1
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Rupert PB, Buerger M, Girard EJ, Frutoso M, Parrilla D, Ng K, Gooley T, Groh V, Strong RK. Preclinical characterization of Pan-NKG2D ligand-binding NKG2D receptor decoys. Heliyon 2024; 10:e28583. [PMID: 38586421 PMCID: PMC10998067 DOI: 10.1016/j.heliyon.2024.e28583] [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] [Received: 12/21/2023] [Revised: 03/18/2024] [Accepted: 03/20/2024] [Indexed: 04/09/2024] Open
Abstract
NKG2D and its ligands are critical regulators of protective immune responses controlling infections and cancer, defining a crucial immune signaling axis. Current therapeutic efforts targeting this axis almost exclusively aim at enhancing NKG2D-mediated effector functions. However, this axis can drive disease processes when dysregulated, in particular, driving stem-like cancer cell reprogramming and tumorigenesis through receptor/ligand self-stimulation on tumor cells. Despite complexities with its structure and biology, we developed multiple novel engineered proteins that functionally serve as axis-blocking NKG2D "decoys" and report biochemical, structural, in vitro, and in vivo evaluation of their functionality.
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Affiliation(s)
- Peter B Rupert
- Division of Basic Science, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Matthew Buerger
- Division of Basic Science, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Emily J Girard
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Marie Frutoso
- Division of Basic Science, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Don Parrilla
- Division of Basic Science, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Kevin Ng
- Division of Basic Science, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Theodore Gooley
- Division of Basic Science, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Veronika Groh
- Division of Basic Science, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Roland K Strong
- Division of Basic Science, Fred Hutchinson Cancer Center, Seattle, WA, United States
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2
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Um S, Jeong H, An JS, Jo SJ, Kim YR, Oh DC, Moon K. Chromatographic Determination of the Absolute Configuration in Sanjoinine A That Increases Nitric Oxide Production. Biomol Ther (Seoul) 2023; 31:566-572. [PMID: 37019875 PMCID: PMC10468421 DOI: 10.4062/biomolther.2023.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/03/2023] [Accepted: 03/09/2023] [Indexed: 04/07/2023] Open
Abstract
A chiral derivatization strategy with phenylglycine methyl ester (PGME) was employed to develop a straightforward method to determine the absolute configurations of N,N-dimethyl amino acids. The PGME derivatives were analyzed using liquid chromatography-mass spectrometry to identify the absolute configurations of various N,N-dimethyl amino acids based on their elution time and order. The established method was applied to assign the absolute configuration of the N,N-dimethyl phenylalanine in sanjoinine A (4), a cyclopeptide alkaloid isolated from Zizyphi Spinosi Semen widely used as herbal medicine for insomnia. Sanjoinine A displayed production of nitric oxide (NO) in LPS-activated RAW 264.7 cells.
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Affiliation(s)
- Soohyun Um
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon 21983, Republic of Korea
| | - Hyeongju Jeong
- College of Pharmacy, Research Institute of Pharmaceutical Sciences, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Joon Soo An
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Se Jin Jo
- College of Pharmacy, Research Institute of Pharmaceutical Sciences, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Young Ran Kim
- College of Pharmacy, Research Institute of Pharmaceutical Sciences, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Dong-Chan Oh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Kyuho Moon
- College of Pharmacy, Research Institute of Pharmaceutical Sciences, Chonnam National University, Gwangju 61186, Republic of Korea
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3
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Ó'Fágáin C. Protein Stability: Enhancement and Measurement. Methods Mol Biol 2023; 2699:369-419. [PMID: 37647007 DOI: 10.1007/978-1-0716-3362-5_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
This chapter defines protein stability, emphasizes its importance, and surveys the field of protein stabilization, with summary reference to a selection of 2014-2021 publications. One can enhance stability, particularly by protein engineering strategies but also by chemical modification and by other means. General protocols are set out on how to measure a given protein's (i) kinetic thermal stability and (ii) oxidative stability and (iii) how to undertake chemical modification of a protein in solution.
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Affiliation(s)
- Ciarán Ó'Fágáin
- School of Biotechnology, Dublin City University, Dublin, Ireland.
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4
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Cook Sangar ML, Girard EJ, Hopping G, Yin C, Pakiam F, Brusniak MY, Nguyen E, Ruff R, Gewe MM, Byrnes-Blake K, Nairn NW, Miller DM, Mehlin C, Strand AD, Mhyre AJ, Correnti CE, Strong RK, Simon JA, Olson JM. A potent peptide-steroid conjugate accumulates in cartilage and reverses arthritis without evidence of systemic corticosteroid exposure. Sci Transl Med 2021; 12:12/533/eaay1041. [PMID: 32132215 DOI: 10.1126/scitranslmed.aay1041] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 01/23/2020] [Indexed: 12/12/2022]
Abstract
On-target, off-tissue toxicity limits the systemic use of drugs that would otherwise reduce symptoms or reverse the damage of arthritic diseases, leaving millions of patients in pain and with limited physical mobility. We identified cystine-dense peptides (CDPs) that rapidly accumulate in cartilage of the knees, ankles, hips, shoulders, and intervertebral discs after systemic administration. These CDPs could be used to concentrate arthritis drugs in joints. A cartilage-accumulating peptide, CDP-11R, reached peak concentration in cartilage within 30 min after administration and remained detectable for more than 4 days. Structural analysis of the peptides by crystallography revealed that the distribution of positive charge may be a distinguishing feature of joint-accumulating CDPs. In addition, quantitative whole-body autoradiography showed that the disulfide-bonded tertiary structure is critical for cartilage accumulation and retention. CDP-11R distributed to joints while carrying a fluorophore imaging agent or one of two different steroid payloads, dexamethasone (dex) and triamcinolone acetonide (TAA). Of the two payloads, the dex conjugate did not advance because the free drug released into circulation was sufficient to cause on-target toxicity. In contrast, the CDP-11R-TAA conjugate alleviated joint inflammation in the rat collagen-induced model of rheumatoid arthritis while avoiding toxicities that occurred with nontargeted steroid treatment at the same molar dose. This conjugate shows promise for clinical development and establishes proof of concept for multijoint targeting of disease-modifying therapeutic payloads.
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Affiliation(s)
- Michelle L Cook Sangar
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Emily J Girard
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Gene Hopping
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Chunfeng Yin
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Fiona Pakiam
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Mi-Youn Brusniak
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Elizabeth Nguyen
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Raymond Ruff
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Mesfin M Gewe
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.,Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | | | | | | | - Christopher Mehlin
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Andrew D Strand
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Andrew J Mhyre
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Colin E Correnti
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Roland K Strong
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Julian A Simon
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.,Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - James M Olson
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
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5
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Giri A, Pant D. Carbonic anhydrase modification for carbon management. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:1294-1318. [PMID: 31797268 DOI: 10.1007/s11356-019-06667-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 10/01/2019] [Indexed: 06/10/2023]
Abstract
Carbonic anhydrase modification (chemical and biological) is an attractive strategy for its diverse application to accelerate the absorption of CO2 from a flue gas with improved activity and stability. This article reports various possibilities of CA modification using metal-ligand homologous chemistry, cross-linking agents, and residue- and group-specific and genetic modifications, and assesses their role in carbon management. Chemically modified carbonic anhydrase is able to improve the absorption of carbon dioxide from a gas stream into mediation compounds with enhanced sequestration and mineral formation. Genetically modified CA polypeptide can also increase carbon dioxide conversion. Chemical modification of CA can be categorized in terms of (i) residue-specific modification (involves protein-ligand interaction in terms of substitution/addition) and group-specific modifications (based on the functional groups of the target CA). For every sustainable change, there should be no/limited toxic or immunological response. In this review, several CA modification pathways and biocompatibility rules are proposed as a theoretical support for emerging research in this area.
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Affiliation(s)
- Anand Giri
- Department of Environmental Sciences, Central University of Himachal Pradesh, Kangra, India
| | - Deepak Pant
- School of Chemical Sciences, Central University of Haryana, Mahendragarh, Haryana, 123029, India.
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6
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Identification of Formaldehyde-Induced Modifications in Diphtheria Toxin. J Pharm Sci 2019; 109:543-557. [PMID: 31678246 DOI: 10.1016/j.xphs.2019.10.047] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 10/17/2019] [Accepted: 10/28/2019] [Indexed: 01/08/2023]
Abstract
Diphtheria toxoid is produced by detoxification of diphtheria toxin with formaldehyde. This study was performed to elucidate the chemical nature and location of formaldehyde-induced modifications in diphtheria toxoid. Diphtheria toxin was chemically modified using 4 different reactions with the following reagents: (1) formaldehyde and NaCNBH3, (2) formaldehyde, (3) formaldehyde and NaCNBH3 followed by formaldehyde and glycine, and (4) formaldehyde and glycine. The modifications were studied by SDS-PAGE, primary amino group determination, and liquid chromatography-electrospray mass spectrometry of chymotryptic digests. Reaction 1 resulted in quantitative dimethylation of all lysine residues. Reaction 2 caused intramolecular cross-links, including the NAD+-binding cavity and the receptor-binding site. Moreover, A fragments and B fragments were cross-linked by formaldehyde on part of the diphtheria toxoid molecules. Reaction 3 resulted in formaldehyde-glycine attachments, including in shielded areas of the protein. The detoxification reaction typically used for vaccine preparation (reaction 4) resulted in a combination of intramolecular cross-links and formaldehyde-glycine attachments. Both the NAD+-binding cavity and the receptor-binding site of diphtheria toxin were chemically modified. Although CD4+ T-cell epitopes were affected to some extent, one universal CD4+ T-cell epitope remained almost completely unaltered by the treatment with formaldehyde and glycine.
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7
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Pawolski D, Heintze C, Mey I, Steinem C, Kröger N. Reconstituting the formation of hierarchically porous silica patterns using diatom biomolecules. J Struct Biol 2018; 204:64-74. [DOI: 10.1016/j.jsb.2018.07.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 07/06/2018] [Accepted: 07/07/2018] [Indexed: 11/15/2022]
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8
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Kish WS, Roach MK, Sachi H, Naik AD, Menegatti S, Carbonell RG. Purification of human erythropoietin by affinity chromatography using cyclic peptide ligands. J Chromatogr B Analyt Technol Biomed Life Sci 2018; 1085:1-12. [DOI: 10.1016/j.jchromb.2018.03.039] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 03/12/2018] [Accepted: 03/24/2018] [Indexed: 10/17/2022]
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9
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Hur J, Jang J, Sim J, Son WS, Ahn HC, Kim TS, Shin YH, Lim C, Lee S, An H, Kim SH, Oh DC, Jo EK, Jang J, Lee J, Suh YG. Conformation-Enabled Total Syntheses of Ohmyungsamycins A and B and Structural Revision of Ohmyungsamycin B. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201711286] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Joonseong Hur
- College of Pharmacy; Seoul National University; 1 Gwanak-ro Gwanak-gu Seoul 08826 Republic of Korea
| | - Jaebong Jang
- College of Pharmacy; Seoul National University; 1 Gwanak-ro Gwanak-gu Seoul 08826 Republic of Korea
| | - Jaehoon Sim
- College of Pharmacy; Seoul National University; 1 Gwanak-ro Gwanak-gu Seoul 08826 Republic of Korea
- College of Pharmacy; CHA University; 120 Haeryong-ro Pocheon Gyeonggi-do 11160 Republic of Korea
| | - Woo Sung Son
- College of Pharmacy; CHA University; 120 Haeryong-ro Pocheon Gyeonggi-do 11160 Republic of Korea
| | - Hee-Chul Ahn
- Department of Pharmacy; Dongguk University; Dongguk-ro 32 Ilsandong-gu, Goyang Geonggi-do 10326 Republic of Korea
| | - Tae Sung Kim
- Department of Microbiology; Chungnam National University School of Medicine; Munhwa-ro 266 Jungku Daejeon 35015 Republic of Korea
| | - Yern-Hyerk Shin
- Natural Products Research Institute; College of Pharmacy; Seoul National University; 1 Gwanak-ro Gwanak-gu Seoul 08826 Republic of Korea
| | - Changjin Lim
- College of Pharmacy; Seoul National University; 1 Gwanak-ro Gwanak-gu Seoul 08826 Republic of Korea
- College of Pharmacy; CHA University; 120 Haeryong-ro Pocheon Gyeonggi-do 11160 Republic of Korea
| | - Seungbeom Lee
- College of Pharmacy; Seoul National University; 1 Gwanak-ro Gwanak-gu Seoul 08826 Republic of Korea
| | - Hongchan An
- College of Pharmacy; Seoul National University; 1 Gwanak-ro Gwanak-gu Seoul 08826 Republic of Korea
| | - Seok-Ho Kim
- College of Pharmacy; CHA University; 120 Haeryong-ro Pocheon Gyeonggi-do 11160 Republic of Korea
| | - Dong-Chan Oh
- Natural Products Research Institute; College of Pharmacy; Seoul National University; 1 Gwanak-ro Gwanak-gu Seoul 08826 Republic of Korea
| | - Eun-Kyeong Jo
- Department of Microbiology; Chungnam National University School of Medicine; Munhwa-ro 266 Jungku Daejeon 35015 Republic of Korea
| | - Jichan Jang
- Division of Applied Life Science; Research Institute of Life Science; Gyeongsang National University; Jinju 52828 Republic of Korea
| | - Jeeyeon Lee
- College of Pharmacy; Seoul National University; 1 Gwanak-ro Gwanak-gu Seoul 08826 Republic of Korea
| | - Young-Ger Suh
- College of Pharmacy; Seoul National University; 1 Gwanak-ro Gwanak-gu Seoul 08826 Republic of Korea
- College of Pharmacy; CHA University; 120 Haeryong-ro Pocheon Gyeonggi-do 11160 Republic of Korea
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10
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Hur J, Jang J, Sim J, Son WS, Ahn HC, Kim TS, Shin YH, Lim C, Lee S, An H, Kim SH, Oh DC, Jo EK, Jang J, Lee J, Suh YG. Conformation-Enabled Total Syntheses of Ohmyungsamycins A and B and Structural Revision of Ohmyungsamycin B. Angew Chem Int Ed Engl 2018; 57:3069-3073. [PMID: 29380472 DOI: 10.1002/anie.201711286] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 12/28/2017] [Indexed: 01/06/2023]
Abstract
The first total syntheses of the bioactive cyclodepsipeptides ohmyungsamycin A and B are described. Key features of our synthesis include the concise preparation of a linear cyclization precursor that consists of N-methyl amides and non-proteinogenic amino acids, and its macrolactamization from a bent conformation. The proposed structure of ohmyungsamycin B was revised based on its synthesis. The cyclic core of the ohmyungsamycins was shown to be responsible for the excellent antituberculosis activity, and ohmyungsamycin variants with truncated chains were evaluated for their biological activity.
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Affiliation(s)
- Joonseong Hur
- College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Jaebong Jang
- College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Jaehoon Sim
- College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea.,College of Pharmacy, CHA University, 120 Haeryong-ro, Pocheon, Gyeonggi-do, 11160, Republic of Korea
| | - Woo Sung Son
- College of Pharmacy, CHA University, 120 Haeryong-ro, Pocheon, Gyeonggi-do, 11160, Republic of Korea
| | - Hee-Chul Ahn
- Department of Pharmacy, Dongguk University, Dongguk-ro 32, Ilsandong-gu, Goyang, Geonggi-do, 10326, Republic of Korea
| | - Tae Sung Kim
- Department of Microbiology, Chungnam National University School of Medicine, Munhwa-ro 266, Jungku, Daejeon, 35015, Republic of Korea
| | - Yern-Hyerk Shin
- Natural Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Changjin Lim
- College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea.,College of Pharmacy, CHA University, 120 Haeryong-ro, Pocheon, Gyeonggi-do, 11160, Republic of Korea
| | - Seungbeom Lee
- College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Hongchan An
- College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Seok-Ho Kim
- College of Pharmacy, CHA University, 120 Haeryong-ro, Pocheon, Gyeonggi-do, 11160, Republic of Korea
| | - Dong-Chan Oh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Eun-Kyeong Jo
- Department of Microbiology, Chungnam National University School of Medicine, Munhwa-ro 266, Jungku, Daejeon, 35015, Republic of Korea
| | - Jichan Jang
- Division of Applied Life Science, Research Institute of Life Science, Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Jeeyeon Lee
- College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Young-Ger Suh
- College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea.,College of Pharmacy, CHA University, 120 Haeryong-ro, Pocheon, Gyeonggi-do, 11160, Republic of Korea
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11
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Hattori Y, Heidenreich D, Ono Y, Sugiki T, Yokoyama KI, Suzuki EI, Fujiwara T, Kojima C. Protein 19F-labeling using transglutaminase for the NMR study of intermolecular interactions. JOURNAL OF BIOMOLECULAR NMR 2017; 68:271-279. [PMID: 28756478 DOI: 10.1007/s10858-017-0125-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 07/14/2017] [Indexed: 06/07/2023]
Abstract
The preparation of stable isotope-labeled proteins is important for NMR studies, however, it is often hampered in the case of eukaryotic proteins which are not readily expressed in Escherichia coli. Such proteins are often conveniently investigated following post-expression chemical isotope tagging. Enzymatic 15N-labeling of glutamine side chains using transglutaminase (TGase) has been applied to several proteins for NMR studies. 19F-labeling is useful for interaction studies due to its high NMR sensitivity and susceptibility. Here, 19F-labeling of glutamine side chains using TGase and 2,2,2-trifluoroethylamine hydrochloride was established for use in an NMR study. This enzymatic 19F-labeling readily provided NMR detection of protein-drug and protein-protein interactions with complexes of about 100 kDa since the surface residues provided a good substrate for TGase. The 19F-labeling method was 3.5-fold more sensitive than 15N-labeling, and could be combined with other chemical modification techniques such as lysine 13C-methylation. 13C-dimethylated-19F-labeled FKBP12 provided more accurate information concerning the FK506 binding site.
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Affiliation(s)
- Yoshikazu Hattori
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka, 565-0871, Japan
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Nishihamaboji, 180, Yamashiro-cho, Tokushima, 770-8514, Japan
| | - David Heidenreich
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka, 565-0871, Japan
- Institute for Pharmaceutical Chemistry and Buchmann Institute for Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse 9, 60438, Frankfurt am Main, Germany
| | - Yuki Ono
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka, 565-0871, Japan
| | - Toshihiko Sugiki
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka, 565-0871, Japan
| | - Kei-Ichi Yokoyama
- Institute for Innovation Ajinomoto Co., Inc, Suzuki-cho 1-1, Kawasaki-ku, Kawasaki, 210-8681, Japan
| | - Ei-Ichiro Suzuki
- Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5, Hodogaya-ku, Yokohama, 240-8501, Japan
| | - Toshimichi Fujiwara
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka, 565-0871, Japan
| | - Chojiro Kojima
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka, 565-0871, Japan.
- Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5, Hodogaya-ku, Yokohama, 240-8501, Japan.
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12
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Kish WS, Sachi H, Naik AD, Roach MK, Bobay BG, Blackburn RK, Menegatti S, Carbonell RG. Design, selection, and development of cyclic peptide ligands for human erythropoietin. J Chromatogr A 2017; 1500:105-120. [DOI: 10.1016/j.chroma.2017.04.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 03/28/2017] [Accepted: 04/10/2017] [Indexed: 11/26/2022]
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13
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Shao LP, Si CM, Mao ZY, Zhou W, Molinski TF, Wei BG, Lin GQ. Synthesis and Structure Revision of Symplocin A. Org Chem Front 2017; 4:995-1004. [PMID: 31007934 DOI: 10.1039/c7qo00052a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Symplocin A, a linear peptide possessing N-terminal N,N-dimethylisoleucine, statine, and valic acid residues, has been synthesized for the first time employing our previously established 'one-pot intramolecular tandem protocol'. Moreover, the stereochemistry of natural symplocin A was unambiguously revised through the confirmation by 1D NMR, 2D NMR, and HPLC comparisons with authentic natural product.
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Affiliation(s)
- Lu-Ping Shao
- Department of Natural Products Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai, 201203, China
| | - Chang-Mei Si
- Department of Natural Products Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai, 201203, China
| | - Zhuo-Ya Mao
- Department of Natural Products Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai, 201203, China
| | - Wen Zhou
- Department of Natural Products Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai, 201203, China
| | - Tadeusz F Molinski
- Department of Chemistry and Biochemistry and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Dr, La Jolla, California 92093-0358, United States
| | - Bang-Guo Wei
- Department of Natural Products Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai, 201203, China
| | - Guo-Qiang Lin
- Department of Natural Products Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai, 201203, China
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14
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Abstract
This article defines protein stability, emphasizes its importance and surveys the field of protein stabilization, with summary reference to a selection of 2009-2015 publications. One can enhance stability by, in particular, protein engineering strategies and by chemical modification (including conjugation) in solution. General protocols are set out on how to measure a given protein's (1) kinetic thermal stability, and (2) oxidative stability, and (3) how to undertake chemical modification of a protein in solution.
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Affiliation(s)
- Ciarán Ó'Fágáin
- School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland.
- National Centre for Sensor Research, Dublin City University, Glasnevin, Dublin 9, Ireland.
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15
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Reddy BS, Chary VN, Pavankumar P, Prabhakar S. Characterization of N-methylated amino acids by GC-MS after ethyl chloroformate derivatization. JOURNAL OF MASS SPECTROMETRY : JMS 2016; 51:638-650. [PMID: 28239971 DOI: 10.1002/jms.3788] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 05/13/2016] [Accepted: 05/16/2016] [Indexed: 06/06/2023]
Abstract
Methylation is an essential metabolic process in the biological systems, and it is significant for several biological reactions in living organisms. Methylated compounds are known to be involved in most of the bodily functions, and some of them serve as biomarkers. Theoretically, all α-amino acids can be methylated, and it is possible to encounter them in most animal/plant samples. But the analytical data, especially the mass spectral data, are available only for a few of the methylated amino acids. Thus, it is essential to generate mass spectral data and to develop mass spectrometry methods for the identification of all possible methylated amino acids for future metabolomic studies. In this study, all N-methyl and N,N-dimethyl amino acids were synthesized by the methylation of α-amino acids and characterized by a GC-MS method. The methylated amino acids were derivatized with ethyl chloroformate and analyzed by GC-MS under EI and methane/CI conditions. The EI mass spectra of ethyl chloroformate derivatives of N-methyl (1-18) and N,N-dimethyl amino acids (19-35) showed abundant [M-COOC2 H5 ]+ ions. The fragment ions due to loss of C2 H4 , CO2 , (CO2 + C2 H4 ) from [M-COOC2 H5 ]+ were of structure indicative for 1-18. The EI spectra of 19-35 showed less number of fragment ions when compared with those of 1-18. The side chain group (R) caused specific fragment ions characteristic to its structure. The methane/CI spectra of the studied compounds showed [M + H]+ ions to substantiate their molecular weights. The detected EI fragment ions were characteristic of the structure that made easy identification of the studied compounds, including isomeric/isobaric compounds. Fragmentation patterns of the studied compounds (1-35) were confirmed by high-resolution mass spectra data and further substantiated by the data obtained from 13 C2 -labeled glycines and N-ethoxycarbonyl methoxy esters. The method was applied to human plasma samples for the identification of amino acids and methylated amino acids. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- B Sudarshana Reddy
- Academy of Scientific and Innovative Research, CSIR-Indian Institute of Chemical Technology, Hyderabad, 500 007, Telangana, India
- National Centre for Mass Spectrometry, CSIR-Indian Institute of Chemical Technology, Hyderabad, 500 007, Telangana, India
| | - V Naresh Chary
- National Centre for Mass Spectrometry, CSIR-Indian Institute of Chemical Technology, Hyderabad, 500 007, Telangana, India
| | - P Pavankumar
- Academy of Scientific and Innovative Research, CSIR-Indian Institute of Chemical Technology, Hyderabad, 500 007, Telangana, India
- National Centre for Mass Spectrometry, CSIR-Indian Institute of Chemical Technology, Hyderabad, 500 007, Telangana, India
| | - S Prabhakar
- Academy of Scientific and Innovative Research, CSIR-Indian Institute of Chemical Technology, Hyderabad, 500 007, Telangana, India
- National Centre for Mass Spectrometry, CSIR-Indian Institute of Chemical Technology, Hyderabad, 500 007, Telangana, India
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16
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Naresh Chary V, Sudarshana Reddy B, Kumar CD, Srinivas R, Prabhakar S. Characterization of N,N-dimethyl amino acids by electrospray ionization-tandem mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2015; 50:771-781. [PMID: 26259661 DOI: 10.1002/jms.3588] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 02/23/2015] [Accepted: 02/23/2015] [Indexed: 06/04/2023]
Abstract
Methylation is an essential metabolic process for a number of critical reactions in the body. Methyl groups are involved in the healthy function of the body life processes, by conducting methylation process involving specific enzymes. In these processes, various amino acids are methylated, and the occurrence of methylated amino acids in nature is diverse. Nowadays, mass-spectrometric-based identification of small molecules as biomarkers for diseases is a growing research. Although all dimethyl amino acids are metabolically important molecules, mass spectral data are available only for a few of them in the literature. In this study, we report synthesis and characterization of all dimethyl amino acids, by electrospray ionization-tandem mass spectrometry (MS/MS) experiments on protonated molecules. The MS/MS spectra of all the studied dimethyl amino acids showed preliminary loss of H2O + CO to form corresponding immonium ions. The other product ions in the spectra are highly characteristic of the methyl groups on the nitrogen and side chain of the amino acids. The amino acids, which are isomeric and isobaric with the studied dimethyl amino acids, gave distinctive MS/MS spectra. The study also included MS/MS analysis of immonium ions of dimethyl amino acids that provide information on side chain structure, and it is further tested to determine the N-terminal amino acid of the peptides.
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Affiliation(s)
- V Naresh Chary
- National Centre for Mass Spectrometry, CSIR-Indian Institute of Chemical Technology, Hyderabad, 500 007, Telangana, India
| | - B Sudarshana Reddy
- National Centre for Mass Spectrometry, CSIR-Indian Institute of Chemical Technology, Hyderabad, 500 007, Telangana, India
- Academy of Scientific and Innovative Research, CSIR-Indian Institute of Chemical Technology, Hyderabad, 500 007, Telangana, India
| | - Ch Dinesh Kumar
- National Centre for Mass Spectrometry, CSIR-Indian Institute of Chemical Technology, Hyderabad, 500 007, Telangana, India
| | - R Srinivas
- National Centre for Mass Spectrometry, CSIR-Indian Institute of Chemical Technology, Hyderabad, 500 007, Telangana, India
| | - S Prabhakar
- National Centre for Mass Spectrometry, CSIR-Indian Institute of Chemical Technology, Hyderabad, 500 007, Telangana, India
- Academy of Scientific and Innovative Research, CSIR-Indian Institute of Chemical Technology, Hyderabad, 500 007, Telangana, India
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17
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Hattori Y, Furuita K, Ohki I, Ikegami T, Fukada H, Shirakawa M, Fujiwara T, Kojima C. Utilization of lysine ¹³C-methylation NMR for protein-protein interaction studies. JOURNAL OF BIOMOLECULAR NMR 2013; 55:19-31. [PMID: 23224986 DOI: 10.1007/s10858-012-9675-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2012] [Accepted: 09/10/2012] [Indexed: 05/20/2023]
Abstract
Chemical modification is an easy way for stable isotope labeling of non-labeled proteins. The reductive (13)C-methylation of the amino group of the lysine side-chain by (13)C-formaldehyde is a post-modification and is applicable to most proteins since this chemical modification specifically and quickly proceeds under mild conditions such as 4 °C, pH 6.8, overnight. (13)C-methylation has been used for NMR to study the interactions between the methylated proteins and various molecules, such as small ligands, nucleic acids and peptides. Here we applied lysine (13)C-methylation NMR to monitor protein-protein interactions. The affinity and the intermolecular interaction sites of methylated ubiquitin with three ubiquitin-interacting proteins were successfully determined using chemical-shift perturbation experiments via the (1)H-(13)C HSQC spectra of the (13)C-methylated-lysine methyl groups. The lysine (13)C-methylation NMR results also emphasized the importance of the usage of side-chain signals to monitor the intermolecular interaction sites, and was applicable to studying samples with concentrations in the low sub-micromolar range.
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Affiliation(s)
- Yoshikazu Hattori
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
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18
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An unusual dimeric structure and assembly for TLR4 regulator RP105-MD-1. Nat Struct Mol Biol 2011; 18:1028-35. [PMID: 21857663 DOI: 10.1038/nsmb.2106] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2010] [Accepted: 06/14/2011] [Indexed: 12/29/2022]
Abstract
RP105-MD-1 modulates the TLR4-MD-2-mediated, innate immune response against bacterial lipopolysaccharide (LPS). The crystal structure of the bovine 1:1 RP105-MD-1 complex bound to a putative endogenous lipid at 2.9 Å resolution shares a similar overall architecture to its homolog TLR4-MD-2 but assembles into an unusual 2:2 homodimer that differs from any other known TLR-ligand assembly. The homodimer is assembled in a head-to-head orientation that juxtaposes the N-terminal leucine-rich repeats (LRRs) of the two RP105 chains, rather than the usual tail-to-tail configuration of C-terminal LRRs in ligand-activated TLR dimers, such as TLR1-TRL2, TLR2-TLR6, TLR3-TLR3 and TLR4-TLR4. Another unusual interaction is mediated by an RP105-specific asparagine-linked glycan, which wedges MD-1 into the co-receptor binding concavity on RP105. This unique mode of assembly represents a new paradigm for TLR complexes and suggests a molecular mechanism for regulating LPS responses.
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Abstract
This article defines protein stability, emphasizes its importance and surveys some notable recent publications (2004-2008) in the field of protein stability/stabilization. Knowledge of the factors stabilizing proteins has emerged from denaturation studies and from study of thermophilic (and other extremophilic) proteins. One can enhance stability by protein engineering strategies, the judicious use of solutes and additives, immobilization, and chemical modification in solution. General protocols are set out on how to measure the kinetic thermal stability of a given protein and how to undertake chemical modification of a protein in solution.
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Affiliation(s)
- Ciarán O'Fágáin
- School of Biotechnology and National Centre for Sensor Research, Dublin City University, Dublin, Ireland.
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20
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Shao B, Tang C, Heinecke JW, Oram JF. Oxidation of apolipoprotein A-I by myeloperoxidase impairs the initial interactions with ABCA1 required for signaling and cholesterol export. J Lipid Res 2010; 51:1849-58. [PMID: 20064972 DOI: 10.1194/jlr.m004085] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A key cardioprotective effect of high-density lipoprotein involves the interaction of its major protein, apolipoprotein A-I (apoA-I) with ATP-binding cassette transporter A1 (ABCA1), a macrophage cholesterol exporter. ApoA-I is thought to remove cholesterol from macrophages by a cascade of events. First it binds directly to ABCA1, activating signaling pathways, and then it binds to and solubilizes lipid domains generated by ABCA1. HDL isolated from human atherosclerotic lesions and blood of subjects with established coronary artery disease contains elevated levels of 3-chlorotyrosine and 3-nitrotyrosine, two characteristic products of myeloperoxidase (MPO), a heme protein secreted by macrophages. Here we show that chlorination (but not nitration) of apoA-I by the MPO pathway impairs its ability to interact directly with ABCA1, to activate the Janus kinase 2 signaling pathway, and to promote efflux of cellular cholesterol. In contrast, oxidation of apoA-I has little effect on its ability to stabilize ABCA1 protein or to solubilize phospholipids. Our results indicate that chlorination of apoA-I by the MPO pathway selectively inhibits two critical early events in cholesterol efflux: (1) the binding of apoA-I to ABCA1 and (2) the activation of a key signaling pathway. Therefore, oxidation of apoA-I in the artery wall by MPO-generated chlorinating intermediates may contribute to atherogenesis by impairing cholesterol efflux from macrophages.
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Affiliation(s)
- Baohai Shao
- Division of Metabolism, Endocrinology and Nutrition, Department of Medicine, University of Washington, Seattle, WA 98195, USA.
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21
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Yang H, Gurgel P, Carbonell R. Hexamer peptide affinity resins that bind the Fc region of human immunoglobulin G. ACTA ACUST UNITED AC 2008. [DOI: 10.1111/j.1747-0285.2006.00342.x] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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22
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Bandyopadhyay U, Kaushik S, Varticovski L, Cuervo AM. The chaperone-mediated autophagy receptor organizes in dynamic protein complexes at the lysosomal membrane. Mol Cell Biol 2008; 28:5747-63. [PMID: 18644871 PMCID: PMC2546938 DOI: 10.1128/mcb.02070-07] [Citation(s) in RCA: 374] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2007] [Revised: 12/26/2007] [Accepted: 07/02/2008] [Indexed: 01/09/2023] Open
Abstract
Chaperone-mediated autophagy (CMA) is a selective type of autophagy by which specific cytosolic proteins are sent to lysosomes for degradation. Substrate proteins bind to the lysosomal membrane through the lysosome-associated membrane protein type 2A (LAMP-2A), one of the three splice variants of the lamp2 gene, and this binding is limiting for their degradation via CMA. However, the mechanisms of substrate binding and uptake remain unknown. We report here that LAMP-2A organizes at the lysosomal membrane into protein complexes of different sizes. The assembly and disassembly of these complexes are a very dynamic process directly related to CMA activity. Substrate proteins only bind to monomeric LAMP-2A, while the efficient translocation of substrates requires the formation of a particular high-molecular-weight LAMP-2A complex. The two major chaperones related to CMA, hsc70 and hsp90, play critical roles in the functional dynamics of the LAMP-2A complexes at the lysosomal membrane. Thus, we have identified a novel function for hsc70 in the disassembly of LAMP-2A from these complexes, whereas the presence of lysosome-associated hsp90 is essential to preserve the stability of LAMP-2A at the lysosomal membrane.
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Affiliation(s)
- Urmi Bandyopadhyay
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
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23
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Zhang C, Cuervo AM. Restoration of chaperone-mediated autophagy in aging liver improves cellular maintenance and hepatic function. Nat Med 2008; 14:959-65. [PMID: 18690243 PMCID: PMC2722716 DOI: 10.1038/nm.1851] [Citation(s) in RCA: 380] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2008] [Accepted: 06/23/2008] [Indexed: 12/14/2022]
Abstract
Chaperone-mediated autophagy (CMA), a selective mechanism for degradation of cytosolic proteins in lysosomes, contributes to the removal of altered proteins as part of the cellular quality-control systems. We have previously found that CMA activity declines in aged organisms and have proposed that this failure in cellular clearance could contribute to the accumulation of altered proteins, the abnormal cellular homeostasis and, eventually, the functional loss characteristic of aged organisms. To determine whether these negative features of aging can be prevented by maintaining efficient autophagic activity until late in life, in this work we have corrected the CMA defect in aged rodents. We have generated a double transgenic mouse model in which the amount of the lysosomal receptor for CMA, previously shown to decrease in abundance with age, can be modulated. We have analyzed in this model the consequences of preventing the age-dependent decrease in receptor abundance in aged rodents at the cellular and organ levels. We show here that CMA activity is maintained until advanced ages if the decrease in the receptor abundance is prevented and that preservation of autophagic activity is associated with lower intracellular accumulation of damaged proteins, better ability to handle protein damage and improved organ function.
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Affiliation(s)
- Cong Zhang
- Department of Developmental and Molecular Biology, Marion Bessin Liver Research Center and Institute for Aging Research, 1300 Morris Park Avenue, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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24
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Samuel-Landtiser M, Zachariah C, Williams CR, Edison AS, Long JR. Incorporation of isotopically enriched amino acids. ACTA ACUST UNITED AC 2008; Chapter 26:Unit 26.3. [PMID: 18429325 DOI: 10.1002/0471140864.ps2603s47] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The incorporation of isotope labels into proteins is extremely useful for the application of nuclear magnetic resonance (NMR), X-ray or neutron-diffraction crystallography, and mass spectrometry (MS) methodologies to investigate the structure and dynamics of proteins. This unit presents methods for incorporating isotopic labels into proteins via expression in E. coli and baculovirus transfected Sf9 insect cells or through cell-free means. The unit also presents methods for introducing isotopic labels by chemical means into synthetic peptides by solid phase peptide synthesis or into isolated proteins by chemical modification of labile protein groups.
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25
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Abstract
This unit describes group-specific modifications of amino groups. These reactions remain valid tools for early-stage evaluation of structure-function relationships, but are now valued even more for their applications in the preparation of bioconjugates, affinity columns, biosensors, and tagged macromolecules. Protocols are provided here for reaction of amino groups with succinimidyl esters and isothiocyanates. These methods are broadly useful for the stable coupling to proteins of groups with useful, non-native functional properties. These include biotin for detection or recovery, fluorescent groups for biophysics or cytochemistry, cross-linking reagents for making bioconjugates, or metal-chelators that permit proteins to be loaded with radioisotopes for medical imaging or antitumor therapy. These applications require accurate product characterization, which preferably is performed by mass spectrometry, as described in this unit as a support procedure. A protocol employing succinic or acetic anhydrides to change the charge state of protein amino groups is provided here, as is a procedure for reductive alkylation that leaves their charge unaltered but converts primary amines to secondary or tertiary amines.
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26
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Kaushik S, Massey AC, Mizushima N, Cuervo AM. Constitutive activation of chaperone-mediated autophagy in cells with impaired macroautophagy. Mol Biol Cell 2008; 19:2179-92. [PMID: 18337468 DOI: 10.1091/mbc.e07-11-1155] [Citation(s) in RCA: 240] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Three different types of autophagy-macroautophagy, microautophagy, and chaperone-mediated autophagy (CMA)-contribute to degradation of intracellular components in lysosomes in mammalian cells. Although some level of basal macroautophagy and CMA activities has been described in different cell types and tissues, these two pathways are maximally activated under stress conditions. Activation of these two pathways is often sequential, suggesting the existence of some level of cross-talk between both stress-related autophagic pathways. In this work, we analyze the consequences of blockage of macroautophagy on CMA activity. Using mouse embryonic fibroblasts deficient in Atg5, an autophagy-related protein required for autophagosome formation, we have found that blockage of macroautophagy leads to up-regulation of CMA, even under basal conditions. Interestingly, different mechanisms contribute to the observed changes in CMA-related proteins and the consequent activation of CMA during basal and stress conditions in these macroautophagy-deficient cells. This work supports a direct cross-talk between these two forms of autophagy, and it identifies changes in the lysosomal compartment that underlie the basis for the communication between both autophagic pathways.
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Affiliation(s)
- Susmita Kaushik
- Departments of Anatomy and Structural Biology and Developmental and Molecular Biology, Marion Bessin Liver Research Center and Institute for Aging Research, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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27
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Krusemark CJ, Ferguson JT, Wenger CD, Kelleher NL, Belshaw PJ. Global amine and acid functional group modification of proteins. Anal Chem 2008; 80:713-20. [PMID: 18184016 PMCID: PMC2364710 DOI: 10.1021/ac7019317] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A sequential reaction methodology is employed for the complete derivatization of protein thiols, amines, and acids in high purity under denaturing conditions. Following standard thiol alkylation, protein amines are modified via reductive methylation with formaldehyde and pyridine-borane. Protein acids are subsequently amidated under buffered conditions in DMSO using the coupling reagent (7-azabenzotriazol-1-yloxy)tripyrrolidinophosphonium hexafluorophosphate. The generality of the approach is demonstrated with four proteins and with several amines yielding near-quantitative transformations as characterized by high-resolution Fourier transform mass spectrometry. The developed approach has numerous implications for protein characterization and general protein chemistry. Applications in mass spectrometry (MS) based proteomics of intact proteins (top-down MS) are explored, including the addition of stable isotopes for relative quantitation and protein identification through functional group counting. The methodology can be used for altering the physical and chemical properties of proteins, as demonstrated with amidation to modify protein isoelectric point and through derivatization with quaternary amines. Additionally, the chemistry has applications in the semisynthesis of monodisperse polymers based on protein scaffolds. We prepare proteins modified with azides and alkynes to enable further functionalization via copper(I)-catalyzed 1,3-dipolar Huisgen cycloaddition ("click") chemistry.
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28
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Doxorubicin coupled to lactosaminated albumin: effect of heterogeneity in drug load on conjugate disposition and hepatocellular carcinoma uptake in rats. Eur J Pharm Sci 2007; 33:191-8. [PMID: 18201877 DOI: 10.1016/j.ejps.2007.11.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2007] [Revised: 11/26/2007] [Accepted: 11/28/2007] [Indexed: 11/24/2022]
Abstract
Coupling to lactosaminated human albumin (L-HSA) makes doxorubicin (DOXO) an effective drug against chemically induced rat hepatocellular carcinomas (HCCs). In the conjugate there is a large heterogeneity in the number of DOXO molecules bound to one L-HSA molecule. After lyophilization, the molecules with the higher DOXO load form large complexes (C-DOXOL), whereas those with low drug load (C-DOXOS) have the size of the carrier L-HSA. In the present experiments, we demonstrated that in C-DOXOL the molecules are not linked by covalent bonds, but are strongly aggregated probably because of mutual drug-drug interaction between the DOXO residues. In healthy rats and in animals with HCCs which received the same dose (1 microg/g) of DOXO injected in C-DOXOL or in C-DOXOS forms, penetration of the drug in tumors and in tissues was more rapid after administration of the former complex. Three hours after injection of both conjugate forms the intracellular release of DOXO from the carrier was completed. The AUCs from 0.5 to 4h of the levels of the released DOXO in HCCs, surrounding liver and bone marrow of animals injected with C-DOXOL were similar to those calculated in animals given C-DOXOS. This suggests that after administration of the dose of DOXO used in the present experiments the conjugate molecules with lower or higher drug load can exert comparable pharmacological and toxic effects.
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29
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Sumper M, Hett R, Lehmann G, Wenzl S. A Code for Lysine Modifications of a Silica Biomineralizing Silaffin Protein. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200702413] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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30
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Sumper M, Hett R, Lehmann G, Wenzl S. A Code for Lysine Modifications of a Silica Biomineralizing Silaffin Protein. Angew Chem Int Ed Engl 2007; 46:8405-8. [PMID: 17899579 DOI: 10.1002/anie.200702413] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Manfred Sumper
- Lehrstuhl Biochemie I, Universität Regensburg, 93040 Regensburg, Germany.
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31
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Shek PYI, Zhao J, Ke Y, Siu KWM, Hopkinson AC. Fragmentations of protonated arginine, lysine and their methylated derivatives: concomitant losses of carbon monoxide or carbon dioxide and an amine. J Phys Chem A 2007; 110:8282-96. [PMID: 16821812 DOI: 10.1021/jp055426k] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The fragmentation pathways of protonated arginine, protonated N(alpha),N(alpha)-dimethylarginine, the N(alpha),N(alpha),N(alpha)-trimethylarginine ion, three protonated N(epsilon),N(epsilon)-dimethyllysines, and three permanent lysine ions in which the charge is fixed by trimethylation are reported. Ion assignment was facilitated by (15)N-labeling and deuterium substitution. The chemistries are dominated by charge-induced elimination of the amino groups as neutrals, including dimethylamine, trimethylamine and guanidine. Competitive losses of the alpha-amino and side-chain amino groups were observed; these losses led to intermediates that had different structures and different subsequent dissociation reactions. Concomitant losses of CO or CO(2) with these amines were also commonly observed. However, the ionic products of amine losses did not subsequently lose CO or CO(2), suggesting strongly that in these concomitant eliminations, it is the CO or CO(2) that was first eliminated, followed immediately by the loss of the amine. Results of density functional theory calculations on protonated arginine and protonated N(alpha),N(alpha)-dimethylarginine reveal that, in such concomitant eliminations, the dissociating complex is vibrationally hot and the intermediate ion formed by losing CO or CO(2) can immediately dissociate to eliminate the amine.
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Affiliation(s)
- P Y Iris Shek
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University, 4700 Keele Street, Toronto, Ontario, Canada M3J 1P3
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32
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Di Stefano G, Fiume L, Baglioni M, Busi C, Chieco P, Kratz F, Mattioli A. Coupling of lactose molecules to the carrier protein hinders the spleen and bone marrow uptake of doxorubicin conjugated with human albumin. Eur J Pharm Sci 2007; 30:136-42. [PMID: 17218086 DOI: 10.1016/j.ejps.2006.10.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2006] [Accepted: 10/28/2006] [Indexed: 11/21/2022]
Abstract
Several attempts have been made to enhance doxorubicin (DOXO) concentrations in tumour cells by drug conjugation with human albumin (HSA). HSA-DOXO has the drawback of causing DOXO accumulation in spleen and bone marrow, with a consequent leucopoenia not produced when lactose molecules are coupled to the carrier protein. In the present experiments we demonstrated that the effect of HSA lactosamination is not a consequence of a more rapid disappearance from the bloodstream of the lactosaminated conjugate (L-HSA-DOXO), which is rapidly internalized by the liver through the asialoglycoprotein receptor, but is due to a hindered uptake by spleen and bone marrow cells caused by the coupled lactose molecules. Experiments in vitro showed that HSA-DOXO produced an inhibition of murine macrophage proliferation not caused by L-HSA-DOXO. This result can be explained by higher amounts of the former conjugate entering in these cells and suggests macrophages as the cell type responsible for the spleen and bone marrow internalization of HSA-DOXO hindered by lactose coupling. Importantly, lactosamination of HSA did not reduce the marked uptake of HSA-DOXO by chemically induced rat hepatocellular carcinoma. L-HSA-DOXO, by avoiding DOXO accumulation in bone marrow is an attractive candidate for clinical trials against tumors which were found to actively internalize this conjugate in laboratory animals, such as hepatocellular carcinoma.
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MESH Headings
- Animals
- Antibiotics, Antineoplastic/chemistry
- Antibiotics, Antineoplastic/pharmacokinetics
- Antibiotics, Antineoplastic/pharmacology
- Bone Marrow/metabolism
- Carbon Radioisotopes
- Carcinoma, Hepatocellular/chemically induced
- Carcinoma, Hepatocellular/metabolism
- Carcinoma, Hepatocellular/prevention & control
- Cell Proliferation/drug effects
- Diethylnitrosamine/toxicity
- Dose-Response Relationship, Drug
- Doxorubicin/chemistry
- Doxorubicin/pharmacokinetics
- Doxorubicin/pharmacology
- Drug Carriers
- Female
- Humans
- Lactose/chemistry
- Liver Neoplasms, Experimental/chemically induced
- Liver Neoplasms, Experimental/metabolism
- Liver Neoplasms, Experimental/prevention & control
- Lymphocytes/cytology
- Lymphocytes/drug effects
- Lymphocytes/metabolism
- Macrophages/cytology
- Macrophages/drug effects
- Macrophages/metabolism
- Male
- Mice
- Rats
- Rats, Wistar
- Serum Albumin/chemistry
- Spleen/metabolism
- Time Factors
- Tumor Cells, Cultured
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Affiliation(s)
- Giuseppina Di Stefano
- Department of Experimental Pathology, University of Bologna, via San Giacomo, 14-40126 Bologna, Italy
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Tenni R, Sonaggere M, Viola M, Bartolini B, Tira ME, Rossi A, Orsini E, Ruggeri A, Ottani V. Self-aggregation of fibrillar collagens I and II involves lysine side chains. Micron 2006; 37:640-7. [PMID: 16714119 DOI: 10.1016/j.micron.2006.01.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2005] [Revised: 01/31/2006] [Accepted: 01/31/2006] [Indexed: 10/25/2022]
Abstract
Several properties of fibrillar collagens depend on abundance and position of ionic amino acids. We recently demonstrated that N-methylation and N-acetylation of Lys/Hyl amino group did not significantly alter the thermal stability of the triple helical conformation and that the binding of modified collagens I and II to decorin is lost only on N-acetylation. The positive charge at physiological pH of Lys/Hyl side chains is preserved only by N-methylation. We report here the new aspect of the influence of the same modifications on collagen self-aggregation in neutral conditions. Three collagen preparations are very differently affected by N-methylation: acid-soluble type I collagen maintains the ability to form banded fibrils with 67-nm periodicity, whereas almost no structured aggregates were detected for pepsin-soluble type I collagen; pepsin-soluble type II collagen forms a very different supramolecular species, known as segment long spacing (SLS). N-acetylation blocks the formation of banded fibrils in neutral conditions (as did all other chemical modifications reported in the literature), demonstrating that the positive charge of Lys/Hyl amino groups is essential for self-aggregation. Kinetic measurements by turbidimetry showed a sizeable increase of absorbance only for the two N-methylated samples forming specific supramolecular aggregates; however, the derivatization affects aggregation kinetics by increasing lag time and decreasing maximum slope of absorbance variation, and lowers aggregation competency. We discuss that the effects of N-methylation on self-aggregation are caused by fewer or weaker salt bridges and by decrease of hydrogen bonding potential and conclude that protonated Lys side chains are involved in the fibril formation process.
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Affiliation(s)
- Ruggero Tenni
- Dipartimento di Biochimica, A. Castellani, University of Pavia, via Taramelli 3b, 27100 Pavia, Italy
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Sumper M, Lehmann G. Silica Pattern Formation in Diatoms: Species-Specific Polyamine Biosynthesis. Chembiochem 2006; 7:1419-27. [PMID: 16888733 DOI: 10.1002/cbic.200600184] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Diatoms are eukaryotic, unicellular algae that are well known for the intricate architecture of their silica-based cell walls. Species identification is mainly based on variations of their hierarchically organized silica structures. Particularly striking silica frameworks are found among diatoms that belong to the genus Coscinodiscus. Recent work indicates an important role for long-chain polyamines in guiding silica precipitation as well as in silica-pattern formation. Here we demonstrate that polyamines, even if isolated from closely related diatom species, exhibit substantial structural differences. Structural variations include the overall chain length, the degree of methylation, positions of secondary amino functionalities, and, unexpectedly, site-specific incorporation of a quaternary ammonium functionality. These findings support a specific role for polyamines in creating silica nanostructures.
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Affiliation(s)
- Manfred Sumper
- Lehrstuhl Biochemie I, Universität Regensburg, 93040 Regensburg, Germany.
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Affiliation(s)
- Luigi Aurelio
- Department of Chemistry, La Trobe University, Victoria 3086, Australia
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36
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Sumper M, Brunner E, Lehmann G. Biomineralization in diatoms: Characterization of novel polyamines associated with silica. FEBS Lett 2005; 579:3765-9. [PMID: 15963992 DOI: 10.1016/j.febslet.2005.06.001] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2005] [Accepted: 06/01/2005] [Indexed: 10/25/2022]
Abstract
Pattern formation during silica biomineralization in diatoms appears to depend on long-chain polyamines as well as proteins covalently modified with polyamines (silaffins). Recently, the complete genome of the diatom Thalassiosira pseudonana has been sequenced making this species an attractive model organism for future studies on biomineralization. Mass- and NMR-spectroscopic analysis of the long-chain polyamines from this diatom species reveals the existence of a complex population with as yet unknown structural features. These include complex methylation patterns, different attachment moieties as well as the existence of quaternary ammonium functionalities.
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Affiliation(s)
- Manfred Sumper
- Lehrstuhl Biochemie I, Universität Regensburg, D-93040 Regensburg, Germany.
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37
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Sell DR, Monnier VM. Conversion of Arginine into Ornithine by Advanced Glycation in Senescent Human Collagen and Lens Crystallins. J Biol Chem 2004; 279:54173-84. [PMID: 15489230 DOI: 10.1074/jbc.m408946200] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Long lived proteins undergo age-related postsynthetic modifications that destabilize them by altering their conformation, charge, and helicity, thereby enhancing their resistance toward proteolysis and propensity to aggregate. The unexpected finding of substantial amounts of ornithine, the nonprotein amino acid, and decarbamidation product of arginine in acid hydrolysates of lens crystallins and skin collagen led us to investigate its source and mechanism of formation. In order to exclude ornithine formation as an artifact of acid hydrolysis, proteins were reductively alkylated with formaldehyde to convert ornithine to dimethyl-ornithine. The proteins were assayed for carboxymethyl-ornithine and glycated ornithine ("furornithine") by liquid chromatography coupled to electrospray ionization mass spectrometry. Ornithine in acid hydrolysates of human lens and skin proteins increased from 1 to 15 nmol/mg protein from ages 10 to 90 years, whereas dimethyl-ornithine increased from 0.5 to 15 and from 0 to 5 nmol/mg protein, respectively. Carboxymethyl-ornithine and furornithine increased with age in lens and skin from approximately 0 to 60 and 0 to 180 pmol/mg protein, respectively. In collagen, ornithine was elevated above levels of nondiabetic controls only when both diabetes and end stage renal disease were present. The age-related increase of these modifications provides evidence for substantial in vivo formation of ornithine in aging human tissue proteins. The mechanism of ornithine formation is not known, but data suggest that arginine-derived advanced glycation end products might serve as precursors for the in vivo conversion of ornithine from arginine.
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Affiliation(s)
- David R Sell
- Institute of Pathology, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, USA.
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38
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Wenzl S, Deutzmann R, Hett R, Hochmuth E, Sumper M. Quaternary Ammonium Groups in Silica-Associated Proteins. Angew Chem Int Ed Engl 2004; 43:5933-6. [PMID: 15547898 DOI: 10.1002/anie.200461236] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Stephan Wenzl
- Lehrstuhl Biochemie I, Universität Regensburg, 93040 Regensburg, Germany
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39
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Wenzl S, Deutzmann R, Hett R, Hochmuth E, Sumper M. Quaternary Ammonium Groups in Silica-Associated Proteins. Angew Chem Int Ed Engl 2004. [DOI: 10.1002/ange.200461236] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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40
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Kiffin R, Christian C, Knecht E, Cuervo AM. Activation of chaperone-mediated autophagy during oxidative stress. Mol Biol Cell 2004; 15:4829-40. [PMID: 15331765 PMCID: PMC524731 DOI: 10.1091/mbc.e04-06-0477] [Citation(s) in RCA: 442] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2004] [Revised: 08/03/2004] [Accepted: 08/18/2004] [Indexed: 02/06/2023] Open
Abstract
Oxidatively damaged proteins accumulate with age in almost all cell types and tissues. The activity of chaperone-mediated autophagy (CMA), a selective pathway for the degradation of cytosolic proteins in lysosomes, decreases with age. We have analyzed the possible participation of CMA in the removal of oxidized proteins in rat liver and cultured mouse fibroblasts. Added to the fact that CMA substrates, when oxidized, are more efficiently internalized into lysosomes, we have found a constitutive activation of CMA during oxidative stress. Oxidation-induced activation of CMA correlates with higher levels of several components of the lysosomal translocation complex, but in particular of the lumenal chaperone, required for substrate uptake, and of the lysosomal membrane protein (lamp) type 2a, previously identified as a receptor for this pathway. In contrast with the well characterized mechanism of CMA activation during nutritional stress, which does not require de novo synthesis of the receptor, oxidation-induced activation of CMA is attained through transcriptional up-regulation of lamp2a. We conclude that CMA is activated during oxidative stress and that the higher activity of this pathway under these conditions, along with the higher susceptibility of the oxidized proteins to be taken up by lysosomes, both contribute to the efficient removal of oxidized proteins.
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Affiliation(s)
- Roberta Kiffin
- Department of Anatomy and Structural Biology, Marion Bessin Liver Research Center, Albert Einstein College of Medicine, Bronx, NY 1046, USA
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41
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Wang G, De J, Schoeniger JS, Roe DC, Carbonell RG. A hexamer peptide ligand that binds selectively to staphylococcal enterotoxin B: isolation from a solid phase combinatorial library. ACTA ACUST UNITED AC 2004; 64:51-64. [PMID: 15251031 DOI: 10.1111/j.1399-3011.2004.00170.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
By screening a solid-phase combinatorial peptide library, a short peptide ligand, YYWLHH, has been discovered that binds with high affinity and selectivity to staphylococcal enterotoxin B (SEB), but only weakly to other SEs that share sequence and structural homology with SEB. Using column affinity chromatography with an immobilized YYWLHH stationary phase, it was possible to separate SEB quantitatively from Staphylococcus aureus fermentation broth, a complex mixture of proteins, carbohydrates and other biomolecules. The immobilized peptide was also used to purify native SEB from a mixture containing denatured and hydrolyzed SEB, and showed little cross-reactivity with other SEs. To our knowledge this is the first report of a highly specific short peptide ligand for SEB. Such a ligand is a potential candidate to replace antibodies for detection, removal and purification strategies for SEB.
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Affiliation(s)
- G Wang
- Department of Chemical Engineering, North Carolina State University, 1017 Main Campus Drive, Centennial Campus, Partner's Building I, Suite 3200, Box 7006, Raleigh, NC 27695-7006, USA
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42
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Metz B, Kersten GFA, Hoogerhout P, Brugghe HF, Timmermans HAM, de Jong A, Meiring H, ten Hove J, Hennink WE, Crommelin DJA, Jiskoot W. Identification of formaldehyde-induced modifications in proteins: reactions with model peptides. J Biol Chem 2003; 279:6235-43. [PMID: 14638685 DOI: 10.1074/jbc.m310752200] [Citation(s) in RCA: 411] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Formaldehyde is a well known cross-linking agent that can inactivate, stabilize, or immobilize proteins. The purpose of this study was to map the chemical modifications occurring on each natural amino acid residue caused by formaldehyde. Therefore, model peptides were treated with excess formaldehyde, and the reaction products were analyzed by liquid chromatography-mass spectrometry. Formaldehyde was shown to react with the amino group of the N-terminal amino acid residue and the side-chains of arginine, cysteine, histidine, and lysine residues. Depending on the peptide sequence, methylol groups, Schiff-bases, and methylene bridges were formed. To study intermolecular cross-linking in more detail, cyanoborohydride or glycine was added to the reaction solution. The use of cyanoborohydride could easily distinguish between peptides containing a Schiff-base or a methylene bridge. Formaldehyde and glycine formed a Schiff-base adduct, which was rapidly attached to primary N-terminal amino groups, arginine and tyrosine residues, and, to a lesser degree, asparagine, glutamine, histidine, and tryptophan residues. Unexpected modifications were found in peptides containing a free N-terminal amino group or an arginine residue. Formaldehyde-glycine adducts reacted with the N terminus by means of two steps: the N terminus formed an imidazolidinone, and then the glycine was attached via a methylene bridge. Two covalent modifications occurred on an arginine-containing peptide: (i) the attachment of one glycine molecule to the arginine residue via two methylene bridges, and (ii) the coupling of two glycine molecules via four methylene bridges. Remarkably, formaldehyde did not generate intermolecular cross-links between two primary amino groups. In conclusion, the use of model peptides enabled us to determine the reactivity of each particular cross-link reaction as a function of the reaction conditions and to identify new reaction products after incubation with formaldehyde.
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Affiliation(s)
- Bernard Metz
- Unit Research and Development, The Netherlands Vaccine Institute, 3720 AL Bilthoven, The Netherlands
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43
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Dam TK, Brewer CF. Carbohydrate-lectin cross-linking interactions: structural, thermodynamic, and biological studies. Methods Enzymol 2003; 362:455-86. [PMID: 12968382 DOI: 10.1016/s0076-6879(03)01031-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Affiliation(s)
- Tarun K Dam
- Departments of Molecular Pharmacology, and Microbiology and Immunology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, USA
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44
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Giudici C, Viola M, Tira ME, Forlino A, Tenni R. Molecular stability of chemically modified collagen triple helices. FEBS Lett 2003; 547:170-6. [PMID: 12860408 DOI: 10.1016/s0014-5793(03)00715-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Ionic residues influence the stability of collagen triple helices and play a relevant role in the spontaneous aggregation of fibrillar collagens. Collagen types I and II and some of their CNBr peptides were chemically modified in mild conditions with two different protocols. Primary amino groups of Lys and Hyl were N-methylated by formaldehyde in reducing conditions or N-acetylated by sulfosuccinimidyl acetate. The positive charge of amino groups at physiological pH was maintained after the former modification, whereas it was lost after the latter. These chemical derivatizations did not significantly alter the stability of the triple helical conformation of peptide trimeric species. Also the enthalpic change on denaturation was largely unaffected by derivatizations. This implies that no significant variation of weak bonds, either in number or overall strength, and of entropy occur on modification. These properties can probably be explained by the fact that chemically modified groups maintain the ability to form hydrogen bonds.
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Affiliation(s)
- Camilla Giudici
- Dipartimento di Biochimica A. Castellani, University of Pavia, via Taramelli 3b, 27100, Pavia, Italy
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45
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Di Stefano G, Kratz F, Lanza M, Fiume L. Doxorubicin coupled to lactosaminated human albumin remains confined within mouse liver cells after the intracellular release from the carrier. Dig Liver Dis 2003; 35:428-33. [PMID: 12868680 DOI: 10.1016/s1590-8658(03)00212-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
BACKGROUND The hepatocyte receptor for asialoglycoproteins, which binds and internalises galactosyl terminating peptides, was found to be expressed also on the cells of the majority of hepatocarcinomas. AIMS To verify whether doxorubicin coupling to lactosaminated albumin, a galactosyl terminating neoglycoprotein, produces selective drug accumulation in hepatocytes with reduced concentrations in extra-hepatic tissues, thus facilitating the use of the drug in hepatocarcinoma treatment. METHODS Doxorubicin concentrations were measured in organs of mice injected with the free or coupled drug. RESULTS In mice injected with the coupled drug, the ratios between doxorubicin concentrations in liver and those in heart, intestine, spleen and kidney were 8-14 times higher than in animals that received the same dose of the free drug. CONCLUSIONS Due to the very efficient liver targeting of doxorubicin, the lactosaminated human albumin-doxorubicin conjugate appears to have the potential of improving the chemotherapy of hepatocellular carcinomas through the asialoglycoprotein receptor.
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Affiliation(s)
- G Di Stefano
- Department of Experimental Pathology, University of Bologna, Via San Giacomo 14, 40126 Bologna, Italy
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46
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Stahelin RV, Long F, Diraviyam K, Bruzik KS, Murray D, Cho W. Phosphatidylinositol 3-phosphate induces the membrane penetration of the FYVE domains of Vps27p and Hrs. J Biol Chem 2002; 277:26379-88. [PMID: 12006563 DOI: 10.1074/jbc.m201106200] [Citation(s) in RCA: 124] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The FYVE domain mediates the recruitment of proteins involved in membrane trafficking and cell signaling to phosphatidylinositol 3-phosphate (PtdIns(3)P)-containing membranes. To elucidate the mechanism by which the FYVE domain interacts with PtdIns(3)P-containing membranes, we measured the membrane binding of the FYVE domains of yeast Vps27p and Drosophila hepatocyte growth factor-regulated tyrosine kinase substrate and their mutants by surface plasmon resonance and monolayer penetration analyses. These measurements as well as electrostatic potential calculation show that PtdIns(3)P specifically induces the membrane penetration of the FYVE domains and increases their membrane residence time by decreasing the positive charge surrounding the hydrophobic tip of the domain and causing local conformational changes. Mutations of hydrophobic residues located close to the PtdIns(3)P-binding pocket or an Arg residue directly involved in PtdIns(3)P binding abrogated the penetration of the FYVE domains into the monolayer, the packing density of which is comparable with that of biological membranes and large unilamellar vesicles. Based on these results, we propose a mechanism of the membrane binding of the FYVE domain in which the domain first binds to the PtdIns(3)P-containing membrane by specific PtdIns(3)P binding and nonspecific electrostatic interactions, which is then followed by the PtdIns(3)P-induced partial membrane penetration of the domain.
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Affiliation(s)
- Robert V Stahelin
- Department of Chemistry, University of Illinois, Chicago, Illinois 60607, USA
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47
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Di Stefano G, Busi C, Fiume L. Floxuridine coupling with lactosaminated human albumin to increase drug efficacy on liver micrometastases. Dig Liver Dis 2002; 34:439-46. [PMID: 12132792 DOI: 10.1016/s1590-8658(02)80042-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
BACKGROUND Conjugates of nucleoside analogues with galactosyl terminating peptides selectively enter hepatocytes through the asialoglycoprotein receptor. After intracellular release from the carrier, the drugs partly exit from hepatic cells into hepatic blood. AIMS To establish whether administration of a conjugate of floxuridine with lactosaminated human albumin selectively enhances drug concentrations in hepatic blood. Floxuridine is a fluoropyrimidine active on human colorectal cancer, a tumour which metastasises first to the liver. METHODS In rats injected with free or conjugated floxuridine, plasma levels of the drug were determined in hepatic veins and in inferior vena cava, in order to measure drug concentrations in hepatic blood and in the systemic circulation, respectively. RESULTS Ratios between floxuridine levels in hepatic veins and those in systemic circulation were found to be seven times higher in rats injected with the conjugate (p=0.000). CONCLUSIONS The present results suggest that coupling to lactosaminated albumin might improve the effect of floxuridine in adjuvant chemotherapy of colorectal cancer by exposing the cells of liver micrometastases (nourished by hepatic sinusoids) to enhanced drug concentrations.
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Affiliation(s)
- G Di Stefano
- Department of Experimental Pathology, University of Bologna, Italy
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48
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Di Stefano G, Lanza M, Busi C, Barbieri L, Fiume L. Conjugates of nucleoside analogs with lactosaminated human albumin to selectively increase the drug levels in liver blood: requirements for a regional chemotherapy. J Pharmacol Exp Ther 2002; 301:638-42. [PMID: 11961068 DOI: 10.1124/jpet.301.2.638] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Nucleoside analogs (NAs) conjugated with galactosyl terminating peptides selectively enter hepatocytes via the asialoglycoprotein receptor and, after intracellular release from the carrier, partly exit from these cells into the bloodstream, resulting in higher concentrations in liver blood than in systemic circulation. Therefore, conjugates of anticancer NAs can be exploited to accomplish a loco-regional noninvasive treatment of liver micrometastases. In the present experiments we studied whether the enhancement of drug levels in liver blood achieved when NAs are given in the coupled form depends on the rate of drug elimination from the bloodstream. Three NAs, adenine arabinoside (ara-A), 5-fluoro-2'-deoxyuridine (FUdR), and 2',2'-difluorodeoxycytidine, were coupled with lactosaminated human albumin, a galactosyl terminating carrier. In rats that received an intravenous bolus injection of these conjugates, we compared the drug concentrations in liver blood to those in the systemic circulation. We found that enhanced levels of NAs in liver blood were only achieved by administering the conjugates of the drugs (ara-A and FUdR), which are rapidly cleared from the bloodstream. Increased drug levels also were obtained when ara-A and FUdR conjugates were slowly infused (a way of administration often used for anticancer drugs). The experiments also showed that galactosyl terminating conjugates of NAs might have the potential to produce a therapeutic effect only when the coupled drugs are active at low blood concentrations, since the amounts of drugs introduced into hepatocytes and released by these cells in the bloodstream cannot be increased when the receptor for the hepatic uptake of galactosyl terminating peptides is saturated.
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49
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Tenni R, Viola M, Welser F, Sini P, Giudici C, Rossi A, Tira ME. Interaction of decorin with CNBr peptides from collagens I and II. Evidence for multiple binding sites and essential lysyl residues in collagen. EUROPEAN JOURNAL OF BIOCHEMISTRY 2002; 269:1428-37. [PMID: 11874457 DOI: 10.1046/j.1432-1033.2002.02784.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Decorin is a small leucine-rich chondroitin/dermatan sulfate proteoglycan reported to interact with fibrillar collagens through its protein core and to localize at d and e bands of the collagen fibril banding pattern. Using a solid-phase assay, we have determined the interaction of peptides derived by CNBr cleavage of type I and type II collagen with decorin extracted from bovine tendon and its protein core and with a recombinant decorin preparation. At least five peptides have been found to interact with all three decorin samples. The interaction of peptides with tendon decorin has a dissociation constant in the nanomolar range. The triple helical conformation of the peptide trimeric species is a necessary requisite for the binding. All positive peptides have a region within the d and e bands of collagen fibrils. Two chemical derivatives of collagens and of positive peptides were prepared by N-acetylation and N-methylation of the primary amino group of Lys/Hyl side chains. Chemical modifications performed in mild conditions do not significantly alter the thermal stability of peptide trimeric species whereas they affect the interaction with decorin: N-acetylation eliminates both the positive charge and the binding to decorin, whereas N-methylation preserves the cationic character and modulates the binding. We conclude that decorin makes contacts with multiple sites in type I collagen and probably also in type II collagen and that some collagen Lys/Hyl residues are essential for the binding.
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Affiliation(s)
- Ruggero Tenni
- Dipartimento di Biochimica A. Castellani, University of Pavia, Italy.
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50
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Ghosh M, Mandal DK. Analysis of equilibrium dissociation and unfolding in denaturants of soybean agglutinin and two of its derivatives. Int J Biol Macromol 2001; 29:273-80. [PMID: 11718824 DOI: 10.1016/s0141-8130(01)00175-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The equilibrium denaturation of tetrameric soybean agglutinin (SBA) in urea and guanidine hydrochloride (GdnHCl) has been examined by steady-state fluorescence and size-exclusion chromatography. The denaturation of SBA reveals two distinct and separable transitions: dissociation (native tetramer<-->tertiary monomer) and unfolding (tertiary monomer<-->unfolded monomer). The urea denaturation curves of N-dimethyl and acetyl derivatives of SBA are also similar to unmodified lectin but the midpoints, [D](1/2), are shifted to lower denaturant concentrations. The free energy of stabilization of tertiary structure (DeltaG(u,aq)) of SBA is estimated to be 4.5-4.6 kcal mol(-1), which shows a decrease by approximately 10-15% for both N-dimethyl SBA and acetyl-SBA. The free energy term (DeltaG(d, aq)) for the relative stability of the quaternary structure of SBA and its derivatives shows that the decrease in stability relative to SBA occurs by <10% for N-dimethyl SBA while for acetyl-SBA, this occurs by approximately 30%. However, the m values depicting the dependence of free energy on denaturant concentration for SBA and its derivatives are similar for dissociation as well as unfolding, which suggest similar denaturation pathways of unmodified and modified SBA.
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Affiliation(s)
- M Ghosh
- Department of Chemistry, Presidency College, 86/1 College Street, 700 073, Calcutta, India
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