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Fakhrutdinov AN, Karlinskii BY, Minyaev ME, Ananikov VP. Unusual Effect of Impurities on the Spectral Characterization of 1,2,3-Triazoles Synthesized by the Cu-Catalyzed Azide-Alkyne Click Reaction. J Org Chem 2021; 86:11456-11463. [PMID: 34310134 DOI: 10.1021/acs.joc.1c00943] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The analysis of products synthesized by Cu-catalyzed click reactions can be complicated due to the presence of metal impurities in isolated substances, which may "selectively" distort some signals in NMR spectra. Such a pronounced impurity effect was found in both 1H and 13C NMR spectra for a number of 1,4-substituted 1,2,3-triazoles. Recording of the full undistorted spectra is possible with additional product treatment, with more thorough purification, or by recording the spectra at low temperatures. The reasons for the distortion and disappearance of signals have been thoroughly studied; it was shown that impurities of paramagnetic metal ions in small amounts lead to this effect. Here, we want to deliver a warning message to the community: when all NMR signals in a spectrum are distorted, this situation is easy to detect. However, if only a few signals are "selectively" removed by impurities and the rest of the spectrum appears normal, this situation is much harder to notice. Therefore, incorrect conclusions about chemical structure may be obtained. Here, we demonstrated the example of Cu2+ ions, but one may anticipate a similar effect for other paramagnetic metal contaminants if the organic molecule has a functional group capable of coordination (heteroatom or a multiple bond).
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Affiliation(s)
- Artem N Fakhrutdinov
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospekt 47, Moscow 119991, Russia
| | - Bogdan Ya Karlinskii
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospekt 47, Moscow 119991, Russia
| | - Mikhail E Minyaev
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospekt 47, Moscow 119991, Russia
| | - Valentine P Ananikov
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospekt 47, Moscow 119991, Russia
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2
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Buck M. Letting go: Deep computational modeling insights into pH-dependent calcium affinity. J Biol Chem 2021; 297:100974. [PMID: 34280436 PMCID: PMC8350533 DOI: 10.1016/j.jbc.2021.100974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Calcium and other cofactors can feature as key additions to a molecular interface, to the extent that the cofactor is completely buried in the bound state. How can such an interaction be regulated then? The answer: By facilitating a switch through an allosteric network. Although a number of unbinding mechanisms are being characterized, an extensive computational study by Joswig et al. reveals a detailed model for the pattern recognition receptor langerin.
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Affiliation(s)
- Matthias Buck
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, Ohio, USA.
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3
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Wang H, Li Q, Zhang J, Zhang H, Shu Y, Zhao Z, Jiang W, Du L, Phillips DL, Lam JWY, Sung HHY, Williams ID, Lu R, Tang BZ. Visualization and Manipulation of Solid-State Molecular Motions in Cocrystallization Processes. J Am Chem Soc 2021; 143:9468-9477. [PMID: 34152134 DOI: 10.1021/jacs.1c02594] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Solid-state molecular motions (SSMM) play a critical role in adjusting behaviors and properties of materials. However, research on SSMM, especially for multicomponent systems, suffers from various problems and is rarely explored. Herein, through collaboration with cocrystal engineering, visualization and manipulation of SSMM in two-component systems, namely, FSBO ((E)-2-(4-fluorostyryl)benzo[d]oxazole)/TCB (1,2,4,5-tetracyanobenzene) and PVBO ((E)-2-(2-(pyridin-4-yl)vinyl)benzo[d]oxazole)/TCB, were realized. The obtained yellow-emissive F/T (FSBO/TCB) cocrystal displayed turn-on fluorescence, and the green-emissive P/T (PVBO/TCB) cocrystal presented redder emission, both of which exhibited an aggregation-induced emission property. At varied pressure and temperature, the grinding mixtures of FSBO/TCB and PVBO/TCB displayed different molecular motions that were readily observed through the fluorescence signal. Notably, even without grinding, FSBO and TCB molecules could move over for 4 mm in a 1D tube. The unique emission changes induced by SSMM were applied in information storage and dynamic anticounterfeiting. This work not only visualized and manipulated SSMM but offered more insights for multicomponent study in aggregate science.
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Affiliation(s)
- Haoran Wang
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Department of Chemical and Biomedical Engineering, Institute for Advanced Study, and Guangdong Hong Kong Macro Joint Laboratory of Optoelectronic and Magnetic Functional Materials, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China.,State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130000, China
| | - Qiyao Li
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Department of Chemical and Biomedical Engineering, Institute for Advanced Study, and Guangdong Hong Kong Macro Joint Laboratory of Optoelectronic and Magnetic Functional Materials, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Jianyu Zhang
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Department of Chemical and Biomedical Engineering, Institute for Advanced Study, and Guangdong Hong Kong Macro Joint Laboratory of Optoelectronic and Magnetic Functional Materials, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Haoke Zhang
- MOE Key Laboratory of Macromolecules Synthesis of Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou 310027, China
| | - Yuanhong Shu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130000, China
| | - Zheng Zhao
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 210009, China
| | - Wei Jiang
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 210009, China
| | - Lili Du
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - David Lee Phillips
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Jacky W Y Lam
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Department of Chemical and Biomedical Engineering, Institute for Advanced Study, and Guangdong Hong Kong Macro Joint Laboratory of Optoelectronic and Magnetic Functional Materials, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Herman H Y Sung
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Department of Chemical and Biomedical Engineering, Institute for Advanced Study, and Guangdong Hong Kong Macro Joint Laboratory of Optoelectronic and Magnetic Functional Materials, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Ian D Williams
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Department of Chemical and Biomedical Engineering, Institute for Advanced Study, and Guangdong Hong Kong Macro Joint Laboratory of Optoelectronic and Magnetic Functional Materials, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Ran Lu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130000, China
| | - Ben Zhong Tang
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Department of Chemical and Biomedical Engineering, Institute for Advanced Study, and Guangdong Hong Kong Macro Joint Laboratory of Optoelectronic and Magnetic Functional Materials, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China.,AIE Institute, Guangzhou Development Distinct, Huangpu, Guangzhou 510530, China
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4
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An intrinsically disordered motif regulates the interaction between the p47 adaptor and the p97 AAA+ ATPase. Proc Natl Acad Sci U S A 2020; 117:26226-26236. [PMID: 33028677 DOI: 10.1073/pnas.2013920117] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
VCP/p97, an enzyme critical to proteostasis, is regulated through interactions with protein adaptors targeting it to specific cellular tasks. One such adaptor, p47, forms a complex with p97 to direct lipid membrane remodeling. Here, we use NMR and other biophysical methods to study the structural dynamics of p47 and p47-p97 complexes. Disordered regions in p47 are shown to be critical in directing intra-p47 and p47-p97 interactions via a pair of previously unidentified linear motifs. One of these, an SHP domain, regulates p47 binding to p97 in a manner that depends on the nucleotide state of p97. NMR and electron cryomicroscopy data have been used as restraints in molecular dynamics trajectories to develop structural ensembles for p47-p97 complexes in adenosine diphosphate (ADP)- and adenosine triphosphate (ATP)-bound conformations, highlighting differences in interactions in the two states. Our study establishes the importance of intrinsically disordered regions in p47 for the formation of functional p47-p97 complexes.
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Zhang J, He B, Wu W, Alam P, Zhang H, Gong J, Song F, Wang Z, Sung HHY, Williams ID, Wang Z, Lam JWY, Tang BZ. Molecular Motions in AIEgen Crystals: Turning on Photoluminescence by Force-Induced Filament Sliding. J Am Chem Soc 2020; 142:14608-14618. [DOI: 10.1021/jacs.0c06305] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Jing Zhang
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering, Research Center for Tissue Restoration and Reconstruction, Institute for Advanced Study, Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Benzhao He
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering, Research Center for Tissue Restoration and Reconstruction, Institute for Advanced Study, Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
- HKUST-Shenzhen Research Institute, No. 9 Yuexing first RD, South Area, Hi-tech Park, Nanshan, Shenzhen 518057, China
| | - Wenjie Wu
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering, Research Center for Tissue Restoration and Reconstruction, Institute for Advanced Study, Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Parvej Alam
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering, Research Center for Tissue Restoration and Reconstruction, Institute for Advanced Study, Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Han Zhang
- Center for Aggregation-Induced Emission, SCUT-HKUST Joint Research Institute, State Key Laboratory of Luminescent Materials and Devices, South China University of Technology, Guangzhou 510640, China
| | - Junyi Gong
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering, Research Center for Tissue Restoration and Reconstruction, Institute for Advanced Study, Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Fengyan Song
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering, Research Center for Tissue Restoration and Reconstruction, Institute for Advanced Study, Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Zaiyu Wang
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering, Research Center for Tissue Restoration and Reconstruction, Institute for Advanced Study, Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Herman H. Y. Sung
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering, Research Center for Tissue Restoration and Reconstruction, Institute for Advanced Study, Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Ian D. Williams
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering, Research Center for Tissue Restoration and Reconstruction, Institute for Advanced Study, Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Zhiming Wang
- Center for Aggregation-Induced Emission, SCUT-HKUST Joint Research Institute, State Key Laboratory of Luminescent Materials and Devices, South China University of Technology, Guangzhou 510640, China
| | - Jacky W. Y. Lam
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering, Research Center for Tissue Restoration and Reconstruction, Institute for Advanced Study, Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
- HKUST-Shenzhen Research Institute, No. 9 Yuexing first RD, South Area, Hi-tech Park, Nanshan, Shenzhen 518057, China
| | - Ben Zhong Tang
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering, Research Center for Tissue Restoration and Reconstruction, Institute for Advanced Study, Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
- HKUST-Shenzhen Research Institute, No. 9 Yuexing first RD, South Area, Hi-tech Park, Nanshan, Shenzhen 518057, China
- Center for Aggregation-Induced Emission, SCUT-HKUST Joint Research Institute, State Key Laboratory of Luminescent Materials and Devices, South China University of Technology, Guangzhou 510640, China
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6
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Alam P, Leung NLC, Cheng Y, Zhang H, Liu J, Wu W, Kwok RTK, Lam JWY, Sung HHY, Williams ID, Tang BZ. Spontaneous and Fast Molecular Motion at Room Temperature in the Solid State. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201813554] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Parvej Alam
- Department of Chemistry Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction and Institute for Advanced Study The Hong Kong University of Science and Technology Clear Water Bay Kowloon, Hong Kong China
| | - Nelson L. C. Leung
- Department of Chemistry Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction and Institute for Advanced Study The Hong Kong University of Science and Technology Clear Water Bay Kowloon, Hong Kong China
| | - Yanhua Cheng
- Department of Chemistry Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction and Institute for Advanced Study The Hong Kong University of Science and Technology Clear Water Bay Kowloon, Hong Kong China
| | - Haoke Zhang
- Department of Chemistry Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction and Institute for Advanced Study The Hong Kong University of Science and Technology Clear Water Bay Kowloon, Hong Kong China
| | - Junkai Liu
- Department of Chemistry Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction and Institute for Advanced Study The Hong Kong University of Science and Technology Clear Water Bay Kowloon, Hong Kong China
| | - Wenjie Wu
- Department of Chemistry Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction and Institute for Advanced Study The Hong Kong University of Science and Technology Clear Water Bay Kowloon, Hong Kong China
| | - Ryan T. K. Kwok
- Department of Chemistry Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction and Institute for Advanced Study The Hong Kong University of Science and Technology Clear Water Bay Kowloon, Hong Kong China
| | - Jacky W. Y. Lam
- Department of Chemistry Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction and Institute for Advanced Study The Hong Kong University of Science and Technology Clear Water Bay Kowloon, Hong Kong China
| | - Herman H. Y. Sung
- Department of Chemistry Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction and Institute for Advanced Study The Hong Kong University of Science and Technology Clear Water Bay Kowloon, Hong Kong China
| | - Ian D. Williams
- Department of Chemistry Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction and Institute for Advanced Study The Hong Kong University of Science and Technology Clear Water Bay Kowloon, Hong Kong China
| | - Ben Zhong Tang
- Department of Chemistry Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction and Institute for Advanced Study The Hong Kong University of Science and Technology Clear Water Bay Kowloon, Hong Kong China
- HKUST-Shenzhen Research Institute No. 9 Yuexing 1st Rd, South Area, Hi-tech Park, Nanshan Shenzhen 518057 China
- Centre for Aggregation-induced emission SCUT-HKUST Joint Research Laboratory State Key Laboratory of Luminescent Materials and Devices South China University of Technology Guangzhou 510640 China
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7
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Alam P, Leung NLC, Cheng Y, Zhang H, Liu J, Wu W, Kwok RTK, Lam JWY, Sung HHY, Williams ID, Tang BZ. Spontaneous and Fast Molecular Motion at Room Temperature in the Solid State. Angew Chem Int Ed Engl 2019; 58:4536-4540. [DOI: 10.1002/anie.201813554] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 01/22/2019] [Indexed: 12/22/2022]
Affiliation(s)
- Parvej Alam
- Department of Chemistry Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction and Institute for Advanced Study The Hong Kong University of Science and Technology Clear Water Bay Kowloon, Hong Kong China
| | - Nelson L. C. Leung
- Department of Chemistry Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction and Institute for Advanced Study The Hong Kong University of Science and Technology Clear Water Bay Kowloon, Hong Kong China
| | - Yanhua Cheng
- Department of Chemistry Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction and Institute for Advanced Study The Hong Kong University of Science and Technology Clear Water Bay Kowloon, Hong Kong China
| | - Haoke Zhang
- Department of Chemistry Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction and Institute for Advanced Study The Hong Kong University of Science and Technology Clear Water Bay Kowloon, Hong Kong China
| | - Junkai Liu
- Department of Chemistry Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction and Institute for Advanced Study The Hong Kong University of Science and Technology Clear Water Bay Kowloon, Hong Kong China
| | - Wenjie Wu
- Department of Chemistry Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction and Institute for Advanced Study The Hong Kong University of Science and Technology Clear Water Bay Kowloon, Hong Kong China
| | - Ryan T. K. Kwok
- Department of Chemistry Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction and Institute for Advanced Study The Hong Kong University of Science and Technology Clear Water Bay Kowloon, Hong Kong China
| | - Jacky W. Y. Lam
- Department of Chemistry Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction and Institute for Advanced Study The Hong Kong University of Science and Technology Clear Water Bay Kowloon, Hong Kong China
| | - Herman H. Y. Sung
- Department of Chemistry Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction and Institute for Advanced Study The Hong Kong University of Science and Technology Clear Water Bay Kowloon, Hong Kong China
| | - Ian D. Williams
- Department of Chemistry Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction and Institute for Advanced Study The Hong Kong University of Science and Technology Clear Water Bay Kowloon, Hong Kong China
| | - Ben Zhong Tang
- Department of Chemistry Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction and Institute for Advanced Study The Hong Kong University of Science and Technology Clear Water Bay Kowloon, Hong Kong China
- HKUST-Shenzhen Research Institute No. 9 Yuexing 1st Rd, South Area, Hi-tech Park, Nanshan Shenzhen 518057 China
- Centre for Aggregation-induced emission SCUT-HKUST Joint Research Laboratory State Key Laboratory of Luminescent Materials and Devices South China University of Technology Guangzhou 510640 China
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8
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Novakovic M, Cousin SF, Jaroszewicz MJ, Rosenzweig R, Frydman L. Looped-PROjected SpectroscopY (L-PROSY): A simple approach to enhance backbone/sidechain cross-peaks in 1H NMR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2018; 294:169-180. [PMID: 30064051 DOI: 10.1016/j.jmr.2018.07.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 07/10/2018] [Accepted: 07/13/2018] [Indexed: 05/08/2023]
Abstract
Cross-relaxation and isotropic mixing phenomena leading to the Nuclear Overhauser Effect (NOE) and to the TOCSY experiment, lie at the center of structural determinations by NMR. 2D TOCSY and NOESY exploit these polarization transfer effects to determine inter-site connectivities and molecular geometries under physiologically-relevant conditions. Among these sequences' drawback, particularly for the case of NOEs, are a lack of sensitivity arising from small structurally-relevant cross peaks. The present study explores the application of multiple Zeno-like projective measurements, to enhance the cross-peaks between spectrally distinct groups in proteins -in particular between amide and aliphatic protons. The enhancement is based on repeating the projection done by Ramsey or TOCSY blocks multiple times, in what we refer to as Looped, PROjected Spectroscopy (L-PROSY). This leads to a reset of the amide/aliphatic transfer processes; the initial slopes of the NOE- or J-transfer effects thus define the cross-peak growth, and a faster cross-peak buildup is achieved upon looping these transfers over the allotted time T1. These projections also help to better preserve the magnetization originating in the amides, resulting in an overall improvement in sensitivity. L-PROSY's usefulness is demonstrated by incorporating it into two widely used protein NMR experiments: 2D 15N-1H HMQC-NOESY and 15N-filtered 2D NOESY. Different parameters dictating the overall SNR improvement, particularly the protein correlation times and the amide-water chemical exchange rates, were examined, and L-PROSY's enhancements resulted for all tested proteins. The largest cross-peak enhancements were observed for unstructured proteins, where chemical exchanges with the solvent of the kind that tend to average out NOE cross-peaks in conventional NMR, boost L-PROSY's cross-peaks by replenishing the amide's magnetizations within each loop. Enhanced cross-peaks were also found in extensions involving TOCSY-based experiments when applied to proteins with unfolded segments.
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Affiliation(s)
- Mihajlo Novakovic
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Samuel F Cousin
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Michael J Jaroszewicz
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Rina Rosenzweig
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Lucio Frydman
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel.
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9
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Tsafou K, Tiwari PB, Forman-Kay JD, Metallo SJ, Toretsky JA. Targeting Intrinsically Disordered Transcription Factors: Changing the Paradigm. J Mol Biol 2018; 430:2321-2341. [PMID: 29655986 DOI: 10.1016/j.jmb.2018.04.008] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 03/21/2018] [Accepted: 04/05/2018] [Indexed: 12/21/2022]
Abstract
Increased understanding of intrinsically disordered proteins (IDPs) and protein regions has revolutionized our view of the relationship between protein structure and function. Data now support that IDPs can be functional in the absence of a single, fixed, three-dimensional structure. Due to their dynamic morphology, IDPs have the ability to display a range of kinetics and affinity depending on what the system requires, as well as the potential for large-scale association. Although several studies have shed light on the functional properties of IDPs, the class of intrinsically disordered transcription factors (TFs) is still poorly characterized biophysically due to their combination of ordered and disordered sequences. In addition, TF modulation by small molecules has long been considered a difficult or even impossible task, limiting functional probe development. However, with evolving technology, it is becoming possible to characterize TF structure-function relationships in unprecedented detail and explore avenues not available or not considered in the past. Here we provide an introduction to the biophysical properties of intrinsically disordered TFs and we discuss recent computational and experimental efforts toward understanding the role of intrinsically disordered TFs in biology and disease. We describe a series of successful TF targeting strategies that have overcome the perception of the "undruggability" of TFs, providing new leads on drug development methodologies. Lastly, we discuss future challenges and opportunities to enhance our understanding of the structure-function relationship of intrinsically disordered TFs.
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Affiliation(s)
- K Tsafou
- Department of Oncology and Pediatrics, Georgetown University, 3970 Reservoir Road Northwest, Washington, DC 20057, USA
| | - P B Tiwari
- Department of Oncology and Pediatrics, Georgetown University, 3970 Reservoir Road Northwest, Washington, DC 20057, USA
| | - J D Forman-Kay
- Molecular Medicine, The Hospital for Sick Children, Toronto M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Toronto M5G 1X8, Canada
| | - S J Metallo
- Department of Chemistry, Georgetown University, Washington, DC 20057, USA
| | - J A Toretsky
- Department of Oncology and Pediatrics, Georgetown University, 3970 Reservoir Road Northwest, Washington, DC 20057, USA.
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10
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Bondarenko V, Wells M, Xu Y, Tang P. Solution NMR Studies of Anesthetic Interactions with Ion Channels. Methods Enzymol 2018; 603:49-66. [PMID: 29673534 DOI: 10.1016/bs.mie.2018.01.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
NMR spectroscopy is one of the major tools to provide atomic resolution protein structural information. It has been used to elucidate the molecular details of interactions between anesthetics and ion channels, to identify anesthetic binding sites, and to characterize channel dynamics and changes introduced by anesthetics. In this chapter, we present solution NMR methods essential for investigating interactions between ion channels and general anesthetics, including both volatile and intravenous anesthetics. Case studies are provided with a focus on pentameric ligand-gated ion channels and the voltage-gated sodium channel NaChBac.
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Affiliation(s)
- Vasyl Bondarenko
- University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Marta Wells
- University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Yan Xu
- University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Pei Tang
- University of Pittsburgh School of Medicine, Pittsburgh, PA, United States.
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11
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Opuni KFM, Al-Majdoub M, Yefremova Y, El-Kased RF, Koy C, Glocker MO. Mass spectrometric epitope mapping. MASS SPECTROMETRY REVIEWS 2018; 37:229-241. [PMID: 27403762 DOI: 10.1002/mas.21516] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 06/23/2016] [Indexed: 06/06/2023]
Abstract
Mass spectrometric epitope mapping has become a versatile method to precisely determine a soluble antigen's partial structure that directly interacts with an antibody in solution. Typical lengths of investigated antigens have increased up to several 100 amino acids while experimentally determined epitope peptides have decreased in length to on average 10-15 amino acids. Since the early 1990s more and more sophisticated methods have been developed and have forwarded a bouquet of suitable approaches for epitope mapping with immobilized, temporarily immobilized, and free-floating antibodies. While up to now monoclonal antibodies have been mostly used in epitope mapping experiments, the applicability of polyclonal antibodies has been proven. The antibody's resistance towards enzymatic proteolysis has been of key importance for the two mostly applied methods: epitope excision and epitope extraction. Sample consumption has dropped to low pmol amounts on both, the antigen and the antibody. While adequate in-solution sample handling has been most important for successful epitope mapping, mass spectrometric analysis has been found the most suitable read-out method from early on. The rapidity by which mass spectrometric epitope mapping nowadays is executed outperforms all alternative methods. Thus, it can be asserted that mass spectrometric epitope mapping has reached a state of maturity, which allows it to be used in any mass spectrometry laboratory. After 25 years of constant and steady improvements, its application to clinical samples, for example, for patient characterization and stratification, is anticipated in the near future. © 2016 Wiley Periodicals, Inc. Mass Spec Rev 37:229-241, 2018.
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Affiliation(s)
- Kwabena F M Opuni
- Proteome Center Rostock, University Medicine and Natural Science Faculty, University of Rostock, Rostock, Germany
| | - Mahmoud Al-Majdoub
- Proteome Center Rostock, University Medicine and Natural Science Faculty, University of Rostock, Rostock, Germany
| | - Yelena Yefremova
- Proteome Center Rostock, University Medicine and Natural Science Faculty, University of Rostock, Rostock, Germany
| | - Reham F El-Kased
- Microbiology and Immunology Faculty of Pharmacy, The British University in Egypt, Cairo, Egypt
| | - Cornelia Koy
- Proteome Center Rostock, University Medicine and Natural Science Faculty, University of Rostock, Rostock, Germany
| | - Michael O Glocker
- Proteome Center Rostock, University Medicine and Natural Science Faculty, University of Rostock, Rostock, Germany
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12
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Current Solution NMR Techniques for Structure-Function Studies of Proteins and RNA Molecules. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1105:43-58. [DOI: 10.1007/978-981-13-2200-6_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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13
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VanSchouwen B, Ahmed R, Milojevic J, Melacini G. Functional dynamics in cyclic nucleotide signaling and amyloid inhibition. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1529-1543. [PMID: 28911813 DOI: 10.1016/j.bbapap.2017.09.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 08/29/2017] [Accepted: 09/07/2017] [Indexed: 12/28/2022]
Abstract
It is now established that understanding the molecular basis of biological function requires atomic resolution maps of both structure and dynamics. Here, we review several illustrative examples of functional dynamics selected from our work on cyclic nucleotide signaling and amyloid inhibition. Although fundamentally diverse, a central aspect common to both fields is that function can only be rationalized by considering dynamic equilibria between distinct states of the accessible free energy landscape. The dynamic exchange between ground and excited states of signaling proteins is essential to explain auto-inhibition and allosteric activation. The dynamic exchange between non-toxic monomeric species and toxic oligomers of amyloidogenic proteins provides a foundation to understand amyloid inhibition. NMR ideally probes both types of dynamic exchange at atomic resolution. Specifically, we will show how NMR was utilized to reveal the dynamical basis of cyclic nucleotide affinity, selectivity, agonism and antagonism in multiple eukaryotic cAMP and cGMP receptors. We will also illustrate how NMR revealed the mechanism of action of plasma proteins that act as extracellular chaperones and inhibit the self-association of the prototypical amyloidogenic Aβ peptide. The examples outlined in this review illustrate the widespread implications of functional dynamics and the power of NMR as an indispensable tool in molecular pharmacology and pathology.
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Affiliation(s)
- Bryan VanSchouwen
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario, Canada
| | - Rashik Ahmed
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Julijana Milojevic
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario, Canada
| | - Giuseppe Melacini
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario, Canada; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada.
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14
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Complementary uses of small angle X-ray scattering and X-ray crystallography. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1623-1630. [PMID: 28743534 DOI: 10.1016/j.bbapap.2017.07.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 07/10/2017] [Accepted: 07/20/2017] [Indexed: 12/11/2022]
Abstract
Most proteins function within networks and, therefore, protein interactions are central to protein function. Although stable macromolecular machines have been extensively studied, dynamic protein interactions remain poorly understood. Small-angle X-ray scattering probes the size, shape and dynamics of proteins in solution at low resolution and can be used to study samples in a large range of molecular weights. Therefore, it has emerged as a powerful technique to study the structure and dynamics of biomolecular systems and bridge fragmented information obtained using high-resolution techniques. Here we review how small-angle X-ray scattering can be combined with other structural biology techniques to study protein dynamics. This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman.
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15
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Pederson K, Chalmers GR, Gao Q, Elnatan D, Ramelot TA, Ma LC, Montelione GT, Kennedy MA, Agard DA, Prestegard JH. NMR characterization of HtpG, the E. coli Hsp90, using sparse labeling with 13C-methyl alanine. JOURNAL OF BIOMOLECULAR NMR 2017; 68:225-236. [PMID: 28653216 PMCID: PMC5546222 DOI: 10.1007/s10858-017-0123-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 06/22/2017] [Indexed: 05/03/2023]
Abstract
A strategy for acquiring structural information from sparsely isotopically labeled large proteins is illustrated with an application to the E. coli heat-shock protein, HtpG (high temperature protein G), a 145 kDa dimer. It uses 13C-alanine methyl labeling in a perdeuterated background to take advantage of the sensitivity and resolution of Methyl-TROSY spectra, as well as the backbone-centered structural information from 1H-13C residual dipolar couplings (RDCs) of alanine methyl groups. In all, 40 of the 47 expected crosspeaks were resolved and 36 gave RDC data. Assignments of crosspeaks were partially achieved by transferring assignments from those made on individual domains using triple resonance methods. However, these were incomplete and in many cases the transfer was ambiguous. A genetic algorithm search for consistency between predictions based on domain structures and measurements for chemical shifts and RDCs allowed 60% of the 40 resolved crosspeaks to be assigned with confidence. Chemical shift changes of these crosspeaks on adding an ATP analog to the apo-protein are shown to be consistent with structural changes expected on comparing previous crystal structures for apo- and complex- structures. RDCs collected on the assigned alanine methyl peaks are used to generate a new solution model for the apo-protein structure.
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Affiliation(s)
- Kari Pederson
- Complex Carbohydrate Research Center, University of Georgia, Athens, USA
| | - Gordon R Chalmers
- Complex Carbohydrate Research Center, University of Georgia, Athens, USA
- Department of Computer Science, University of Georgia, Athens, USA
| | - Qi Gao
- Complex Carbohydrate Research Center, University of Georgia, Athens, USA
| | - Daniel Elnatan
- Department of Biochemistry and Biophysics, Howard Hughes Medical Institute, University of California, San Francisco, USA
| | - Theresa A Ramelot
- Department of Chemistry and Biochemistry, Miami University, Oxford, USA
| | - Li-Chung Ma
- Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, The State University of New Jersey, Piscataway, USA
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, USA
| | - Gaetano T Montelione
- Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, The State University of New Jersey, Piscataway, USA
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, USA
| | - Michael A Kennedy
- Department of Chemistry and Biochemistry, Miami University, Oxford, USA
| | - David A Agard
- Department of Biochemistry and Biophysics, Howard Hughes Medical Institute, University of California, San Francisco, USA
| | - James H Prestegard
- Complex Carbohydrate Research Center, University of Georgia, Athens, USA.
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16
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Lakomek NA, Penzel S, Lends A, Cadalbert R, Ernst M, Meier BH. Microsecond Dynamics in Ubiquitin Probed by Solid-State 15
N NMR Spectroscopy R
1ρ
Relaxation Experiments under Fast MAS (60-110 kHz). Chemistry 2017; 23:9425-9433. [DOI: 10.1002/chem.201701738] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Indexed: 11/07/2022]
Affiliation(s)
- Nils-Alexander Lakomek
- Laboratory of Physical Chemistry; ETH Zurich; Vladimir-Prelog Weg 2 8093 Zurich Switzerland
| | - Susanne Penzel
- Laboratory of Physical Chemistry; ETH Zurich; Vladimir-Prelog Weg 2 8093 Zurich Switzerland
| | - Alons Lends
- Laboratory of Physical Chemistry; ETH Zurich; Vladimir-Prelog Weg 2 8093 Zurich Switzerland
| | - Riccardo Cadalbert
- Laboratory of Physical Chemistry; ETH Zurich; Vladimir-Prelog Weg 2 8093 Zurich Switzerland
| | - Matthias Ernst
- Laboratory of Physical Chemistry; ETH Zurich; Vladimir-Prelog Weg 2 8093 Zurich Switzerland
| | - Beat H. Meier
- Laboratory of Physical Chemistry; ETH Zurich; Vladimir-Prelog Weg 2 8093 Zurich Switzerland
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17
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Zhuravleva A, Korzhnev DM. Protein folding by NMR. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2017; 100:52-77. [PMID: 28552172 DOI: 10.1016/j.pnmrs.2016.10.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Revised: 10/17/2016] [Accepted: 10/17/2016] [Indexed: 06/07/2023]
Abstract
Protein folding is a highly complex process proceeding through a number of disordered and partially folded nonnative states with various degrees of structural organization. These transiently and sparsely populated species on the protein folding energy landscape play crucial roles in driving folding toward the native conformation, yet some of these nonnative states may also serve as precursors for protein misfolding and aggregation associated with a range of devastating diseases, including neuro-degeneration, diabetes and cancer. Therefore, in vivo protein folding is often reshaped co- and post-translationally through interactions with the ribosome, molecular chaperones and/or other cellular components. Owing to developments in instrumentation and methodology, solution NMR spectroscopy has emerged as the central experimental approach for the detailed characterization of the complex protein folding processes in vitro and in vivo. NMR relaxation dispersion and saturation transfer methods provide the means for a detailed characterization of protein folding kinetics and thermodynamics under native-like conditions, as well as modeling high-resolution structures of weakly populated short-lived conformational states on the protein folding energy landscape. Continuing development of isotope labeling strategies and NMR methods to probe high molecular weight protein assemblies, along with advances of in-cell NMR, have recently allowed protein folding to be studied in the context of ribosome-nascent chain complexes and molecular chaperones, and even inside living cells. Here we review solution NMR approaches to investigate the protein folding energy landscape, and discuss selected applications of NMR methodology to studying protein folding in vitro and in vivo. Together, these examples highlight a vast potential of solution NMR in providing atomistic insights into molecular mechanisms of protein folding and homeostasis in health and disease.
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Affiliation(s)
- Anastasia Zhuravleva
- Astbury Centre for Structural Molecular Biology and Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom.
| | - Dmitry M Korzhnev
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT 06030, USA.
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18
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Macek P, Kerfah R, Boeri Erba E, Crublet E, Moriscot C, Schoehn G, Amero C, Boisbouvier J. Unraveling self-assembly pathways of the 468-kDa proteolytic machine TET2. SCIENCE ADVANCES 2017; 3:e1601601. [PMID: 28435872 PMCID: PMC5384809 DOI: 10.1126/sciadv.1601601] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 02/10/2017] [Indexed: 05/03/2023]
Abstract
The spontaneous formation of biological higher-order structures from smaller building blocks, called self-assembly, is a fundamental attribute of life. Although the protein self-assembly is a time-dependent process that occurs at the molecular level, its current understanding originates either from static structures of trapped intermediates or from modeling. Nuclear magnetic resonance (NMR) spectroscopy has the unique ability to monitor structural changes in real time; however, its size limitation and time-resolution constraints remain a challenge when studying the self-assembly of large biological particles. We report the application of methyl-specific isotopic labeling combined with relaxation-optimized NMR spectroscopy to overcome both size- and time-scale limitations. We report for the first time the self-assembly process of a half-megadalton protein complex that was monitored at the structural level, including the characterization of intermediate states, using a mutagenesis-free strategy. NMR was used to obtain individual kinetics data on the different transient intermediates and the formation of final native particle. In addition, complementary time-resolved electron microscopy and native mass spectrometry were used to characterize the low-resolution structures of oligomerization intermediates.
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Affiliation(s)
- Pavel Macek
- Université Grenoble Alpes, Institut de
Biologie Structurale (IBS), Grenoble, France
- CEA, IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
| | - Rime Kerfah
- Université Grenoble Alpes, Institut de
Biologie Structurale (IBS), Grenoble, France
- CEA, IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
| | - Elisabetta Boeri Erba
- Université Grenoble Alpes, Institut de
Biologie Structurale (IBS), Grenoble, France
- CEA, IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
| | - Elodie Crublet
- Université Grenoble Alpes, Institut de
Biologie Structurale (IBS), Grenoble, France
- CEA, IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
| | - Christine Moriscot
- Université Grenoble Alpes, Institut de
Biologie Structurale (IBS), Grenoble, France
- CEA, IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
| | - Guy Schoehn
- Université Grenoble Alpes, Institut de
Biologie Structurale (IBS), Grenoble, France
- CEA, IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
| | - Carlos Amero
- Centro de Investigaciones Químicas, IICBA,
Universidad Autónoma del Estado de Morelos, México
- Corresponding author. (C.A.);
(J.B.)
| | - Jerome Boisbouvier
- Université Grenoble Alpes, Institut de
Biologie Structurale (IBS), Grenoble, France
- CEA, IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
- Corresponding author. (C.A.);
(J.B.)
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19
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Süssmuth RD, Mainz A. Nonribosomal Peptide Synthesis-Principles and Prospects. Angew Chem Int Ed Engl 2017; 56:3770-3821. [PMID: 28323366 DOI: 10.1002/anie.201609079] [Citation(s) in RCA: 529] [Impact Index Per Article: 75.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Indexed: 01/05/2023]
Abstract
Nonribosomal peptide synthetases (NRPSs) are large multienzyme machineries that assemble numerous peptides with large structural and functional diversity. These peptides include more than 20 marketed drugs, such as antibacterials (penicillin, vancomycin), antitumor compounds (bleomycin), and immunosuppressants (cyclosporine). Over the past few decades biochemical and structural biology studies have gained mechanistic insights into the highly complex assembly line of nonribosomal peptides. This Review provides state-of-the-art knowledge on the underlying mechanisms of NRPSs and the variety of their products along with detailed analysis of the challenges for future reprogrammed biosynthesis. Such a reprogramming of NRPSs would immediately spur chances to generate analogues of existing drugs or new compound libraries of otherwise nearly inaccessible compound structures.
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Affiliation(s)
- Roderich D Süssmuth
- Technische Universität Berlin, Institut für Chemie, Strasse des 17. Juni 124, 10623, Berlin, Germany
| | - Andi Mainz
- Technische Universität Berlin, Institut für Chemie, Strasse des 17. Juni 124, 10623, Berlin, Germany
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20
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Süssmuth RD, Mainz A. Nicht-ribosomale Peptidsynthese - Prinzipien und Perspektiven. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201609079] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Roderich D. Süssmuth
- Technische Universität Berlin; Institut für Chemie; Straße des 17. Juni 124 10623 Berlin Deutschland
| | - Andi Mainz
- Technische Universität Berlin; Institut für Chemie; Straße des 17. Juni 124 10623 Berlin Deutschland
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21
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Unfolding the mechanism of the AAA+ unfoldase VAT by a combined cryo-EM, solution NMR study. Proc Natl Acad Sci U S A 2016; 113:E4190-9. [PMID: 27402735 DOI: 10.1073/pnas.1603980113] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The AAA+ (ATPases associated with a variety of cellular activities) enzymes play critical roles in a variety of homeostatic processes in all kingdoms of life. Valosin-containing protein-like ATPase of Thermoplasma acidophilum (VAT), the archaeal homolog of the ubiquitous AAA+ protein Cdc48/p97, functions in concert with the 20S proteasome by unfolding substrates and passing them on for degradation. Here, we present electron cryomicroscopy (cryo-EM) maps showing that VAT undergoes large conformational rearrangements during its ATP hydrolysis cycle that differ dramatically from the conformational states observed for Cdc48/p97. We validate key features of the model with biochemical and solution methyl-transverse relaxation optimized spectroscopY (TROSY) NMR experiments and suggest a mechanism for coupling the energy of nucleotide hydrolysis to substrate unfolding. These findings illustrate the unique complementarity between cryo-EM and solution NMR for studies of molecular machines, showing that the structural properties of VAT, as well as the population distributions of conformers, are similar in the frozen specimens used for cryo-EM and in the solution phase where NMR spectra are recorded.
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