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Narayan M. The Non-native Disulfide-Bond-Containing Landscape Orthogonal to the Oxidative Protein-Folding Trajectory: A Necessary Evil? J Phys Chem B 2022; 126:10273-10284. [PMID: 36472840 DOI: 10.1021/acs.jpcb.2c04648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Oxidative protein folding describes the process by which disulfide-bond-containing proteins mature from their ribosomal, fully reduced and unfolded, origins. Over the past 40 years, a number of exemplar proteins including bovine pancreatic ribonuclease A (RNaseA), bovine pancreatic trypsin inhibitor (BPTI), and hen egg-white lysozyme (HEWL), among others, have provided rich insight into the nature of the intermolecular interactions that drive the formation of the native, biologically active fold. In this Review Article, we revisit the oxidative folding process of RNase A with a focus on reconciling the role of non-native disulfide-bond-containing species that populate the oxidative folding landscape. Toward gaining such an understanding, we project the regeneration pathway onto a Cartesian coordinate system. This helps not only to recognize the magnitude of the seemingly "fruitless", non-native disulfide-bond-containing species that lie orthogonal to the "native-protein-forming" reaction progress but also to reconcile a role for their existence in the regenerative trajectory. Finally, we superimpose the folding funnel onto the regeneration trajectory to draw parallels between oxidative folders and conformational folders (proteins that lack disulfide bonds). The overall objective is to provide the reader with a semi-quantitative description of oxidative protein folding and the barriers to successful regeneration while underscoring a role of seemingly fruitless intermediates.
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Affiliation(s)
- Mahesh Narayan
- Department of Chemistry and Biochemistry, University of Texas at El Paso, El Paso, Texas 79968, United States
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Towards a generic prototyping approach for therapeutically-relevant peptides and proteins in a cell-free translation system. Nat Commun 2022; 13:260. [PMID: 35017494 PMCID: PMC8752827 DOI: 10.1038/s41467-021-27854-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 12/17/2021] [Indexed: 11/23/2022] Open
Abstract
Advances in peptide and protein therapeutics increased the need for rapid and cost-effective polypeptide prototyping. While in vitro translation systems are well suited for fast and multiplexed polypeptide prototyping, they suffer from misfolding, aggregation and disulfide-bond scrambling of the translated products. Here we propose that efficient folding of in vitro produced disulfide-rich peptides and proteins can be achieved if performed in an aggregation-free and thermodynamically controlled folding environment. To this end, we modify an E. coli-based in vitro translation system to allow co-translational capture of translated products by affinity matrix. This process reduces protein aggregation and enables productive oxidative folding and recycling of misfolded states under thermodynamic control. In this study we show that the developed approach is likely to be generally applicable for prototyping of a wide variety of disulfide-constrained peptides, macrocyclic peptides with non-native bonds and antibody fragments in amounts sufficient for interaction analysis and biological activity assessment. Generic approach for rapid prototyping is essential for the progress of synthetic biology. Here the authors modify the cell-free translation system to control protein aggregation and folding and validate the approach by using single conditions for prototyping of various disulfide-constrained polypeptides.
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Matsusaki M, Okada R, Tanikawa Y, Kanemura S, Ito D, Lin Y, Watabe M, Yamaguchi H, Saio T, Lee YH, Inaba K, Okumura M. Functional Interplay between P5 and PDI/ERp72 to Drive Protein Folding. BIOLOGY 2021; 10:biology10111112. [PMID: 34827105 PMCID: PMC8615271 DOI: 10.3390/biology10111112] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/21/2021] [Accepted: 10/27/2021] [Indexed: 11/16/2022]
Abstract
P5 is one of protein disulfide isomerase family proteins (PDIs) involved in endoplasmic reticulum (ER) protein quality control that assists oxidative folding, inhibits protein aggregation, and regulates the unfolded protein response. P5 reportedly interacts with other PDIs via intermolecular disulfide bonds in cultured cells, but it remains unclear whether complex formation between P5 and other PDIs is involved in regulating enzymatic and chaperone functions. Herein, we established the far-western blot method to detect non-covalent interactions between P5 and other PDIs and found that PDI and ERp72 are partner proteins of P5. The enzymatic activity of P5-mediated oxidative folding is up-regulated by PDI, while the chaperone activity of P5 is stimulated by ERp72. These findings shed light on the mechanism by which the complex formations among PDIs drive to synergistically accelerate protein folding and prevents aggregation. This knowledge has implications for understanding misfolding-related pathology.
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Affiliation(s)
- Motonori Matsusaki
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, 6-3, Aramakiaza Aoba, Aoba-ku, Sendai 980-8578, Japan; (M.M.); (S.K.); (M.W.)
- Institute of Advanced Medical Sciences, Tokushima University, 3-18-15, Kuramoto-cho, Tokushima 770-8503, Japan;
| | - Rina Okada
- School of Science and Technology, Kwansei Gakuin University, 2-1, Gakuen, Sanda 669-1337, Japan; (R.O.); (Y.T.); (H.Y.)
| | - Yuya Tanikawa
- School of Science and Technology, Kwansei Gakuin University, 2-1, Gakuen, Sanda 669-1337, Japan; (R.O.); (Y.T.); (H.Y.)
| | - Shingo Kanemura
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, 6-3, Aramakiaza Aoba, Aoba-ku, Sendai 980-8578, Japan; (M.M.); (S.K.); (M.W.)
- School of Science and Technology, Kwansei Gakuin University, 2-1, Gakuen, Sanda 669-1337, Japan; (R.O.); (Y.T.); (H.Y.)
| | - Dai Ito
- Department of Brain and Cognitive Science, Daegu Gyeongbuk Institute of Science and Technology, 333, Techno Jungang Daero, Daegu 42988, Korea;
| | - Yuxi Lin
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, 162, Yeongudanji-ro, Ochang-eup, Cheongwon-gu, Cheongju-si 28119, Korea; (Y.L.); (Y.-H.L.)
| | - Mai Watabe
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, 6-3, Aramakiaza Aoba, Aoba-ku, Sendai 980-8578, Japan; (M.M.); (S.K.); (M.W.)
| | - Hiroshi Yamaguchi
- School of Science and Technology, Kwansei Gakuin University, 2-1, Gakuen, Sanda 669-1337, Japan; (R.O.); (Y.T.); (H.Y.)
| | - Tomohide Saio
- Institute of Advanced Medical Sciences, Tokushima University, 3-18-15, Kuramoto-cho, Tokushima 770-8503, Japan;
| | - Young-Ho Lee
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, 162, Yeongudanji-ro, Ochang-eup, Cheongwon-gu, Cheongju-si 28119, Korea; (Y.L.); (Y.-H.L.)
- Bio-Analytical Science, University of Science and Technology, 217, Gajeong-ro, Yuseong-gu, Daejeon 34113, Korea
- Graduate School of Analytical Science and Technology, Chungnam National University, 99, Daehak-ro, Yuseong-gu, Daejeon 34134, Korea
- Research Headquarters, Korea Brain Research Institute, 61, Cheomdan-ro, Dong-gu, Daegu 41068, Korea
| | - Kenji Inaba
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan;
| | - Masaki Okumura
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, 6-3, Aramakiaza Aoba, Aoba-ku, Sendai 980-8578, Japan; (M.M.); (S.K.); (M.W.)
- Correspondence: ; Tel.: +81-22-795-5764
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Context-dependent monoclonal antibodies against protein carbamidomethyl-cysteine. PLoS One 2020; 15:e0242376. [PMID: 33232360 PMCID: PMC7685443 DOI: 10.1371/journal.pone.0242376] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 11/01/2020] [Indexed: 02/07/2023] Open
Abstract
Protein sulfhydryl residues participate in key structural and biochemical functions. Alterations in sulfhydryl status, regulated by either reversible redox reactions or by permanent covalent capping, may be challenging to identify. To advance the detection of protein sulfhydryl groups, we describe the production of new Rabbit monoclonal antibodies that react with carbamidomethyl-cysteine (CAM-cys), a product of iodoacetamide (IAM) labeling of protein sulfhydryl residues. These antibodies bind to proteins labeled with IAM (but not N-ethylmaleimide (NEM) or acrylamide) and identify multiple protein bands when applied to Western blots of cell lysates treated with IAM. The monoclonal antibodies label a subset of CAM-cys modified peptide sequences and purified proteins (human von Willebrand Factor (gene:vWF), Jagged 1 (gene:JAG1), Laminin subunit alpha 2 (gene:LAMA2), Thrombospondin-2 (gene:TSP2), and Collagen IV (gene:COL4)) but do not recognize specific proteins such as Bovine serum albumin (gene:BSA) and human Thrombospondin-1 (gene:TSP1), Biglycan (gene:BGN) and Decorin (gene:DCN). Scanning mutants of the peptide sequence used to generate the CAM-cys antibodies elucidated residues required for context dependent reactivity. In addition to recognition of in vitro labeled proteins, the antibodies were used to identify selected sulfhydryl-containing proteins from living cells that were pulse labeled with IAM. Further development of novel CAM-cys monoclonal antibodies in conjunction with other biochemical tools may complement current methods for sulfhydryl detection within specific proteins. Moreover, CAM-cys reactive reagents may be useful when there is a need to label subpopulations of proteins.
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Mechanisms of Disulfide Bond Formation in Nascent Polypeptides Entering the Secretory Pathway. Cells 2020; 9:cells9091994. [PMID: 32872499 PMCID: PMC7565403 DOI: 10.3390/cells9091994] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 08/26/2020] [Accepted: 08/28/2020] [Indexed: 12/16/2022] Open
Abstract
Disulfide bonds are an abundant feature of proteins across all domains of life that are important for structure, stability, and function. In eukaryotic cells, a major site of disulfide bond formation is the endoplasmic reticulum (ER). How cysteines correctly pair during polypeptide folding to form the native disulfide bond pattern is a complex problem that is not fully understood. In this paper, the evidence for different folding mechanisms involved in ER-localised disulfide bond formation is reviewed with emphasis on events that occur during ER entry. Disulfide formation in nascent polypeptides is discussed with focus on (i) its mechanistic relationship with conformational folding, (ii) evidence for its occurrence at the co-translational stage during ER entry, and (iii) the role of protein disulfide isomerase (PDI) family members. This review highlights the complex array of cellular processes that influence disulfide bond formation and identifies key questions that need to be addressed to further understand this fundamental process.
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