4; 3,3-d2) acid precursors.
{"title":"A simple and cost-effective protocol for high-yield expression of deuterated and selectively isoleucine/leucine/valine methyl protonated proteins in Escherichia coli grown in shaker flasks","authors":"Mengli Cai, Ying Huang, John Lloyd, Robert Craigie, G. Marius Clore","doi":"10.1007/s10858-021-00357-x","DOIUrl":"https://doi.org/10.1007/s10858-021-00357-x","url":null,"abstract":"<p>A simple and cost-effective protocol is presented for expression of perdeuterated, Ile/Leu/Val <sup>1</sup>H/<sup>13</sup>C methyl protonated proteins from 100?ml cultures in M9?++?/D<sub>2</sub>O medium induced at high (OD<sub>600</sub>?~?10) cell density in shaker flasks. This protocol, which is an extension of our previous protocols for expression of <sup>2</sup>H/<sup>15</sup>N/<sup>13</sup>C and <sup>1</sup>H/<sup>13</sup>C labeled proteins, yields comparable quantities of protein from 100?ml cell culture to those obtained using a conventional 1 L culture with M9/D<sub>2</sub>O medium, while using three-fold less α-ketoisovaleric (1,2,3,4-<sup>13</sup>C<sub>4</sub>; 3,4′,4′,4′-d<sub>4</sub>) and α-ketobutyric (<sup>13</sup>C<sub>4</sub>; 3,3-d<sub>2</sub>) acid precursors.</p>","PeriodicalId":613,"journal":{"name":"Journal of Biomolecular NMR","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2021-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10858-021-00357-x","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4159519","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-01-27DOI: 10.1007/s10858-020-00354-6
Layara Akemi Abiko, Marco Rogowski, Antoine Gautier, Gebhard Schertler, Stephan Grzesiek
G protein-coupled receptors (GPCRs) are transmembrane signal transducers which regulate many key physiological process. Since their discovery, their analysis has been limited by difficulties in obtaining sufficient amounts of the receptors in high-quality, functional form from heterologous expression hosts. Albeit highly attractive because of its simplicity and the ease of isotope labeling for NMR studies, heterologous expression of functional GPCRs in E. coli has proven particularly challenging due to the absence of the more evolved protein expression and folding machinery of higher eukaryotic hosts. Here we first give an overview on the previous strategies for GPCR E. coli expression and then describe the development of an optimized robust protocol for the E. coli expression and purification of two mutants of the turkey β1-adrenergic receptor (β1AR) uniformly or selectively labeled in 15N or 2H,15N. These mutants had been previously optimized for thermal stability using insect cell expression and used successfully in crystallographic and NMR studies. The same sequences were then used for E. coli expression. Optimization of E. coli expression was achieved by a quantitative analysis of losses of receptor material at each step of the solubilization and purification procedure. Final yields are 0.2–0.3?mg receptor per liter culture. Whereas both expressed mutants are well folded and competent for orthosteric ligand binding, the less stable YY-β1AR mutant also comprises the two native tyrosines Y5.58 and Y7.53, which enable G protein binding. High-quality 1H-15N TROSY spectra were obtained for E. coli-expressed YY-β1AR in three different functional states (antagonist, agonist, and agonist?+?G protein-mimicking nanobody-bound), which are identical to spectra obtained of the same forms of the receptor expressed in insect cells. NdeI and AgeI restriction sites introduced into the expression plasmid allow for the easy replacement of the receptor gene by other GPCR genes of interest, and the provided quantitative workflow analysis may guide the respective adaptation of the purification protocol.
{"title":"Efficient production of a functional G protein-coupled receptor in E. coli for structural studies","authors":"Layara Akemi Abiko, Marco Rogowski, Antoine Gautier, Gebhard Schertler, Stephan Grzesiek","doi":"10.1007/s10858-020-00354-6","DOIUrl":"https://doi.org/10.1007/s10858-020-00354-6","url":null,"abstract":"<p>G protein-coupled receptors (GPCRs) are transmembrane signal transducers which regulate many key physiological process. Since their discovery, their analysis has been limited by difficulties in obtaining sufficient amounts of the receptors in high-quality, functional form from heterologous expression hosts. Albeit highly attractive because of its simplicity and the ease of isotope labeling for NMR studies, heterologous expression of functional GPCRs in <i>E. coli</i> has proven particularly challenging due to the absence of the more evolved protein expression and folding machinery of higher eukaryotic hosts. Here we first give an overview on the previous strategies for GPCR <i>E. coli</i> expression and then describe the development of an optimized robust protocol for the <i>E. coli</i> expression and purification of two mutants of the turkey β<sub>1</sub>-adrenergic receptor (β<sub>1</sub>AR) uniformly or selectively labeled in <sup>15</sup>N or <sup>2</sup>H,<sup>15</sup>N. These mutants had been previously optimized for thermal stability using insect cell expression and used successfully in crystallographic and NMR studies. The same sequences were then used for <i>E. coli</i> expression. Optimization of <i>E. coli</i> expression was achieved by a quantitative analysis of losses of receptor material at each step of the solubilization and purification procedure. Final yields are 0.2–0.3?mg receptor per liter culture. Whereas both expressed mutants are well folded and competent for orthosteric ligand binding, the less stable YY-β<sub>1</sub>AR mutant also comprises the two native tyrosines Y<sup>5.58</sup> and Y<sup>7.53</sup>, which enable G protein binding. High-quality <sup>1</sup>H-<sup>15</sup>N TROSY spectra were obtained for <i>E. coli</i>-expressed YY-β<sub>1</sub>AR in three different functional states (antagonist, agonist, and agonist?+?G protein-mimicking nanobody-bound), which are identical to spectra obtained of the same forms of the receptor expressed in insect cells. NdeI and AgeI restriction sites introduced into the expression plasmid allow for the easy replacement of the receptor gene by other GPCR genes of interest, and the provided quantitative workflow analysis may guide the respective adaptation of the purification protocol.</p>","PeriodicalId":613,"journal":{"name":"Journal of Biomolecular NMR","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2021-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10858-020-00354-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"5044170","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-01-25DOI: 10.1007/s10858-020-00355-5
Lorna J. Smith, Wilfred F. van Gunsteren, Bartosz Stankiewicz, Niels Hansen
Values of 3J-couplings as obtained from NMR experiments on proteins cannot easily be used to determine protein structure due to the difficulty of accounting for the high sensitivity of intermediate 3J-coupling values (4–8?Hz) to the averaging period that must cover the conformational variability of the torsional angle related to the 3J-coupling, and due to the difficulty of handling the multiple-valued character of the inverse Karplus relation between torsional angle and 3J-coupling. Both problems can be solved by using 3J-coupling time-averaging local-elevation restraining MD simulation. Application to the protein hen egg white lysozyme using 213 backbone and side-chain 3J-coupling restraints shows that a conformational ensemble compatible with the experimental data can be obtained using this technique, and that accounting for averaging and the ability of the algorithm to escape from local minima for the torsional angle induced by the Karplus relation, are essential for a comprehensive use of 3J-coupling data in protein structure determination.
{"title":"On the use of 3J-coupling NMR data to derive structural information on proteins","authors":"Lorna J. Smith, Wilfred F. van Gunsteren, Bartosz Stankiewicz, Niels Hansen","doi":"10.1007/s10858-020-00355-5","DOIUrl":"https://doi.org/10.1007/s10858-020-00355-5","url":null,"abstract":"<p>Values of <sup>3</sup><i>J</i>-couplings as obtained from NMR experiments on proteins cannot easily be used to determine protein structure due to the difficulty of accounting for the high sensitivity of intermediate <sup>3</sup><i>J</i>-coupling values (4–8?Hz) to the averaging period that must cover the conformational variability of the torsional angle related to the <sup>3</sup><i>J</i>-coupling, and due to the difficulty of handling the multiple-valued character of the inverse Karplus relation between torsional angle and <sup>3</sup><i>J</i>-coupling. Both problems can be solved by using <sup>3</sup><i>J</i>-coupling time-averaging local-elevation restraining MD simulation. Application to the protein hen egg white lysozyme using 213 backbone and side-chain <sup>3</sup><i>J</i>-coupling restraints shows that a conformational ensemble compatible with the experimental data can be obtained using this technique, and that accounting for averaging and the ability of the algorithm to escape from local minima for the torsional angle induced by the Karplus relation, are essential for a comprehensive use of <sup>3</sup><i>J</i>-coupling data in protein structure determination.</p>","PeriodicalId":613,"journal":{"name":"Journal of Biomolecular NMR","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2021-01-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10858-020-00355-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"5338680","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-01-21DOI: 10.1007/s10858-020-00356-4
Arthur Hinterholzer, Vesna Stanojlovic, Christof Regl, Christian G. Huber, Chiara Cabrele, Mario Schubert
The monitoring of non-enzymatic post-translational modifications (PTMs) in therapeutic proteins is important to ensure drug safety and efficacy. Together with methionine and asparagine, aspartic acid (Asp) is very sensitive to spontaneous alterations. In particular, Asp residues can undergo isomerization and peptide-bond hydrolysis, especially when embedded in sequence motifs that are prone to succinimide formation or when followed by proline (Pro). As Asp and isoAsp have the same mass, and the Asp-Pro peptide-bond cleavage may lead to an unspecific mass difference of?+?18?Da under native conditions or in the case of disulfide-bridged cleavage products, it is challenging to directly detect and characterize such modifications by mass spectrometry (MS). Here we propose a 2D?NMR-based approach for the unambiguous identification of isoAsp and the products of Asp-Pro peptide-bond cleavage, namely N-terminal Pro and C-terminal Asp, and demonstrate its applicability to proteins including a therapeutic monoclonal antibody (mAb). To choose the ideal pH conditions under which the NMR signals of isoAsp and C-terminal Asp are distinct from other random coil signals, we determined the pKa values of isoAsp and C-terminal Asp in short peptides. The characteristic 1H-13C chemical shift correlations of isoAsp, N-terminal Pro and C-terminal Asp under standardized conditions were used to identify these PTMs in lysozyme and in the therapeutic mAb rituximab (MabThera) upon prolonged storage under acidic conditions (pH 4–5) and 40?°C. The results show that the application of our 2D?NMR-based protocol is straightforward and allows detecting chemical changes of proteins that may be otherwise unnoticed with other analytical methods.
{"title":"Detecting aspartate isomerization and backbone cleavage after aspartate in intact proteins by NMR spectroscopy","authors":"Arthur Hinterholzer, Vesna Stanojlovic, Christof Regl, Christian G. Huber, Chiara Cabrele, Mario Schubert","doi":"10.1007/s10858-020-00356-4","DOIUrl":"https://doi.org/10.1007/s10858-020-00356-4","url":null,"abstract":"<p>The monitoring of non-enzymatic post-translational modifications (PTMs) in therapeutic proteins is important to ensure drug safety and efficacy. Together with methionine and asparagine, aspartic acid (Asp) is very sensitive to spontaneous alterations. In particular, Asp residues can undergo isomerization and peptide-bond hydrolysis, especially when embedded in sequence motifs that are prone to succinimide formation or when followed by proline (Pro). As Asp and isoAsp have the same mass, and the Asp-Pro peptide-bond cleavage may lead to an unspecific mass difference of?+?18?Da under native conditions or in the case of disulfide-bridged cleavage products, it is challenging to directly detect and characterize such modifications by mass spectrometry (MS). Here we propose a 2D?NMR-based approach for the unambiguous identification of isoAsp and the products of Asp-Pro peptide-bond cleavage, namely N-terminal Pro and C-terminal Asp, and demonstrate its applicability to proteins including a therapeutic monoclonal antibody (mAb). To choose the ideal pH conditions under which the NMR signals of isoAsp and C-terminal Asp are distinct from other random coil signals, we determined the pK<sub>a</sub> values of isoAsp and C-terminal Asp in short peptides. The characteristic <sup>1</sup>H-<sup>13</sup>C chemical shift correlations of isoAsp, N-terminal Pro and C-terminal Asp under standardized conditions were used to identify these PTMs in lysozyme and in the therapeutic mAb rituximab (MabThera) upon prolonged storage under acidic conditions (pH 4–5) and 40?°C. The results show that the application of our 2D?NMR-based protocol is straightforward and allows detecting chemical changes of proteins that may be otherwise unnoticed with other analytical methods.</p>","PeriodicalId":613,"journal":{"name":"Journal of Biomolecular NMR","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2021-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10858-020-00356-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4823097","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2020-11-25DOI: 10.1007/s10858-020-00352-8
Jan H. Overbeck, Werner Kremer, Remco Sprangers
{"title":"Correction to: A suite of 19F based relaxation dispersion experiments to assess biomolecular motions","authors":"Jan H. Overbeck, Werner Kremer, Remco Sprangers","doi":"10.1007/s10858-020-00352-8","DOIUrl":"https://doi.org/10.1007/s10858-020-00352-8","url":null,"abstract":"","PeriodicalId":613,"journal":{"name":"Journal of Biomolecular NMR","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2020-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10858-020-00352-8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"5370578","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2020-11-13DOI: 10.1007/s10858-020-00351-9
Raymond S. Norton, Wolfgang Jahnke
{"title":"Correction to: NMR in pharmaceutical discovery and development","authors":"Raymond S. Norton, Wolfgang Jahnke","doi":"10.1007/s10858-020-00351-9","DOIUrl":"https://doi.org/10.1007/s10858-020-00351-9","url":null,"abstract":"","PeriodicalId":613,"journal":{"name":"Journal of Biomolecular NMR","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2020-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10858-020-00351-9","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4551653","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2020-11-02DOI: 10.1007/s10858-020-00353-7
Sebastian Hiller
Advanced NMR methods combined with biophysical techniques have recently provided unprecedented insight into structure and dynamics of molecular chaperones and their interaction with client proteins. These studies showed that several molecular chaperones are able to dissolve aggregation-prone polypeptides in aqueous solution. Furthermore, chaperone-bound clients often feature fluid-like backbone dynamics and chaperones have a denaturing effect on clients. Interestingly, these effects that chaperones have on client proteins resemble the effects of known chaotropic substances. Following this analogy, chaotropicity could be a fruitful concept to describe, quantify and rationalize molecular chaperone function. In addition, the observations raise the possibility that at least some molecular chaperones might share functional similarities with chaotropes. We discuss these concepts and outline future research in this direction.
{"title":"Molecular chaperones and their denaturing effect on client proteins","authors":"Sebastian Hiller","doi":"10.1007/s10858-020-00353-7","DOIUrl":"https://doi.org/10.1007/s10858-020-00353-7","url":null,"abstract":"<p>Advanced NMR methods combined with biophysical techniques have recently provided unprecedented insight into structure and dynamics of molecular chaperones and their interaction with client proteins. These studies showed that several molecular chaperones are able to dissolve aggregation-prone polypeptides in aqueous solution. Furthermore, chaperone-bound clients often feature fluid-like backbone dynamics and chaperones have a denaturing effect on clients. Interestingly, these effects that chaperones have on client proteins resemble the effects of known chaotropic substances. Following this analogy, chaotropicity could be a fruitful concept to describe, quantify and rationalize molecular chaperone function. In addition, the observations raise the possibility that at least some molecular chaperones might share functional similarities with chaotropes. We discuss these concepts and outline future research in this direction.</p>","PeriodicalId":613,"journal":{"name":"Journal of Biomolecular NMR","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2020-11-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10858-020-00353-7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4100820","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2020-10-28DOI: 10.1007/s10858-020-00347-5
Mikael Karjalainen, Helena Tossavainen, Maarit Hellman, Perttu Permi
Unidirectional coherence transfer is highly efficient in intrinsically disordered proteins (IDPs). Their elevated ps-ns timescale dynamics ensures long transverse (T2) relaxation times allowing sophisticated coherence transfer pathway selection in comparison to folded proteins. 1Hα-detection ensures non-susceptibility to chemical exchange with the solvent and enables chemical shift assignment of consecutive proline residues, typically abundant in IDPs. However, many IDPs undergo a disorder-to-order transition upon interaction with their target protein, which leads to the loss of the favorable relaxation properties. Long coherence transfer routes now result in prohibitively large decrease in sensitivity. We introduce a novel 4D 1Hα-detected experiment HACANCOi, together with its 3D implementation, which warrant high sensitivity for the assignment of proline-rich regions in IDPs in complex with a globular protein. The experiment correlates 1Hαi, 13Cαi, 15Ni and (^{13} C^{prime}_{i}) spins by transferring the magnetization concomitantly from 13Cαi to 15Ni and (^{13} C^{prime}_{i}). The B1 domain of protein G (GB1), and the enteropathogenic E.coli EspF in complex with human SNX9 SH3, serve as model systems to demonstrate the attainable sensitivity and successful sequential assignment.
{"title":"HACANCOi: a new Hα-detected experiment for backbone resonance assignment of intrinsically disordered proteins","authors":"Mikael Karjalainen, Helena Tossavainen, Maarit Hellman, Perttu Permi","doi":"10.1007/s10858-020-00347-5","DOIUrl":"https://doi.org/10.1007/s10858-020-00347-5","url":null,"abstract":"<p>Unidirectional coherence transfer is highly efficient in intrinsically disordered proteins (IDPs). Their elevated ps-ns timescale dynamics ensures long transverse (T<sub>2</sub>) relaxation times allowing sophisticated coherence transfer pathway selection in comparison to folded proteins. <sup>1</sup>H<sup>α</sup>-detection ensures non-susceptibility to chemical exchange with the solvent and enables chemical shift assignment of consecutive proline residues, typically abundant in IDPs. However, many IDPs undergo a disorder-to-order transition upon interaction with their target protein, which leads to the loss of the favorable relaxation properties. Long coherence transfer routes now result in prohibitively large decrease in sensitivity. We introduce a novel 4D <sup>1</sup>H<sup>α</sup>-detected experiment HACANCOi, together with its 3D implementation, which warrant high sensitivity for the assignment of proline-rich regions in IDPs in complex with a globular protein. The experiment correlates <sup>1</sup>H<sup>α</sup><sub>i</sub>, <sup>13</sup>C<sup>α</sup><sub>i</sub>, <sup>15</sup>N<sub>i</sub> and <span>(^{13} C^{prime}_{i})</span> spins by transferring the magnetization concomitantly from <sup>13</sup>C<sup>α</sup><sub>i</sub> to <sup>15</sup>N<sub>i</sub> and <span>(^{13} C^{prime}_{i})</span>. The B1 domain of protein G (GB1), and the enteropathogenic <i>E.</i> <i>coli</i> EspF in complex with human SNX9 SH3, serve as model systems to demonstrate the attainable sensitivity and successful sequential assignment.</p>","PeriodicalId":613,"journal":{"name":"Journal of Biomolecular NMR","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2020-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10858-020-00347-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"5102118","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}