1
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Toyama Y, Shimada I. Quantitative analysis of the slow exchange process by 19F NMR in the presence of scalar and dipolar couplings: applications to the ribose 2'- 19F probe in nucleic acids. JOURNAL OF BIOMOLECULAR NMR 2024:10.1007/s10858-024-00446-7. [PMID: 38918317 DOI: 10.1007/s10858-024-00446-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 06/10/2024] [Indexed: 06/27/2024]
Abstract
Solution NMR spectroscopy is a particularly powerful technique for characterizing the functional dynamics of biomolecules, which is typically achieved through the quantitative characterization of chemical exchange processes via the measurement of spin relaxation rates. In addition to the conventional nuclei such as 15N and 13C, which are abundant in biomolecules, fluorine-19 (19F) has recently garnered attention and is being widely used as a site-specific spin probe. While 19F offers the advantages of high sensitivity and low background, it can be susceptible to artifacts in quantitative relaxation analyses due to a multitude of dipolar and scalar coupling interactions with nearby 1H spins. In this study, we focused on the ribose 2'-19F spin probe in nucleic acids and investigated the effects of 1H-19F spin interactions on the quantitative characterization of slow exchange processes on the millisecond time scale. We demonstrated that the 1H-19F dipolar coupling can significantly affect the interpretation of 19F chemical exchange saturation transfer (CEST) experiments when 1H decoupling is applied, while the 1H-19F interactions have a lesser impact on Carr-Purcell-Meiboom-Gill relaxation dispersion applications. We also proposed a modified CEST scheme to alleviate these artifacts along with experimental verifications on self-complementary RNA systems. The theoretical framework presented in this study can be widely applied to various 19F spin systems where 1H-19F interactions are operative, further expanding the utility of 19F relaxation-based NMR experiments.
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Affiliation(s)
- Yuki Toyama
- Laboratory for Dynamic Structure of Biomolecules, RIKEN Center for Biosystems Dynamics Research (BDR), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
| | - Ichio Shimada
- Laboratory for Dynamic Structure of Biomolecules, RIKEN Center for Biosystems Dynamics Research (BDR), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4, Kagamiyama, Higashi-Hiroshima, 739-8528, Japan.
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2
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Kumar A, Madhurima K, Naganathan AN, Vallurupalli P, Sekhar A. Probing excited state 1Hα chemical shifts in intrinsically disordered proteins with a triple resonance-based CEST experiment: Application to a disorder-to-order switch. Methods 2023; 218:198-209. [PMID: 37607621 PMCID: PMC7615522 DOI: 10.1016/j.ymeth.2023.08.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/14/2023] [Accepted: 08/16/2023] [Indexed: 08/24/2023] Open
Abstract
Over 40% of eukaryotic proteomes and 15% of bacterial proteomes are predicted to be intrinsically disordered based on their amino acid sequence. Intrinsically disordered proteins (IDPs) exist as heterogeneous ensembles of interconverting conformations and pose a challenge to the structure-function paradigm by apparently functioning without possessing stable structural elements. IDPs play a prominent role in biological processes involving extensive intermolecular interaction networks and their inherently dynamic nature facilitates their promiscuous interaction with multiple structurally diverse partner molecules. NMR spectroscopy has made pivotal contributions to our understanding of IDPs because of its unique ability to characterize heterogeneity at atomic resolution. NMR methods such as Chemical Exchange Saturation Transfer (CEST) and relaxation dispersion have enabled the detection of 'invisible' excited states in biomolecules which are transiently and sparsely populated, yet central for function. Here, we develop a 1Hα CEST pulse sequence which overcomes the resonance overlap problem in the 1Hα-13Cα plane of IDPs by taking advantage of the superior resolution in the 1H-15N correlation spectrum. In this sequence, magnetization is transferred after 1H CEST using a triple resonance coherence transfer pathway from 1Hα (i) to 1HN(i + 1) during which the 15N(t1) and 1HN(t2) are frequency labelled. This approach is integrated with spin state-selective CEST for eliminating spurious dips in CEST profiles resulting from dipolar cross-relaxation. We apply this sequence to determine the excited state 1Hα chemical shifts of the intrinsically disordered DNA binding domain (CytRN) of the bacterial cytidine repressor (CytR), which transiently acquires a functional globally folded conformation. The structure of the excited state, calculated using 1Hα chemical shifts in conjunction with other excited state NMR restraints, is a three-helix bundle incorporating a helix-turn-helix motif that is vital for binding DNA.
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Affiliation(s)
- Ajith Kumar
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, Karnataka, India
| | - Kulkarni Madhurima
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, Karnataka, India
| | - Athi N Naganathan
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Pramodh Vallurupalli
- Tata Institute of Fundamental Research Hyderabad, 36/P, Gopanpally Village, Serilingampally Mandal, Ranga Reddy District, Hyderabad 500046, India
| | - Ashok Sekhar
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, Karnataka, India.
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3
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Rational design of hairpin RNA excited states reveals multi-step transitions. Nat Commun 2022; 13:1523. [PMID: 35314698 PMCID: PMC8938425 DOI: 10.1038/s41467-022-29194-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 02/01/2022] [Indexed: 11/25/2022] Open
Abstract
RNA excited states represent a class of high-energy-level and thus low-populated conformational states of RNAs that are sequestered within the free energy landscape until being activated by cellular cues. In recent years, there has been growing interest in structural and functional studies of these transient states, but the rational design of excited states remains unexplored. Here we developed a method to design small hairpin RNAs with predefined excited states that exchange with ground states through base pair reshuffling, and verified these transient states by combining NMR relaxation dispersion technique and imino chemical shift prediction. Using van’t Hoff analysis and accelerated molecular dynamics simulations, a mechanism of multi-step sequential transition has been revealed. The efforts made in this study will expand the scope of RNA rational design, and also contribute towards improved predictions of RNA secondary structure. RNA molecules exhibit conformational fluctuations between ground states and excited states. Here the authors designed and verified small hairpin RNAs with predefined secondary structure reshufflings. In light of Van’t Hoff analysis and accelerated molecular dynamics simulation, a mechanism of multistep sequential transition has been revealed.
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4
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Liu B, Shi H, Rangadurai A, Nussbaumer F, Chu CC, Erharter KA, Case DA, Kreutz C, Al-Hashimi HM. A quantitative model predicts how m 6A reshapes the kinetic landscape of nucleic acid hybridization and conformational transitions. Nat Commun 2021; 12:5201. [PMID: 34465779 PMCID: PMC8408185 DOI: 10.1038/s41467-021-25253-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 07/21/2021] [Indexed: 11/18/2022] Open
Abstract
N6-methyladenosine (m6A) is a post-transcriptional modification that controls gene expression by recruiting proteins to RNA sites. The modification also slows biochemical processes through mechanisms that are not understood. Using temperature-dependent (20°C-65°C) NMR relaxation dispersion, we show that m6A pairs with uridine with the methylamino group in the anti conformation to form a Watson-Crick base pair that transiently exchanges on the millisecond timescale with a singly hydrogen-bonded low-populated (1%) mismatch-like conformation in which the methylamino group is syn. This ability to rapidly interchange between Watson-Crick or mismatch-like forms, combined with different syn:anti isomer preferences when paired (~1:100) versus unpaired (~10:1), explains how m6A robustly slows duplex annealing without affecting melting at elevated temperatures via two pathways in which isomerization occurs before or after duplex annealing. Our model quantitatively predicts how m6A reshapes the kinetic landscape of nucleic acid hybridization and conformational transitions, and provides an explanation for why the modification robustly slows diverse cellular processes.
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Affiliation(s)
- Bei Liu
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
| | - Honglue Shi
- Department of Chemistry, Duke University, Durham, NC, USA
| | - Atul Rangadurai
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
| | - Felix Nussbaumer
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Chia-Chieh Chu
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
- Department of Chemistry, University of Chicago, Chicago, IL, USA
| | - Kevin Andreas Erharter
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - David A Case
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, USA
| | - Christoph Kreutz
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Hashim M Al-Hashimi
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA.
- Department of Chemistry, Duke University, Durham, NC, USA.
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5
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Chemical shift prediction of RNA imino groups: application toward characterizing RNA excited states. Nat Commun 2021; 12:1595. [PMID: 33707433 PMCID: PMC7952389 DOI: 10.1038/s41467-021-21840-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 02/10/2021] [Indexed: 11/26/2022] Open
Abstract
NH groups in proteins or nucleic acids are the most challenging target for chemical shift prediction. Here we show that the RNA base pair triplet motif dictates imino chemical shifts in its central base pair. A lookup table is established that links each type of base pair triplet to experimental chemical shifts of the central base pair, and can be used to predict imino chemical shifts of RNAs to remarkable accuracy. Strikingly, the semiempirical method can well interpret the variations of chemical shifts for different base pair triplets, and is even applicable to non-canonical motifs. This finding opens an avenue for predicting chemical shifts of more complicated RNA motifs. Furthermore, we combine the imino chemical shift prediction with NMR relaxation dispersion experiments targeting both 15N and 1HN of the imino group, and verify a previously characterized excited state of P5abc subdomain including an earlier speculated non-native G•G mismatch. Prediction of chemical shifts is critical for extracting structural and dynamic information from biomolecular NMR data. Here the authors report an RNA imino group chemical shift predictor, showing that the imino chemical shifts of a residue are dictated by the surrounding base pair triplet.
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Agarwal PK, Bernard DN, Bafna K, Doucet N. Enzyme dynamics: Looking beyond a single structure. ChemCatChem 2020; 12:4704-4720. [PMID: 33897908 PMCID: PMC8064270 DOI: 10.1002/cctc.202000665] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Indexed: 12/23/2022]
Abstract
Conventional understanding of how enzymes function strongly emphasizes the role of structure. However, increasing evidence clearly indicates that enzymes do not remain fixed or operate exclusively in or close to their native structure. Different parts of the enzyme (from individual residues to full domains) undergo concerted motions on a wide range of time-scales, including that of the catalyzed reaction. Information obtained on these internal motions and conformational fluctuations has so far uncovered and explained many aspects of enzyme mechanisms, which could not have been understood from a single structure alone. Although there is wide interest in understanding enzyme dynamics and its role in catalysis, several challenges remain. In addition to technical difficulties, the vast majority of investigations are performed in dilute aqueous solutions, where conditions are significantly different than the cellular milieu where a large number of enzymes operate. In this review, we discuss recent developments, several challenges as well as opportunities related to this topic. The benefits of considering dynamics as an integral part of the enzyme function can also enable new means of biocatalysis, engineering enzymes for industrial and medicinal applications.
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Affiliation(s)
- Pratul K. Agarwal
- Department of Physiological Sciences and High-Performance Computing Center, Oklahoma State University, Stillwater, Oklahoma 74078
- Arium BioLabs, 2519 Caspian Drive, Knoxville, Tennessee 37932
| | - David N. Bernard
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique (INRS), Université du Québec, 531 Boulevard des Prairies, Laval, Quebec, H7V 1B7, Canada
| | - Khushboo Bafna
- Department of Chemistry and Chemical Biology, and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180
| | - Nicolas Doucet
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique (INRS), Université du Québec, 531 Boulevard des Prairies, Laval, Quebec, H7V 1B7, Canada
- PROTEO, the Quebec Network for Research on Protein Function, Structure, and Engineering, 1045 Avenue de la Médecine, Université Laval, Québec, QC, G1V 0A6, Canada
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7
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Shi H, Liu B, Nussbaumer F, Rangadurai A, Kreutz C, Al-Hashimi HM. NMR Chemical Exchange Measurements Reveal That N6-Methyladenosine Slows RNA Annealing. J Am Chem Soc 2019; 141:19988-19993. [PMID: 31826614 DOI: 10.1021/jacs.9b10939] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
N6-Methyladenosine (m6A) is an abundant epitranscriptomic modification that plays important roles in many aspects of RNA metabolism. While m6A is thought to mainly function by recruiting reader proteins to specific RNA sites, the modification can also reshape RNA-protein and RNA-RNA interactions by altering RNA structure mainly by destabilizing base pairing. Little is known about how m6A and other epitranscriptomic modifications might affect the kinetic rates of RNA folding and other conformational transitions that are also important for cellular activity. Here, we used NMR R1ρ relaxation dispersion and chemical exchange saturation transfer to noninvasively and site-specifically measure nucleic acid hybridization kinetics. The methodology was validated on two DNA duplexes and then applied to examine how a single m6A alters the hybridization kinetics in two RNA duplexes. The results show that m6A minimally impacts the rate constant for duplex dissociation, changing koff by ∼1-fold but significantly slows the rate of duplex annealing, decreasing kon by ∼7-fold. A reduction in the annealing rate was observed robustly for two different sequence contexts at different temperatures, both in the presence and absence of Mg2+. We propose that rotation of the N6-methyl group from the preferred syn conformation in the unpaired nucleotide to the energetically disfavored anti conformation required for Watson-Crick pairing is responsible for the reduced annealing rate. The results help explain why in mRNA m6A slows down tRNA selection and more generally suggest that m6A may exert cellular functions by reshaping the kinetics of RNA conformational transitions.
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Affiliation(s)
- Honglue Shi
- Department of Chemistry , Duke University , Durham , North Carolina 27710 , United States
| | - Bei Liu
- Department of Biochemistry , Duke University School of Medicine , Durham , North Carolina 27710 , United States
| | - Felix Nussbaumer
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI) , University of Innsbruck , 6020 Innsbruck , Austria
| | - Atul Rangadurai
- Department of Biochemistry , Duke University School of Medicine , Durham , North Carolina 27710 , United States
| | - Christoph Kreutz
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI) , University of Innsbruck , 6020 Innsbruck , Austria
| | - Hashim M Al-Hashimi
- Department of Chemistry , Duke University , Durham , North Carolina 27710 , United States.,Department of Biochemistry , Duke University School of Medicine , Durham , North Carolina 27710 , United States
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8
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Yu XC, Hu Y, Ding J, Li H, Jin C. Structural basis and mechanism of the unfolding-induced activation of HdeA, a bacterial acid response chaperone. J Biol Chem 2018; 294:3192-3206. [PMID: 30573682 DOI: 10.1074/jbc.ra118.006398] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 12/17/2018] [Indexed: 11/06/2022] Open
Abstract
The role of protein structural disorder in biological functions has gained increasing attention in the past decade. The bacterial acid-resistant chaperone HdeA belongs to a group of "conditionally disordered" proteins, because it is inactive in its well-structured state and becomes activated via an order-to-disorder transition under acid stress. However, the mechanism for unfolding-induced activation remains unclear because of a lack of experimental information on the unfolded state conformation and the chaperone-client interactions. Herein, we used advanced solution NMR methods to characterize the activated-state conformation of HdeA under acidic conditions and identify its client-binding sites. We observed that the structure of activated HdeA becomes largely disordered and exposes two hydrophobic patches essential for client interactions. Furthermore, using the pH-dependent chemical exchange saturation transfer (CEST) NMR method, we identified three acid-sensitive regions that act as structural locks in regulating the exposure of the two client-binding sites during the activation process, revealing a multistep activation mechanism of HdeA's chaperone function at the atomic level. Our results highlight the role of intrinsic protein disorder in chaperone function and the self-inhibitory role of ordered structures under nonstress conditions, offering new insights for improving our understanding of protein structure-function paradigms.
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Affiliation(s)
- Xing-Chi Yu
- From the College of Chemistry and Molecular Engineering.,Beijing Nuclear Magnetic Resonance Center
| | - Yunfei Hu
- From the College of Chemistry and Molecular Engineering, .,Beijing Nuclear Magnetic Resonance Center
| | - Jienv Ding
- Beijing Nuclear Magnetic Resonance Center.,College of Life Sciences
| | - Hongwei Li
- From the College of Chemistry and Molecular Engineering.,Beijing Nuclear Magnetic Resonance Center
| | - Changwen Jin
- From the College of Chemistry and Molecular Engineering, .,Beijing Nuclear Magnetic Resonance Center.,College of Life Sciences.,Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China
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9
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Abstract
The phenomenon of chemical or conformational exchange in NMR spectroscopy has enabled detailed characterization of time-dependent aspects of biomolecular function, including folding, molecular recognition, allostery, and catalysis, on timescales from microsecond to second. Importantly, NMR methods based on a variety of spin relaxation parameters have been developed that provide quantitative information on interconversion kinetics, thermodynamic properties, and structural features of molecular states populated to a fraction of a percent at equilibrium and otherwise unobservable by other NMR approaches. The ongoing development of more sophisticated experimental techniques and the necessity to apply these methods to larger and more complex molecular systems engenders a corresponding need for theoretical advances describing such techniques and facilitating data analysis in applications. This review surveys current aspects of the theory of chemical exchange, as utilized in ZZ-exchange; Hahn and Carr-Purcell-Meiboom-Gill (CPMG) spin-echo; and R1ρ, chemical exchange saturation transfer (CEST), and dark state saturation transfer (DEST) spin-locking experiments. The review emphasizes theoretical results for kinetic topologies with more than two interconverting states, both to obtain compact analytical forms suitable for data analysis and to establish conditions for distinguishability between alternative kinetic schemes.
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Affiliation(s)
- Arthur G Palmer
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, United States.
| | - Hans Koss
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, United States
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10
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Zhang W, Niu X, Ding J, Hu Y, Jin C. Intra- and inter-protein couplings of backbone motions underlie protein thiol-disulfide exchange cascade. Sci Rep 2018; 8:15448. [PMID: 30337655 PMCID: PMC6193951 DOI: 10.1038/s41598-018-33766-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 10/06/2018] [Indexed: 11/09/2022] Open
Abstract
The thioredoxin (Trx)-coupled arsenate reductase (ArsC) is a family of enzymes that catalyzes the reduction of arsenate to arsenite in the arsenic detoxification pathway. The catalytic cycle involves a series of relayed intramolecular and intermolecular thiol-disulfide exchange reactions. Structures at different reaction stages have been determined, suggesting significant conformational fluctuations along the reaction pathway. Herein, we use two state-of-the-art NMR methods, the chemical exchange saturation transfer (CEST) and the CPMG-based relaxation dispersion (CPMG RD) experiments, to probe the conformational dynamics of B. subtilis ArsC in all reaction stages, namely the enzymatic active reduced state, the intra-molecular C10-C82 disulfide-bonded intermediate state, the inactive oxidized state, and the inter-molecular disulfide-bonded protein complex with Trx. Our results reveal highly rugged energy landscapes in the active reduced state, and suggest global collective motions in both the C10-C82 disulfide-bonded intermediate and the mixed-disulfide Trx-ArsC complex.
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Affiliation(s)
- Wenbo Zhang
- College of Life Sciences, Peking University, Beijing, 100871, China.,Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing, 100871, China
| | - Xiaogang Niu
- College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China.,Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing, 100871, China
| | - Jienv Ding
- College of Life Sciences, Peking University, Beijing, 100871, China.,Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing, 100871, China.,National Institutes of Health, DHHS 1050 Boyles Street, Frederick, MD, 21702, USA
| | - Yunfei Hu
- College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China. .,Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing, 100871, China. .,Medical College of Soochow University, Suzhou, 215123, China.
| | - Changwen Jin
- College of Life Sciences, Peking University, Beijing, 100871, China. .,College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China. .,Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing, 100871, China. .,Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, 100871, China.
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11
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Yuwen T, Bouvignies G, Kay LE. Exploring methods to expedite the recording of CEST datasets using selective pulse excitation. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2018; 292:1-7. [PMID: 29753980 DOI: 10.1016/j.jmr.2018.04.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 04/23/2018] [Accepted: 04/24/2018] [Indexed: 06/08/2023]
Abstract
Chemical Exchange Saturation Transfer (CEST) has emerged as a powerful tool for studies of biomolecular conformational exchange involving the interconversion between a major, visible conformer and one or more minor, invisible states. Applications typically entail recording a large number of 2D datasets, each of which differs in the position of a weak radio frequency field, so as to generate a CEST profile for each nucleus from which the chemical shifts of spins in the invisible state(s) are obtained. Here we compare a number of band-selective CEST schemes for speeding up the process using either DANTE or cosine-modulated excitation approaches. We show that while both are essentially identical for applications such as 15N CEST, in cases where the probed spins are dipolar or scalar coupled to other like spins there can be advantages for the cosine-excitation scheme.
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Affiliation(s)
- Tairan Yuwen
- Departments of Molecular Genetics, Biochemistry and Chemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada.
| | - Guillaume Bouvignies
- Laboratoire des biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France.
| | - Lewis E Kay
- Departments of Molecular Genetics, Biochemistry and Chemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada; Hospital for Sick Children, Program in Molecular Medicine, 555 University Avenue, Toronto, Ontario M5G 1X8, Canada.
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12
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Yuwen T, Kay LE. A new class of CEST experiment based on selecting different magnetization components at the start and end of the CEST relaxation element: an application to 1H CEST. JOURNAL OF BIOMOLECULAR NMR 2018; 70:93-102. [PMID: 29352366 DOI: 10.1007/s10858-017-0161-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 12/22/2017] [Indexed: 06/07/2023]
Abstract
Chemical exchange saturation transfer (CEST) experiments are becoming increasingly popular for investigating biomolecular exchange dynamics with rates on the order of approximately 50-500 s-1 and a rich toolkit of different methods has emerged over the past few years. Typically, experiments are based on the evolution of longitudinal magnetization, or in some cases two-spin order, during a fixed CEST relaxation delay, with the same class of magnetization prepared at the start and selected at end of the CEST period. Here we present a pair of TROSY-based pulse schemes for recording amide and methyl 1H CEST profiles where longitudinal magnetization at the start evolves to produce two-spin order that is then selected at the completion of the CEST element. This selection process subtracts out contributions from 1H-1H cross-relaxation on the fly that would otherwise complicate analysis of the data. It also obviates the need to record spin-state selective CEST profiles as an alternative to eliminating NOE effects, leading to significant improvements in sensitivity. The utility of the approach is demonstrated on a sample of a cavity mutant of T4 lysozyme that undergoes chemical exchange between conformations where the cavity is free and occupied.
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Affiliation(s)
- Tairan Yuwen
- Departments of Molecular Genetics, Biochemistry and Chemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Lewis E Kay
- Departments of Molecular Genetics, Biochemistry and Chemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada.
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON, M5G 0A4, Canada.
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13
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Ziarek JJ, Baptista D, Wagner G. Recent developments in solution nuclear magnetic resonance (NMR)-based molecular biology. J Mol Med (Berl) 2017. [PMID: 28643003 DOI: 10.1007/s00109-017-1560-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Visualizing post-translational modifications, conformations, and interaction surfaces of protein structures at atomic resolution underpins the development of novel therapeutics to combat disease. As computational resources expand, in silico calculations coupled with experimentally derived structures and functional assays have led to an explosion in structure-based drug design (SBDD) with several compounds in clinical trials. It is increasingly clear that "hidden" transition-state structures along activation trajectories can be harnessed to develop novel classes of allosteric inhibitors. The goal of this mini-review is to empower the clinical researcher with a general knowledge of the strengths and weaknesses of nuclear magnetic resonance (NMR) spectroscopy in molecular medicine. Although NMR can determine protein structures at atomic resolution, its unrivaled strength lies in sensing subtle changes in a nuclei's chemical environment as a result of intrinsic conformational dynamics, solution conditions, and binding interactions. These can be recorded at atomic resolution, without explicit structure determination, and then incorporated with static structures or molecular dynamics simulations to produce a complete biological picture.
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Affiliation(s)
- Joshua J Ziarek
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Ave, Boston, MA, 02115, USA
| | - Diego Baptista
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Ave, Boston, MA, 02115, USA
| | - Gerhard Wagner
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Ave, Boston, MA, 02115, USA.
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