Pauline Defant, Christof Regl, Christian G. Huber, Mario Schubert
{"title":"The NMR signature of maltose-based glycation in full-length proteins","authors":"Pauline Defant, Christof Regl, Christian G. Huber, Mario Schubert","doi":"10.1007/s10858-023-00432-5","DOIUrl":"10.1007/s10858-023-00432-5","url":null,"abstract":"<div><p>Reducing sugars can spontaneously react with free amines in protein side chains leading to posttranslational modifications (PTMs) called glycation. In contrast to glycosylation, glycation is a non-enzymatic modification with consequences on the overall charge, solubility, aggregation susceptibility and functionality of a protein. Glycation is a critical quality attribute of therapeutic monoclonal antibodies. In addition to glucose, also disaccharides like maltose can form glycation products. We present here a detailed NMR analysis of the Amadori product formed between proteins and maltose. For better comparison, data collection was done under denaturing conditions using 7 M urea-d<sub>4</sub> in D<sub>2</sub>O. The here presented correlation patterns serve as a signature and can be used to identify maltose-based glycation in any protein that can be denatured. In addition to the model protein BSA, which can be readily glycated, we present data of the biotherapeutic abatacept containing maltose in its formulation buffer. With this contribution, we demonstrate that NMR spectroscopy is an independent method for detecting maltose-based glycation, that is suited for cross-validation with other methods.</p></div>","PeriodicalId":613,"journal":{"name":"Journal of Biomolecular NMR","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2023-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10981599/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138796146","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}
Sungsool Wi, Conggang Li, Karen Pham, Woonghee Lee, Lucio Frydman
{"title":"Short and long range 2D 15N–15N NMR correlations among peptide groups by novel solid state dipolar mixing schemes","authors":"Sungsool Wi, Conggang Li, Karen Pham, Woonghee Lee, Lucio Frydman","doi":"10.1007/s10858-023-00429-0","DOIUrl":"10.1007/s10858-023-00429-0","url":null,"abstract":"<div><p>A recently developed homonuclear dipolar recoupling scheme, Adiabatic Linearly FREquency Swept reCOupling (AL FRESCO), was applied to record two-dimensional (2D) <sup>15</sup>N–<sup>15</sup>N correlations on uniformly <sup>15</sup>N-labeled GB1 powders. A major feature exploited in these <sup>15</sup>N–<sup>15</sup>N correlations was AL FRESCO’s remarkably low RF power demands, which enabled seconds-long mixing schemes when establishing direct correlations. These <sup>15</sup>N–<sup>15</sup>N mixing schemes proved efficient regardless of the magic-angle spinning (MAS) rate and, being nearly free from dipolar truncation effects, they enabled the detection of long-range, weak dipolar couplings, even in the presence of strong short-range dipolar couplings. This led to a connectivity information that was significantly better than that obtained with spontaneously proton-driven, <sup>15</sup>N spin-diffusion experiments. An indirect approach producing long-range <sup>15</sup>N–<sup>15</sup>N correlations was also tested, relying on short (ms-long) <sup>1</sup>H<sup>N</sup>–<sup>1</sup>H<sup>N</sup> mixings schemes while applying AL FRESCO chirped pulses along the <sup>15</sup>N channel. These indirect mixing schemes produced numerous long-distance N<sub>i</sub>–N<sub>i±n</sub> (n = 2 − 5) correlations, that might be useful for characterizing three-dimensional arrangements in proteins. Once again, these AL FRESCO mediated experiments proved more informative than variants based on spin-diffusion-based <sup>1</sup>H<sup>N</sup>–<sup>1</sup>H<sup>N</sup> counterparts.</p></div>","PeriodicalId":613,"journal":{"name":"Journal of Biomolecular NMR","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2023-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138691562","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}
Francisco Mendoza-Hoffmann, Canyong Guo, Yanzhuo Song, Dandan Feng, Lingyun Yang, Kurt Wüthrich
{"title":"19F-NMR studies of the impact of different detergents and nanodiscs on the A2A adenosine receptor","authors":"Francisco Mendoza-Hoffmann, Canyong Guo, Yanzhuo Song, Dandan Feng, Lingyun Yang, Kurt Wüthrich","doi":"10.1007/s10858-023-00430-7","DOIUrl":"10.1007/s10858-023-00430-7","url":null,"abstract":"<div><p>For the A<sub>2A</sub> adenosine receptor (A<sub>2A</sub>AR), a class A G-protein-coupled receptor (GPCR), reconstituted in <i>n</i>-dodecyl-<i>β</i>-D-maltoside (DDM)/cholesteryl hemisuccinate (CHS) mixed micelles, previous <sup>19</sup>F-NMR studies revealed the presence of multiple simultaneously populated conformational states. Here, we study the influence of a different detergent, lauryl maltose neopentyl glycol (LMNG) in mixed micelles with CHS, and of lipid bilayer nanodiscs on these conformational equilibria. The populations of locally different substates are pronouncedly different in DDM/CHS and LMNG/CHS micelles, whereas the A<sub>2A</sub>AR conformational manifold in LMNG/CHS micelles is closely similar to that in the lipid bilayer nanodiscs. Considering that nanodiscs represent a closer match of the natural lipid bilayer membrane, these observations support that LMNG/CHS micelles are a good choice for reconstitution trials of class A GPCRs for NMR studies in solution.</p></div>","PeriodicalId":613,"journal":{"name":"Journal of Biomolecular NMR","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2023-12-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138585223","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}
Alexander R. Davis, Elijah T. Roberts, I. Jonathan Amster, Adam W. Barb
{"title":"Uniform [13C,15N]-labeled and glycosylated IgG1 Fc expressed in Saccharomyces cerevisiae","authors":"Alexander R. Davis, Elijah T. Roberts, I. Jonathan Amster, Adam W. Barb","doi":"10.1007/s10858-023-00428-1","DOIUrl":"10.1007/s10858-023-00428-1","url":null,"abstract":"<div><p>Despite the prevalence and importance of glycoproteins in human biology, methods for isotope labeling suffer significant limitations. Common prokaryotic platforms do not produce mammalian post-translation modifications that are essential to the function of many human glycoproteins, including immunoglobulin G1 (IgG1). Mammalian expression systems require complex media and thus introduce significant costs to achieve uniform labeling. Expression with Pichia is available, though expertise and equipment requirements surpass <i>E. coli</i> culture. We developed a system utilizing <i>Saccharomyces cerevisiae</i>, [<sup>13</sup>C]-glucose, and [<sup>15</sup>N]-ammonium chloride with complexity comparable to <i>E. coli</i>. Here we report two vectors for expressing the crystallizable fragment (Fc) of IgG1 for secretion into the culture medium, utilizing the ADH2 or DDI2 promoters. We also report a strategy to optimize the expression yield using orthogonal Taguchi arrays. Lastly, we developed two different media formulations, a standard medium which provides 86–92% <sup>15</sup>N and 30% <sup>13</sup>C incorporation into the polypeptide, or a rich medium which provides 98% <sup>15</sup>N and 95% <sup>13</sup>C incorporation as determined by mass spectrometry. This advance represents an expression and optimization strategy accessible to experimenters with the capability to grow and produce proteins for NMR-based experiments using <i>E. coli</i>.</p></div>","PeriodicalId":613,"journal":{"name":"Journal of Biomolecular NMR","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2023-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138290066","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}
Sina Kazemi, Anna Lopata, Andreas Kniss, Lukas Pluska, Peter Güntert, Thomas Sommer, Thomas F. Prisner, Alberto Collauto, Volker Dötsch
{"title":"Efficient determination of the accessible conformation space of multi-domain complexes based on EPR PELDOR data","authors":"Sina Kazemi, Anna Lopata, Andreas Kniss, Lukas Pluska, Peter Güntert, Thomas Sommer, Thomas F. Prisner, Alberto Collauto, Volker Dötsch","doi":"10.1007/s10858-023-00426-3","DOIUrl":"10.1007/s10858-023-00426-3","url":null,"abstract":"<div><p>Many proteins can adopt multiple conformations which are important for their function. This is also true for proteins and domains that are covalently linked to each other. One important example is ubiquitin, which can form chains of different conformations depending on which of its lysine side chains is used to form an isopeptide bond with the C-terminus of another ubiquitin molecule. Similarly, ubiquitin gets covalently attached to active-site residues of E2 ubiquitin-conjugating enzymes. Due to weak interactions between ubiquitin and its interaction partners, these covalent complexes adopt multiple conformations. Understanding the function of these complexes requires the characterization of the entire accessible conformation space and its modulation by interaction partners. Long-range (1.8–10 nm) distance restraints obtained by EPR spectroscopy in the form of probability distributions are ideally suited for this task as not only the mean distance but also information about the conformation dynamics is encoded in the experimental data. Here we describe a computational method that we have developed based on well-established structure determination software using NMR restraints to calculate the accessible conformation space using PELDOR/DEER data.</p></div>","PeriodicalId":613,"journal":{"name":"Journal of Biomolecular NMR","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2023-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10687113/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"107590024","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}
{"title":"5D solid-state NMR spectroscopy for facilitated resonance assignment","authors":"Alexander Klein, Suresh K. Vasa, Rasmus Linser","doi":"10.1007/s10858-023-00424-5","DOIUrl":"10.1007/s10858-023-00424-5","url":null,"abstract":"<div><p><sup>1</sup>H-detected solid-state NMR spectroscopy has been becoming increasingly popular for the characterization of protein structure, dynamics, and function. Recently, we showed that higher-dimensionality solid-state NMR spectroscopy can aid resonance assignments in large micro-crystalline protein targets to combat ambiguity (Klein et al., Proc. Natl. Acad. Sci. U.S.A. 2022). However, assignments represent both, a time-limiting factor and one of the major practical disadvantages within solid-state NMR studies compared to other structural-biology techniques from a very general perspective. Here, we show that 5D solid-state NMR spectroscopy is not only justified for high-molecular-weight targets but will also be a realistic and practicable method to streamline resonance assignment in small to medium-sized protein targets, which such methodology might not have been expected to be of advantage for. Using a combination of non-uniform sampling and the signal separating algorithm for spectral reconstruction on a deuterated and proton back-exchanged micro-crystalline protein at fast magic-angle spinning, direct amide-to-amide correlations in five dimensions are obtained with competitive sensitivity compatible with common hardware and measurement time commitments. The self-sufficient backbone walks enable efficient assignment with very high confidence and can be combined with higher-dimensionality sidechain-to-backbone correlations from protonated preparations into minimal sets of experiments to be acquired for simultaneous backbone and sidechain assignment. The strategies present themselves as potent alternatives for efficient assignment compared to the traditional assignment approaches in 3D, avoiding user misassignments derived from ambiguity or loss of overview and facilitating automation. This will ease future access to NMR-based characterization for the typical solid-state NMR targets at fast MAS.</p></div>","PeriodicalId":613,"journal":{"name":"Journal of Biomolecular NMR","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2023-11-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10687145/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71520147","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}
Leonardo Querci, Deborah Grifagni, Inês B. Trindade, José Malanho Silva, Ricardo O. Louro, Francesca Cantini, Mario Piccioli
{"title":"Paramagnetic NMR to study iron sulfur proteins: 13C detected experiments illuminate the vicinity of the metal center","authors":"Leonardo Querci, Deborah Grifagni, Inês B. Trindade, José Malanho Silva, Ricardo O. Louro, Francesca Cantini, Mario Piccioli","doi":"10.1007/s10858-023-00425-4","DOIUrl":"10.1007/s10858-023-00425-4","url":null,"abstract":"<div><p>The robustness of NMR coherence transfer in proximity of a paramagnetic center depends on the relaxation properties of the nuclei involved. In the case of Iron-Sulfur Proteins, different pulse schemes or different parameter sets often provide complementary results. Tailored versions of HCACO and CACO experiments significantly increase the number of observed C<sup>α</sup>/C’ connectivities in highly paramagnetic systems, by recovering many resonances that were lost due to paramagnetic relaxation. Optimized <sup>13</sup>C direct detected experiments can significantly extend the available assignments, improving the overall knowledge of these systems. The different relaxation properties of C<sup>α</sup> and C’ nuclei are exploited in CACO vs COCA experiments and the complementarity of the two experiments is used to obtain structural information. The two [Fe<sub>2</sub>S<sub>2</sub>]<sup>+</sup> clusters containing NEET protein CISD3 and the one [Fe<sub>4</sub>S<sub>4</sub>]<sup>2+</sup> cluster containing HiPIP protein PioC have been taken as model systems. We show that tailored experiments contribute to decrease the blind sphere around the cluster, to extend resonance assignment of cluster bound cysteine residues and to retrieve details on the topology of the iron-bound ligand residues.</p></div>","PeriodicalId":613,"journal":{"name":"Journal of Biomolecular NMR","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2023-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10687126/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49673020","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}
Theresa Höfurthner, Giorgia Toscano, Georg Kontaxis, Andreas Beier, Moriz Mayer, Leonhard Geist, Darryl B. McConnell, Harald Weinstabl, Roman Lichtenecker, Robert Konrat
{"title":"Synthesis of a 13C-methylene-labeled isoleucine precursor as a useful tool for studying protein side-chain interactions and dynamics","authors":"Theresa Höfurthner, Giorgia Toscano, Georg Kontaxis, Andreas Beier, Moriz Mayer, Leonhard Geist, Darryl B. McConnell, Harald Weinstabl, Roman Lichtenecker, Robert Konrat","doi":"10.1007/s10858-023-00427-2","DOIUrl":"10.1007/s10858-023-00427-2","url":null,"abstract":"<div><p>In this study, we present the synthesis and incorporation of a metabolic isoleucine precursor compound for selective methylene labeling. The utility of this novel α-ketoacid isotopologue is shown by incorporation into the protein Brd4-BD1, which regulates gene expression by binding to acetylated histones. High quality single quantum <sup>13</sup>C−<sup>1</sup> H-HSQC were obtained, as well as triple quantum HTQC spectra, which are superior in terms of significantly increased <sup>13</sup>C-T<sub>2</sub> times. Additionally, large chemical shift perturbations upon ligand binding were observed. Our study thus proves the great sensitivity of this precursor as a reporter for side-chain dynamic studies and for investigations of CH-π interactions in protein-ligand complexes.</p></div>","PeriodicalId":613,"journal":{"name":"Journal of Biomolecular NMR","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2023-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10981609/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41187718","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}
Andrea Estefania Lopez Giraldo, Zowie Werner, Mehdi Rahimi, Woonghee Lee
{"title":"Breaking boundaries: TINTO in POKY for computer vision-based NMR walking strategies","authors":"Andrea Estefania Lopez Giraldo, Zowie Werner, Mehdi Rahimi, Woonghee Lee","doi":"10.1007/s10858-023-00423-6","DOIUrl":"10.1007/s10858-023-00423-6","url":null,"abstract":"<div><p>Nuclear magnetic resonance is a crucial technique for studying biological complexes, as it provides precise structural and dynamic information at the atomic level. However, the process of assigning resonances can be time-consuming and challenging, particularly in cases where peaks overlap, or the data quality is poor. In this paper, we present TINTO (Two and three-dimensional Imaging for NMR sTrip Operation via CV/ML), an advanced semiautomatic toolset for NMR resonance assignment. TINTO comprises two separate tools, each tailored for either two-dimensional or three-dimensional imaging. The toolset utilizes a computer-vision approach and a machine learning approach, specifically structural similarity index and principal components analysis, to perform visual similarity searches of resonances and quickly locate similar strips, and in that way overcome the challenges associated with peak overlap without requiring peak picking. Our tool offers a user-friendly interface and has the potential to enhance the efficiency and accuracy of NMR resonance assignment, particularly in complex cases. This advancement holds promising implications for furthering our understanding of biological systems at the molecular level. TINTO is pre-installed in the POKY suite, which is available at https://poky.clas.ucdenver.edu.</p></div>","PeriodicalId":613,"journal":{"name":"Journal of Biomolecular NMR","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2023-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41113412","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}
Matej Dzurov, Šárka Pospíšilová, Michaela Krafčíková, Lukáš Trantírek, Lucy Vojtová, Jan Ryneš
{"title":"A thermosensitive gel matrix for bioreactor-assisted in-cell NMR of nucleic acids and proteins","authors":"Matej Dzurov, Šárka Pospíšilová, Michaela Krafčíková, Lukáš Trantírek, Lucy Vojtová, Jan Ryneš","doi":"10.1007/s10858-023-00422-7","DOIUrl":"10.1007/s10858-023-00422-7","url":null,"abstract":"<div><p>Introducing the flow through the bioreactor has revolutionized in-cell NMR spectroscopy by prolonging the measurement time available to acquire spectral information about biomacromolecules in metabolically active cells. Bioreactor technology relies on immobilizer matrices, which secure cells in the active volume of the NMR coil and enable uniform perfusion of the growth medium, supplying fresh nutrients to the cells while removing toxic byproducts of their metabolism. The main drawbacks of commonly used matrices include the inability to recover intact cells post-measurement for additional analyses and/or requirements for specific operating temperatures. Here, we report on the development and characterization of a set of thermosensitive and nontoxic triblock copolymers based on poly(D,L-lactide)-<i>b</i>-poly(ethylene glycol)-<i>b</i>-poly(D,L-lactide) (PLA-PEG-PLA). Here, we show for the first time that these copolymers are suitable as immobilizer matrices for the acquisition of in-cell NMR spectra of nucleic acids and proteins over a commonly used sample temperature range of 15–40 °C and, importantly, allow recovery of cells after completion of in-cell NMR spectra acquisition. We compared the performances of currently used matrices in terms of cell viability (dye exclusion assays), cellular metabolism (1D <sup>31</sup>P NMR), and quality of in-cell NMR spectra of two model biomacromolecules (hybrid double-stranded/i-motif DNA and ubiquitin). Our results demonstrate the suitability and advantages of PLA-PEG-PLA copolymers for application in bioreactor-assisted in-cell NMR.</p></div>","PeriodicalId":613,"journal":{"name":"Journal of Biomolecular NMR","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2023-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10687187/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10189696","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}