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Qin SY, He JH, Zhao Y, Yang YL, Zhang AQ, Lei X. Programming Peptide Liquid Crystal Media to Acquire Independent Sets of Residual Dipolar Couplings and Enantiodiscrimination in Multiple Solvent Systems. Anal Chem 2023; 95:17759-17765. [PMID: 37996077 DOI: 10.1021/acs.analchem.3c03777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2023]
Abstract
Multiple independent sets of residual dipolar couplings (RDCs) acquired by relying on different alignment media show the great potential for de novo structure determination of organic compounds. However, this methodology is severely compromised by the limited availability of multialignment media. In this work, an engineering strategy was developed to program the oligopeptide amphiphiles (OPAs) to create different peptide liquid crystal (LC) media for the acquisition of independent sets of RDCs. With no need for de novo design on peptide sequences, the molecular alignment can be simply modulated by varying the length of the hydrophobic tails within OPAs. Relying on these programmed peptide LC media, five independent sets of RDCs were extracted in a highly efficient and accurate manner. Because of the similar bulk composition of OPAs, this approach offers the significant advantage in circumventing the possible incompatibilities of analytes with one or several different alignment media, therefore avoiding the analysis complication. Notably, these peptide LC media show enantiodifferentiating properties, and the enantiodiscriminating capabilities could also be optimized through the programmed strategy. Furthermore, we show that these media are compatible with different polar solvents, allowing the possible de novo structure elucidation of organic compounds with varied polarities and solubilities.
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Affiliation(s)
- Si-Yong Qin
- Hubei Engineering Technology Research Centre of Energy Polymer Materials, School of Chemistry and Materials Science, South-Central Minzu University, Wuhan 430074, China
- Key Laboratory of Analytical Chemistry of the State Ethnic Affairs Commission, School of Chemistry and Materials Science, South-Central Minzu University, Wuhan 430074, China
| | - Jin-Hao He
- Hubei Engineering Technology Research Centre of Energy Polymer Materials, School of Chemistry and Materials Science, South-Central Minzu University, Wuhan 430074, China
| | - You Zhao
- Hubei Engineering Technology Research Centre of Energy Polymer Materials, School of Chemistry and Materials Science, South-Central Minzu University, Wuhan 430074, China
| | - Yan-Ling Yang
- School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan 430074, P. R. China
| | - Ai-Qing Zhang
- Hubei Engineering Technology Research Centre of Energy Polymer Materials, School of Chemistry and Materials Science, South-Central Minzu University, Wuhan 430074, China
| | - Xinxiang Lei
- School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan 430074, P. R. China
- State Key Laboratory of Applied Organic Chemistry, Lanzhou Magnetic Resonance Center, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
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Wang M, Song X, Chen J, Chen X, Zhang X, Yang Y, Liu Z, Yao L. Intracellular environment can change protein conformational dynamics in cells through weak interactions. SCIENCE ADVANCES 2023; 9:eadg9141. [PMID: 37478178 PMCID: PMC10361600 DOI: 10.1126/sciadv.adg9141] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 06/21/2023] [Indexed: 07/23/2023]
Abstract
Conformational dynamics is important for protein functions, many of which are performed in cells. How the intracellular environment may affect protein conformational dynamics is largely unknown. Here, loop conformational dynamics is studied for a model protein in Escherichia coli cells by using nuclear magnetic resonance (NMR) spectroscopy. The weak interactions between the protein and surrounding macromolecules in cells hinder the protein rotational diffusion, which extends the dynamic detection timescale up to microseconds by the NMR spin relaxation method. The loop picosecond to microsecond dynamics is confirmed by nanoparticle-assisted spin relaxation and residual dipolar coupling methods. The loop interactions with the intracellular environment are perturbed through point mutation of the loop sequence. For the sequence of the protein that interacts stronger with surrounding macromolecules, the loop becomes more rigid in cells. In contrast, the mutational effect on the loop dynamics in vitro is small. This study provides direct evidence that the intracellular environment can modify protein loop conformational dynamics through weak interactions.
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Affiliation(s)
- Mengting Wang
- Qingdao New Energy Shandong Laboratory, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiangfei Song
- Qingdao New Energy Shandong Laboratory, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
| | - Jingfei Chen
- Qingdao New Energy Shandong Laboratory, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
| | - Xiaoxu Chen
- Qingdao New Energy Shandong Laboratory, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xueying Zhang
- Qingdao New Energy Shandong Laboratory, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ying Yang
- Qingdao New Energy Shandong Laboratory, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
| | - Zhijun Liu
- National Facility for Protein Science, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Lishan Yao
- Qingdao New Energy Shandong Laboratory, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
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Shen Y, Bax A. Synergism between x-ray crystallography and NMR residual dipolar couplings in characterizing protein dynamics. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2023; 10:040901. [PMID: 37448874 PMCID: PMC10338066 DOI: 10.1063/4.0000192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 06/23/2023] [Indexed: 07/15/2023]
Abstract
The important role of structural dynamics in protein function is widely recognized. Thermal or B-factors and their anisotropy, seen in x-ray analysis of protein structures, report on the presence of atomic coordinate heterogeneity that can be attributed to motion. However, their quantitative evaluation in terms of protein dynamics by x-ray ensemble refinement remains challenging. NMR spectroscopy provides quantitative information on the amplitudes and time scales of motional processes. Unfortunately, with a few exceptions, the NMR data do not provide direct insights into the atomic details of dynamic trajectories. Residual dipolar couplings, measured by solution NMR, are very precise parameters reporting on the time-averaged bond-vector orientations and may offer the opportunity to derive correctly weighted dynamic ensembles of structures for cases where multiple high-resolution x-ray structures are available. Applications to the SARS-CoV-2 main protease, Mpro, and ubiquitin highlight this complementarity of NMR and crystallography for quantitative assessment of internal motions.
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Affiliation(s)
| | - Ad Bax
- Author to whom correspondence should be addressed:
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Lin Y, Li J, Qin SY, Sun H, Yang YL, Navarro-Vázquez A, Lei X. Programmable alignment media from self-assembled oligopeptide amphiphiles for the measurement of independent sets of residual dipolar couplings in organic solvents. Chem Sci 2022; 13:5838-5845. [PMID: 35685790 PMCID: PMC9131869 DOI: 10.1039/d2sc01057g] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 04/14/2022] [Indexed: 11/27/2022] Open
Abstract
NMR spectroscopy in anisotropic media has emerged as a powerful technique for the structural elucidation of organic molecules. Its application requires weak alignment of analytes by means of suitable alignment media. Although a number of alignment media, that are compatible with organic solvents, have been introduced in the last 20 years, acquiring a number of independent, non-linearly related sets of anisotropic NMR data from the same organic solvent system remains a formidable challenge, which is however crucial for the alignment simulations and deriving dynamic and structural information of organic molecules unambiguously. Herein, we introduce a programmable strategy to construct several distinct peptide-based alignment media by adjusting the amino acid sequence, which allows us to measure independent sets of residual dipolar couplings (RDCs) in a highly efficient and accurate manner. This study opens a new avenue for de novo structure determination of organic compounds without requiring prior structural information. We report a programmable strategy to construct multi-alignment media via peptide self-assembly for the measurement of independent sets of residual dipolar couplings (RDCs).![]()
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Affiliation(s)
- Yuexiao Lin
- School of Pharmaceutical Sciences, South-Central University for Nationalities Wuhan 430074 China
| | - Jiaqian Li
- School of Pharmaceutical Sciences, South-Central University for Nationalities Wuhan 430074 China
| | - Si-Yong Qin
- Key Laboratory of Analytical Chemistry of the State Ethnic Affairs Commission, South-Central University for Nationalities Wuhan 430074 China
| | - Han Sun
- Group of Structural Chemistry and Computational Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) 13125 Berlin Germany
| | - Yan-Ling Yang
- School of Pharmaceutical Sciences, South-Central University for Nationalities Wuhan 430074 China
| | - Armando Navarro-Vázquez
- Departamento de Química Fundamental, Universidade Federal de Pernambuco Cidade Universitária CEP 50740-540 Recife PE Brazil
| | - Xinxiang Lei
- School of Pharmaceutical Sciences, South-Central University for Nationalities Wuhan 430074 China .,Key Laboratory of Analytical Chemistry of the State Ethnic Affairs Commission, South-Central University for Nationalities Wuhan 430074 China
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Ma B, Chen JL, Cui CY, Yang F, Gong YJ, Su XC. Rigid, Highly Reactive and Stable DOTA-like Tags Containing a Thiol-Specific Phenylsulfonyl Pyridine Moiety for Protein Modification and NMR Analysis*. Chemistry 2021; 27:16145-16152. [PMID: 34595784 DOI: 10.1002/chem.202102495] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Indexed: 11/06/2022]
Abstract
Site specific installation of a paramagnetic ion with magnetic anisotropy in a biomolecule generates valuable structural restraints, such as pseudocontact shifts (PCSs) and residual dipolar couplings (RDCs). These paramagnetic effects can be used to characterize the structures, interactions and dynamics of biological macromolecules and their complexes. Two single-armed DOTA-like tags, BrPSPy-DO3M(S)A-Ln and BrPSPy-6M-DO3M(S)A-Ln, each containing a thiol-specific reacting group, that is, a phenylsulfonyl pyridine moiety, are demonstrated as rigid, reactive and stable paramagnetic tags for protein modification by formation of a reducing resistant thioether bond between the protein and the tag. The two tags present high reactivity with the solvent exposed thiol group in aqueous solution at room temperature. The introduction of Br at the meta-position in pyridine enhances the reactivity of 4-phenylsulfonyl pyridine towards the solvent exposed thiol group in a protein, whereas the ortho-methyl group in pyridine increases the rigidity of the tag in the protein conjugates. The high performance of these two tags has been demonstrated in different cysteine mutants of ubiquitin and GB1. The high reactivity and rigidity of these two tags can be added in the toolbox of paramagnetic tags suitable for the high-resolution NMR measurements of biological macromolecules and their complexes.
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Affiliation(s)
- Bo Ma
- State Key Laboratory of Elemento-organic Chemistry, College of Chemistry, Nankai University, Weijin Road 94, Tianjin, 300071, P.R. China
| | - Jia-Liang Chen
- State Key Laboratory of Elemento-organic Chemistry, College of Chemistry, Nankai University, Weijin Road 94, Tianjin, 300071, P.R. China
| | - Chao-Yu Cui
- State Key Laboratory of Elemento-organic Chemistry, College of Chemistry, Nankai University, Weijin Road 94, Tianjin, 300071, P.R. China
| | - Feng Yang
- State Key Laboratory of Elemento-organic Chemistry, College of Chemistry, Nankai University, Weijin Road 94, Tianjin, 300071, P.R. China
| | - Yan-Jun Gong
- State Key Laboratory of Elemento-organic Chemistry, College of Chemistry, Nankai University, Weijin Road 94, Tianjin, 300071, P.R. China
| | - Xun-Cheng Su
- State Key Laboratory of Elemento-organic Chemistry, College of Chemistry, Nankai University, Weijin Road 94, Tianjin, 300071, P.R. China
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Chiliveri SC, Robertson AJ, Shen Y, Torchia DA, Bax A. Advances in NMR Spectroscopy of Weakly Aligned Biomolecular Systems. Chem Rev 2021; 122:9307-9330. [PMID: 34766756 DOI: 10.1021/acs.chemrev.1c00730] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The measurement and application of residual dipolar couplings (RDCs) in solution NMR studies of biological macromolecules has become well established over the past quarter of a century. Numerous methods for generating the requisite anisotropic orientational molecular distribution have been demonstrated, each with its specific strengths and weaknesses. In parallel, an enormous number of pulse schemes have been introduced to measure the many different types of RDCs, ranging from the most widely measured backbone amide 15N-1H RDCs, to 1H-1H RDCs and couplings between low-γ nuclei. Applications of RDCs range from structure validation and refinement to the determination of relative domain orientations, the measurement of backbone and domain motions, and de novo structure determination. Nevertheless, it appears that the power of the RDC methodology remains underutilized. This review aims to highlight the practical aspects of sample preparation and RDC measurement while describing some of the most straightforward applications that take advantage of the exceptionally precise information contained in such data. Some emphasis will be placed on more recent developments that enable the accurate measurement of RDCs in larger systems, which is key to the ongoing shift in focus of biological NMR spectroscopy from structure determination toward gaining improved understanding of how molecular flexibility drives protein function.
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Affiliation(s)
- Sai Chaitanya Chiliveri
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Angus J Robertson
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Yang Shen
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Dennis A Torchia
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Ad Bax
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
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