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Choi S, Park YS, Lee KW, Park YJ, Jang HJ, Kim DM, Yoo TH. Sensitive Methods to Detect Single-Stranded Nucleic Acids of Food Pathogens Based on Cell-Free Protein Synthesis and Retroreflection Signal Detection. J Agric Food Chem 2024; 72:3783-3792. [PMID: 38346351 DOI: 10.1021/acs.jafc.3c07785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Cell-free protein synthesis (CFPS) has recently gained considerable attention as a new platform for developing methods to detect various molecules, ranging from small chemicals to biological macromolecules. Retroreflection has been used as an alternative signal to develop analytical methods because it can be detected by using a simple instrument comprising a white light source and a camera. Here, we report a novel reporter protein that couples the capability of CFPS and the simplicity of retroreflection signal detection. The design of the reporter was based on two pairs of protein-peptide interactions, SpyCatcher003-SpyTag003 and MDM2-PMI(N8A). MDM2-MDM2-SpyCatcher003 was decided as the reporter protein, and the two peptides, SpyTag003 and PMI(N8A), were immobilized on the surfaces of retroreflective Janus particles and microfluidic chips, respectively. The developed retroreflection signal detection system was combined with a previously reported CFPS reaction that can transduce the presence of a single-stranded nucleic acid into protein synthesis. The resulting methods were applied to detect 16S rRNAs of several foodborne pathogens. Concentration-dependent relationships were observed over a range of 10° fM to 102 pM, with the limits of detection being single-digit femtomolar concentrations. Considering the designability of the CFPS system for other targets, the retroreflection signal detection method will enable the development of novel methods to detect various molecules.
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Affiliation(s)
- Sunjoo Choi
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea
| | - Ye Seop Park
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea
| | - Kyung Won Lee
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea
| | - Yu Jin Park
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, Daejeon 34134, Korea
| | - Hee Ju Jang
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea
| | - Dong-Myung Kim
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, Daejeon 34134, Korea
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea
- Department of Applied Chemistry and Biological Engineering, Ajou University, Suwon 16499, Korea
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2
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Park YS, Choi S, Jang HJ, Yoo TH. Assay methods based on proximity-enhanced reactions for detecting non-nucleic acid molecules. Front Bioeng Biotechnol 2023; 11:1188313. [PMID: 37456730 PMCID: PMC10343955 DOI: 10.3389/fbioe.2023.1188313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 06/21/2023] [Indexed: 07/18/2023] Open
Abstract
Accurate and reliable detection of biological molecules such as nucleic acids, proteins, and small molecules is essential for the diagnosis and treatment of diseases. While simple homogeneous assays have been developed and are widely used for detecting nucleic acids, non-nucleic acid molecules such as proteins and small molecules are usually analyzed using methods that require time-consuming procedures and highly trained personnel. Recently, methods using proximity-enhanced reactions (PERs) have been developed for detecting non-nucleic acids. These reactions can be conducted in a homogeneous liquid phase via a single-step procedure. Herein, we review three assays based on PERs for the detection of non-nucleic acid molecules: proximity ligation assay, proximity extension assay, and proximity proteolysis assay.
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Affiliation(s)
- Ye Seop Park
- Department of Molecular Science and Technology, Ajou University, Suwon, Republic of Korea
| | - Sunjoo Choi
- Department of Molecular Science and Technology, Ajou University, Suwon, Republic of Korea
| | - Hee Ju Jang
- Department of Molecular Science and Technology, Ajou University, Suwon, Republic of Korea
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, Suwon, Republic of Korea
- Department of Applied Chemistry and Biological Engineering, Ajou University, Suwon, Republic of Korea
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3
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Park HJ, Kim Y, Lee KW, Gwon M, Yoon HC, Yoo TH. Coupling hCG-based protease sensors with a commercial pregnancy test strip for simple analyses of protease activities. Biosens Bioelectron 2023; 235:115364. [PMID: 37207580 DOI: 10.1016/j.bios.2023.115364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 04/03/2023] [Accepted: 04/28/2023] [Indexed: 05/21/2023]
Abstract
Proteases play an essential role in many cellular processes, and consequently, abnormalities in their activities are related to various diseases. Methods have been developed to measure the activity of these enzymes, but most involve sophisticated instruments or complicated procedures, which hampers the development of a point-of-care test (POCT). Here, we propose a strategy for developing simple and sensitive methods to analyze protease activity using commercial pregnancy test strips that detect human chorionic gonadotropin (hCG). hCG was engineered to have site-specific conjugated biotin and a peptide sequence, which can be cleaved by a target protease, between hCG and biotin. hCG protein was immobilized on streptavidin-coated beads, resulting in a protease sensor. The hCG-immobilized beads were too large to flow through the membrane of the hCG test strip and yielded only one band in the control line. When the peptide linker was hydrolyzed by the target protease, hCG was released from the beads, and the signal appeared in both the control and test lines. Three protease sensors for matrix metalloproteinase-2, caspase-3, and thrombin were constructed by replacing the protease-cleavable peptide linker. The combination of the protease sensors and a commercial pregnancy strip enabled the specific detection of each protease in the picomolar range, with a 30-min incubation of the hCG-immobilized beads and samples. The modular design of the protease sensor and simple assay procedure will facilitate the development of POCTs for various protease disease markers.
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Affiliation(s)
- Hyeon Ji Park
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Yengtong-gu, Suwon, 16499, South Korea
| | - Yuseon Kim
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Yengtong-gu, Suwon, 16499, South Korea
| | - Kyung Won Lee
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Yengtong-gu, Suwon, 16499, South Korea
| | - Minji Gwon
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Yengtong-gu, Suwon, 16499, South Korea
| | - Hyun C Yoon
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Yengtong-gu, Suwon, 16499, South Korea; Department of Applied Chemistry and Biological Engineering, Ajou University, 206 World cup-ro, Yengtong-gu, Suwon, 16499, South Korea.
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Yengtong-gu, Suwon, 16499, South Korea; Department of Applied Chemistry and Biological Engineering, Ajou University, 206 World cup-ro, Yengtong-gu, Suwon, 16499, South Korea.
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Heo GY, Kim HJ, Kalantar D, Jung CY, Kim HW, Park JT, Chang TI, Yoo TH, Kang SW, Rhee CM, Kalantar-Zadeh K, Han SH. Association between Fiber Intake and Risk of Incident Chronic Kidney Disease: The UK Biobank Study. J Nutr Health Aging 2023; 27:1018-1027. [PMID: 37997724 DOI: 10.1007/s12603-023-1998-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 09/13/2023] [Indexed: 11/25/2023]
Abstract
OBJECTIVES Dietary fiber intake is associated with a lower risk of diabetes, cardiovascular disease, and cancer. However, it is unknown whether dietary fiber has a beneficial effect on preventing the development of chronic kidney disease (CKD). DESIGN, SETTING, PARTICIPANTS AND MEASUREMENTS Using the UK Biobank prospective cohort, 110,412 participants who completed at least one dietary questionnaire and had an estimated glomerular filtration rate ≥60 mL/min/1.73 m2, urinary albumin-to-creatinine ratio <30 mg/g, and no history of CKD were included. The primary exposure was total dietary fiber density, calculated by dividing the absolute amount of daily total fiber intake by total energy intake (g/1,000 kcal). We separately examined soluble and insoluble fiber densities as additional predictors. The primary outcome was incident CKD based on diagnosis codes. RESULTS A total of 3,507 (3.2%) participants developed incident CKD during a median follow-up of 9.9 years. In a multivariable cause-specific model, the adjusted hazard ratios (aHRs; 95% confidence intervals [CIs]) for incident CKD were 0.85 (0.77-0.94), 0.78 (0.70-0.86), and 0.76 (0.68-0.86), respectively, for the second, third, and highest quartiles of dietary fiber density (reference: lowest quartile). In a continuous model, the aHR for each +∆1.0g/1,000 kcal increase in dietary fiber density was 0.97 (95% CI, 0.95-0.99). This pattern of associations was similar for both soluble and insoluble fiber densities and did not differ across subgroups of sex, age, body mass index, hypertension, diabetes, smoking, and inflammation. CONCLUSION Increased fiber intake was associated with a lower risk of CKD in this large well-characterized cohort.
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Affiliation(s)
- G Y Heo
- Seung Hyeok Han, MD, Ph.D. Yonsei University, Institute of Kidney Disease Research, College of Medicine, Department of Internal Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea, Phone: 82-2-2228-1984; Fax: 82-2-393-6884; E-mail: , (https://orcid.org/0000-0001-7923-5635)
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Pagar AD, Jeon H, Khobragade TP, Sarak S, Giri P, Lim S, Yoo TH, Ko BJ, Yun H. Non-Canonical Amino Acid-Based Engineering of (R)-Amine Transaminase. Front Chem 2022; 10:839636. [PMID: 35295971 PMCID: PMC8918476 DOI: 10.3389/fchem.2022.839636] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 02/07/2022] [Indexed: 01/07/2023] Open
Abstract
Non-canonical amino acids (ncAAs) have been utilized as an invaluable tool for modulating the active site of the enzymes, probing the complex enzyme mechanisms, improving catalytic activity, and designing new to nature enzymes. Here, we report site-specific incorporation of p-benzoyl phenylalanine (pBpA) to engineer (R)-amine transaminase previously created from d-amino acid aminotransferase scaffold. Replacement of the single Phe88 residue at the active site with pBpA exhibits a significant 15-fold and 8-fold enhancement in activity for 1-phenylpropan-1-amine and benzaldehyde, respectively. Reshaping of the enzyme’s active site afforded an another variant F86A/F88pBpA, with 30% higher thermostability at 55°C without affecting parent enzyme activity. Moreover, various racemic amines were successfully resolved by transaminase variants into (S)-amines with excellent conversions (∼50%) and enantiomeric excess (>99%) using pyruvate as an amino acceptor. Additionally, kinetic resolution of the 1-phenylpropan-1-amine was performed using benzaldehyde as an amino acceptor, which is cheaper than pyruvate. Our results highlight the utility of ncAAs for designing enzymes with enhanced functionality beyond the limit of 20 canonical amino acids.
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Affiliation(s)
- Amol D. Pagar
- Department of Systems Biotechnology, Konkuk University, Seoul, South Korea
| | - Hyunwoo Jeon
- Department of Systems Biotechnology, Konkuk University, Seoul, South Korea
| | | | - Sharad Sarak
- Department of Systems Biotechnology, Konkuk University, Seoul, South Korea
| | - Pritam Giri
- Department of Systems Biotechnology, Konkuk University, Seoul, South Korea
| | - Seonga Lim
- Department of Systems Biotechnology, Konkuk University, Seoul, South Korea
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
| | - Byoung Joon Ko
- School of Biopharmaceutical and Medical Sciences, Sungshin Women’s University, Seoul, South Korea
| | - Hyungdon Yun
- Department of Systems Biotechnology, Konkuk University, Seoul, South Korea
- *Correspondence: Hyungdon Yun,
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Park HJ, Jung C, Yoo TH. Development of one-step isothermal methods to detect RNAs using hairpin-loop signal converters and proximity proteolysis reaction. Biosens Bioelectron 2022; 197:113769. [PMID: 34773751 DOI: 10.1016/j.bios.2021.113769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/27/2021] [Accepted: 11/02/2021] [Indexed: 11/28/2022]
Abstract
Ribonucleic acids (RNAs) provide valuable information for biological systems and act as important indicators of disease states. RNAs are diverse in size and structure, and various strategies have been proposed for the detection of nucleic acids; however, developing them into point-of-care (POC) tests has been challenging as most of them consist of complex time-consuming steps. Here, we propose a strategy to assay RNAs using a hairpin-loop (HP) converter and proximity proteolysis reaction (PPR). Interaction between the loop part of HP and its target exposes a single strand of nucleotides, which acts as the template for PPR. A pair of protease and zymogen-conjugated nucleic acids associates with the adjacent regions of the template, resulting in an enhanced proteolysis reaction between protease and zymogen. The activated zymogen then generates a color signal through the hydrolysis of a chromogenic substrate. The combination of HP converter and PPR allowed the same pair of protease- and zymogen-nucleic acids to be used for different RNAs. Guidelines were provided for designing HP converters based on computational analyses and experimental characterizations. This strategy using an HP converter and PPR has been successfully applied to develop simple isothermal methods for the detection of various RNAs, including several microRNAs and KRAS mRNA, in the picomolar range in 1 h. The simplicity of designing HP converters and the beneficial properties of PPR as POC tests would enable the development of novel methods to detect RNAs under low-resource conditions.
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Affiliation(s)
- Hyeon Ji Park
- Department of Molecular Science and Technology, Ajou University, 206 World Cup-ro, Yengtong-gu, Suwon, 16499, South Korea
| | - Cheulhee Jung
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, South Korea
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, 206 World Cup-ro, Yengtong-gu, Suwon, 16499, South Korea; Department of Applied Chemistry and Biological Engineering, Ajou University, 206 World Cup-ro, Yengtong-gu, Suwon, 16499, South Korea.
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7
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Lee BS, Choi WJ, Lee SW, Ko BJ, Yoo TH. Towards Engineering an Orthogonal Protein Translation Initiation System. Front Chem 2021; 9:772648. [PMID: 34765589 PMCID: PMC8576571 DOI: 10.3389/fchem.2021.772648] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 10/14/2021] [Indexed: 11/24/2022] Open
Abstract
In the last two decades, methods to incorporate non-canonical amino acids (ncAAs) into specific positions of a protein have advanced significantly; these methods have become general tools for engineering proteins. However, almost all these methods depend on the translation elongation process, and strategies leveraging the initiation process have rarely been reported. The incorporation of a ncAA specifically at the translation initiation site enables the installation of reactive groups for modification at the N-termini of proteins, which are attractive positions for introducing abiological groups with minimal structural perturbations. In this study, we attempted to engineer an orthogonal protein translation initiation system. Introduction of the identity elements of Escherichia coli initiator tRNA converted an engineered Methanococcus jannaschii tRNATyr into an initiator tRNA. The engineered tRNA enabled the site-specific incorporation of O-propargyl-l-tyrosine (OpgY) into the amber (TAG) codon at the translation initiation position but was inactive toward the elongational TAG codon. Misincorporation of Gln was detected, and the engineered system was demonstrated only with OpgY. We expect further engineering of the initiator tRNA for improved activity and specificity to generate an orthogonal translation initiation system.
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Affiliation(s)
- Byeong Sung Lee
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
| | - Woon Jong Choi
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
| | - Sang Woo Lee
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
| | - Byoung Joon Ko
- School of Biopharmaceutical and Medical Sciences, Sungshin Women's University, Seoul, South Korea
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea.,Department of Applied Chemistry and Biological Engineering, Ajou University, Suwon, South Korea
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8
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Park HJ, Kim Y, Yoo TH. One-pot colorimetric detection of molecules based on proximity proteolysis reaction. Biosens Bioelectron 2021; 188:113349. [PMID: 34030090 DOI: 10.1016/j.bios.2021.113349] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 05/10/2021] [Accepted: 05/12/2021] [Indexed: 01/06/2023]
Abstract
Various types of molecules serve as biomarkers of diseases, and numerous methods have been reported to detect and quantify them. Recently, research efforts have been made to develop point-of-care (POC) tests, which contribute to early diagnoses of diseases, particularly in resource-limited settings. An assay performed in a homogeneous phase is an obvious route to develop these methods. Here, simple homogeneous methods based on proximity proteolysis reactions (PPR) are reported to detect biological molecules. A typical PPR system has been designed such that the proteolysis reaction between protease and zymogen is enhanced in the presence of a target analyte. The activated zymogen generates a color signal by hydrolyzing a chromophore. A protease and zymogen are linked to target binders using specific hybridization between complementary single-stranded DNAs, and several molecules, including proteins, antibodies, aptamers, and small molecules, are used as target binders. The developed assay methods successfully detected several kinds of analytes at subnanomolar concentrations with the one-step procedure and color signal. The modular design of the PPR-based assay will enable the development of simple POC diagnostics for various biomarkers.
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Affiliation(s)
- Hyeon Ji Park
- Department of Molecular Science and Technology, Ajou University, 206 World Cup-ro, Yengtong-gu, Suwon, 16499, South Korea
| | - Yuseon Kim
- Department of Molecular Science and Technology, Ajou University, 206 World Cup-ro, Yengtong-gu, Suwon, 16499, South Korea
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, 206 World Cup-ro, Yengtong-gu, Suwon, 16499, South Korea; Department of Applied Chemistry and Biological Engineering, Ajou University, 206 World Cup-ro, Yengtong-gu, Suwon, 16499, South Korea.
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9
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Pagar AD, Patil MD, Flood DT, Yoo TH, Dawson PE, Yun H. Recent Advances in Biocatalysis with Chemical Modification and Expanded Amino Acid Alphabet. Chem Rev 2021; 121:6173-6245. [PMID: 33886302 DOI: 10.1021/acs.chemrev.0c01201] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The two main strategies for enzyme engineering, directed evolution and rational design, have found widespread applications in improving the intrinsic activities of proteins. Although numerous advances have been achieved using these ground-breaking methods, the limited chemical diversity of the biopolymers, restricted to the 20 canonical amino acids, hampers creation of novel enzymes that Nature has never made thus far. To address this, much research has been devoted to expanding the protein sequence space via chemical modifications and/or incorporation of noncanonical amino acids (ncAAs). This review provides a balanced discussion and critical evaluation of the applications, recent advances, and technical breakthroughs in biocatalysis for three approaches: (i) chemical modification of cAAs, (ii) incorporation of ncAAs, and (iii) chemical modification of incorporated ncAAs. Furthermore, the applications of these approaches and the result on the functional properties and mechanistic study of the enzymes are extensively reviewed. We also discuss the design of artificial enzymes and directed evolution strategies for enzymes with ncAAs incorporated. Finally, we discuss the current challenges and future perspectives for biocatalysis using the expanded amino acid alphabet.
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Affiliation(s)
- Amol D Pagar
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
| | - Mahesh D Patil
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
| | - Dillon T Flood
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Yeongtong-gu, Suwon 16499, Korea
| | - Philip E Dawson
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Hyungdon Yun
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
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10
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Park J, Lee S, Kim Y, Yoo TH. Methods to generate site-specific conjugates of antibody and protein. Bioorg Med Chem 2021; 30:115946. [DOI: 10.1016/j.bmc.2020.115946] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 12/07/2020] [Accepted: 12/09/2020] [Indexed: 02/07/2023]
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Kim B, Lee SS, Yoo TH, Kim JM. Viscoelastic particle focusing in human biofluids. Electrophoresis 2020; 42:2238-2245. [PMID: 33314214 DOI: 10.1002/elps.202000280] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/29/2020] [Accepted: 12/07/2020] [Indexed: 11/08/2022]
Abstract
Saliva and blood plasma are non-Newtonian viscoelastic fluids that play essential roles in the transport of particulate matters (e.g., food and blood cells). However, whether the viscoelasticity of such biofluids alters the dynamics of suspended particles is still unknown. In this study, we report that under pressure-driven microflows of both human saliva and blood plasma, spherical particles laterally migrate and form a focused stream along the channel centerline by their viscoelastic properties. We observed that the particle focusing varied among samples on the basis of sampling times/donors, thereby demonstrating that the viscoelasticity of the human biofluids can be affected by their compositions. We showed that the particle focusing, observed in bovine submaxillary mucin solutions, intensified with the increase in mucin concentration. We expect that the findings from this study will contribute to the understanding of the physiological roles of viscoelasticity of human biofluids.
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Affiliation(s)
- Bookun Kim
- Department of Energy Systems Research, Ajou University, Suwon, Republic of Korea
| | - Sung Sik Lee
- Institute of Biochemistry, ETH Zurich, Zurich, Switzerland.,Scientific Center for Optical and Electron Microscopy, ETH Zurich, Zurich, Switzerland
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, Suwon, Republic of Korea
| | - Ju Min Kim
- Department of Energy Systems Research, Ajou University, Suwon, Republic of Korea.,Department of Chemical Engineering, Ajou University, Suwon, Republic of Korea
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Nasir A, Ashok S, Shim JY, Park S, Yoo TH. Recent Progress in the Understanding and Engineering of Coenzyme B 12-Dependent Glycerol Dehydratase. Front Bioeng Biotechnol 2020; 8:500867. [PMID: 33224925 PMCID: PMC7674605 DOI: 10.3389/fbioe.2020.500867] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 09/17/2020] [Indexed: 01/21/2023] Open
Abstract
Coenzyme B12-dependent glycerol dehydratase (GDHt) catalyzes the dehydration reaction of glycerol in the presence of adenosylcobalamin to yield 3-hydroxypropanal (3-HPA), which can be converted biologically to versatile platform chemicals such as 1,3-propanediol and 3-hydroxypropionic acid. Owing to the increased demand for biofuels, developing biological processes based on glycerol, which is a byproduct of biodiesel production, has attracted considerable attention recently. In this review, we will provide updates on the current understanding of the catalytic mechanism and structure of coenzyme B12-dependent GDHt, and then summarize the results of engineering attempts, with perspectives on future directions in its engineering.
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Affiliation(s)
- Abdul Nasir
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
| | | | - Jeung Yeop Shim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea
| | - Sunghoon Park
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea.,Department of Applied Chemistry and Biological Engineering, Ajou University, Suwon, South Korea
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13
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Park W, Lee KM, Lee BS, Kim YJ, Joo SH, Kwak SK, Yoo TH, Kwon O. Rücktitelbild: Hydrogen‐Bond Free Energy of Local Biological Water (Angew. Chem. 18/2020). Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202003884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Won‐Woo Park
- Department of Chemistry School of Natural Science Ulsan National Institute of Science and Technology Ulsan 44919 Republic of Korea
| | - Kyung Min Lee
- Department of Energy Engineering School of Energy and Chemical Engineering Ulsan National Institute of Science and Technology Ulsan 44919 Republic of Korea
| | - Byeong Sung Lee
- Department of Molecular Science and Technology Ajou University Suwon 16499 Republic of Korea
| | - Young Jae Kim
- Department of Chemistry School of Natural Science Ulsan National Institute of Science and Technology Ulsan 44919 Republic of Korea
- Center for Soft and Living Matter Institute for Basic Science (IBS) Ulsan 44919 Republic of Korea
| | - Se Hun Joo
- Department of Energy Engineering School of Energy and Chemical Engineering Ulsan National Institute of Science and Technology Ulsan 44919 Republic of Korea
| | - Sang Kyu Kwak
- Department of Energy Engineering School of Energy and Chemical Engineering Ulsan National Institute of Science and Technology Ulsan 44919 Republic of Korea
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology Ajou University Suwon 16499 Republic of Korea
| | - Oh‐Hoon Kwon
- Department of Chemistry School of Natural Science Ulsan National Institute of Science and Technology Ulsan 44919 Republic of Korea
- Center for Soft and Living Matter Institute for Basic Science (IBS) Ulsan 44919 Republic of Korea
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Park W, Lee KM, Lee BS, Kim YJ, Joo SH, Kwak SK, Yoo TH, Kwon O. Back Cover: Hydrogen‐Bond Free Energy of Local Biological Water (Angew. Chem. Int. Ed. 18/2020). Angew Chem Int Ed Engl 2020. [DOI: 10.1002/anie.202003884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Won‐Woo Park
- Department of Chemistry School of Natural Science Ulsan National Institute of Science and Technology Ulsan 44919 Republic of Korea
| | - Kyung Min Lee
- Department of Energy Engineering School of Energy and Chemical Engineering Ulsan National Institute of Science and Technology Ulsan 44919 Republic of Korea
| | - Byeong Sung Lee
- Department of Molecular Science and Technology Ajou University Suwon 16499 Republic of Korea
| | - Young Jae Kim
- Department of Chemistry School of Natural Science Ulsan National Institute of Science and Technology Ulsan 44919 Republic of Korea
- Center for Soft and Living Matter Institute for Basic Science (IBS) Ulsan 44919 Republic of Korea
| | - Se Hun Joo
- Department of Energy Engineering School of Energy and Chemical Engineering Ulsan National Institute of Science and Technology Ulsan 44919 Republic of Korea
| | - Sang Kyu Kwak
- Department of Energy Engineering School of Energy and Chemical Engineering Ulsan National Institute of Science and Technology Ulsan 44919 Republic of Korea
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology Ajou University Suwon 16499 Republic of Korea
| | - Oh‐Hoon Kwon
- Department of Chemistry School of Natural Science Ulsan National Institute of Science and Technology Ulsan 44919 Republic of Korea
- Center for Soft and Living Matter Institute for Basic Science (IBS) Ulsan 44919 Republic of Korea
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Park WW, Lee KM, Lee BS, Kim YJ, Joo SH, Kwak SK, Yoo TH, Kwon OH. Hydrogen-Bond Free Energy of Local Biological Water. Angew Chem Int Ed Engl 2020; 59:7089-7096. [PMID: 32112494 DOI: 10.1002/anie.202002025] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Indexed: 11/09/2022]
Abstract
Here, we propose an experimental methodology based on femtosecond-resolved fluorescence spectroscopy to measure the hydrogen (H)-bond free energy of water at protein surfaces under isothermal conditions. A demonstration was conducted by installing a non-canonical isostere of tryptophan (7-azatryptophan) at the surface of a coiled-coil protein to exploit the photoinduced proton transfer of its chromophoric moiety, 7-azaindole. The H-bond free energy of this biological water was evaluated by comparing the rates of proton transfer, sensitive to the hydration environment, at the protein surface and in bulk water, and it was found to be higher than that of bulk water by 0.4 kcal mol-1 . The free-energy difference is dominated by the entropic cost in the H-bond network among water molecules at the hydrophilic and charged protein surface. Our study opens a door to accessing the energetics and dynamics of local biological water to give insight into its roles in protein structure and function.
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Affiliation(s)
- Won-Woo Park
- Department of Chemistry, School of Natural Science, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
| | - Kyung Min Lee
- Department of Energy Engineering, School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
| | - Byeong Sung Lee
- Department of Molecular Science and Technology, Ajou University, Suwon, 16499, Republic of Korea
| | - Young Jae Kim
- Department of Chemistry, School of Natural Science, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea.,Center for Soft and Living Matter, Institute for Basic Science (IBS), Ulsan, 44919, Republic of Korea
| | - Se Hun Joo
- Department of Energy Engineering, School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
| | - Sang Kyu Kwak
- Department of Energy Engineering, School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, Suwon, 16499, Republic of Korea
| | - Oh-Hoon Kwon
- Department of Chemistry, School of Natural Science, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea.,Center for Soft and Living Matter, Institute for Basic Science (IBS), Ulsan, 44919, Republic of Korea
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Affiliation(s)
- Won‐Woo Park
- Department of Chemistry School of Natural Science Ulsan National Institute of Science and Technology Ulsan 44919 Republic of Korea
| | - Kyung Min Lee
- Department of Energy Engineering School of Energy and Chemical Engineering Ulsan National Institute of Science and Technology Ulsan 44919 Republic of Korea
| | - Byeong Sung Lee
- Department of Molecular Science and Technology Ajou University Suwon 16499 Republic of Korea
| | - Young Jae Kim
- Department of Chemistry School of Natural Science Ulsan National Institute of Science and Technology Ulsan 44919 Republic of Korea
- Center for Soft and Living Matter Institute for Basic Science (IBS) Ulsan 44919 Republic of Korea
| | - Se Hun Joo
- Department of Energy Engineering School of Energy and Chemical Engineering Ulsan National Institute of Science and Technology Ulsan 44919 Republic of Korea
| | - Sang Kyu Kwak
- Department of Energy Engineering School of Energy and Chemical Engineering Ulsan National Institute of Science and Technology Ulsan 44919 Republic of Korea
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology Ajou University Suwon 16499 Republic of Korea
| | - Oh‐Hoon Kwon
- Department of Chemistry School of Natural Science Ulsan National Institute of Science and Technology Ulsan 44919 Republic of Korea
- Center for Soft and Living Matter Institute for Basic Science (IBS) Ulsan 44919 Republic of Korea
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Min MW, Kim CE, Chauhan S, Park HJ, Park CS, Yoo TH, Kang TJ. Identification of peptide inhibitors of matrix metalloproteinase 1 using an in-house assay system for the enzyme. Enzyme Microb Technol 2019; 127:65-69. [DOI: 10.1016/j.enzmictec.2019.04.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 04/08/2019] [Accepted: 04/19/2019] [Indexed: 11/30/2022]
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Achek A, Shah M, Seo JY, Kwon HK, Gui X, Shin HJ, Cho EY, Lee BS, Kim DJ, Lee SH, Yoo TH, Kim MS, Choi S. Linear and Rationally Designed Stapled Peptides Abrogate TLR4 Pathway and Relieve Inflammatory Symptoms in Rheumatoid Arthritis Rat Model. J Med Chem 2019; 62:6495-6511. [PMID: 31283217 DOI: 10.1021/acs.jmedchem.9b00061] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A mounting evidence exists for the despicable role of the aberrant immune response in the pathogenesis of rheumatoid arthritis (RA), where toll-like receptor 4 (TLR4) can activate synovial fibroblasts that lead to the chronic inflammation and joint destruction, thus making TLR4 a potent drug target in RA. We report that novel TLR4-antagonizing peptide, PIP2, inhibits the induction of inflammatory biomarkers in vitro as well as in vivo. Systemically, PIP2 inhibits the lipopolysaccharide (LPS)-elicited TNF-α, IL-6, and IL-12p40 in a mouse model. The rationally designed cyclic derivative, cPIP2, is capable of inhibiting LPS-induced proinflammatory cytokines at significantly lower concentration as compared to PIP2 (PIP2 IC50 = 20 μM, cPIP2 IC50 = 5 μM). Finally, cPIP2 was able to relieve the inflammatory symptoms and synovial tissue destruction in the RA rat model. Cumulatively, these data suggest that PIP2 and cPIP2 hold strong promise for the development of peptide-based immunotherapeutics that could be of great value in curbing TLR-related immune complications including RA.
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Affiliation(s)
- Asma Achek
- Department of Molecular Science and Technology , Ajou University , Suwon 16499 , Korea
| | - Masaud Shah
- Department of Molecular Science and Technology , Ajou University , Suwon 16499 , Korea
| | - Ji Young Seo
- Department of Molecular Science and Technology , Ajou University , Suwon 16499 , Korea
| | - Hyuk-Kwon Kwon
- Department of Orthopedics and Rehabilitation , Yale University School of Medicine , New Haven , Connecticut 06520-8071 , United States
| | - Xiangai Gui
- Department of Molecular Science and Technology , Ajou University , Suwon 16499 , Korea
| | - Hyeon-Jun Shin
- Department of Molecular Science and Technology , Ajou University , Suwon 16499 , Korea
| | - Eun-Young Cho
- Department of Molecular Science and Technology , Ajou University , Suwon 16499 , Korea
| | - Byeong Sung Lee
- Department of Molecular Science and Technology , Ajou University , Suwon 16499 , Korea
| | - Dong-Jin Kim
- Division of Nephrology, Department of Internal Medicine , Kyung Hee University Hospital at Gangdong , Seoul 05278 , Korea
| | - Sang Ho Lee
- Division of Nephrology, Department of Internal Medicine , Kyung Hee University Hospital at Gangdong , Seoul 05278 , Korea
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology , Ajou University , Suwon 16499 , Korea
| | - Moon Suk Kim
- Department of Molecular Science and Technology , Ajou University , Suwon 16499 , Korea
| | - Sangdun Choi
- Department of Molecular Science and Technology , Ajou University , Suwon 16499 , Korea
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Lee BS, Lee Y, Park J, Jeong BS, Jo M, Jung ST, Yoo TH. Construction of an immunotoxin via site-specific conjugation of anti-Her2 IgG and engineered Pseudomonas exotoxin A. J Biol Eng 2019; 13:56. [PMID: 31285754 PMCID: PMC6588878 DOI: 10.1186/s13036-019-0188-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 06/12/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Immunotoxins consisting of a toxin from bacteria or plants and a targeting module have been developed as potent anti-cancer therapeutics. The majority of them, especially those in preclinical or clinical testing stages, are fusion proteins of a toxin and antibody fragment. Immunotoxins based on full-length antibodies are less studied, even though the fragment crystallizable (Fc) domain plays an important role in regulating the concentration of immunoglobulin G (IgG) in the serum and in antibody-mediated immune responses against pathogens. RESULTS We devised a method to site-specifically conjugate IgG and another protein using a cysteine residue introduced into the IgG and a bio-orthogonally reactive unnatural amino acid incorporated into the other protein. The human epidermal growth factor receptor 2 (Her2)-targeting IgG, trastuzumab, was engineered to have an unpaired cysteine in the heavy chain, and an unnatural amino acid with the azido group was incorporated into an engineered Pseudomonas exotoxin A (PE24). The two protein molecules were conjugated site-specifically using a bifunctional linker having dibenzocyclooctyne and maleimide groups. Binding to Her2 and interaction with various Fc receptors of trastuzumab were not affected by the conjugation with PE24. The trastuzumab-PE24 conjugate was cytotoxic to Her2-overexpressing cell lines, which involved the inhibition of cellular protein synthesis due to the modification of elongation factor-2. CONCLUSIONS We constructed the site-specifically conjugated immunotoxin based on IgG and PE24, which induced target-specific cytotoxicity. To evaluate the molecule as a cancer therapeutic, animal studies are planned to assess tumor regression, half-life in blood, and in vivo immunogenicity. In addition, we expect that the site-specific conjugation method can be used to develop other antibody-protein conjugates for applications in therapeutics and diagnostics.
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Affiliation(s)
- Byeong Sung Lee
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Yeongtong-gu, Suwon, 16499 South Korea
| | - Yumi Lee
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Yeongtong-gu, Suwon, 16499 South Korea
| | - Jisoo Park
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Yeongtong-gu, Suwon, 16499 South Korea
| | - Bo Seok Jeong
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Yeongtong-gu, Suwon, 16499 South Korea
| | - Migyeong Jo
- Department of Applied Chemistry, Kookmin University, 77 Jeongneung-ro, Seongbuk-gu, Seoul, 02707 South Korea
| | - Sang Taek Jung
- Department of Biomedical Sciences, Graduate School of Medicine, Korea University, Seongbuk-gu, Seoul, 02841 South Korea
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Yeongtong-gu, Suwon, 16499 South Korea
- Department of Applied Chemistry and Biological Engineering, Ajou University, 206 World cup-ro, Yeongtong-gu, Suwon, 16499 South Korea
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20
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Mitrofanova A, Mallela SK, Ducasa GM, Yoo TH, Rosenfeld-Gur E, Zelnik ID, Molina J, Varona Santos J, Ge M, Sloan A, Kim JJ, Pedigo C, Bryn J, Volosenco I, Faul C, Zeidan YH, Garcia Hernandez C, Mendez AJ, Leibiger I, Burke GW, Futerman AH, Barisoni L, Ishimoto Y, Inagi R, Merscher S, Fornoni A. SMPDL3b modulates insulin receptor signaling in diabetic kidney disease. Nat Commun 2019; 10:2692. [PMID: 31217420 PMCID: PMC6584700 DOI: 10.1038/s41467-019-10584-4] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 05/15/2019] [Indexed: 12/22/2022] Open
Abstract
Sphingomyelin phosphodiesterase acid-like 3b (SMPDL3b) is a lipid raft enzyme that regulates plasma membrane (PM) fluidity. Here we report that SMPDL3b excess, as observed in podocytes in diabetic kidney disease (DKD), impairs insulin receptor isoform B-dependent pro-survival insulin signaling by interfering with insulin receptor isoforms binding to caveolin-1 in the PM. SMPDL3b excess affects the production of active sphingolipids resulting in decreased ceramide-1-phosphate (C1P) content as observed in human podocytes in vitro and in kidney cortexes of diabetic db/db mice in vivo. Podocyte-specific Smpdl3b deficiency in db/db mice is sufficient to restore kidney cortex C1P content and to protect from DKD. Exogenous administration of C1P restores IR signaling in vitro and prevents established DKD progression in vivo. Taken together, we identify SMPDL3b as a modulator of insulin signaling and demonstrate that supplementation with exogenous C1P may represent a lipid therapeutic strategy to treat diabetic complications such as DKD.
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Affiliation(s)
- A Mitrofanova
- Katz Family Division of Nephrology and Hypertension, Department of Medicine, University of Miami, Miller School of Medicine, Miami, 33136, FL, USA
- Peggy and Harold Katz Family Drug Discovery Center, University of Miami, Miller School of Medicine, Miami, 33136, FL, USA
- Department of Surgery, University of Miami, Miller School of Medicine, Miami, 33136, FL, USA
| | - S K Mallela
- Katz Family Division of Nephrology and Hypertension, Department of Medicine, University of Miami, Miller School of Medicine, Miami, 33136, FL, USA
- Peggy and Harold Katz Family Drug Discovery Center, University of Miami, Miller School of Medicine, Miami, 33136, FL, USA
| | - G M Ducasa
- Katz Family Division of Nephrology and Hypertension, Department of Medicine, University of Miami, Miller School of Medicine, Miami, 33136, FL, USA
- Peggy and Harold Katz Family Drug Discovery Center, University of Miami, Miller School of Medicine, Miami, 33136, FL, USA
- Department of Molecular and Cellular Pharmacology, University of Miami, Miller School of Medicine, Miami, 33136, FL, USA
| | - T H Yoo
- Katz Family Division of Nephrology and Hypertension, Department of Medicine, University of Miami, Miller School of Medicine, Miami, 33136, FL, USA
- Peggy and Harold Katz Family Drug Discovery Center, University of Miami, Miller School of Medicine, Miami, 33136, FL, USA
- Department of Internal Medicine, College of Medicine, Yonsei University, Seoul, 03722, Korea
| | - E Rosenfeld-Gur
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - I D Zelnik
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - J Molina
- Katz Family Division of Nephrology and Hypertension, Department of Medicine, University of Miami, Miller School of Medicine, Miami, 33136, FL, USA
- Peggy and Harold Katz Family Drug Discovery Center, University of Miami, Miller School of Medicine, Miami, 33136, FL, USA
| | - J Varona Santos
- Katz Family Division of Nephrology and Hypertension, Department of Medicine, University of Miami, Miller School of Medicine, Miami, 33136, FL, USA
- Peggy and Harold Katz Family Drug Discovery Center, University of Miami, Miller School of Medicine, Miami, 33136, FL, USA
| | - M Ge
- Katz Family Division of Nephrology and Hypertension, Department of Medicine, University of Miami, Miller School of Medicine, Miami, 33136, FL, USA
- Peggy and Harold Katz Family Drug Discovery Center, University of Miami, Miller School of Medicine, Miami, 33136, FL, USA
- Department of Molecular and Cellular Pharmacology, University of Miami, Miller School of Medicine, Miami, 33136, FL, USA
| | - A Sloan
- Katz Family Division of Nephrology and Hypertension, Department of Medicine, University of Miami, Miller School of Medicine, Miami, 33136, FL, USA
- Peggy and Harold Katz Family Drug Discovery Center, University of Miami, Miller School of Medicine, Miami, 33136, FL, USA
| | - J J Kim
- Katz Family Division of Nephrology and Hypertension, Department of Medicine, University of Miami, Miller School of Medicine, Miami, 33136, FL, USA
- Peggy and Harold Katz Family Drug Discovery Center, University of Miami, Miller School of Medicine, Miami, 33136, FL, USA
| | - C Pedigo
- Katz Family Division of Nephrology and Hypertension, Department of Medicine, University of Miami, Miller School of Medicine, Miami, 33136, FL, USA
- Peggy and Harold Katz Family Drug Discovery Center, University of Miami, Miller School of Medicine, Miami, 33136, FL, USA
- Department of Internal Medicine, Yale University School of Medicine, New Haven, 06510, CT, USA
| | - J Bryn
- Katz Family Division of Nephrology and Hypertension, Department of Medicine, University of Miami, Miller School of Medicine, Miami, 33136, FL, USA
- Peggy and Harold Katz Family Drug Discovery Center, University of Miami, Miller School of Medicine, Miami, 33136, FL, USA
| | - I Volosenco
- Katz Family Division of Nephrology and Hypertension, Department of Medicine, University of Miami, Miller School of Medicine, Miami, 33136, FL, USA
- Peggy and Harold Katz Family Drug Discovery Center, University of Miami, Miller School of Medicine, Miami, 33136, FL, USA
- Lewis Gale Medical Center, Salem, 24153, VI, USA
| | - C Faul
- Katz Family Division of Nephrology and Hypertension, Department of Medicine, University of Miami, Miller School of Medicine, Miami, 33136, FL, USA
- Peggy and Harold Katz Family Drug Discovery Center, University of Miami, Miller School of Medicine, Miami, 33136, FL, USA
- Division of Nephrology, Department of Medicine, University of Alabama at Birmingham, Birmingham, 35233, AL, USA
| | - Y H Zeidan
- Peggy and Harold Katz Family Drug Discovery Center, University of Miami, Miller School of Medicine, Miami, 33136, FL, USA
- Department of Radiation Oncology, University of Miami, Miller School of Medicine, Miami, 33136, FL, USA
- Department of Radiation Oncology, American University of Beirut, Beirut, 1107 2020, Lebanon
| | - C Garcia Hernandez
- Katz Family Division of Nephrology and Hypertension, Department of Medicine, University of Miami, Miller School of Medicine, Miami, 33136, FL, USA
- Peggy and Harold Katz Family Drug Discovery Center, University of Miami, Miller School of Medicine, Miami, 33136, FL, USA
- Department of Radiation Oncology, University of Miami, Miller School of Medicine, Miami, 33136, FL, USA
| | - A J Mendez
- Diabetes Research Institute, University of Miami, Miller School of Medicine, Miami, 33136, FL, USA
| | - I Leibiger
- The Rolf Luft Research Center for Diabetes and Endocrinology, Karolinska Institutet, Stockholm, 17176, Sweden
| | - G W Burke
- Department of Surgery, University of Miami, Miller School of Medicine, Miami, 33136, FL, USA
- Diabetes Research Institute, University of Miami, Miller School of Medicine, Miami, 33136, FL, USA
| | - A H Futerman
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - L Barisoni
- Department of Pathology, University of Miami, Miller School of Medicine, Miami, 33136, FL, USA
| | - Y Ishimoto
- Division of Nephrology and Endocrinology, University of Tokyo Graduate School of Medicine, Tokyo, 113-8654, Japan
- Division of CKD Pathophysiology, University of Tokyo Graduate School of Medicine, Tokyo, 113-8654, Japan
| | - R Inagi
- Division of Nephrology and Endocrinology, University of Tokyo Graduate School of Medicine, Tokyo, 113-8654, Japan
- Division of CKD Pathophysiology, University of Tokyo Graduate School of Medicine, Tokyo, 113-8654, Japan
| | - S Merscher
- Katz Family Division of Nephrology and Hypertension, Department of Medicine, University of Miami, Miller School of Medicine, Miami, 33136, FL, USA
- Peggy and Harold Katz Family Drug Discovery Center, University of Miami, Miller School of Medicine, Miami, 33136, FL, USA
| | - A Fornoni
- Katz Family Division of Nephrology and Hypertension, Department of Medicine, University of Miami, Miller School of Medicine, Miami, 33136, FL, USA.
- Peggy and Harold Katz Family Drug Discovery Center, University of Miami, Miller School of Medicine, Miami, 33136, FL, USA.
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Kim B, Lee SS, Yoo TH, Kim S, Kim SY, Choi SH, Kim JM. Normal stress difference-driven particle focusing in nanoparticle colloidal dispersion. Sci Adv 2019; 5:eaav4819. [PMID: 31187058 PMCID: PMC6555624 DOI: 10.1126/sciadv.aav4819] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 04/29/2019] [Indexed: 06/09/2023]
Abstract
Colloidal dispersion has elastic properties due to Brownian relaxation process. However, experimental evidence for the elastic properties, characterized with normal stress differences, is elusive in shearing colloidal dispersion, particularly at low Péclet numbers (Pe < 1). Here, we report that single micrometer-sized polystyrene (PS) beads, suspended in silica nanoparticle dispersion (8 nm radius; 22%, v/v), laterally migrate and form a tightly focused stream by the normal stress differences, generated in pressure-driven microtube flow at low Pe. The nanoparticle dispersion was expected to behave as a Newtonian fluid because of its ultrashort relaxation time (2 μs), but large shear strain experienced by the PS beads causes the notable non-Newtonian behavior. We demonstrate that the unique rheological properties of the nanoparticle dispersion generate the secondary flow in perpendicular to mainstream in a noncircular conduit, and the elastic properties of blood plasma-constituting protein solutions are elucidated by the colloidal dynamics of protein molecules.
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Affiliation(s)
- Bookun Kim
- Department of Energy Systems Research, Ajou University, Suwon 16499, Republic of Korea
| | - Sung Sik Lee
- Institute of Biochemistry, ETH Zurich, Zurich CH-8093, Switzerland
- Scientific Center for Optical and Electron Microscopy, ETH Zurich, Zurich CH-8093, Switzerland
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Republic of Korea
| | - Sunhyung Kim
- Corporate R&D, LG Chem, Gwacheon 13818, Republic of Korea
| | - So Youn Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Soo-Hyung Choi
- Department of Chemical Engineering, Hongik University, Seoul 04066, Republic of Korea
| | - Ju Min Kim
- Department of Energy Systems Research, Ajou University, Suwon 16499, Republic of Korea
- Department of Chemical Engineering, Ajou University, Suwon 16499, Republic of Korea
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22
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Jang YJ, Lee KH, Yoo TH, Kim DM. Interfacing a Personal Glucose Meter with Cell-Free Protein Synthesis for Rapid Analysis of Amino Acids. Anal Chem 2019; 91:2531-2535. [DOI: 10.1021/acs.analchem.8b05526] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yeon-Jae Jang
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea
| | - Kyung-Ho Lee
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, 206 Worldcup-ro, Yeongtong-gu, Suwon 16499, Korea
| | - Dong-Myung Kim
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea
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Abstract
Nucleic acid analysis plays an important role in diagnosing diseases as well as understanding biology. Despite advances in technology, there is still a need to develop a rapid and simple method to detect specific nucleic acids, especially in remote locations and low-resource cases. Here, we proposed a proximity proteolysis reaction in which the reaction between protease and zymogen is enhanced in the presence of a target molecule. The pair of proteins was site-specifically modified with oligonucleotides, and the conjugates were used to develop a method of detecting nucleic acids. Target DNA and RNA could be detected in less than 1 h at sub-nanomolar concentrations based on an absorbance signal. The assay method was resistant to interference by biological matrixes, and its sensitivity could be improved when combined with an isothermal nucleic acid amplification method. The results demonstrated the feasibility of this proximity proteolysis reaction as a new platform technology for detecting specific nucleic acid sequences.
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Affiliation(s)
- Hyeon Ji Park
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Yengtong-gu, Suwon 16499, Korea
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Yengtong-gu, Suwon 16499, Korea
- Department of Applied Chemistry and Biological Engineering, Ajou University, 206 World cup-ro, Yengtong-gu, Suwon 16499, Korea
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24
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Abstract
Conjugation of antibody has expanded its applications in therapeutics and diagnostics, and various methods have been developed based on chemical or enzymatic reactions. However, the majority of them have focused on synthetic molecules such as small molecules, nucleic acids, or synthetic materials, but site-specific conjugation of antibody with protein cargo has rarely been demonstrated. In this Communication, we report a PEptide-DIrected Photo-cross-linking (PEDIP) reaction for site-specific conjugation of IgG with protein using an Fc-binding peptide and a photoreactive amino acid analogue, and demonstrate this method by developing an immunotoxin composed of a Her2-targeting IgG (trastuzumab) and an engineered Pseudomonas exotoxin A (PE24). The ADP-ribosylation of eukaryotic elongation factor-2 by the bacterial toxin inhibits the ribosomal translation of protein, and the trastuzumab-PE24 conjugate exhibited the cytotoxicity toward Her2-overexpressing cell lines. The PEDIP reaction can also be applied for many other types of cargo with slight modifications of the method.
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Affiliation(s)
| | | | - Byoung Joon Ko
- New Drug Development Center , Osong Medical Innovative Foundation , 123 Osongsaengmyeong-ro , Osong-eup, Cheongju , 28160 , Korea
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25
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Seok JY, Yang J, Choi SJ, Lim HG, Choi UJ, Kim KJ, Park S, Yoo TH, Jung GY. Directed evolution of the 3-hydroxypropionic acid production pathway by engineering aldehyde dehydrogenase using a synthetic selection device. Metab Eng 2018; 47:113-120. [PMID: 29545147 DOI: 10.1016/j.ymben.2018.03.009] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 03/09/2018] [Accepted: 03/09/2018] [Indexed: 12/30/2022]
Abstract
3-Hydroxypropionic acid (3-HP) is an important platform chemical, and biological production of 3-HP from glycerol as a carbon source using glycerol dehydratase (GDHt) and aldehyde dehydrogenase (ALDH) has been revealed to be effective because it involves a relatively simple metabolic pathway and exhibits higher yield and productivity than other biosynthetic pathways. Despite the successful attempts of 3-HP production from glycerol, the biological process suffers from problems arising from low activity and inactivation of the two enzymes. To apply the directed evolutionary approach to engineer the 3-HP production system, we constructed a synthetic selection device using a 3-HP-responsive transcription factor and developed a selection approach for screening 3-HP-producing microorganisms. The method was applied to an ALDH library, specifically aldehyde-binding site library of alpha-ketoglutaric semialdehyde dehydrogenase (KGSADH). Only two serial cultures resulted in enrichment of strains showing increased 3-HP production, and an isolated KGSADH variant enzyme exhibited a 2.79-fold higher catalytic efficiency toward its aldehyde substrate than the wild-type one. This approach will provide the simple and efficient tool to engineer the pathway enzymes in metabolic engineering.
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Affiliation(s)
- Joo Yeon Seok
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Jina Yang
- School of Chemical and Biological Engineering, Institute of Chemical Process, Seoul National University, 1 Gwanak-Ro, Gwanak-Gu, Seoul 08826, Republic of Korea
| | - Sang Jin Choi
- Department of Molecular Science and Technology, Ajou University, 206 Worldcup-Ro, Yeongtong-Gu, Suwon 16499, Republic of Korea
| | - Hyun Gyu Lim
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Un Jong Choi
- Department of Molecular Science and Technology, Ajou University, 206 Worldcup-Ro, Yeongtong-Gu, Suwon 16499, Republic of Korea
| | - Kyung-Jin Kim
- School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daehak-Ro 80, Buk-Ku, Daegu 702-701, Republic of Korea
| | - Sunghoon Park
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), UNIST-Gil 50, Eonyang-Eup, Ulju-Gun, Ulsan 449419, Republic of Korea
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, 206 Worldcup-Ro, Yeongtong-Gu, Suwon 16499, Republic of Korea.
| | - Gyoo Yeol Jung
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea; Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea.
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26
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Heo CH, Cho MK, Shin S, Yoo TH, Kim HM. Real-time monitoring of vesicle pH in an endocytic pathway using an EGF-conjugated two-photon probe. Chem Commun (Camb) 2018; 52:14007-14010. [PMID: 27853757 DOI: 10.1039/c6cc08036g] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Herein, we developed a ratiometric two-photon probe (BHS3-EGF), derived from a pH sensitive dye and epidermal growth factor (EGF), for real-time monitoring and quantitative analysis of acidic luminal pH values during endocytic pathway activity. Two-photon microscopy imaging with BHS3-EGF allows the quantitative analysis of pH distributions of single vesicles and their dynamics in receptor-mediated endocytosis in real-time.
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Affiliation(s)
- Cheol Ho Heo
- Department of Energy Systems Research, Ajou University, Suwon 443-749, Korea.
| | - Myoung Ki Cho
- Department of Energy Systems Research, Ajou University, Suwon 443-749, Korea.
| | - Seunggun Shin
- Department of Molecular Science and Technology, Ajou University, Suwon 433-721, Korea.
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, Suwon 433-721, Korea.
| | - Hwan Myung Kim
- Department of Energy Systems Research, Ajou University, Suwon 443-749, Korea.
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Abstract
The use of biomimetic scaffolds for bone tissue engineering has been studied for a long time. Biomimetic scaffolds can assist and accelerate bone regeneration that is similar to that of authentic tissue, which represents the environment of cells in a living organism. Currently, numerous biomaterials have been reported for use as a biomimetic scaffold. This review focuses on the design of biomimetic scaffolds, kinds of biomaterials and methods used to fabricate biomimetic scaffolds, growth factors used with biomimetic scaffold for bone regeneration, mobilization of biological agents into biomimetic scaffolds, and studies on (pre)clinical bone regeneration from biomimetic scaffolds. Then, future prospects for biomimetic scaffolds are discussed.
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Affiliation(s)
- Joon Yeong Park
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
| | - Seung Hun Park
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
| | - Mal Geum Kim
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
| | - Sang-Hyug Park
- Department of Biomedical Engineering, Pukyong National University, Busan, South Korea
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
| | - Moon Suk Kim
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea.
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28
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Park YS, Choi UJ, Nam NH, Choi SJ, Nasir A, Lee SG, Kim KJ, Jung GY, Choi S, Shim JY, Park S, Yoo TH. Engineering an aldehyde dehydrogenase toward its substrates, 3-hydroxypropanal and NAD +, for enhancing the production of 3-hydroxypropionic acid. Sci Rep 2017; 7:17155. [PMID: 29214999 PMCID: PMC5719400 DOI: 10.1038/s41598-017-15400-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 10/25/2017] [Indexed: 11/09/2022] Open
Abstract
3-Hydroxypropionic acid (3-HP) can be produced via the biological route involving two enzymatic reactions: dehydration of glycerol to 3-hydroxypropanal (3-HPA) and then oxidation to 3-HP. However, commercial production of 3-HP using recombinant microorganisms has been hampered with several problems, some of which are associated with the toxicity of 3-HPA and the efficiency of NAD+ regeneration. We engineered α-ketoglutaric semialdehyde dehydrogenase (KGSADH) from Azospirillum brasilense for the second reaction to address these issues. The residues in the binding sites for the substrates, 3-HPA and NAD+, were randomized, and the resulting libraries were screened for higher activity. Isolated KGSADH variants had significantly lower Km values for both the substrates. The enzymes also showed higher substrate specificities for aldehyde and NAD+, less inhibition by NADH, and greater resistance to inactivation by 3-HPA than the wild-type enzyme. A recombinant Pseudomonas denitrificans strain with one of the engineered KGSADH variants exhibited less accumulation of 3-HPA, decreased levels of inactivation of the enzymes, and higher cell growth than that with the wild-type KGSADH. The flask culture of the P. denitrificans strain with the mutant KGSADH resulted in about 40% increase of 3-HP titer (53 mM) compared with that using the wild-type enzyme (37 mM).
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Affiliation(s)
- Ye Seop Park
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Yeongtong-gu, Suwon, 16499, Korea
| | - Un Jong Choi
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Yeongtong-gu, Suwon, 16499, Korea
| | - Nguyen Hoai Nam
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Korea
| | - Sang Jin Choi
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Yeongtong-gu, Suwon, 16499, Korea
| | - Abdul Nasir
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Yeongtong-gu, Suwon, 16499, Korea
| | - Sun-Gu Lee
- Department of Chemical and Biomolecular Engineering, Pusan National University, Pusan, 46241, Korea
| | - Kyung Jin Kim
- School of Life Sciences, Kyungpook National University, Daegu, 41566, Korea
| | - Gyoo Yeol Jung
- Department of Chemical Engineering, Pohang University of Science and Technology, Pohang, 37673, Korea
| | - Sangdun Choi
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Yeongtong-gu, Suwon, 16499, Korea
| | - Jeung Yeop Shim
- Bio R&D Center, Noroo Holdings Co., Ltd, Suwon, 16229, Korea
| | - Sunghoon Park
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Korea.
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Yeongtong-gu, Suwon, 16499, Korea.
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Abstract
In this study, we present a simple and economical method that enables rapid quantification of amino acids based on their polymerization into a signal-generating protein. This method harnesses amino acid-deficient cell-free protein synthesis systems that generate fluorescence signals in response to exogenous amino acids. When premixed with assay samples containing the amino acids in question, incubation of the cell-free synthesis reaction mixture rapidly resulted in the production of sfGFP, the fluorescence intensity of which was linearly proportional to the concentration of the amino acids. The assay method achieved a limit of detection as low as ∼100 nM and was successfully applied to the quantification of disease-related amino acids in biological samples. Compared with standard methods in current use that require chemical derivatization of amino acids and chromatographic equipment, the complementation assay method developed in this work enables the direct translation of amino acid titer into measurable biofluorescence intensity in a much shorter period, providing a more affordable and flexible option for the quantification of amino acids.
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Affiliation(s)
- Yeon-Jae Jang
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University , 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea
| | - Kyung-Ho Lee
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University , 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University , 206 Worldcup-ro, Yeongtong-gu, Suwon 16499, Korea
| | - Dong-Myung Kim
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University , 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea
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Park SH, Kwon JS, Lee BS, Park JH, Lee BK, Yun JH, Lee BY, Kim JH, Min BH, Yoo TH, Kim MS. BMP2-modified injectable hydrogel for osteogenic differentiation of human periodontal ligament stem cells. Sci Rep 2017; 7:6603. [PMID: 28747761 PMCID: PMC5529463 DOI: 10.1038/s41598-017-06911-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 06/19/2017] [Indexed: 12/22/2022] Open
Abstract
This is the first report on the development of a covalently bone morphogenetic protein-2 (BMP2)-immobilized hydrogel that is suitable for osteogenic differentiation of human periodontal ligament stem cells (hPLSCs). O-propargyl-tyrosine (OpgY) was site-specifically incorporated into BMP2 to prepare BMP2-OpgY with an alkyne group. The engineered BMP2-OpgY exhibited osteogenic characteristics after in vitro osteogenic differentiation of hPLSCs, indicating the osteogenic ability of BMP2-OpgY. A methoxy polyethylene glycol-(polycaprolactone-(N3)) block copolymer (MC-N3) was prepared as an injectable in situ-forming hydrogel. BMP2 covalently immobilized on an MC hydrogel (MC-BMP2) was prepared quantitatively by a simple biorthogonal reaction between alkyne groups on BMP2-OpgY and azide groups on MC-N3 via a Cu(I)-catalyzed click reaction. The hPLSCs-loaded MC-BMP2 formed a hydrogel almost immediately upon injection into animals. In vivo osteogenic differentiation of hPLSCs in the MC-BMP2 formulation was confirmed by histological staining and gene expression analyses. Histological staining of hPLSC-loaded MC-BMP2 implants showed evidence of mineralized calcium deposits, whereas hPLSC-loaded MC-Cl or BMP2-OpgY mixed with MC-Cl, implants showed no mineral deposits. Additionally, MC-BMP2 induced higher levels of osteogenic gene expression in hPLSCs than in other groups. In conclusion, BMP2-OpgY covalently immobilized on MC-BMP2 induced osteogenic differentiation of hPLSCs as a noninvasive method for bone tissue engineering.
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Affiliation(s)
- Seung Hun Park
- Department of Molecular Science and Technology, Ajou University, Suwon, 443-749, Korea
| | - Jin Seon Kwon
- Department of Molecular Science and Technology, Ajou University, Suwon, 443-749, Korea
| | - Byeong Sung Lee
- Department of Molecular Science and Technology, Ajou University, Suwon, 443-749, Korea
| | - Ji Hoon Park
- Department of Molecular Science and Technology, Ajou University, Suwon, 443-749, Korea
| | - Bo Keun Lee
- Department of Molecular Science and Technology, Ajou University, Suwon, 443-749, Korea
| | - Jeong-Ho Yun
- Department of Periodontology, School of Dentistry and Institute of Oral Bioscience, Chonbuk National University, Jeonju, 561-712, Korea
| | - Bun Yeoul Lee
- Department of Molecular Science and Technology, Ajou University, Suwon, 443-749, Korea
| | - Jae Ho Kim
- Department of Molecular Science and Technology, Ajou University, Suwon, 443-749, Korea
| | - Byoung Hyun Min
- Department of Molecular Science and Technology, Ajou University, Suwon, 443-749, Korea
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, Suwon, 443-749, Korea.
| | - Moon Suk Kim
- Department of Molecular Science and Technology, Ajou University, Suwon, 443-749, Korea.
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31
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Shin TH, Lee S, Choi KR, Lee DY, Kim Y, Paik MJ, Seo C, Kang S, Jin MS, Yoo TH, Kang SH, Lee G. Quality and freshness of human bone marrow-derived mesenchymal stem cells decrease over time after trypsinization and storage in phosphate-buffered saline. Sci Rep 2017; 7:1106. [PMID: 28439086 PMCID: PMC5430841 DOI: 10.1038/s41598-017-01315-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 03/29/2017] [Indexed: 12/31/2022] Open
Abstract
Human bone marrow-derived mesenchymal stem cells (hBM-MSCs) have been studied for their therapeutic potential. However, evaluating the quality of hBM-MSCs before transplantation remains a challenge. We addressed this issue in the present study by investigating deformation, the expression of genes related to reactive oxygen species (ROS) generation, changes in amino acid profiles, and membrane fluidity in hBM-MSCs. Deformability and cell size were decreased after storage for 6 and 12 h, respectively, in phosphate-buffered saline. Intracellular ROS levels also increased over time, which was associated with altered expression of genes related to ROS generation and amino acid metabolism. Membrane fluidity measurements revealed higher Laurdan generalized polarization values at 6 and 12 h; however, this effect was reversed by N-acetyl-l-cysteine-treatment. These findings indicate that the quality and freshness of hBM-MSCs is lost over time after dissociation from the culture dish for transplantation, highlighting the importance of using freshly trypsinized cells in clinical applications.
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Affiliation(s)
- Tae Hwan Shin
- Department of Molecular Science and Technology, Ajou University, Suwon, Republic of Korea.,Department of Physiology and Department of Biomedical Sciences, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Seungah Lee
- Department of Applied Chemistry and Institute of Natural Sciences, Kyung Hee University, Yongin-si, Republic of Korea
| | - Ki Ryung Choi
- Department of Physiology and Department of Biomedical Sciences, Ajou University School of Medicine, Suwon, Republic of Korea.,Pharmicell Co., Ltd., Sungnam, Republic of Korea
| | - Da Yeon Lee
- Department of Physiology and Department of Biomedical Sciences, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Yongman Kim
- Pharmicell Co., Ltd., Sungnam, Republic of Korea
| | - Man Jeong Paik
- College of Pharmacy, Sunchon National University, Suncheon, Republic of Korea
| | - Chan Seo
- College of Pharmacy, Sunchon National University, Suncheon, Republic of Korea
| | - Seok Kang
- Hanyang University School of Medicine, Seoul, Republic of Korea
| | - Moon Suk Jin
- Biological Sciences, Ajou University, Suwon, Republic of Korea
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, Suwon, Republic of Korea
| | - Seong Ho Kang
- Department of Applied Chemistry and Institute of Natural Sciences, Kyung Hee University, Yongin-si, Republic of Korea.
| | - Gwang Lee
- Department of Physiology and Department of Biomedical Sciences, Ajou University School of Medicine, Suwon, Republic of Korea.
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Son HF, Park S, Yoo TH, Jung GY, Kim KJ. Structural insights into the production of 3-hydroxypropionic acid by aldehyde dehydrogenase from Azospirillum brasilense. Sci Rep 2017; 7:46005. [PMID: 28393833 PMCID: PMC5385487 DOI: 10.1038/srep46005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 03/07/2017] [Indexed: 12/19/2022] Open
Abstract
3-Hydroxypropionic acid (3-HP) is an important platform chemical to be converted to acrylic acid and acrylamide. Aldehyde dehydrogenase (ALDH), an enzyme that catalyzes the reaction of 3-hydroxypropionaldehyde (3-HPA) to 3-HP, determines 3-HP production rate during the conversion of glycerol to 3-HP. To elucidate molecular mechanism of 3-HP production, we determined the first crystal structure of a 3-HP producing ALDH, α-ketoglutarate-semialdehyde dehydrogenase from Azospirillum basilensis (AbKGSADH), in its apo-form and in complex with NAD+. Although showing an overall structure similar to other ALDHs, the AbKGSADH enzyme had an optimal substrate binding site for accepting 3-HPA as a substrate. Molecular docking simulation of 3-HPA into the AbKGSADH structure revealed that the residues Asn159, Gln160 and Arg163 stabilize the aldehyde- and the hydroxyl-groups of 3-HPA through hydrogen bonds, and several hydrophobic residues, such as Phe156, Val286, Ile288, and Phe450, provide the optimal size and shape for 3-HPA binding. We also compared AbKGSADH with other reported 3-HP producing ALDHs for the crucial amino acid residues for enzyme catalysis and substrate binding, which provides structural implications on how these enzymes utilize 3-HPA as a substrate.
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Affiliation(s)
- Hyeoncheol Francis Son
- School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daehak-ro 80, Buk-ku, Daegu 702-701, Korea
| | - Sunghoon Park
- School of Energy and Chemical Engineering, Ulsan national Institute of Science and Technology (UNIST), Ulsan 44919, Korea
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea
| | - Gyoo Yeol Jung
- Department of Chemical Engineering and School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, Korea
| | - Kyung-Jin Kim
- School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daehak-ro 80, Buk-ku, Daegu 702-701, Korea
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Lee BS, Kim S, Ko BJ, Yoo TH. An efficient system for incorporation of unnatural amino acids in response to the four-base codon AGGA in Escherichia coli. Biochim Biophys Acta Gen Subj 2017; 1861:3016-3023. [PMID: 28212794 DOI: 10.1016/j.bbagen.2017.02.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 02/08/2017] [Accepted: 02/09/2017] [Indexed: 01/21/2023]
Abstract
BACKGROUND Adding new amino acids to the set of building blocks for protein synthesis expands the scope of protein engineering, and orthogonal pairs of tRNA and aminoacyl-tRNA synthetase have been developed for incorporating unnatural amino acids (UAAs) into proteins. While diverse systems have been developed to incorporate UAAs in response to the amber codon, less research has been focused on four-base codons despites their advantages. In this study, we report an efficient method to incorporate UAA in response to an AGGA codon in Escherichia coli. RESULTS The Methanococcus jannaschii tyrosyl-tRNA synthetase-tRNACUA(MjTyrRS-MjtRNACUA) orthogonal pair has been engineered to incorporate diverse UAAs in response to the amber codon. To apply the engineered MjTyrRS enzymes for UAAs to a four-base codon suppression, we developed an MjTyrRS-MjtRNAUCCU pair system that enabled incorporation of UAAs in response to the AGGA codon in E. coli. Using this system, we demonstrated that several UAAs could be incorporated quantitatively in the AGGA site. In addition, multiple AGGA codons were successfully suppressed in an E. coli strain when the endogenous tRNACCUArg gene was knocked out. CONCLUSION An efficient system was developed for the incorporation of UAAs in response to the AGGA four-base codon in E. coli, and the method was successfully demonstrated for several UAAs and for multiple AGGA sites. GENERAL SIGNIFICANCE The developed system can expand the repertoire of protein engineering tools based on amino acid analogues in combination with other UAA incorporation methods. This article is part of a Special Issue entitled "Biochemistry of Synthetic Biology - Recent Developments" Guest Editor: Dr. Ilka Heinemann and Dr. Patrick O'Donoghue.
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Affiliation(s)
- Byeong Sung Lee
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Yeongtong-gu, Suwon 16499, Republic of Korea
| | - Suyeon Kim
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Yeongtong-gu, Suwon 16499, Republic of Korea
| | - Byoung Joon Ko
- New Drug Development Center, Osong Medical Innovative Foundation, 123, Osongsaengmyeong-ro, Osong-eup, Cheongju 28160, Republic of Korea
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Yeongtong-gu, Suwon 16499, Republic of Korea; Department of Applied Chemistry and Biological Engineering, Ajou University, 206 World cup-ro, Yeongtong-gu, Suwon 16499, Republic of Korea.
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34
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Kim J, Seok SH, Hong E, Yoo TH, Seo MD, Ryu Y. Crystal structure and characterization of esterase Est25 mutants reveal improved enantioselectivity toward (S)-ketoprofen ethyl ester. Appl Microbiol Biotechnol 2016; 101:2333-2342. [PMID: 27915377 DOI: 10.1007/s00253-016-7989-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 09/25/2016] [Accepted: 11/05/2016] [Indexed: 11/25/2022]
Abstract
Esterases comprise a group of enzymes that catalyze the cleavage and synthesis of ester bonds. They are important in biotechnological applications owing to their enantioselectivity, regioselectivity, broad substrate specificity, and the fact that they do not require cofactors. In a previous study, we isolated the esterase Est25 from a metagenomic library. Est25 showed catalytic activity toward the (R,S)-ketoprofen ethyl ester but had low enantioselectivity toward the (S)-ketoprofen ethyl ester. Because (S)-ketoprofen has stronger anti-inflammatory effects and fewer side effects than (R)-ketoprofen, enantioselectivity of this esterase is important. In this study, we generated Est25 mutants with improved enantioselectivity toward the (S)-ketoprofen ethyl ester; improved enantioselectivity of mutants was established by analysis of their crystal structures. The enantioselectivity of mutants was influenced by substitution of Phe72 and Leu255. Substituting these residues changed the size of the binding pocket and the entrance hole that leads to the active site. The enantioselectivity of Est25 (E = 1.1 ± 0.0) was improved in the mutants F72G (E = 1.9 ± 0.2), L255W (E = 16.1 ± 1.1), and F72G/L255W (E = 60.1 ± 0.5). Finally, characterization of Est25 mutants was performed by determining the optimum reaction conditions, thermostability, effect of additives, and substrate specificity after substituting Phe72 and Leu255.
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Affiliation(s)
- Jinyeong Kim
- Department of Molecular Science and Technology, Ajou University, Suwon, 16499, South Korea
| | | | - Eunsoo Hong
- Department of Molecular Science and Technology, Ajou University, Suwon, 16499, South Korea
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, Suwon, 16499, South Korea
| | - Min-Duk Seo
- Department of Molecular Science and Technology, Ajou University, Suwon, 16499, South Korea. .,College of Pharmacy, Ajou University, Suwon, 16499, South Korea.
| | - Yeonwoo Ryu
- Department of Molecular Science and Technology, Ajou University, Suwon, 16499, South Korea.
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35
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Zhang CQ, Park YM, Yang D, Yoo TH, Yoon HC. Development of a matrix metalloproteinase-2 (MMP-2) biosensing system by integrating an enzyme-mediated color development reaction into a common electronics components setup. BioChip J 2016. [DOI: 10.1007/s13206-016-0306-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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36
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Min SE, Lee KH, Park SW, Yoo TH, Oh CH, Park JH, Yang SY, Kim YS, Kim DM. Cell-free production and streamlined assay of cytosol-penetrating antibodies. Biotechnol Bioeng 2016; 113:2107-12. [DOI: 10.1002/bit.25985] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2015] [Accepted: 03/28/2016] [Indexed: 12/22/2022]
Affiliation(s)
- Seung Eui Min
- Department of Chemical Engineering and Applied Chemistry; Chungnam National University; Daejeon 34134 Korea
| | - Kyung-Ho Lee
- Department of Chemical Engineering and Applied Chemistry; Chungnam National University; Daejeon 34134 Korea
| | - Seong-Wook Park
- Department of Molecular Science and Technology; Ajou University; Suwon Korea
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology; Ajou University; Suwon Korea
| | - Chan Hee Oh
- Department of Bio and Brain Engineering; Korea Advanced Institute of Science and Technology; Daejeon Korea
| | - Ji-Ho Park
- Department of Bio and Brain Engineering; Korea Advanced Institute of Science and Technology; Daejeon Korea
| | - Sung Yun Yang
- Department of Polymer Science and Engineering; Chungnam National University; Daejeon Korea
| | - Yong-Sung Kim
- Department of Molecular Science and Technology; Ajou University; Suwon Korea
| | - Dong-Myung Kim
- Department of Chemical Engineering and Applied Chemistry; Chungnam National University; Daejeon 34134 Korea
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37
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Seo KH, Chu HS, Yoo TH, Lee SG, Won JI. Separation efficiency of free-solution conjugated electrophoresis with drag-tags incorporating a synthetic amino acid. Electrophoresis 2016; 37:818-25. [PMID: 26757485 DOI: 10.1002/elps.201500506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 12/22/2015] [Accepted: 12/29/2015] [Indexed: 11/10/2022]
Abstract
DNA sequencing or separation by conventional capillary electrophoresis with a polymer matrix has some inherent drawbacks, such as the expense of polymer matrix and limitations in sequencing read length. As DNA fragments have a linear charge-to-friction ratio in free solution, DNA fragments cannot be separated by size. However, size-based separation of DNA is possible in free-solution conjugate electrophoresis (FSCE) if a "drag-tag" is attached to DNA fragments because the tag breaks the linear charge-to-friction scaling. Although several previous studies have demonstrated the feasibility of DNA separation by free-solution conjugated electrophoresis, generation of a monodisperse drag-tag and identification of a strong, site-specific conjugation method between a DNA fragment and a drag-tag are challenges that still remain. In this study, we demonstrate an efficient FSCE method by conjugating a biologically synthesized elastin-like polypeptide (ELP) and green fluorescent protein (GFP) to DNA fragments. In addition, to produce strong and site-specific conjugation, a methionine residue in drag-tags is replaced with homopropargylglycine (Hpg), which can be conjugated specifically to a DNA fragment with an azide site.
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Affiliation(s)
- Kyung-Ho Seo
- Department of Chemical Engineering, Hongik University, Seoul, Korea
| | - Hun-Su Chu
- Department of Chemical Engineering, Hongik University, Seoul, Korea.,Material Research Center, SAMSUNG ELECTRONICS Co, Suwon, Korea
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, Suwon, Korea
| | - Sun-Gu Lee
- Department of Chemical Engineering, Pusan National University, Pusan, Korea
| | - Jong-In Won
- Department of Chemical Engineering, Hongik University, Seoul, Korea
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38
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Ravikumar Y, Nadarajan SP, Hyeon Yoo T, Lee CS, Yun H. Incorporating unnatural amino acids to engineer biocatalysts for industrial bioprocess applications. Biotechnol J 2015; 10:1862-76. [DOI: 10.1002/biot.201500153] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 08/13/2015] [Accepted: 09/02/2015] [Indexed: 12/22/2022]
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39
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Abstract
The biological protein synthesis system has been engineered to incorporate unnatural amino acid into proteins, and this has opened up new routes for engineering proteins with novel compositions. While such systems have been successfully applied in research, there remains a need to develop new approaches with respect to the wider application of unnatural amino acids. In this study, we reported a strategy for incorporating unnatural amino acids into proteins by reassigning one of the Arg sense codons, the AGG codon. Using this method, several unnatural amino acids were quantitatively incorporated into the AGG site. Furthermore, we applied the method to multiple AGG sites, and even to tandem AGG sequences. The method developed and described here could be used for engineering proteins with diverse unnatural amino acids, particularly when employed in combination with other methods.
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Affiliation(s)
| | | | | | - Kyoung-Soon Jang
- Division
of Mass Spectrometry Research, Korea Basic Science Institute, 162
Yeongudanji-ro, Ochang-eup, Cheongwon-gu, Cheongju 363-883, Korea
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40
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Ravikumar Y, Nadarajan SP, Yoo TH, Lee CS, Yun H. Unnatural amino acid mutagenesis-based enzyme engineering. Trends Biotechnol 2015; 33:462-70. [PMID: 26088007 DOI: 10.1016/j.tibtech.2015.05.002] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 05/07/2015] [Accepted: 05/13/2015] [Indexed: 02/09/2023]
Abstract
Traditional enzyme engineering relies on substituting one amino acid by one of the other 19 natural amino acids to change the functional properties of an enzyme. However, incorporation of unnatural amino acids (UAAs) has been harnessed to engineer efficient enzymes for biocatalysis. Residue-specific and site-specific in vivo incorporation methods are becoming the preferred approach for producing enzymes with altered or improved functions. We describe the contribution of in vivo UAA incorporation methodologies to enzyme engineering as well as the future prospects for the field, including the integration of UAAs with other new advances in enzyme engineering.
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Affiliation(s)
- Yuvaraj Ravikumar
- School of Biotechnology, Department of Biochemistry, Yeungnam University, Gyeongsan, Gyeongbuk 712-749, Korea
| | | | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, Suwon 443-749, Korea
| | - Chong-soon Lee
- School of Biotechnology, Department of Biochemistry, Yeungnam University, Gyeongsan, Gyeongbuk 712-749, Korea
| | - Hyungdon Yun
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 143-701, Korea.
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41
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Deepankumar K, Nadarajan SP, Mathew S, Lee SG, Yoo TH, Hong EY, Kim BG, Yun H. Engineering Transaminase for Stability Enhancement and Site-Specific Immobilization through Multiple Noncanonical Amino Acids Incorporation. ChemCatChem 2014. [DOI: 10.1002/cctc.201402882] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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42
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Abstract
Non-canonical amino acids (ncAAs) provide powerful tools for engineering the chemical and physical properties of proteins. However, introducing ncAAs into proteins can affect protein properties in unpredictable ways, thus necessitating screening efforts to identify mutants with desirable properties. In this work, we describe an Escherichia coli cell surface display platform for the directed evolution of clickable antibody fragments. This platform enabled isolation of antibody fragments with improved digoxigenin binding and modest affinity maturation in several different ncAA contexts. Azide-functionalized fragments exhibited improved binding kinetics relative to their methionine counterparts, facile chemical modification through azide-alkyne cycloaddition, and retention of binding properties after modification. The results described here suggest new possibilities for protein engineering, including modulation of molecular recognition events by ncAAs and direct screening of libraries of chemically modified proteins.
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Affiliation(s)
- James A Van Deventer
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Boulevard, MC 210-41, Pasadena, CA 91125 (USA); The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139 (USA)
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43
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Kim M, Lee HJ, Oh S, Kim Y, Jung H, Oh MK, Yoon YJ, Yoo TH, Yoon TS, Lee HH. Robust ZnO nanoparticle embedded memory device using vancomycin conjugate and its biorecognition for electrical charging node. Biosens Bioelectron 2014; 56:33-8. [PMID: 24462828 DOI: 10.1016/j.bios.2013.12.049] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Revised: 12/09/2013] [Accepted: 12/20/2013] [Indexed: 10/25/2022]
Abstract
Conjugation of antibiotic vancomycin (VAN) on nanoparticles (NPs) has recently initiated novel works in the nanobiotechnology field. In this study, a bioelectronic structure using VAN conjugated zinc oxide (ZnO) NPs as charge storing elements on metal-pentacene-insulator-silicon (MPIS) device is demonstrated. Highly specific molecular recognition between the VAN and membrane protein unit mimicked from VAN-resistant bacteria is employed as the formation mechanism of self-assembly monolayers (SAMs) of ZnO NPs. The insulator surface is modified with the VAN cognate peptide of L-Ala-D-Glu-L-Lys-D-Ala-D-Ala by chemical activator coupling. Hysteretic behaviors in capacitance versus voltage (C-V) curves are obtained for the charged ZnO NPs exhibiting flatband voltage shifts, which demonstrate the charge storage on the VAN conjugated ZnO NPs. The potential perspective of this study will be a tangible progress of biomolecular electronics implemented by the interface between biomolecules and electronics.
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Affiliation(s)
- Minkeun Kim
- Department of Chemical Engineering, Myongji University, Yongin 449-728, Republic of Korea
| | - Hye-Jin Lee
- Department of Chemical and Biochemical Engineering, Korea University, Seoul 100-715, Republic of Korea
| | - Sewook Oh
- Department of Chemical Engineering, Myongji University, Yongin 449-728, Republic of Korea
| | - Yejin Kim
- Department of Chemical Engineering, Myongji University, Yongin 449-728, Republic of Korea
| | - Hunsang Jung
- Department of Chemical Engineering, Myongji University, Yongin 449-728, Republic of Korea
| | - Min-Kyu Oh
- Department of Chemical and Biochemical Engineering, Korea University, Seoul 100-715, Republic of Korea
| | - Yeo Joon Yoon
- Department of Chemistry, Ewha Womans's University, Seoul 120-750, Republic of Korea
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, Suwon 443-749, Republic of Korea
| | - Tae-Sik Yoon
- Department of Material Science and Engineering, Myongji University, Yongin 449-728, Republic of Korea
| | - Hyun Ho Lee
- Department of Chemical Engineering, Myongji University, Yongin 449-728, Republic of Korea.
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44
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Kim H, Yoon HK, Yoo TH. Correction: Engineering β-lactamase zymogens for use in protease activity assays. Chem Commun (Camb) 2014. [DOI: 10.1039/c4cc90398f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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45
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Abstract
In this report, we engineered β-lactamase zymogens and developed a sensitive protease assay method based on the precursor enzymes.
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Affiliation(s)
- Hajin Kim
- Department of Molecular Science and Technology
- Ajou University
- Yeongtong-gu, South Korea
| | - Hyun Kyung Yoon
- Department of Molecular Science and Technology
- Ajou University
- Yeongtong-gu, South Korea
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology
- Ajou University
- Yeongtong-gu, South Korea
- Department of Applied Chemistry and Biological Engineering
- Ajou University
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46
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Kim HR, Lee MJ, Song JE, Han JH, Yoo TH, Kang SW, Choi KH, Han SH. Drainage failure because of spontaneous fracture of the peritoneal dialysis catheter. Perit Dial Int 2013; 33:218-20. [PMID: 23478378 DOI: 10.3747/pdi.2012.00045] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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47
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Yoon HK, Jung ST, Kim JH, Yoo TH. Recent development of highly sensitive protease assay methods: Signal amplification through enzyme cascades. BIOTECHNOL BIOPROC E 2013; 17:1113-1119. [PMID: 32218678 PMCID: PMC7090753 DOI: 10.1007/s12257-012-0545-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Revised: 08/29/2012] [Accepted: 09/05/2012] [Indexed: 01/10/2023]
Abstract
Proteases are involved in almost all biological processes, and therefore, aberrant activity of many of these enzymes is an important indicator of disease. Various methods have been developed to analyze protease activity, among which, protease assays based on resonance energy transfer are currently used most widely. However, quantitative methods with relatively higher sensitivity are needed, especially for disease diagnosis at early stages. One of the strategies to achieve higher sensitivity is to implement signal amplification of the protease activity. In this review, we briefly summarize the protease assay methods based on resonance energy transfer, and then elaborate the efforts to develop sensitive protease assays through signal amplification by using enzyme cascades.
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Affiliation(s)
- Hyun Kyung Yoon
- Department of Molecular Science and Technology, Ajou University, Suwon, 443-749 Korea
| | - Sang Taek Jung
- Department of Bio and Nano Chemistry, Kookmin University, Seoul, 136-702 Korea
| | - Jae-Ho Kim
- Department of Molecular Science and Technology, Ajou University, Suwon, 443-749 Korea
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, Suwon, 443-749 Korea
- Department of Applied Chemistry and Biological Engineering, Ajou University, Suwon, 443-749 Korea
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48
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Yoon HK, Yoo TH. A novel protease activity assay method based on an engineered autoinhibited protein using an enzyme-linked immunoassay. Analyst 2013; 138:7164-8. [DOI: 10.1039/c3an01336g] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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49
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Abstract
Intrinsically disordered proteins (IDPs), which play key roles in cell signaling and regulation, do not display specific tertiary structure when isolated in solution. Instead, they dynamically explore an ensemble of unfolded configurations, adopting more stable, ordered structures only after binding to their ligands. Whether ligands induce IDP structural changes upon binding or simply bind to pre-existing conformers that are populated within the IDP's structural ensemble is not well understood. Molecular simulations can provide information with the spatiotemporal resolution necessary to resolve these issues. Here, we report on the conformational ensemble of a 15-residue wild-type p53 fragment from the TAD domain and its mutant (TAD-P27L) obtained by replica exchange molecular dynamics simulation using an optimized (fully atomistic, explicit solvent) protein model and the experimental validation of the simulation results. We use a clustering method based on structural similarity to identify conformer states populated by the peptides in solution from the simulated ensemble. We show that p53 populates solution structures that strongly resemble the ligand (MDM2)-bound structure, but at the same time, the conformational free-energy landscape is relatively flat in the absence of the ligand.
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Affiliation(s)
- Jeetain Mittal
- Department of Chemical Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States.
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50
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Soundrarajan N, Sokalingam S, Raghunathan G, Budisa N, Paik HJ, Yoo TH, Lee SG. Conjugation of proteins by installing BIO-orthogonally reactive groups at their N-termini. PLoS One 2012; 7:e46741. [PMID: 23056430 PMCID: PMC3466299 DOI: 10.1371/journal.pone.0046741] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Accepted: 09/04/2012] [Indexed: 01/25/2023] Open
Abstract
N-terminal site-specific modification of a protein has many advantages over methods targeting internal positions, but it is not easy to install reactive groups onto a protein in an N-terminal specific manner. We here report a strategy to incorporate amino acid analogues specifically in the N-terminus of a protein in vivo and demonstrate it by preparing green fluorescent protein (GFP) having bio-orthogonally reactive groups at its N-terminus. In the first step, GFP was engineered to be a foldable, internal methionine-free sequence via the semi-rational mutagenesis of five internal methionine residues and the introduction of mutations for GFP folding enhancement. In the second step, the N-terminus of the engineered protein was modified in vivo with bio-orthogonally functional groups by reassigning functional methionine surrogates such as L-homopropargylglycine and L-azidohomoalanine into the first methionine codon of the engineered internal methionine-free GFP. The N-terminal specific incorporation of unnatural amino acids was confirmed by ESI-MS analysis and the incorporation did not affect significantly the specific activity, refolding rate and folding robustness of the protein. The two proteins which have alkyne or azide groups at their N-termini were conjugated each other by bio-orthogonal Cu(I)-catalyzed click chemistry. The strategy used in this study is expected to facilitate bio-conjugation applications of proteins such as N-terminal specific glycosylation, labeling of fluorescent dyes, and immobilization on solid surfaces.
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Affiliation(s)
| | - Sriram Sokalingam
- Department of Polymer Science and Chemical Engineering, Pusan National University, Busan, South Korea
| | - Govindan Raghunathan
- Department of Polymer Science and Chemical Engineering, Pusan National University, Busan, South Korea
| | - Nediljko Budisa
- Department of Chemistry, Technische Universität Berlin, Franklinstrasse, Berlin, Germany
| | - Hyun-Jong Paik
- Department of Polymer Science and Chemical Engineering, Pusan National University, Busan, South Korea
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
- Department of Applied Chemistry and Biological Engineering, Ajou University, Suwon, South Korea
| | - Sun-Gu Lee
- Department of Polymer Science and Chemical Engineering, Pusan National University, Busan, South Korea
- * E-mail:
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