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Zhao W, Sun Y, Che L, Wang H, Cao A. Conformational Engineering of Flexible Protein Fragments on the Surface of Different Nanoparticles: The Surface-Atom Mobility Rules. ChemMedChem 2025; 20:e202400832. [PMID: 39809713 DOI: 10.1002/cmdc.202400832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2024] [Revised: 01/14/2025] [Accepted: 01/14/2025] [Indexed: 01/16/2025]
Abstract
As a newly emerging technology, conformational engineering (CE) has been gradually displaying the power of producing protein-like nanoparticles (NPs) by tuning flexible protein fragments into their original native conformation on NPs. But apparently, not all types of NPs can serve as scaffolds for CE. To expedite the CE technology on a broader variety of NPs, the essential characteristic of NPs as scaffolds for CE needs to be identified. Herein, we investigate the potential of two distinct types of NPs as scaffolds for CE: CdSe/ZnS quantum dots (QDs), an ionic compound NP, and palladium NPs (PdNPs), a metal NP. The results demonstrate that while QDs cannot support the restoration of the native conformation and function of the complementary-determining region (CDR) fragments of antibodies, PdNPs can. The notably disparate outcomes unequivocally show that the mobility of the surface atoms/adatoms of the NPs or the mobility of the conjugating bonds to the NPs is essential for CE, which allows the conjugated peptides to undergo a conformational change from their initial random conformation to their most stable native conformation under the constraints mimicking the native long-range interactions in the original proteins. This discovery opens the door for CE on more NPs in the future.
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Affiliation(s)
- Wenxian Zhao
- Institute of Nanochemistry and Nanobiology, Shanghai University, Shanghai, 200444, China
| | - Yiwei Sun
- Institute of Nanochemistry and Nanobiology, Shanghai University, Shanghai, 200444, China
| | - Laiyu Che
- Institute of Nanochemistry and Nanobiology, Shanghai University, Shanghai, 200444, China
| | - Haifang Wang
- Institute of Nanochemistry and Nanobiology, Shanghai University, Shanghai, 200444, China
| | - Aoneng Cao
- Institute of Nanochemistry and Nanobiology, Shanghai University, Shanghai, 200444, China
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2
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Zhang Q, Dai J, Deng J, Sun Y, Liu YY, Wang H, Cao A. Gold Nanoparticle-Based Artificial Antibodies as Stable Substitutes for Antibodies in the Immunoassay. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2025:e2412730. [PMID: 40123243 DOI: 10.1002/smll.202412730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2024] [Revised: 02/27/2025] [Indexed: 03/25/2025]
Abstract
Sandwich enzyme-linked immunosorbent assay (ELISA) is a widely used powerful method to detect antigens in complicated environments, due to the high sensitivity and specificity of monoclonal antibodies. Yet, the intrinsic instability of antibodies limits the applications of sandwich ELISA. To overcome the shortcomings of antibodies, we previously demonstrated that a class of gold nanoparticle (AuNP)-based artificial antibody, named goldbody, can be created by "Goldization" technology, i.e., reconstructing the fragments of antibodies on AuNPs. Goldbody has the same binding specificity as the original antibody, but has a much better stability. However, it is still a big challenge to design matched goldbody pairs to develop a sandwich ELISA entirely based on goldbodies. Herein, an anti-EGFR goldbody is designed and synthesized by reconstructing ("Goldization") the "dimerization arm" fragment of EGFR on AuNPs. As expected, this new anti-EGFR goldbody binds to EGFR at a site far away from where the previously developed one binds, allowing the two anti-EGFR goldbodies to bind the same EGFR simultaneously and qualify as a matched pair. Subsequently, a goldbody-based sandwich ELISA is developed, and the goldbodies in the ELISA kit can be used for the detection of EGFR even after preheatment at 100 °C, demonstrating the excellent stability of goldbody.
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Affiliation(s)
- Qiangqiang Zhang
- Institute of Nanochemistry and Nanobiology, Shanghai University, Shanghai, 200444, China
| | - Jingjing Dai
- Institute of Nanochemistry and Nanobiology, Shanghai University, Shanghai, 200444, China
| | - Jiewen Deng
- Institute of Nanochemistry and Nanobiology, Shanghai University, Shanghai, 200444, China
| | - Yiwei Sun
- Institute of Nanochemistry and Nanobiology, Shanghai University, Shanghai, 200444, China
| | - Yuan-Yuan Liu
- Institute of Nanochemistry and Nanobiology, Shanghai University, Shanghai, 200444, China
| | - Haifang Wang
- Institute of Nanochemistry and Nanobiology, Shanghai University, Shanghai, 200444, China
| | - Aoneng Cao
- Institute of Nanochemistry and Nanobiology, Shanghai University, Shanghai, 200444, China
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3
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Das S, Krishnamoorthy J, Kar RK. Estimating the structural and spatial variables of allantoinase enzyme critical for protein adsorption. Biochem Biophys Res Commun 2025; 743:151161. [PMID: 39693939 DOI: 10.1016/j.bbrc.2024.151161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2024] [Revised: 11/25/2024] [Accepted: 12/09/2024] [Indexed: 12/20/2024]
Abstract
Designing enzyme-based sensors necessitates a comprehensive exploration of macromolecular properties. Integrating enzymes with a suitable transducer involves immobilizing them onto a surface, facilitated through adsorption or entrapment techniques. Allantoin, a stable biomarkers metabolite, holds promise for detecting oxidative stress-related complications through its enzyme. In this study, we examined allantoinase from various taxa, with bacterial origin comprising over 70 % of the dataset. Crucial residues such as Asp, His, and Gly in the active binding site and associated hydrophobic area play a critical role in maintaining binding specificity and sensitivity. In this work, we utilized bioinformatics tools to analyze properties such as pI, solubility index, amino acid hydropathy, stability, disordered regions, solvent-accessible surface area, and hydrodynamic parameters. The stability of allantoinase is assessed through surface Cys residues, hydrophobicity, and thermostability. Furthermore, the compactness and spherical geometry of the enzyme, which are crucial for protein adsorption are evaluated through parameters like spatial conformation, asphericity, and hydrodynamic radius distribution. Among the dataset, bacterial allantoinase demonstrates significant adaptability to environmental changes, as indicated by solvent-accessible surface area and instability index. This study highlights the importance of macromolecular properties underscoring their significance in optimizing, calibrating, and ensuring the stability of enzyme-based sensor design.
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Affiliation(s)
- Sheetal Das
- Jyoti and Bhupat Mehta School of Health Sciences and Technology, Indian Institute of Technology Guwahati, Assam, 781039, India
| | | | - Rajiv K Kar
- Jyoti and Bhupat Mehta School of Health Sciences and Technology, Indian Institute of Technology Guwahati, Assam, 781039, India; Centre for Nanotechnology, Indian Institute of Technology Guwahati, Assam, 781039, India.
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Cao A, Wang H. Making nanoparticles protein-like. Nanomedicine (Lond) 2024; 19:1219-1221. [PMID: 38578738 PMCID: PMC11285234 DOI: 10.2217/nnm-2024-0084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 03/14/2024] [Indexed: 04/07/2024] Open
Affiliation(s)
- Aoneng Cao
- Institute of Nanochemistry and Nanobiology, Shanghai University, Shanghai, 200444, China
| | - Haifang Wang
- Institute of Nanochemistry and Nanobiology, Shanghai University, Shanghai, 200444, China
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5
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Singh RP, Mishra A, Chandel SS, Agarwal M, Chawra HS, Singh M, Dubey G. Unlocking New Approaches to Urolithiasis Management Via Nutraceuticals. Curr Pharm Biotechnol 2024; 25:1124-1131. [PMID: 37608670 DOI: 10.2174/1389201024666230821122416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 06/15/2023] [Accepted: 07/06/2023] [Indexed: 08/24/2023]
Abstract
Urolithiasis, commonly known as kidney stones, is characterized by the formation of hard deposits in the urinary tract. These stones can cause severe pain and discomfort, and their management typically involves a combination of medical interventions and lifestyle modifications. According to the literature, 30% and 50% of urolithiasis cases recur. Between 9 and 12% of persons in industrialised countries are predicted to have urolithiasis at some time. Due to the high frequency of stone formation, recurrent nature, and prevalence in adults, it has a significant impact on society, the person, and the health care system. Adopting the best prophylactic measures is crucial in light of these developments to decrease the impact of urolithiasis on individuals and society. In recent years, there has been growing interest in the potential role of nutraceuticals in the management of urolithiasis. Nutraceuticals, such as herbal extracts, vitamins, minerals, and probiotics, have gained recognition for their potential in promoting urinary health and reducing the risk of urolithiasis. These compounds can aid in various ways, including inhibiting crystal formation, enhancing urine pH balance, reducing urinary calcium excretion, and supporting kidney function. Additionally, nutraceuticals can help alleviate symptoms associated with urolithiasis, such as pain and inflammation. While medical interventions remain crucial, incorporating nutraceuticals into a comprehensive management plan can offer a holistic approach to urolithiasis, improving patient outcomes and quality of life. Therefore, nutraceuticals may be a desirable choice for treating and avoiding recurring urolithiasis for patients and medical professionals. Therefore, the present study has focused on nutraceuticals' role in preventing urolithiasis.
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Affiliation(s)
- Ravindra Pal Singh
- Department of Pharmacy, NIMS Institute of Pharmacy, NIMS University Rajasthan, Jaipur, India
| | - Anurag Mishra
- Department of Pharmacy, NIMS Institute of Pharmacy, NIMS University Rajasthan, Jaipur, India
| | | | - Mohit Agarwal
- Department of Pharmacy, NIMS Institute of Pharmacy, NIMS University Rajasthan, Jaipur, India
| | - Himmat Singh Chawra
- Department of Pharmacy, NIMS Institute of Pharmacy, NIMS University Rajasthan, Jaipur, India
| | - Mithilesh Singh
- Department of Pharmacy, NIMS Institute of Pharmacy, NIMS University Rajasthan, Jaipur, India
| | - Gaurav Dubey
- Department of Pharmacy, NIMS Institute of Pharmacy, NIMS University Rajasthan, Jaipur, India
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Wang T, He X, Li M, Shao B, Liu TY. AIMD-Chig: Exploring the conformational space of a 166-atom protein Chignolin with ab initio molecular dynamics. Sci Data 2023; 10:549. [PMID: 37607915 PMCID: PMC10444755 DOI: 10.1038/s41597-023-02465-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 08/11/2023] [Indexed: 08/24/2023] Open
Abstract
Molecular dynamics (MD) simulations have revolutionized the modeling of biomolecular conformations and provided unprecedented insight into molecular interactions. Due to the prohibitive computational overheads of ab initio simulation for large biomolecules, dynamic modeling for proteins is generally constrained on force field with molecular mechanics, which suffers from low accuracy as well as ignores the electronic effects. Here, we report AIMD-Chig, an MD dataset including 2 million conformations of 166-atom protein Chignolin sampled at the density functional theory (DFT) level with 7,763,146 CPU hours. 10,000 conformations were initialized covering the whole conformational space of Chignolin, including folded, unfolded, and metastable states. Ab initio simulations were driven by M06-2X/6-31 G* with a Berendsen thermostat at 340 K. We reported coordinates, energies, and forces for each conformation. AIMD-Chig brings the DFT level conformational space exploration from small organic molecules to real-world proteins. It can serve as the benchmark for developing machine learning potentials for proteins and facilitate the exploration of protein dynamics with ab initio accuracy.
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Affiliation(s)
- Tong Wang
- Microsoft Research AI4Science, Beijing, China.
| | - Xinheng He
- Microsoft Research AI4Science, Beijing, China
- Work done during an internship at Microsoft Research AI4Science, Beijing, China
- State Key Laboratory of Drug Research and CAS Key Laboratory of Receptor Research and, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Mingyu Li
- Microsoft Research AI4Science, Beijing, China
- Work done during an internship at Microsoft Research AI4Science, Beijing, China
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Bin Shao
- Microsoft Research AI4Science, Beijing, China.
| | - Tie-Yan Liu
- Microsoft Research AI4Science, Beijing, China
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Gao T, Liu YY, Lou C, Wang H, Liu Y, Cao A. PEGylation of Goldbody: PEG-aided conformational engineering of peptides on gold nanoparticles. RSC Adv 2022; 12:26123-26133. [PMID: 36275117 PMCID: PMC9475419 DOI: 10.1039/d2ra03903f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 09/07/2022] [Indexed: 11/21/2022] Open
Abstract
It is still a great challenge to engineer flexible non-functional molecules into special conformations to carry out novel functions. Previously, we successfully restored the native conformations and functions of the flexible complementary-determining regions (CDRs) of antibodies on the surface of gold nanoparticles (AuNPs), and created a class of AuNP-based artificial antibodies, denoted as Goldbodies. Yet, in these Goldbodies, there are dozens of CDRs on one Goldbody. Herein, we show that the number of CDRs per Goldbody could be reduced by more than one order of magnitude, by replacing the majority of the CDRs with polyethylene glycol (PEG) with a molecular weight around 600 Da, while the native conformations and functions of the CDRs could still be restored on AuNPs. Also, we find that the PEG with two terminal -SH groups is much better than the PEG with a single -SH group for aiding the restoration of the native conformation of the CDRs on AuNPs. To demonstrate the potential generic applicability of the PEGylation in aiding conformational engineering of peptides, two PEGylated Goldbodies have been created, which can specifically recognize lysozyme and epidermal growth factor receptor, respectively. The PEGylated Goldbodies further prove the mechanism of conformational engineering and the "Confined Lowest Energy Fragments" (CLEFs) hypothesis, and pave the way for future applications of Goldbodies.
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Affiliation(s)
- Tiange Gao
- Institute of Nanochemistry and Nanobiology, Shanghai University Shanghai 200444 China
| | - Yuan-Yuan Liu
- Institute of Nanochemistry and Nanobiology, Shanghai University Shanghai 200444 China
| | - Chenxi Lou
- Institute of Nanochemistry and Nanobiology, Shanghai University Shanghai 200444 China
| | - Haifang Wang
- Institute of Nanochemistry and Nanobiology, Shanghai University Shanghai 200444 China
| | - Yuanfang Liu
- Institute of Nanochemistry and Nanobiology, Shanghai University Shanghai 200444 China
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University Beijing 100871 China
| | - Aoneng Cao
- Institute of Nanochemistry and Nanobiology, Shanghai University Shanghai 200444 China
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8
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Wang Y, Wang X, Gao T, Lou C, Wang H, Liu Y, Cao A. Folding of Flexible Protein Fragments and Design of Nanoparticle-Based Artificial Antibody Targeting Lysozyme. J Phys Chem B 2022; 126:5045-5054. [PMID: 35763806 DOI: 10.1021/acs.jpcb.2c03200] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
It is generally believed that a protein's sequence solely determines its native structure, but how the long- and short-range interactions jointly determine the native structure/conformation of the protein or every local fragment of the protein is still not fully understood. Since most protein fragments are unstructured on their own, direct observation of the folding of flexible protein fragments is very difficult. Interestingly, we show that it is possible to graft the complementary-determining regions (CDRs) of antibodies onto the surface of a gold nanoparticle (AuNP) to create AuNP-based artificial antibodies (denoted as Goldbodies), such as an antilysozyme Goldbody. Goldbodies can specifically recognize the corresponding antigens like the original natural antibodies do, but direct structural evidence for the refolding or restoration of native conformation of the grafted CDRs on AuNPs is still missing and in high demand. Herein we design a new Goldbody that targets an epitope on the lysozyme different from that of the previous antilysozyme Goldbody, and the one circle of helix in the CDR makes it possible to distinguish the unfolded conformation of the free CDR and its folded conformation on AuNPs by circular dichroism (CD) spectroscopy. The refolding of flexible protein fragments on NPs provides unique evidence and inspiration for understanding the fundamental principles of protein folding.
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Affiliation(s)
- Yan Wang
- Institute of Nanochemistry and Nanobiology, Shanghai University, Shanghai 200444, China
| | - Xinping Wang
- Institute of Nanochemistry and Nanobiology, Shanghai University, Shanghai 200444, China
| | - Tiange Gao
- Institute of Nanochemistry and Nanobiology, Shanghai University, Shanghai 200444, China
| | - Chenxi Lou
- Institute of Nanochemistry and Nanobiology, Shanghai University, Shanghai 200444, China
| | - Haifang Wang
- Institute of Nanochemistry and Nanobiology, Shanghai University, Shanghai 200444, China
| | - Yuanfang Liu
- Institute of Nanochemistry and Nanobiology, Shanghai University, Shanghai 200444, China.,Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Aoneng Cao
- Institute of Nanochemistry and Nanobiology, Shanghai University, Shanghai 200444, China
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9
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Xu J, Gao T, Sheng L, Wang Y, Lou C, Wang H, Liu Y, Cao A. Conformationally engineering flexible peptides on silver nanoparticles. iScience 2022; 25:104324. [PMID: 35601913 PMCID: PMC9117549 DOI: 10.1016/j.isci.2022.104324] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/30/2022] [Accepted: 04/25/2022] [Indexed: 11/24/2022] Open
Abstract
Molecular conformational engineering is to engineer flexible non-functional molecules into unique conformations to create novel functions just like natural proteins fold. Obviously, it is a grand challenge with tremendous opportunities. Based on the facts that natural proteins are only marginally stable with a net stabilizing energy roughly equivalent to the energy of two hydrogen bonds, and the energy barriers for the adatom diffusion of some metals are within a similar range, we propose that metal nanoparticles can serve as a general replacement of protein scaffolds to conformationally engineer protein fragments on the surface of nanoparticles. To prove this hypothesis, herein, we successfully restore the antigen-recognizing function of the flexible peptide fragment of a natural anti-lysozyme antibody on the surface of silver nanoparticles, creating a silver nanoparticle-base artificial antibody (Silverbody). A plausible mechanism is proposed, and some general principles for conformational engineering are summarized to guide future studies in this area. A silver NP-based artificial antibody is created by conformational engineering Function emerges on NPs from non-functional peptide by mimicking the protein folding A general mechanism is proposed for the conformational engineering on metal NPs
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Affiliation(s)
- Jia Xu
- Institute of Nanochemistry and Nanobiology, Shanghai University, Shanghai 200444, China
| | - Tiange Gao
- Institute of Nanochemistry and Nanobiology, Shanghai University, Shanghai 200444, China
| | - Lingjie Sheng
- Institute of Nanochemistry and Nanobiology, Shanghai University, Shanghai 200444, China
| | - Yan Wang
- Institute of Nanochemistry and Nanobiology, Shanghai University, Shanghai 200444, China
| | - Chenxi Lou
- Institute of Nanochemistry and Nanobiology, Shanghai University, Shanghai 200444, China
| | - Haifang Wang
- Institute of Nanochemistry and Nanobiology, Shanghai University, Shanghai 200444, China
- Corresponding author
| | - Yuanfang Liu
- Institute of Nanochemistry and Nanobiology, Shanghai University, Shanghai 200444, China
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Aoneng Cao
- Institute of Nanochemistry and Nanobiology, Shanghai University, Shanghai 200444, China
- Corresponding author
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10
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Liu Q, Sheng L, Liu YY, Gao T, Wang H, Liu Y, Cao A. A potential inhibitor of MDM2 by restoring the native conformation of the p53 α-helical peptide on gold nanoparticles. ChemMedChem 2022; 17:e202100623. [PMID: 35037401 DOI: 10.1002/cmdc.202100623] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 11/14/2021] [Indexed: 11/11/2022]
Abstract
Many efforts have been made to develop inhibitors of MDM2 as potential drugs for cancer therapy. In this work, we use our previous developed conformational engineering technique to stabilize the binding conformation of the p53 transcription activation domain (TAD) peptide on gold NPs (AuNPs), and create an AuNP-based anti-MDM2 artificial antibody, denoted as Goldbody, that specifically binds MDM2. Though the free TAD peptide is unstructured, circular dichroism spectra confirm that its α-helical conformation in the original p53 protein is restored on the anti-MDM2 Goldbody, and surface plasmon resonance (SPR) experiments confirm that there is strong specific interaction between the anti-MDM2 Goldbody and MDM2, demonstrating the anti-MDM2 Goldbody as a potential inhibitor of MDM2. This work demonstrates that the conformational engineering technique is not limited to the antigen-antibody systems, but can also be applied more widely in other protein-protein interfaces to create more and more artificial proteins for various biomedical applications.
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Affiliation(s)
- Qi Liu
- Shanghai University, Institute of Nanochemistry and Nanobiology, CHINA
| | - Lingjie Sheng
- Shanghai University, Institute of Nanochemistry and Nanobiology, CHINA
| | - Yuan-Yuan Liu
- Shanghai University, Institute of Nanochemistry and Nanobiology, CHINA
| | - Tiange Gao
- Shanghai University, Institute of Nanochemistry and Nanobiology, CHINA
| | - Haifang Wang
- Shanghai University, Institute of Nanochemistry and Nanobiology, CHINA
| | - Yuanfang Liu
- Peking University, College of Chemistry and Molecular Engineering, CHINA
| | - Aoneng Cao
- Shanghai University, Institute of Nanochemistry and Nanobiology, No.99 Shangda Rd. Rm201, Bldg. E, 200444, Shanghai, CHINA
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