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Shi N, Zheng M, Wu X, Chen N, Jiang L, Chang B, Lu F, Liu F. Construction and Catalytic Study of Affinity Peptide Orientation and Light Crosslinking Immobilized Sucrose Isomerase. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:13401-13408. [PMID: 37647235 DOI: 10.1021/acs.jafc.3c02644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
A novel affinity peptide orientation and light-controlled covalent immobilized method was developed. Sucrose isomerase (SI) was selected as the model enzyme. Molecular simulation was first performed to select the targeted immobilization region. Subsequently, a short peptide (H2N-VNIGGX-COOH, VG) with high affinity to this region was rationally designed. Thereafter, 4-benzoyl-l-phenylalanine with the photosensitive group of benzophenone was introduced. Then, the affinity between the ligand and the SI was validated using molecular dynamics simulation. Thereafter, the SI was directionally immobilized onto the surface of the epoxy resin (EP) guided by VG via photo-crosslinking, and thus the oriented photo-crosslinking enzymes were obtained. The enzymatic activity, thermostability, and reusability of the affinity directional photo-crosslinked immobilized sucrose isomerase (hv-EP-VG-SI) were systematically studied. The oriented immobilization enzymes were significantly improved in recycling and heat resistance. Moreover, hv-EP-VG-SI retained more than 90% of the original activity and 50% of the activity after 11 cycles.
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Affiliation(s)
- Nian Shi
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, National Engineering Laboratory for Industrial Enzymes, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Mingqiang Zheng
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, National Engineering Laboratory for Industrial Enzymes, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Xinming Wu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, National Engineering Laboratory for Industrial Enzymes, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Ning Chen
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, National Engineering Laboratory for Industrial Enzymes, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Luying Jiang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, National Engineering Laboratory for Industrial Enzymes, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Baogen Chang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, National Engineering Laboratory for Industrial Enzymes, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Fuping Lu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, National Engineering Laboratory for Industrial Enzymes, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Fufeng Liu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, National Engineering Laboratory for Industrial Enzymes, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
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Liu X, Jiang L, Li L, Lu F, Liu F. Bionics design of affinity peptide inhibitors for SARS-CoV-2 RBD to block SARS-CoV-2 RBD-ACE2 interactions. Heliyon 2023; 9:e12890. [PMID: 36686609 PMCID: PMC9836997 DOI: 10.1016/j.heliyon.2023.e12890] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 12/30/2022] [Accepted: 01/06/2023] [Indexed: 01/14/2023] Open
Abstract
Coronavirus Disease 2019 (COVID-19), has already posed serious threats and impacts on the health of the population and the country's economy. Therefore, it is of great theoretical significance and practical application value to better understand the process of COVID-19 infection and develop effective therapeutic drugs. It is known that the receptor-binding structural domain (SARS-CoV-2 RBD) on the spike protein of the novel coronavirus directly mediates its interaction with the host receptor angiotensin-converting enzyme 2 (ACE2), and thus blocking SARS-CoV-2 RBD-ACE2 interaction is capable of inhibiting SARS-CoV-2 infection. Firstly, the interaction mechanism between SARS-CoV-2RBD-ACE2 was explored using molecular dynamics simulation (MD) coupled with molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) free energy calculation method. The results of energy analysis showed that the key residues R403, R408, K417, and Y505 of SARS-CoV-2 RBD and the key residues D30, E37, D38, and Y41 of ACE2 were identified. Therefore, according to the hotspot residues of ACE2 and their distribution, a short peptide library of high-affinity SARS-CoV-2 RBD was constructed. And by using molecular docking virtual screening, six short peptides including DDFEDY, DEFEDY, DEYEDY, DFVEDY, DFHEDY, and DSFEDY with high affinity for SARS-CoV-2 RBD were identified. The results of MD simulation further confirmed that DDFEDY, DEYEDY, and DFVEDY are expected to be effective inhibitors. Finally, the allergenicity, toxicity and solubility properties of the three peptide inhibitors were validated.
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Affiliation(s)
- Xiaofeng Liu
- Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education; Tianjin Key Laboratory of Industrial Microbiology, PR China,College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, PR China
| | - Luying Jiang
- Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education; Tianjin Key Laboratory of Industrial Microbiology, PR China,College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, PR China
| | - Li Li
- College of Marine and Environmental Science, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Fuping Lu
- Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education; Tianjin Key Laboratory of Industrial Microbiology, PR China,College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, PR China
| | - Fufeng Liu
- Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education; Tianjin Key Laboratory of Industrial Microbiology, PR China,College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, PR China,Corresponding author. Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education; Tianjin Key Laboratory of Industrial Microbiology, PR China.
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da Fonseca AM, Soares NB, Colares RP, Macedo de Oliveira M, Santos Oliveira L, Marinho GS, Raya Paula de Lima M, da Rocha MN, Dos Santos HS, Marinho ES. Naphthoquinones biflorin and bis-biflorin ( Capraria biflora) as possible inhibitors of the fungus Candida auris polymerase: molecular docking, molecular dynamics, MM/GBSA calculations and in silico drug-likeness study. J Biomol Struct Dyn 2023; 41:11564-11577. [PMID: 36597918 DOI: 10.1080/07391102.2022.2163702] [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: 04/12/2022] [Accepted: 12/24/2022] [Indexed: 01/05/2023]
Abstract
A new worldwide concern has emerged with the recent emergence of infections caused by Candida auris. This reflects its comparative ease of transmission, substantial mortality, and the increasing level of resistance seen in the three major classes of antifungal drugs. Efforts to create a better design for structure-based drugs that described numerous modifications and the search for secondary metabolic structures derived from plant species are likely to reduce the virulence of several fungal pathogens. In this context, the present work aimed to evaluate in silico two naphthoquinones isolated from the roots of Capraria biflora, biflorin, and its dimmer, bis-biflorin, as potential inhibitors of Candida auris polymerase. Based on the simulation performed with the two naphthoquinones, biflorin and bis-biflorin, it can be stated that bis-biflorin showed the best interactions with Candida auris polymerase. Still, biflorin also demonstrated favorable coupling energy. Predictive pharmacokinetic assays suggest that biflorin has high oral bioavailability and more excellent metabolic stability compared to the bis-biflorin analogue. constituting a promising pharmacological tool.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Aluísio Marques da Fonseca
- Mestrado Acadêmico em Sociobiodiversidades e Tecnologias Sustentáveis - MASTS, Instituto de Engenharias e Desenvolvimento Sustentável, Universidade da Integração Internacional da Lusofonia Afro-Brasileira, Acarape, CE, Brazil
| | - Neidelenio Baltazar Soares
- Instituto de Ciências Exatas e da Natureza, Universidade da Integração Internacional da Lusofonia Afro-Brasileira, Acarape, CE, Brazil
| | - Regilany Paulo Colares
- Instituto de Ciências Exatas e da Natureza, Universidade da Integração Internacional da Lusofonia Afro-Brasileira, Acarape, CE, Brazil
| | | | | | - Gabrielle Silva Marinho
- Grupo de Química Teórica e Eletroquímica - GQTE, Universidade Estadual de Ceará, Limoiro do Norte, CE, Brazil
| | - Mira Raya Paula de Lima
- Instituto Federal de Educação Ciência e Tecnologia do Ceará - Campus Juazeiro do Norte, Juazeiro do Norte, CE, Brazil
| | - Matheus Nunes da Rocha
- Grupo de Química Teórica e Eletroquímica - GQTE, Universidade Estadual de Ceará, Limoiro do Norte, CE, Brazil
| | | | - Emmanuel Silva Marinho
- Grupo de Química Teórica e Eletroquímica - GQTE, Universidade Estadual de Ceará, Limoiro do Norte, CE, Brazil
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Alipour M, Motavaf M, Abdolmaleki P, Zali A, Ashrafi F, Safari S, Hajipour-Verdom B. Structural Analysis and Conformational Dynamics of Short Helical Hyperphosphorylated Segments of Tau Protein (Sequence 254–290) in Alzheimer’s Disease: A Molecular Dynamics Simulation Study. Front Mol Biosci 2022; 9:884705. [PMID: 36003083 PMCID: PMC9393928 DOI: 10.3389/fmolb.2022.884705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 06/09/2022] [Indexed: 11/21/2022] Open
Abstract
Alzheimer’s disease (AD) is a progressive neurodegenerative disorder whose early diagnosis leads to a chance for successful treatment and decreases the side effects. Hyperphosphorylation of tau proteins is a pathological hallmark of AD that causes it to lose its attachment ability to the microtubules. Alteration of tau structure due to its hyperphosphorylation is an exciting challenge regarding AD treatments. Here, we aimed to examine the structural alterations of short helical segments of tau protein with one to three phosphorylated sites by molecular dynamics simulation. Results indicated that the interaction of two similar segments with three phosphorylated sites (P-Ser262, 285, and 289) formed a compact and more stable structure than the one phosphorylated site complex (P-Ser262). Moreover, due to the high dynamics of the P-Ser262 complex, several structures were made with different conformational dynamics, but there was only one stable cluster of the P-Ser262, 285, and 289 complex during simulation. It seems that the P-Ser262, 285, and 289 complex plays an important role in the formation of paired helical filaments (PHFs) by forming a stable dimer. Generally, it is important to identify how structural features of segments in tau protein change when the phosphorylated sites increase from one to three sites and their effects on the formation of PHFs for drug design and diagnostic biomarkers.
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Affiliation(s)
- Mozhgan Alipour
- Functional Neurosurgery Research Center, Shohada Tajrish Comprehensive Neurosurgical Center of Excellence, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mahsa Motavaf
- Functional Neurosurgery Research Center, Shohada Tajrish Comprehensive Neurosurgical Center of Excellence, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Parviz Abdolmaleki
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Alireza Zali
- Functional Neurosurgery Research Center, Shohada Tajrish Comprehensive Neurosurgical Center of Excellence, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Farzad Ashrafi
- Functional Neurosurgery Research Center, Shohada Tajrish Comprehensive Neurosurgical Center of Excellence, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Saeid Safari
- Functional Neurosurgery Research Center, Shohada Tajrish Comprehensive Neurosurgical Center of Excellence, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- *Correspondence: Saeid Safari, ; Behnam Hajipour-Verdom,
| | - Behnam Hajipour-Verdom
- Functional Neurosurgery Research Center, Shohada Tajrish Comprehensive Neurosurgical Center of Excellence, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
- *Correspondence: Saeid Safari, ; Behnam Hajipour-Verdom,
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Rahmati S, Torkashvand F, Amanlou M, Bagherzadeh K, Fard Esfahani P, Aghamirza Moghim Aliabadi H, Vaziri B. Computational Engineering of Protein L to Achieve an Optimal Affinity Chromatography Resin for Purification of Antibody Fragments. Anal Chem 2021; 93:15253-15261. [PMID: 34747593 DOI: 10.1021/acs.analchem.1c01871] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Protein L affinity chromatography is a useful method for the purification of antibody fragments containing kappa light chains. In affinity chromatography, increasing the binding affinity leads to increased product purity, recovery, and dynamic binding capacity (DBC). In this study, molecular docking and molecular dynamics simulation techniques were used to design the engineered Protein L with higher affinity to the kappa light chain. Each engineered ligand was produced as a recombinant protein and coupled to a solid matrix. The purity, recovery, and DBC of the engineered resins were evaluated and then compared to those of a commercially available resin. The results showed important parameters for engineering more efficient Protein L ligands for affinity chromatography.
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Affiliation(s)
- Saman Rahmati
- Biotechnology Research Center, Pasteur Institute of Iran, Tehran 1316943551, Iran
| | - Fatemeh Torkashvand
- Biotechnology Research Center, Pasteur Institute of Iran, Tehran 1316943551, Iran
| | - Massoud Amanlou
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran 1417614411, Iran
| | - Kowsar Bagherzadeh
- Eye Research Center, The Five Senses Institute Rassoul Akram Hospital, Iran University of Medical Sciences, Tehran 1445613131, Iran.,Stem Cell and Regenerative Medicine Research Center, Iran University of Medical Sciences, Tehran 1449614535, Iran
| | | | | | - Behrouz Vaziri
- Biotechnology Research Center, Pasteur Institute of Iran, Tehran 1316943551, Iran
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Li E, Wang Y, Zhang D, Fan X, Han Z, Yu F. Siderite/PMS conditioning-pressurized vertical electro-osmotic dewatering process for activated sludge volume reduction: Evolution of protein secondary structure and typical amino acid in EPS. WATER RESEARCH 2021; 201:117352. [PMID: 34157572 DOI: 10.1016/j.watres.2021.117352] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 05/20/2021] [Accepted: 06/07/2021] [Indexed: 06/13/2023]
Abstract
In this study, the siderite/PMS conditioning-pressurized vertical electro-osmotic dewatering (PEOD) process was used to reduce the volume of activated sludge (AS). The changes in water content, cell, extracellular polymeric substances (EPS) distribution, protein secondary structures and typical amino acids in EPS fractions of AS along siderite/PMS conditioning-PEOD process were investigated. Results showed that the final water content (WC) of dewatered AS was 58.02% under the RSM optimized conditioning conditions of 0.05 g/g TSS siderite dosage, 0.23 g/g TSS PMS dosage, 600 kPa mechanical pressure and 20 V voltage. At conditioning and PEOD stages, the bound water content(BWC) of AS decreased by 25.23% and 91.76%, respectively. The HO• and SO4-· generated from siderite activating PMS could lead to the disruption of cells. The ratio of Ala-to Lys (Ala/Lys) showed strong negative correlations with BWC or WC in slime (RBWC2=-0.803, p<0.01; RWC2=-0.771, p<0.01) and TB-EPS (RBWC2=-0.693, p<0.01; RWC2=-0.705, p<0.01), and could be considered as an indicator of AS dewaterability. Compared with raw AS, conditioning led to the occurrence of the denser protein structure in TB-EPS and the looser one in slime. The contact number between Ala-and water decreased in TB-EPS and increased in slime, which indicated that the migration of water adhered in TB-EPS to outer layer. At the DG, MC and EC process, while the looser protein structure in TB-EPS and the denser one in slime occurred, as well as higher contact number between Ala-and water in TB-EPS than that in slime, which indicated that more water flowed outsider of slime than TB-EPS. This implied that the variations of the compactness of protein secondary structures and the contact number between Ala-and water in EPS layers correlated with AS dewaterability.
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Affiliation(s)
- Enrui Li
- College of Environmental Science and Engineering, Beijing Key Lab for Source Control Technology of Water Pollution, Beijing Forestry University, Beijing 100083, China
| | - Yili Wang
- College of Environmental Science and Engineering, Beijing Key Lab for Source Control Technology of Water Pollution, Beijing Forestry University, Beijing 100083, China.
| | - Daxin Zhang
- College of Environmental Science and Engineering, Beijing Key Lab for Source Control Technology of Water Pollution, Beijing Forestry University, Beijing 100083, China
| | - Xiaoyang Fan
- College of Environmental Science and Engineering, Beijing Key Lab for Source Control Technology of Water Pollution, Beijing Forestry University, Beijing 100083, China
| | - Zhibo Han
- College of Environmental Science and Engineering, Beijing Key Lab for Source Control Technology of Water Pollution, Beijing Forestry University, Beijing 100083, China
| | - Fuling Yu
- College of Science, Beijing Forestry University, Beijing 100083, China
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Matos MJB, Pina AS, Roque ACA. Rational design of affinity ligands for bioseparation. J Chromatogr A 2020; 1619:460871. [PMID: 32044126 DOI: 10.1016/j.chroma.2020.460871] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 01/05/2020] [Accepted: 01/08/2020] [Indexed: 11/25/2022]
Abstract
Affinity adsorbents have been the cornerstone in protein purification. The selective nature of the molecular recognition interactions established between an affinity ligands and its target provide the basis for efficient capture and isolation of proteins. The plethora of affinity adsorbents available in the market reflects the importance of affinity chromatography in the bioseparation industry. Ligand discovery relies on the implementation of rational design techniques, which provides the foundation for the engineering of novel affinity ligands. The main goal for the design of affinity ligands is to discover or improve functionality, such as increased stability or selectivity. However, the methodologies must adapt to the current needs, namely to the number and diversity of biologicals being developed, and the availability of new tools for big data analysis and artificial intelligence. In this review, we offer an overview on the development of affinity ligands for bioseparation, including the evolution of rational design techniques, dating back to the years of early discovery up to the current and future trends in the field.
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Affiliation(s)
- Manuel J B Matos
- UCIBIO, Chemistry Department, School of Sciences and Technology, NOVA University of Lisbon, 2829-516 Caparica, Portugal
| | - Ana S Pina
- UCIBIO, Chemistry Department, School of Sciences and Technology, NOVA University of Lisbon, 2829-516 Caparica, Portugal
| | - A C A Roque
- UCIBIO, Chemistry Department, School of Sciences and Technology, NOVA University of Lisbon, 2829-516 Caparica, Portugal.
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8
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Bordelon T, Bobay B, Murphy A, Reese H, Shanahan C, Odeh F, Broussard A, Kormos C, Menegatti S. Translating antibody-binding peptides into peptoid ligands with improved affinity and stability. J Chromatogr A 2019; 1602:284-299. [DOI: 10.1016/j.chroma.2019.05.047] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 05/03/2019] [Accepted: 05/24/2019] [Indexed: 12/18/2022]
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9
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Li D, Gao Y, Pan X, Wei D, Guo B, Yang C, Liu B. MD and DSC study of bioactive structural stability of insulin in various imidazolium ionic liquids. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.01.039] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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10
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Fang YM, Lin DQ, Yao SJ. Review on biomimetic affinity chromatography with short peptide ligands and its application to protein purification. J Chromatogr A 2018; 1571:1-15. [DOI: 10.1016/j.chroma.2018.07.082] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 07/12/2018] [Accepted: 07/29/2018] [Indexed: 10/28/2022]
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Xue A, Zhao WW, Liu X(M, Sun Y. Affinity chromatography of human IgG with octapeptide ligands identified from eleven peptide-ligand candidates. Biochem Eng J 2016. [DOI: 10.1016/j.bej.2015.11.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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12
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Salvalaglio M, Paloni M, Guelat B, Morbidelli M, Cavallotti C. A two level hierarchical model of protein retention in ion exchange chromatography. J Chromatogr A 2015; 1411:50-62. [DOI: 10.1016/j.chroma.2015.07.101] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 07/23/2015] [Accepted: 07/27/2015] [Indexed: 10/23/2022]
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13
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A comprehensive evaluation of mixed mode interactions of HEA and PPA HyperCel™ chromatographic media. J Chromatogr B Analyt Technol Biomed Life Sci 2015; 976-977:68-77. [DOI: 10.1016/j.jchromb.2014.11.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Revised: 11/04/2014] [Accepted: 11/21/2014] [Indexed: 11/18/2022]
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14
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Combined docking, molecular dynamics simulations and spectroscopic studies for the rational design of a dipeptide ligand for affinity chromatography separation of human serum albumin. J Mol Model 2014; 20:2446. [DOI: 10.1007/s00894-014-2446-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 08/26/2014] [Indexed: 01/07/2023]
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15
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Li Y, Liu X, Dong X, Zhang L, Sun Y. Biomimetic design of affinity peptide ligand for capsomere of virus-like particle. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:8500-8508. [PMID: 24976378 DOI: 10.1021/la5017438] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Virus-like particle (VLP) of murine polyomavirus (MPV) is a T = 7d icosahedral capsid that self-assembles from 72 capsomeres (Caps), each of which is a pentamer of major coat protein VP1. VLP has great potential in vaccinology, gene therapy, drug delivery, and materials science. However, its application is hindered by high cost downstream processes, leading to an urgent demand of a highly efficient affinity ligand for the separation and purification of Cap by affinity chromatography. Herein a biomimetic design strategy of an affinity peptide ligand of Cap has been developed on the basis of the binding structure of the C-terminus of minor coat protein (VP2-C) on the inner surface of Cap. The molecular interactions between VP2-C and Cap were first examined using all-atom molecular dynamics (MD) simulations coupled with the molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA) method, where V283, P285, D286, W287, L289, and Y296 of VP2-C were identified as the hot spots. An affinity peptide library (DWXLXLXY, X denotes arbitrary amino acids except cysteine) was then constructed for virtual screening sequently by docking with AUTODOCK VINA, binding structure comparison, and final docking with ROSETTA FlexPepDock. Ten peptide candidates were selected and further confirmed by MD simulations and MM/PBSA, where DWDLRLLY was found to have the highest affinity to Cap. In DWDLRLLY, six residues are favorable for the binding, including W2, L4, L6 and Y8 inheriting from VP2-C, and R5 and L7 selected in the virtual screening. This confirms the high efficiency and accuracy of the biomimetic design strategy. DWDLRLLY was then experimentally validated by a one-step purification of Cap from crude cell lysate using affinity chromatography with the octapeptide immobilized on Sepharose gel. The purified Caps were observed to self-assemble into VLP with consistent structure of authentic MPV.
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Affiliation(s)
- Yanying Li
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology, Tianjin University , Tianjin 300072, People's Republic of China
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16
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Zhao WW, Liu FF, Shi QH, Dong XY, Sun Y. Biomimetic design of affinity peptide ligands for human IgG based on protein A-IgG complex. Biochem Eng J 2014. [DOI: 10.1016/j.bej.2014.03.015] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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17
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A study on the nature of interactions of mixed-mode ligands HEA and PPA HyperCel using phenylglyoxal modified lysozyme. J Chromatogr B Analyt Technol Biomed Life Sci 2014; 960:209-13. [DOI: 10.1016/j.jchromb.2014.04.046] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 04/23/2014] [Indexed: 11/20/2022]
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18
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Bai JS, Bai S, Shi QH, Sun Y. Purification of supercoiled plasmid DNA from clarified bacterial lysate by arginine-affinity chromatography: Effects of spacer arms and ligand density. J Sep Sci 2014; 37:1386-95. [DOI: 10.1002/jssc.201400092] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 03/25/2014] [Accepted: 03/26/2014] [Indexed: 12/21/2022]
Affiliation(s)
- Jin-Shan Bai
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of Ministry of Education; School of Chemical Engineering and Technology, Tianjin University; Tianjin China
| | - Shu Bai
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of Ministry of Education; School of Chemical Engineering and Technology, Tianjin University; Tianjin China
| | - Qing-Hong Shi
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of Ministry of Education; School of Chemical Engineering and Technology, Tianjin University; Tianjin China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin); Tianjin China
| | - Yan Sun
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of Ministry of Education; School of Chemical Engineering and Technology, Tianjin University; Tianjin China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin); Tianjin China
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Zhang L, Zhang C, Sun Y. Biomimetic design of platelet adhesion inhibitors to block integrin α2β1-collagen interactions: II. Inhibitor library, screening, and experimental validation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:4734-4742. [PMID: 24697658 DOI: 10.1021/la4046012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Platelet adhesion on collagen mediated by integrin α2β1 has been proven important in arterial thrombus formation, leading to an exigent demand on development of potent inhibitors for the integrin α2β1-collagen binding. In the present study, a biomimetic design strategy of platelet adhesion inhibitors was established, based on the affinity binding model of integrin proposed in part I. First, a heptapeptide library containing 8000 candidates was designed to functionally mimic the binding motif of integrin α2β1. Then, each heptapeptide in the library was docked onto a collagen molecule for the assessment of its affinity, followed by a screening based on its structure similarity to the original structure in the affinity binding model. Eight candidates were then selected for further screening by molecular dynamics (MD) simulations. Thereafter, three candidates chosen from MD simulations were separately added into the physiological saline containing separated integrin and collagen, to check their abilities for blocking the integrin-collagen interaction using MD simulations. Of these three candidates, significant inhibition was observed in the presence of LWWNSYY. Finally, the binding affinity of LWWNSYY for collagen was demonstrated by isothermal titration calorimetry. Moreover, significant inhibition of platelet adhesion in the presence of LWWNSYY has been experimentally validated. This work has thus developed an effective strategy for the biomimetic design of peptide-based platelet adhesion inhibitors.
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Affiliation(s)
- Lin Zhang
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology, Tianjin University , Tianjin 300072, People's Republic of China
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Fasoli E, Reyes YR, Guzman OM, Rosado A, Cruz VR, Borges A, Martinez E, Bansal V. Para-aminobenzamidine linked regenerated cellulose membranes for plasminogen activator purification: effect of spacer arm length and ligand density. J Chromatogr B Analyt Technol Biomed Life Sci 2013; 930:13-21. [PMID: 23703544 DOI: 10.1016/j.jchromb.2013.04.025] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Revised: 04/10/2013] [Accepted: 04/12/2013] [Indexed: 11/25/2022]
Abstract
Despite membrane-based separations offering superior alternative to packed bed chromatographic processes, there has been a substantial lacuna in their actual application to separation processes. One of the major reasons behind this is the lack of availability of appropriately modified or end-group modifiable membranes. In this paper, an affinity membrane was developed using a commercially available serine protease inhibitor, para-aminobenzamidine (pABA). The membrane modification was optimized for protein binding capacity by varying: (i) the length of the spacer arm (SA; 5-atoms, 7-atoms, and 14-atoms) linking the ligand to membrane surface; (ii) the affinity ligand (pABA) density on membrane surface (5-25nmol/cm(2)). Resulting membranes were tested for their ability to bind plasminogen activators (PAs) from mono- and multi-component systems in batch mode. The membrane containing pABA linked through 7-atoms SA but similar ligand density as in the case of 5- or 14-atoms long SA was found to bind up to 1.6-times higher amounts of PA per nmoles of immobilized ligand from conditioned HeLa cell culture media. However, membranes with similar ligand densities but different lengths of SA, showed comparable binding capacities in mono-component system. In addition, the length of SA did not affect the selectivity of the ligand for PA. A clear inverse linear correlation was observed between ligand density and binding capacity until the point of PA binding optima was reached (11±1.0nmol/cm(2)) in mono- and multi-component systems for 7- as well as 14-atoms SA. Up to 200-fold purification was achieved in a single step separation of PA from HeLa conditioned media using these affinity membranes. The issues of ligand leaching and reuse of the membranes were also investigated. An extensive regeneration procedure allowed the preservation of approximately 95% of the PA binding capacity of the membranes even after five cycles of use.
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Affiliation(s)
- Ezio Fasoli
- Department of Chemistry, University of Puerto Rico at Humacao, CUH Station, Humacao, PR 00792, USA
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He X, Lin R, He H, Sun M, Xiao D. Chiral Separation of Ketoprofen on a Chirobiotic T Column and Its Chiral Recognition Mechanisms. Chromatographia 2012. [DOI: 10.1007/s10337-012-2352-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Sheng S, Kong F. Separation of antigens and antibodies by immunoaffinity chromatography. PHARMACEUTICAL BIOLOGY 2012; 50:1038-1044. [PMID: 22480305 DOI: 10.3109/13880209.2011.653493] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
CONTEXT Affinity chromatography is an efficient antibody, antigen and protein separation method based on the interaction between specific immobilized ligands and target antibody, antigen, and so on. Populations of available ligands can be used to separate antibodies or their Fab fragments. Similarly, antigens can be isolated by immunoaffinity chromatography (IAC) on immobilized antibodies of low affinity. OBJECTIVE This review describes the advantages, the applications, as well as the drawbacks, of IAC in the separation and purification of antibodies and antigens. METHODS The present review discussed all types of purification and isolation of antibodies and antigens by IAC, including purification of antibodies using immobilized and synthetic mimic proteins A, G and L; isolation of Fab fragments of antibodies; separation of antibodies against different antigen forms; isolation of antigens by immobilized antibodies and so on. These methods come from over 60 references compiled from all major databases. RESULTS Purification of antigens with antibodies should choose low-affinity antibodies to avoid denaturation of most proteins. Concern for cost and safety, prompted research activities focused on novel synthetic ligands with improved properties such as lower cost, avoidance of the risk of contamination associated with natural ligands of human or animal origin to isolate antibodies and antigens. CONCLUSION It is anticipated that the improvements of IAC will have impact not only on large-scale production of antibodies but also on the generation of new affinity-based methods for the increasing number of proteins and antibody derivatives available by protein engineering and the proteomics revolution.
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Affiliation(s)
- Shuai Sheng
- Department of Hematology, Liaoning Medical University, Jinzhou, Liaoning, People's Republic of China
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Freed AS, Garde S, Cramer SM. Molecular Simulations of Multimodal Ligand–Protein Binding: Elucidation of Binding Sites and Correlation with Experiments. J Phys Chem B 2011; 115:13320-7. [DOI: 10.1021/jp2038015] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Alexander S. Freed
- The Howard P. Isermann Department of Chemical and Biological Engineering, and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York
| | - Shekhar Garde
- The Howard P. Isermann Department of Chemical and Biological Engineering, and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York
| | - Steven M. Cramer
- The Howard P. Isermann Department of Chemical and Biological Engineering, and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York
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Zhao G, Bai S, Sun Y. Development of a displacer-immobilized ligand docking scheme for displacer screening for protein displacement chromatography. Biochem Eng J 2011. [DOI: 10.1016/j.bej.2011.03.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Feng J, Fu LX, Wang J, Wang W, Li JH, Qiao YT, Sun PC, Yuan Z. A comparison study between polymeric ligand and monomeric ligand for oligopeptide adsorption. J Colloid Interface Sci 2011; 355:478-85. [DOI: 10.1016/j.jcis.2010.12.045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2010] [Revised: 12/12/2010] [Accepted: 12/14/2010] [Indexed: 11/27/2022]
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Zhao G, Dong XY, Sun Y. Ligands for mixed-mode protein chromatography: Principles, characteristics and design. J Biotechnol 2009; 144:3-11. [DOI: 10.1016/j.jbiotec.2009.04.009] [Citation(s) in RCA: 134] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2009] [Revised: 04/10/2009] [Accepted: 04/23/2009] [Indexed: 11/24/2022]
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Sun Y, Liu FF, Shi QH. Approaches to high-performance preparative chromatography of proteins. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2009; 113:217-254. [PMID: 19373447 DOI: 10.1007/10_2008_32] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Preparative liquid chromatography is widely used for the purification of chemical and biological substances. Different from high-performance liquid chromatography for the analysis of many different components at minimized sample loading, high-performance preparative chromatography is of much larger scale and should be of high resolution and high capacity at high operation speed and low to moderate pressure drop. There are various approaches to this end. For biochemical engineers, the traditional way is to model and optimize a purification process to make it exert its maximum capability. For high-performance separations, however, we need to improve chromatographic technology itself. We herein discuss four approaches in this review, mainly based on the recent studies in our group. The first is the development of high-performance matrices, because packing material is the central component of chromatography. Progress in the fabrication of superporous materials in both beaded and monolithic forms are reviewed. The second topic is the discovery and design of affinity ligands for proteins. In most chromatographic methods, proteins are separated based on their interactions with the ligands attached to the surface of porous media. A target-specific ligand can offer selective purification of desired proteins. Third, electrochromatography is discussed. An electric field applied to a chromatographic column can induce additional separation mechanisms besides chromatography, and result in electrokinetic transport of protein molecules and/or the fluid inside pores, thus leading to high-performance separations. Finally, expanded-bed adsorption is described for process integration to reduce separation steps and process time.
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Affiliation(s)
- Yan Sun
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China,
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