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Dasgupta S, Ghosh N, Bhattacharyya P, Roy Chowdhury S, Chaudhury K. Metabolomics of asthma, COPD, and asthma-COPD overlap: an overview. Crit Rev Clin Lab Sci 2023; 60:153-170. [PMID: 36420874 DOI: 10.1080/10408363.2022.2140329] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The two common progressive lung diseases, asthma and chronic obstructive pulmonary disease (COPD), are the leading causes of morbidity and mortality worldwide. Asthma-COPD overlap, referred to as ACO, is another complex pulmonary disease that manifests itself with features of both asthma and COPD. The disease has no clear diagnostic or therapeutic guidelines, thereby making both diagnosis and treatment challenging. Though a number of studies on ACO have been documented, gaps in knowledge regarding the pathophysiologic mechanism of this disorder exist. Addressing this issue is an urgent need for improved diagnostic and therapeutic management of the disease. Metabolomics, an increasingly popular technique, reveals the pathogenesis of complex diseases and holds promise in biomarker discovery. This comprehensive narrative review, comprising 99 original research articles in the last five years (2017-2022), summarizes the scientific advances in terms of metabolic alterations in patients with asthma, COPD, and ACO. The analytical tools, nuclear magnetic resonance (NMR), gas chromatography-mass spectrometry (GC-MS), and liquid chromatography-mass spectrometry (LC-MS), commonly used to study the expression of the metabolome, are discussed. Challenges frequently encountered during metabolite identification and quality assessment are highlighted. Bridging the gap between phenotype and metabotype is envisioned in the future.
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Affiliation(s)
- Sanjukta Dasgupta
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Nilanjana Ghosh
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, India
| | | | | | - Koel Chaudhury
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, India
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2
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Anaraki MT, Lysak DH, Downey K, Kock FVC, You X, Majumdar RD, Barison A, Lião LM, Ferreira AG, Decker V, Goerling B, Spraul M, Godejohann M, Helm PA, Kleywegt S, Jobst K, Soong R, Simpson MJ, Simpson AJ. NMR spectroscopy of wastewater: A review, case study, and future potential. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2021; 126-127:121-180. [PMID: 34852923 DOI: 10.1016/j.pnmrs.2021.08.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 08/12/2021] [Accepted: 08/13/2021] [Indexed: 06/13/2023]
Abstract
NMR spectroscopy is arguably the most powerful tool for the study of molecular structures and interactions, and is increasingly being applied to environmental research, such as the study of wastewater. With over 97% of the planet's water being saltwater, and two thirds of freshwater being frozen in the ice caps and glaciers, there is a significant need to maintain and reuse the remaining 1%, which is a precious resource, critical to the sustainability of most life on Earth. Sanitation and reutilization of wastewater is an important method of water conservation, especially in arid regions, making the understanding of wastewater itself, and of its treatment processes, a highly relevant area of environmental research. Here, the benefits, challenges and subtleties of using NMR spectroscopy for the analysis of wastewater are considered. First, the techniques available to overcome the specific challenges arising from the nature of wastewater (which is a complex and dilute matrix), including an examination of sample preparation and NMR techniques (such as solvent suppression), in both the solid and solution states, are discussed. Then, the arsenal of available NMR techniques for both structure elucidation (e.g., heteronuclear, multidimensional NMR, homonuclear scalar coupling-based experiments) and the study of intermolecular interactions (e.g., diffusion, nuclear Overhauser and saturation transfer-based techniques) in wastewater are examined. Examples of wastewater NMR studies from the literature are reviewed and potential areas for future research are identified. Organized by nucleus, this review includes the common heteronuclei (13C, 15N, 19F, 31P, 29Si) as well as other environmentally relevant nuclei and metals such as 27Al, 51V, 207Pb and 113Cd, among others. Further, the potential of additional NMR methods such as comprehensive multiphase NMR, NMR microscopy and hyphenated techniques (for example, LC-SPE-NMR-MS) for advancing the current understanding of wastewater are discussed. In addition, a case study that combines natural abundance (i.e. non-concentrated), targeted and non-targeted NMR to characterize wastewater, along with in vivo based NMR to understand its toxicity, is included. The study demonstrates that, when applied comprehensively, NMR can provide unique insights into not just the structure, but also potential impacts, of wastewater and wastewater treatment processes. Finally, low-field NMR, which holds considerable future potential for on-site wastewater monitoring, is briefly discussed. In summary, NMR spectroscopy is one of the most versatile tools in modern science, with abilities to study all phases (gases, liquids, gels and solids), chemical structures, interactions, interfaces, toxicity and much more. The authors hope this review will inspire more scientists to embrace NMR, given its huge potential for both wastewater analysis in particular and environmental research in general.
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Affiliation(s)
- Maryam Tabatabaei Anaraki
- Environmental NMR Center, University of Toronto Scarborough, 1265 Military Trail, Toronto M1C1A4, Canada
| | - Daniel H Lysak
- Environmental NMR Center, University of Toronto Scarborough, 1265 Military Trail, Toronto M1C1A4, Canada
| | - Katelyn Downey
- Environmental NMR Center, University of Toronto Scarborough, 1265 Military Trail, Toronto M1C1A4, Canada
| | - Flávio Vinicius Crizóstomo Kock
- Environmental NMR Center, University of Toronto Scarborough, 1265 Military Trail, Toronto M1C1A4, Canada; Department of Chemistry, Federal University of São Carlos-SP (UFSCar), São Carlos, SP, Brazil
| | - Xiang You
- Environmental NMR Center, University of Toronto Scarborough, 1265 Military Trail, Toronto M1C1A4, Canada
| | - Rudraksha D Majumdar
- Environmental NMR Center, University of Toronto Scarborough, 1265 Military Trail, Toronto M1C1A4, Canada; Synex Medical, 2 Bloor Street E, Suite 310, Toronto, ON M4W 1A8, Canada
| | - Andersson Barison
- NMR Center, Federal University of Paraná, CP 19081, 81530-900 Curitiba, PR, Brazil
| | - Luciano Morais Lião
- NMR Center, Institute of Chemistry, Universidade Federal de Goiás, Goiânia 74690-900, Brazil
| | | | - Venita Decker
- Bruker Biospin GmbH, Silberstreifen 4, 76287 Rheinstetten, Germany
| | | | - Manfred Spraul
- Bruker Biospin GmbH, Silberstreifen 4, 76287 Rheinstetten, Germany
| | | | - Paul A Helm
- Environmental Monitoring & Reporting Branch, Ontario Ministry of the Environment, Toronto M9P 3V6, Canada
| | - Sonya Kleywegt
- Technical Assessment and Standards Development Branch, Ontario Ministry of the Environment, Conservation and Parks, Toronto, ON M4V 1M2, Canada
| | - Karl Jobst
- Memorial University of Newfoundland, St. John's, NL A1C 5S7, Canada
| | - Ronald Soong
- Environmental NMR Center, University of Toronto Scarborough, 1265 Military Trail, Toronto M1C1A4, Canada
| | - Myrna J Simpson
- Environmental NMR Center, University of Toronto Scarborough, 1265 Military Trail, Toronto M1C1A4, Canada
| | - Andre J Simpson
- Environmental NMR Center, University of Toronto Scarborough, 1265 Military Trail, Toronto M1C1A4, Canada.
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Sadeghi S, Lee WK, Kong SN, Shetty A, Drum CL. Oral administration of protein nanoparticles: An emerging route to disease treatment. Pharmacol Res 2020; 158:104685. [DOI: 10.1016/j.phrs.2020.104685] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 02/06/2020] [Accepted: 02/07/2020] [Indexed: 01/20/2023]
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Li N, Shi K, Rao T, Banerjee S, Aihara H. Structural insights into the promiscuous DNA binding and broad substrate selectivity of fowlpox virus resolvase. Sci Rep 2020; 10:393. [PMID: 31941902 PMCID: PMC6962361 DOI: 10.1038/s41598-019-56825-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 12/17/2019] [Indexed: 01/07/2023] Open
Abstract
Fowlpox virus resolvase (Fpr) is an endonuclease that cleaves a broad range of branched DNA structures, including the Holliday junction (HJ), with little sequence-specificity. To better understand the mechanisms underlying its relaxed substrate specificity, we determined the crystal structures of Fpr and that in a novel complex with HJ at 3.1-Å resolution. In the Fpr-HJ complex, two Fpr dimers use several distinct regions to interact with different DNA structural motifs, showing versatility in DNA-binding. Biochemical and solution NMR data support the existence of non-canonical modes of HJ interaction in solution. The binding of Fpr to various DNA motifs are mediated by its flat DNA-binding surface, which is centered on a short loop spanning K61 to I72 and flanked by longer α-helices at the outer edges, and basic side grooves near the dimer interface. Replacing the Fpr loop K61~I72 with a longer loop from Thermus thermophilus RuvC (E71~A87) endows Fpr with an enhanced selectivity toward HJ cleavage but with a target sequence preference distinct from that of RuvC, highlighting a unique role of this loop region in Fpr-HJ interaction. Our work helps explain the broad substrate selectivity of Fpr and suggests a possible mode of its association with poxvirus hairpin telomeres.
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Affiliation(s)
- Na Li
- 0000000419368657grid.17635.36Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6-155 Jackson Hall, 321 Church Street S.E. Minneapolis, Minneapolis, MN 55455 USA ,0000 0001 0703 7066grid.412099.7Present Address: College of Biological Engineering, Henan University of Technology, Zhengzhou, 450001 People’s Republic of China
| | - Ke Shi
- 0000000419368657grid.17635.36Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6-155 Jackson Hall, 321 Church Street S.E. Minneapolis, Minneapolis, MN 55455 USA
| | - Timsi Rao
- 0000000419368657grid.17635.36Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6-155 Jackson Hall, 321 Church Street S.E. Minneapolis, Minneapolis, MN 55455 USA
| | - Surajit Banerjee
- 0000 0001 1939 4845grid.187073.aNortheastern Collaborative Access Team, Cornell University, Advanced Photon Source, Lemont, Illinois 60439 USA
| | - Hideki Aihara
- 0000000419368657grid.17635.36Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6-155 Jackson Hall, 321 Church Street S.E. Minneapolis, Minneapolis, MN 55455 USA
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Grudziąż K, Zawadzka-Kazimierczuk A, Koźmiński W. High-dimensional NMR methods for intrinsically disordered proteins studies. Methods 2018; 148:81-87. [PMID: 29705209 DOI: 10.1016/j.ymeth.2018.04.031] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Accepted: 04/24/2018] [Indexed: 01/16/2023] Open
Abstract
Intrinsically disordered proteins (IDPs) are getting more and more interest of the scientific community. Nuclear magnetic resonance (NMR) is often a technique of choice for these studies, as it provides atomic-resolution information on structure, dynamics and interactions of IDPs. Nonetheless, NMR spectra of IDPs are typically extraordinary crowded, comparing to those of structured proteins. To overcome this problem, high-dimensional NMR experiments can be used, which allow for a better peak separation. In the present review different aspects of such experiments are discussed, from data acquisition and processing to analysis, focusing on experiments for resonance assignment.
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Affiliation(s)
- Katarzyna Grudziąż
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Anna Zawadzka-Kazimierczuk
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Wiktor Koźmiński
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland.
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6
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Stärtzel P. Arginine as an Excipient for Protein Freeze-Drying: A Mini Review. J Pharm Sci 2018; 107:960-967. [DOI: 10.1016/j.xphs.2017.11.015] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 10/26/2017] [Accepted: 11/16/2017] [Indexed: 12/14/2022]
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Kheddo P, Bramham JE, Dearman RJ, Uddin S, van der Walle CF, Golovanov AP. Investigating Liquid–Liquid Phase Separation of a Monoclonal Antibody Using Solution-State NMR Spectroscopy: Effect of Arg·Glu and Arg·HCl. Mol Pharm 2017; 14:2852-2860. [DOI: 10.1021/acs.molpharmaceut.7b00418] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Priscilla Kheddo
- Manchester
Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester, M1 7DN, U.K
| | - Jack E. Bramham
- Manchester
Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester, M1 7DN, U.K
| | - Rebecca J. Dearman
- School
of Biological Sciences, The University of Manchester, Manchester, M13 9PL, U.K
| | - Shahid Uddin
- Formulation
Sciences, MedImmune Ltd., Aaron Klug Building, Granta Park, Cambridge, CB21 6GH, U.K
| | | | - Alexander P. Golovanov
- Manchester
Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester, M1 7DN, U.K
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Kheddo P, Cliff MJ, Uddin S, van der Walle CF, Golovanov AP. Characterizing monoclonal antibody formulations in arginine glutamate solutions using 1H NMR spectroscopy. MAbs 2016; 8:1245-1258. [PMID: 27589351 PMCID: PMC5058632 DOI: 10.1080/19420862.2016.1214786] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Assessing how excipients affect the self-association of monoclonal antibodies (mAbs) requires informative and direct in situ measurements for highly concentrated solutions, without sample dilution or perturbation. This study explores the application of solution nuclear magnetic resonance (NMR) spectroscopy for characterization of typical mAb behavior in formulations containing arginine glutamate. The data show that the analysis of signal intensities in 1D 1H NMR spectra, when compensated for changes in buffer viscosity, is invaluable for identifying conditions where protein-protein interactions are minimized. NMR-derived molecular translational diffusion rates for concentrated solutions are less useful than transverse relaxation rates as parameters defining optimal formulation. Furthermore, NMR reports on the solution viscosity and mAb aggregation during accelerated stability study assessment, generating data consistent with that acquired by size-exclusion chromatography. The methodology developed here offers NMR spectroscopy as a new tool providing complementary information useful to formulation development of mAbs and other large therapeutic proteins.
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Affiliation(s)
- Priscilla Kheddo
- a Manchester Institute of Biotechnology, University of Manchester , Manchester , UK.,b School of Chemistry, University of Manchester , Manchester , UK
| | - Matthew J Cliff
- a Manchester Institute of Biotechnology, University of Manchester , Manchester , UK
| | - Shahid Uddin
- c Formulation Sciences, MedImmune Ltd , Granta Park, Cambridge , UK
| | | | - Alexander P Golovanov
- a Manchester Institute of Biotechnology, University of Manchester , Manchester , UK.,b School of Chemistry, University of Manchester , Manchester , UK
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9
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Kheddo P, Tracka M, Armer J, Dearman RJ, Uddin S, van der Walle CF, Golovanov AP. The effect of arginine glutamate on the stability of monoclonal antibodies in solution. Int J Pharm 2014; 473:126-33. [PMID: 24992318 PMCID: PMC4162492 DOI: 10.1016/j.ijpharm.2014.06.053] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Revised: 06/26/2014] [Accepted: 06/27/2014] [Indexed: 12/21/2022]
Abstract
Finding excipients which mitigate protein self-association and aggregation is an important task during formulation. Here, the effect of an equimolar mixture of l-Arg and l-Glu (Arg·Glu) on colloidal and conformational stability of four monoclonal antibodies (mAb1–mAb4) at different pH is explored, with the temperatures of the on-set of aggregation (Tagg) and unfolding (Tm1) measured by static light scattering and intrinsic fluorescence, respectively. Arg·Glu increased the Tagg of all four mAbs in concentration-dependent manner, especially as pH increased to neutral. Arg·Glu also increased Tm1 of the least thermally stable mAb3, but without similar direct effect on the Tm1 of other mAbs. Raising pH itself from 5 to 7 increased Tm1 for all four mAbs. Selected mAb formulations were assessed under accelerated stability conditions for the monomer fraction remaining in solution after storage. The aggregation of mAb3 was suppressed to a greater extent by Arg·Glu than by Arg·HCl. Furthermore, Arg·Glu suppressed the aggregation of mAb1 at neutral pH such that the fraction monomer was near to that at the more typical formulation pH of 5.5. We conclude that Arg·Glu can suppress mAb aggregation with increasing temperature/pH and, importantly, under accelerated stability conditions at weakly acidic to neutral pH.
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Affiliation(s)
- Priscilla Kheddo
- Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK; Faculty of Life Sciences, University of Manchester, Manchester M13 9PL, UK
| | | | | | - Rebecca J Dearman
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PL, UK
| | - Shahid Uddin
- MedImmune Ltd., Granta Park, Cambridge CB21 6GH, UK
| | | | - Alexander P Golovanov
- Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK; Faculty of Life Sciences, University of Manchester, Manchester M13 9PL, UK.
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10
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Foot JN, Feracci M, Dominguez C. Screening protein--single stranded RNA complexes by NMR spectroscopy for structure determination. Methods 2014; 65:288-301. [PMID: 24096002 PMCID: PMC3959648 DOI: 10.1016/j.ymeth.2013.09.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Revised: 09/16/2013] [Accepted: 09/24/2013] [Indexed: 12/23/2022] Open
Abstract
In the past few years, RNA molecules have been revealed to be at the center of numerous biological processes. Long considered as passive molecules transferring genetic information from DNA to proteins, it is now well established that RNA molecules play important regulatory roles. Associated with that, the number of identified RNA binding proteins (RBPs) has increased considerably and mutations in RNA molecules or RBP have been shown to cause various diseases, such as cancers. It is therefore crucial to understand at the molecular level how these proteins specifically recognise their RNA targets in order to design new generation drug therapies targeting protein-RNA complexes. Nuclear magnetic resonance (NMR) is a particularly well-suited technique to study such protein-RNA complexes at the atomic level and can provide valuable information for new drug discovery programs. In this article, we describe the NMR strategy that we and other laboratories use for screening optimal conditions necessary for structural studies of protein-single stranded RNA complexes, using two proteins, Sam68 and T-STAR, as examples.
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Affiliation(s)
- Jaelle N Foot
- Department of Biochemistry, Henry Wellcome Laboratories of Structural Biology, University of Leicester, UK
| | - Mikael Feracci
- Department of Biochemistry, Henry Wellcome Laboratories of Structural Biology, University of Leicester, UK
| | - Cyril Dominguez
- Department of Biochemistry, Henry Wellcome Laboratories of Structural Biology, University of Leicester, UK.
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Fukuda M, Kameoka D, Torizawa T, Saitoh S, Yasutake M, Imaeda Y, Koga A, Mizutani A. Thermodynamic and fluorescence analyses to determine mechanisms of IgG1 stabilization and destabilization by arginine. Pharm Res 2013; 31:992-1001. [PMID: 24287623 DOI: 10.1007/s11095-013-1221-2] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Accepted: 09/30/2013] [Indexed: 11/24/2022]
Abstract
PURPOSE To investigate mechanisms governing the stabilization and destabilization of immunoglobulin (IgG1) by arginine (Arg). METHODS The effects of Arg on the aggregation/degradation, thermodynamic stability, hydrophobicity, and aromatic residues of IgG1 were respectively investigated by size-exclusion chromatography, differential scanning calorimetry, probe fluorescence, and intrinsic fluorescence. RESULTS Arg monohydrochloride (Arg-HCl) suppressed IgG1 aggregation at near-neutral pH, but facilitated aggregation and degradation at acidic pH or at high storage temperature. Equimolar mixtures of Arg and aspartic acid (Asp) or glutamic acid (Glu) suppressed aggregation without facilitating degradation even at high temperature. Arg-HCl decreased the thermodynamic stability of IgG1 by enthalpic loss, which was counteracted by using Asp or Glu as a counterion for Arg. The suppression of aggregation by Arg-HCl was well correlated with the decrease in hydrophobicity of IgG1. The intrinsic fluorescence of IgG1 was unaffected by Arg-HCl. CONCLUSIONS Suppression of IgG1 aggregation can be attributed to the interaction between Arg and hydrophobic residues; on the other hand, facilitation of aggregation and degradation is presumably due to the interaction between Arg and some acidic residues, which could be competitively inhibited by simultaneously adding either Asp or Glu.
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Affiliation(s)
- Masakazu Fukuda
- Product Engineering Department, Chugai Pharmaceutical Co., Ltd., 5-5-1 Ukima, Kita-ku, Tokyo, 115-8543, Japan,
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12
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Waudby CA, Launay H, Cabrita LD, Christodoulou J. Protein folding on the ribosome studied using NMR spectroscopy. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2013; 74:57-75. [PMID: 24083462 PMCID: PMC3991860 DOI: 10.1016/j.pnmrs.2013.07.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2013] [Revised: 07/17/2013] [Accepted: 07/17/2013] [Indexed: 05/11/2023]
Abstract
NMR spectroscopy is a powerful tool for the investigation of protein folding and misfolding, providing a characterization of molecular structure, dynamics and exchange processes, across a very wide range of timescales and with near atomic resolution. In recent years NMR methods have also been developed to study protein folding as it might occur within the cell, in a de novo manner, by observing the folding of nascent polypeptides in the process of emerging from the ribosome during synthesis. Despite the 2.3 MDa molecular weight of the bacterial 70S ribosome, many nascent polypeptides, and some ribosomal proteins, have sufficient local flexibility that sharp resonances may be observed in solution-state NMR spectra. In providing information on dynamic regions of the structure, NMR spectroscopy is therefore highly complementary to alternative methods such as X-ray crystallography and cryo-electron microscopy, which have successfully characterized the rigid core of the ribosome particle. However, the low working concentrations and limited sample stability associated with ribosome-nascent chain complexes means that such studies still present significant technical challenges to the NMR spectroscopist. This review will discuss the progress that has been made in this area, surveying all NMR studies that have been published to date, and with a particular focus on strategies for improving experimental sensitivity.
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14
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Structures of the Sgt2/SGTA dimerization domain with the Get5/UBL4A UBL domain reveal an interaction that forms a conserved dynamic interface. Cell Rep 2012; 2:1620-32. [PMID: 23142665 DOI: 10.1016/j.celrep.2012.10.010] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Revised: 09/25/2012] [Accepted: 10/08/2012] [Indexed: 10/27/2022] Open
Abstract
In the cytoplasm, the correct delivery of membrane proteins is an essential and highly regulated process. The posttranslational targeting of the important tail-anchor membrane (TA) proteins has recently been under intense investigation. A specialized pathway, called the guided entry of TA proteins (GET) pathway in yeast and the transmembrane domain recognition complex (TRC) pathway in vertebrates, recognizes endoplasmic-reticulum-targeted TA proteins and delivers them through a complex series of handoffs. An early step is the formation of a complex between Sgt2/SGTA, a cochaperone with a presumed ubiquitin-like-binding domain (UBD), and Get5/UBL4A, a ubiquitin-like domain (UBL)-containing protein. We structurally characterize this UBD/UBL interaction for both yeast and human proteins. This characterization is supported by biophysical studies that demonstrate that complex formation is mediated by electrostatics, generating an interface that has high-affinity with rapid kinetics. In total, this work provides a refined model of the interplay of Sgt2 homologs in TA targeting.
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15
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Brockmann C, Soucek S, Kuhlmann SI, Mills-Lujan K, Kelly SM, Yang JC, Iglesias N, Stutz F, Corbett AH, Neuhaus D, Stewart M. Structural basis for polyadenosine-RNA binding by Nab2 Zn fingers and its function in mRNA nuclear export. Structure 2012; 20:1007-18. [PMID: 22560733 PMCID: PMC3384006 DOI: 10.1016/j.str.2012.03.011] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2012] [Revised: 03/19/2012] [Accepted: 03/26/2012] [Indexed: 01/19/2023]
Abstract
Polyadenylation regulation and efficient nuclear export of mature mRNPs both require the polyadenosine-RNA-binding protein, Nab2, which contains seven CCCH Zn fingers. We describe here the solution structure of fingers 5-7, which are necessary and sufficient for high-affinity polyadenosine-RNA binding, and identify key residues involved. These Zn fingers form a single structural unit. Structural coherence is lost in the RNA-binding compromised Nab2-C437S mutant, which also suppresses the rat8-2 allele of RNA helicase Dbp5. Structure-guided Nab2 variants indicate that dbp5(rat8-2) suppression is more closely linked to hyperadenylation and suppression of mutant alleles of the nuclear RNA export adaptor, Yra1, than to affinity for polyadenosine-RNA. These results indicate that, in addition to modulating polyA tail length, Nab2 has an unanticipated function associated with generating export-competent mRNPs, and that changes within fingers 5-7 lead to suboptimal assembly of mRNP export complexes that are more easily disassembled by Dbp5 upon reaching the cytoplasm.
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Affiliation(s)
- Christoph Brockmann
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
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16
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Daubner GM, Cléry A, Jayne S, Stevenin J, Allain FHT. A syn-anti conformational difference allows SRSF2 to recognize guanines and cytosines equally well. EMBO J 2011; 31:162-74. [PMID: 22002536 DOI: 10.1038/emboj.2011.367] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2011] [Accepted: 09/12/2011] [Indexed: 11/09/2022] Open
Abstract
SRSF2 (SC35) is a key player in the regulation of alternative splicing events and binds degenerated RNA sequences with similar affinity in nanomolar range. We have determined the solution structure of the SRSF2 RRM bound to the 5'-UCCAGU-3' and 5'-UGGAGU-3' RNA, both identified as SRSF2 binding sites in the HIV-1 tat exon 2. RNA recognition is achieved through a novel sandwich-like structure with both termini forming a positively charged cavity to accommodate the four central nucleotides. To bind both RNA sequences equally well, SRSF2 forms a nearly identical network of intermolecular interactions by simply flipping the bases of the two consecutive C or G nucleotides into either anti or syn conformation. We validate this unusual mode of RNA recognition functionally by in-vitro and in-vivo splicing assays and propose a 5'-SSNG-3' (S=C/G) high-affinity binding consensus sequence for SRSF2. In conclusion, in addition to describe for the first time the RNA recognition mode of SRSF2, we provide the precise consensus sequence to identify new putative binding sites for this splicing factor.
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Affiliation(s)
- Gerrit M Daubner
- Institute of Molecular Biology and Biophysics, ETH Zürich, Zürich, Switzerland
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Dominguez C, Schubert M, Duss O, Ravindranathan S, Allain FHT. Structure determination and dynamics of protein-RNA complexes by NMR spectroscopy. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2011; 58:1-61. [PMID: 21241883 DOI: 10.1016/j.pnmrs.2010.10.001] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2010] [Accepted: 04/24/2010] [Indexed: 05/30/2023]
Affiliation(s)
- Cyril Dominguez
- Institute for Molecular Biology and Biophysics, ETH Zürich, CH-8093 Zürich, Switzerland
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Kwan AH, Mobli M, Gooley PR, King GF, Mackay JP. Macromolecular NMR spectroscopy for the non-spectroscopist. FEBS J 2011; 278:687-703. [PMID: 21214860 DOI: 10.1111/j.1742-4658.2011.08004.x] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
NMR spectroscopy is a powerful tool for studying the structure, function and dynamics of biological macromolecules. However, non-spectroscopists often find NMR theory daunting and data interpretation nontrivial. As the first of two back-to-back reviews on NMR spectroscopy aimed at non-spectroscopists, the present review first provides an introduction to the basics of macromolecular NMR spectroscopy, including a discussion of typical sample requirements and what information can be obtained from simple NMR experiments. We then review the use of NMR spectroscopy for determining the 3D structures of macromolecules and examine how to judge the quality of NMR-derived structures.
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Affiliation(s)
- Ann H Kwan
- School of Molecular Bioscience, University of Sydney, New South Wales, Australia
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Vostrikov VV, Daily AE, Greathouse DV, Koeppe RE. Charged or aromatic anchor residue dependence of transmembrane peptide tilt. J Biol Chem 2010; 285:31723-30. [PMID: 20667827 PMCID: PMC2951244 DOI: 10.1074/jbc.m110.152470] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2010] [Revised: 07/15/2010] [Indexed: 01/13/2023] Open
Abstract
The membrane-spanning segments of integral membrane proteins often are flanked by aromatic or charged amino acid residues, which may "anchor" the transmembrane orientation. Single spanning transmembrane peptides such as those of the WALP family, acetyl-GWW(LA)(n)LWWA-amide, furthermore adopt a moderate average tilt within lipid bilayer membranes. To understand the anchor residue dependence of the tilt, we introduce Leu-Ala "spacers" between paired anchors and in some cases replace the outer tryptophans. The resulting peptides, acetyl-GX(2)ALW(LA)(6)LWLAX(22)A-amide, have Trp, Lys, Arg, or Gly in the two X positions. The apparent average orientations of the core helical sequences were determined in oriented phosphatidylcholine bilayer membranes of varying thickness using solid-state (2)H NMR spectroscopy. When X is Lys, Arg, or Gly, the direction of the tilt is essentially constant in different lipids and presumably is dictated by the tryptophans (Trp(5) and Trp(19)) that flank the inner helical core. The Leu-Ala spacers are no longer helical. The magnitude of the apparent helix tilt furthermore scales nicely with the bilayer thickness except when X is Trp. When X is Trp, the direction of tilt is less well defined in each phosphatidylcholine bilayer and varies up to 70° among 1,2-dioleoyl-sn-glycero-3-phosphocholine, 1,2-dimyristoyl-sn-glycero-3-phosphocholine, and 1,2-dilauroyl-sn-glycero-3-phosphocholine bilayer membranes. Indeed, the X = Trp case parallels earlier observations in which WALP family peptides having multiple Trp anchors show little dependence of the apparent tilt magnitude on bilayer thickness. The results shed new light on the interactions of arginine, lysine, tryptophan, and even glycine at lipid bilayer membrane interfaces.
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Affiliation(s)
- Vitaly V. Vostrikov
- From the Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701
| | - Anna E. Daily
- From the Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701
| | - Denise V. Greathouse
- From the Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701
| | - Roger E. Koeppe
- From the Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701
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Bermel W, Tkach EN, Sobol AG, Golovanov AP. Simultaneous measurement of residual dipolar couplings for proteins in complex using the isotopically discriminated NMR approach. J Am Chem Soc 2009; 131:8564-70. [DOI: 10.1021/ja901602c] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Wolfgang Bermel
- Bruker Biospin GmbH, Silberstreifen 4, 76287 Rheinstetten, Germany, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia, and Faculty of Life Sciences and Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Elena N. Tkach
- Bruker Biospin GmbH, Silberstreifen 4, 76287 Rheinstetten, Germany, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia, and Faculty of Life Sciences and Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Alexander G. Sobol
- Bruker Biospin GmbH, Silberstreifen 4, 76287 Rheinstetten, Germany, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia, and Faculty of Life Sciences and Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Alexander P. Golovanov
- Bruker Biospin GmbH, Silberstreifen 4, 76287 Rheinstetten, Germany, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia, and Faculty of Life Sciences and Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
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