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Teimouri H, Medvedeva A, Kolomeisky AB. Physical-Chemical Features Selection Reveals That Differences in Dipeptide Compositions Correlate Most with Protein-Protein Interactions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.27.582345. [PMID: 38464064 PMCID: PMC10925282 DOI: 10.1101/2024.02.27.582345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
The ability to accurately predict protein-protein interactions is critically important for our understanding of major cellular processes. However, current experimental and computational approaches for identifying them are technically very challenging and still have limited success. We propose a new computational method for predicting protein-protein interactions using only primary sequence information. It utilizes a concept of physical-chemical similarity to determine which interactions will most probably occur. In our approach, the physical-chemical features of protein are extracted using bioinformatics tools for different organisms, and then they are utilized in a machine-learning method to identify successful protein-protein interactions via correlation analysis. It is found that the most important property that correlates most with the protein-protein interactions for all studied organisms is dipeptide amino acid compositions. The analysis is specifically applied to the bacterial two-component system that includes histidine kinase and transcriptional response regulators. Our theoretical approach provides a simple and robust method for quantifying the important details of complex mechanisms of biological processes.
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Affiliation(s)
- Hamid Teimouri
- Department of Chemistry, Rice University, Houston, Texas, United States
- Center for Theoretical Biological Physics, Rice University, Houston, Texas, United States
| | - Angela Medvedeva
- Department of Chemistry, Rice University, Houston, Texas, United States
- Center for Theoretical Biological Physics, Rice University, Houston, Texas, United States
| | - Anatoly B. Kolomeisky
- Department of Chemistry, Rice University, Houston, Texas, United States
- Center for Theoretical Biological Physics, Rice University, Houston, Texas, United States
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas, United States
- Department of Physics and Astronomy, Rice University, Houston, TX, United States
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2
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Immobilization of carbonic anhydrase in a hydrophobic poly(ionic liquid): A new functional solid for CO2 capture. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2022.108639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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3
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Luan P, Li Y, Huang C, Dong L, Ma T, Liu J, Gao J, Liu Y, Jiang Y. Design of De Novo Three-Enzyme Nanoreactors for Stereodivergent Synthesis of α-Substituted Cyclohexanols. ACS Catal 2022. [DOI: 10.1021/acscatal.2c02136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Pengqian Luan
- School of Chemical Engineering and Technology, Hebei University of Technology, Tianjin 300130, China
| | - Yongxing Li
- School of Chemical Engineering and Technology, Hebei University of Technology, Tianjin 300130, China
| | - Chen Huang
- School of Chemical Engineering and Technology, Hebei University of Technology, Tianjin 300130, China
| | - Lele Dong
- School of Chemical Engineering and Technology, Hebei University of Technology, Tianjin 300130, China
| | - Teng Ma
- School of Chemical Engineering and Technology, Hebei University of Technology, Tianjin 300130, China
| | - Jianqiao Liu
- School of Chemical Engineering and Technology, Hebei University of Technology, Tianjin 300130, China
| | - Jing Gao
- School of Chemical Engineering and Technology, Hebei University of Technology, Tianjin 300130, China
| | - Yunting Liu
- School of Chemical Engineering and Technology, Hebei University of Technology, Tianjin 300130, China
| | - Yanjun Jiang
- School of Chemical Engineering and Technology, Hebei University of Technology, Tianjin 300130, China
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
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4
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Lin L, Luo C, Li C, Chen X, Cui H. A Novel Biocompatible Ternary Nanoparticle with High Antibacterial Activity: Synthesis, Characterization, and Its Application in Beef Preservation. Foods 2022; 11:foods11030438. [PMID: 35159588 PMCID: PMC8834416 DOI: 10.3390/foods11030438] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 01/28/2022] [Accepted: 01/29/2022] [Indexed: 01/27/2023] Open
Abstract
Edible nanoparticles containing antibacterial agents are one of the effective strategies to control foodborne diseases. Herein, novel ternary nanoparticles (TNP) were prepared from rosemary essential oil (REO), nisin and Lycium barbarum polysaccharides (LBP) through hydrophobic and electrostatic interaction. The average particle size of TNP was 211.5 nm, and its encapsulation efficiency reached 86.6%. After the addition of LBP, the physical stability, thermal stability and storage stability of TNP were significantly improved. In vitro, compared with the control group, the population of S. aureus and E. coli O157:H7 in the TNP-treated group was reduced by 2.386 log CFU/mL and 1.966 log CFU/mL, respectively, on the fifth day. The free radical scavenging rate of TNP was 63.15%. The application of TNP on beef presented favorable preservation effects without affecting its color and texture. Therefore, the synthesis strategy of TNP has important reference significance for the research and development of new food antibacterial agents.
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Affiliation(s)
- Lin Lin
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China; (L.L.); (C.L.); (X.C.)
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha 410007, China;
| | - Chencheng Luo
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China; (L.L.); (C.L.); (X.C.)
| | - Changzhu Li
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha 410007, China;
| | - Xiaochen Chen
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China; (L.L.); (C.L.); (X.C.)
| | - Haiying Cui
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China; (L.L.); (C.L.); (X.C.)
- Correspondence:
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5
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Kumar A, Singh NK, Ghosh D, Radhakrishna M. Understanding the role of hydrophobic patches in protein disaggregation. Phys Chem Chem Phys 2021; 23:12620-12629. [PMID: 34075973 DOI: 10.1039/d1cp00954k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Protein folding is a very complex process and, so far, the mechanism of folding still intrigues the research community. Despite a large conformational space available (O(1047) for a 100 amino acid residue), most proteins fold into their native state within a very short time. While small proteins fold relatively fast (a few microseconds) large globular proteins may take as long as several milliseconds to fold. During the folding process, the protein synthesized in the ribosome is exposed to the crowded environment of the cell and is easily prone to misfolding and aggregation due to interactions with other proteins or biomacromolecules present within the cell. These large proteins, therefore, rely on chaperones for their folding and repair. Chaperones are known to have hydrophobic patchy domains that play a crucial role in shielding the protein against misfolding and disaggregation of aggregated proteins. In the current article, Monte Carlo simulations carried out in the framework of the hydrophobic-polar (H-P) lattice model indicate that hydrophobic patchy domains drastically reduce the inter-protein interactions and are efficient in disaggregating proteins. The effectiveness of the disaggregation depends on the size and distribution of these patches on the surface and also on the strength of the interaction between the protein and the surface. Further, our results indicate that when the patch is complementary to the exposed hydrophobic patch of the protein, protein disaggregation is accompanied by stabilization of the protein even relative to its bulk behavior due to favorable protein-surface interactions. We believe that these findings shed light on the role of the class of chaperones known as heat shock proteins (Hsps) on protein disaggregation and refolding.
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Affiliation(s)
- Avishek Kumar
- Discipline of Chemical Engineering, Indian Institute of Technology (IIT) Gandhinagar, Palaj, Gandhinagar, Gujarat-382355, India.
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6
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High Stabilization of Enzymes Immobilized on Rigid Hydrophobic Glyoxyl-Supports: Generation of Hydrophilic Environments on Support Surfaces. Catalysts 2020. [DOI: 10.3390/catal10060676] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Very rigid supports are useful for enzyme immobilization to design continuous flow reactors and/or to work in non-conventional media. Among them, epoxy-methacrylic supports are easily functionalized with glyoxyl groups, which makes them ideal candidates for enzyme stabilization via multipoint covalent immobilization. However, these supports present highly hydrophobic surfaces, which might promote very undesirable effects on enzyme activity and/or stability. The hydrophilization of the support surface after multipoint enzyme immobilization is proposed here as an alternative to reduce these undesirable effects. The remaining aldehyde groups on the support are modified with aminated hydrophilic small molecules (glycine, lysine or aspartic acid) in the presence of 2-picoline borane. The penicillin G acylase from Escherichia coli (PGA) and alcohol dehydrogenase from Thermus thermophilus HB27 (ADH2) were immobilized on glyoxyl-functionalized agarose, Relizyme and Relisorb. Despite the similar density of aldehyde groups displayed by functionalized supports, their stabilization effects on immobilized enzymes were quite different: up to 300-fold lower by hydrophobic supports than by highly hydrophilic glyoxyl-agarose. A dramatic increase in the protein stabilities was shown when a hydrophilization treatment of the hydrophobic support surface was done. The PGA immobilized on the glyoxyl-Relisorb hydrophilized with aspartic acid becomes 280-fold more stable than without any treatment, and it is even more stable than the PGA immobilized on the glyoxyl agarose.
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7
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Wang H, Zhang L, Wang Y, Li J, Du G, Kang Z. Engineering the heparin-binding pocket to enhance the catalytic efficiency of a thermostable heparinase III from Bacteroides thetaiotaomicron. Enzyme Microb Technol 2020; 137:109549. [DOI: 10.1016/j.enzmictec.2020.109549] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 02/26/2020] [Accepted: 03/08/2020] [Indexed: 02/06/2023]
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8
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Kumar A, Ghosh D, Radhakrishna M. Surface Patterning for Enhanced Protein Stability: Insights from Molecular Simulations. J Phys Chem B 2019; 123:8363-8369. [DOI: 10.1021/acs.jpcb.9b05663] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Avishek Kumar
- Department of Chemical Engineering, Indian Institute of Technology (IIT) Gandhinagar, Palaj, Gandhinagar, Gujarat 382355, India
| | - Deepshikha Ghosh
- Department of Chemical Engineering, Indian Institute of Technology (IIT) Gandhinagar, Palaj, Gandhinagar, Gujarat 382355, India
| | - Mithun Radhakrishna
- Department of Chemical Engineering, Indian Institute of Technology (IIT) Gandhinagar, Palaj, Gandhinagar, Gujarat 382355, India
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9
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Li J, Pan D, Yi J, Hao L, Kang Q, Liu X, Lu L, Lu J. Protective effect of β-cyclodextrin on stability of nisin and corresponding interactions involved. Carbohydr Polym 2019; 223:115115. [PMID: 31426993 DOI: 10.1016/j.carbpol.2019.115115] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 07/18/2019] [Accepted: 07/20/2019] [Indexed: 12/20/2022]
Abstract
Nisin has been extensively employed in food industry as an antimicrobial peptide, but the proteolytic degradation and interference by food components resulted in the decrease of its antimicrobial activity. This study intends to explore the protective effect of β-cyclodextrin (β-CD) on nisin and corresponding interactions involved. The antibacterial experiments indicated that the combination of nisin and β-CD could provide a better antibacterial effect on cooked pork meat. Spectral analysis with UV-vis and fluorescence spectroscopy showed that the micro-environment of nisin could be influenced by β-CD. Tricine-SDS-PAGE results exhibited that the combination of nisin and β-CD could delay the degradation of nisin and improve its stability in the presence of trypsin. In sum, the study provided a potential approach to improve the stability of nisin, especially in the presence of trypsin.
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Affiliation(s)
- Jingjing Li
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Dan Pan
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Juanjuan Yi
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Limin Hao
- The Quartermaster Research Institute of Engineering and Technology, Academy of Military Sciences PLA China, Beijing 100010, China
| | - Qiaozhen Kang
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Xin Liu
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Laizheng Lu
- Zhengzhou Mindtek Biotechnology Co. Ltd, Zhengzhou, Henan 450001, China
| | - Jike Lu
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China.
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10
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Torktaz I, Karkhane AA, Hemmat J. Rational engineering of Cel5E from Clostridium thermocellum to improve its thermal stability and catalytic activity. Appl Microbiol Biotechnol 2018; 102:8389-8402. [DOI: 10.1007/s00253-018-9204-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 06/16/2018] [Accepted: 06/25/2018] [Indexed: 10/28/2022]
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11
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Parashar SK, Srivastava SK, Dutta NN, Garlapati VK. Engineering aspects of immobilized lipases on esterification: A special emphasis of crowding, confinement and diffusion effects. Eng Life Sci 2018; 18:308-316. [PMID: 32624910 DOI: 10.1002/elsc.201700082] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Revised: 11/08/2017] [Accepted: 01/24/2018] [Indexed: 11/10/2022] Open
Abstract
Cross-linked enzyme crystal (CLEC) and sol-gel entrapped pseudomonas sp. lipase were investigated for the esterification of lauric acid with ethanol by considering the effects of reaction conditions on reaction rate. The activation energy for the reaction was estimated to be 1097.58 J/mol and 181.75 J/mol for sol-gel and CLEC entrapped lipase respectively. CLEC lipase exhibited a marginal internal diffusion effect on reaction rate over sol-gel lipases and found to be interesting. The overall reaction mechanism was found to conform to the Ping Pong Bi Bi mechanism. The higher efficiency of sol-gel lipases over CLEC lipases in esterification reaction is mainly due to the combined effects of crowding, confinement and diffusional limitations.
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Affiliation(s)
- Surendra Kumar Parashar
- Department of Chemical Engineering/Chemistry Jaypee University of Engineering and Technology Guna Madhya Pradesh India
| | - Sunil Kumar Srivastava
- Department of Chemical Engineering/Chemistry Jaypee University of Engineering and Technology Guna Madhya Pradesh India
| | - N N Dutta
- Department of Chemical Engineering/Chemistry Jaypee University of Engineering and Technology Guna Madhya Pradesh India
| | - Vijay Kumar Garlapati
- Department of Biotechnology and Bioinformatics Jaypee University of Information Technology Waknaghat Himachal Pradesh India
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12
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Nabavi Zadeh PS, Zezzi do Valle Gomes M, Abrahamsson M, Palmqvist AEC, Åkerman B. Measuring viscosity inside mesoporous silica using protein-bound molecular rotor probe. Phys Chem Chem Phys 2018; 20:23202-23213. [DOI: 10.1039/c8cp01063c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Fluorescence spectroscopy of protein-bound molecular rotors Cy3 and Cy5 is used to monitor the effective viscosity inside the pores of two types of mesoporous silica (SBA-15 and MCF) with pore diameters between 8.9 and 33 nm.
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Affiliation(s)
- Pegah S. Nabavi Zadeh
- Chalmers University of Technology
- Department of Chemistry and Chemical Engineering
- Physical Chemistry
- SE-41296 Gothenburg
- Sweden
| | - Milene Zezzi do Valle Gomes
- Chalmers University of Technology
- Department of Chemistry and Chemical Engineering
- Applied Chemistry
- SE-41296 Gothenburg
- Sweden
| | - Maria Abrahamsson
- Chalmers University of Technology
- Department of Chemistry and Chemical Engineering
- Physical Chemistry
- SE-41296 Gothenburg
- Sweden
| | - Anders E. C. Palmqvist
- Chalmers University of Technology
- Department of Chemistry and Chemical Engineering
- Applied Chemistry
- SE-41296 Gothenburg
- Sweden
| | - Björn Åkerman
- Chalmers University of Technology
- Department of Chemistry and Chemical Engineering
- Physical Chemistry
- SE-41296 Gothenburg
- Sweden
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13
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14
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Zezzi do Valle Gomes M, Palmqvist AEC. Influence of operating conditions and immobilization on activity of alcohol dehydrogenase for the conversion of formaldehyde to methanol. NEW J CHEM 2017. [DOI: 10.1039/c7nj02028g] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Improved activity of alcohol dehydrogenase by immobilization in octyl-functionalized siliceous mesostructured cellular foams and tuning of pressure and formaldehyde concentration.
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Affiliation(s)
- Milene Zezzi do Valle Gomes
- Chalmers University of Technology, Department of Chemistry and Chemical Engineering, Applied Chemistry
- Gothenburg
- Sweden
| | - Anders E. C. Palmqvist
- Chalmers University of Technology, Department of Chemistry and Chemical Engineering, Applied Chemistry
- Gothenburg
- Sweden
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15
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Kahar UM, Sani MH, Chan KG, Goh KM. Immobilization of α-Amylase from Anoxybacillus sp. SK3-4 on ReliZyme and Immobead Supports. Molecules 2016; 21:E1196. [PMID: 27618002 PMCID: PMC6273902 DOI: 10.3390/molecules21091196] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 09/04/2016] [Accepted: 09/05/2016] [Indexed: 01/13/2023] Open
Abstract
α-Amylase from Anoxybacillus sp. SK3-4 (ASKA) is a thermostable enzyme that produces a high level of maltose from starches. A truncated ASKA (TASKA) variant with improved expression and purification efficiency was characterized in an earlier study. In this work, TASKA was purified and immobilized through covalent attachment on three epoxide (ReliZyme EP403/M, Immobead IB-150P, and Immobead IB-150A) and an amino-epoxide (ReliZyme HFA403/M) activated supports. Several parameters affecting immobilization were analyzed, including the pH, temperature, and quantity (mg) of enzyme added per gram of support. The influence of the carrier surface properties, pore sizes, and lengths of spacer arms (functional groups) on biocatalyst performances were studied. Free and immobilized TASKAs were stable at pH 6.0-9.0 and active at pH 8.0. The enzyme showed optimal activity and considerable stability at 60 °C. Immobilized TASKA retained 50% of its initial activity after 5-12 cycles of reuse. Upon degradation of starches and amylose, only immobilized TASKA on ReliZyme HFA403/M has comparable hydrolytic ability with the free enzyme. To the best of our knowledge, this is the first report of an immobilization study of an α-amylase from Anoxybacillus spp. and the first report of α-amylase immobilization using ReliZyme and Immobeads as supports.
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Affiliation(s)
- Ummirul Mukminin Kahar
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, Skudai 81310, Johor, Malaysia.
| | - Mohd Helmi Sani
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, Skudai 81310, Johor, Malaysia.
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia.
| | - Kian Mau Goh
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, Skudai 81310, Johor, Malaysia.
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16
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Wang H, Black CT, Akcora P. Elastic Properties of Protein Functionalized Nanoporous Polymer Films. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:151-158. [PMID: 26672623 DOI: 10.1021/acs.langmuir.5b04334] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Retaining the conformational structure and bioactivity of immobilized proteins is important for biosensor designs and drug delivery systems. Confined environments often lead to changes in conformation and functions of proteins. In this study, lysozyme is chemically tethered into nanopores of polystyrene thin films, and submicron pores in poly(methyl methacrylate) films are functionalized with streptavidin. Nanoindentation experiments show that stiffness of streptavidin increases with decreasing submicron pore sizes. Lysozymes in polystyrene nanopores are found to behave stiffer than the submicron pore sizes and still retain their specific bioactivity relative to the proteins on flat surfaces. Our results show that protein functionalized ordered nanoporous polystyrene/poly(methyl methacrylate) films present heterogeneous elasticity and can be used to study interactions between free proteins and designed surfaces.
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Affiliation(s)
- Haoyu Wang
- Department of Chemical Engineering and Materials Science, Stevens Institute of Technology , 1 Castle Point on Hudson, Hoboken, New Jersey 07030, United States
| | - Charles T Black
- Center for Functional Nanomaterials, Brookhaven National Laboratory , Upton, New York 11973, United States
| | - Pinar Akcora
- Department of Chemical Engineering and Materials Science, Stevens Institute of Technology , 1 Castle Point on Hudson, Hoboken, New Jersey 07030, United States
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17
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Kumar-Krishnan S, Chakaravarthy S, Hernandez-Rangel A, Prokhorov E, Luna-Bárcenas G, Esparza R, Meyyappan M. Chitosan supported silver nanowires as a platform for direct electrochemistry and highly sensitive electrochemical glucose biosensing. RSC Adv 2016. [DOI: 10.1039/c5ra24259b] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Chitosan supported silver nanowire (CS/AgNWs) based enzyme electrodes for highly sensitive glucose sensing.
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Affiliation(s)
- Siva Kumar-Krishnan
- Cinvestav Queretaro
- Querétaro QRO
- México
- Centro de Física Aplicada y Tecnología Avanzada
- Universidad Nacional Autónoma de México
| | - S. Chakaravarthy
- Programa de Doctorado en Nanociencias y Nanotecnología, CINVESTAV-IPN
- México
| | | | | | | | - Rodrigo Esparza
- Centro de Física Aplicada y Tecnología Avanzada
- Universidad Nacional Autónoma de México
- Santiago de Querétaro
- México
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18
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Zhang Y, Feng WX, Legrand YM, Supuran CT, Su CY, Barboiu M. Dynameric host frameworks for the activation of lipase through H-bond and interfacial encapsulation. Chem Commun (Camb) 2016; 52:13768-13770. [DOI: 10.1039/c6cc08399d] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The encapsulation of lipase by dynamic polymers – dynamers – was used to activate enzymatic reactions.
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Affiliation(s)
- Yan Zhang
- Institut Européen des Membranes
- Adaptive Supramolecular Nanosystems Group
- F-34095 Montpellier
- France
| | - Wei-Xu Feng
- Lehn Institute of Functional Materials
- School of Chemistry and Chemical Engineering
- Sun Yat-Sen University
- Guangzhou 510275
- China
| | - Yves-Marie Legrand
- Institut Européen des Membranes
- Adaptive Supramolecular Nanosystems Group
- F-34095 Montpellier
- France
| | - Claudiu T. Supuran
- Università degli Studi di Firenze
- Neurofarba Department
- Sezione di Scienze Farmaceutiche
- 50019 Sesto Fiorentino
- Italy
| | - Cheng-Yong Su
- Lehn Institute of Functional Materials
- School of Chemistry and Chemical Engineering
- Sun Yat-Sen University
- Guangzhou 510275
- China
| | - Mihail Barboiu
- Institut Européen des Membranes
- Adaptive Supramolecular Nanosystems Group
- F-34095 Montpellier
- France
- Lehn Institute of Functional Materials
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19
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Zhang Y, Legrand YM, Petit E, Supuran CT, Barboiu M. Dynamic encapsulation and activation of carbonic anhydrase in multivalent dynameric host matrices. Chem Commun (Camb) 2016; 52:4053-5. [DOI: 10.1039/c6cc00796a] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The encapsulation of carbonic anhydrase by reversible dynamic polymers–dynamers was used to activate enzymatic reactions.
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Affiliation(s)
- Yan Zhang
- Institut Européen des Membranes
- Adaptive Supramolecular Nanosystems Group
- F-34095 Montpellier
- France
| | - Yves-Marie Legrand
- Institut Européen des Membranes
- Adaptive Supramolecular Nanosystems Group
- F-34095 Montpellier
- France
| | - Eddy Petit
- Institut Européen des Membranes
- Adaptive Supramolecular Nanosystems Group
- F-34095 Montpellier
- France
| | - Claudiu T. Supuran
- Università degli Studi di Firenze
- Polo Scientifico
- Laboratorio di Chimica Bio-inorganica
- 50019 Sesto Fiorentino
- Italy
| | - Mihail Barboiu
- Institut Européen des Membranes
- Adaptive Supramolecular Nanosystems Group
- F-34095 Montpellier
- France
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20
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Liu J, Yang Q, Li C. Towards efficient chemical synthesis via engineering enzyme catalysis in biomimetic nanoreactors. Chem Commun (Camb) 2015. [PMID: 26208044 DOI: 10.1039/c5cc04590h] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Biocatalysis with immobilized enzymes as catalysts holds enormous promise in developing more efficient and sustainable processes for the synthesis of fine chemicals, chiral pharmaceuticals and biomass feedstocks. Despite the appealing potentials, nowadays the industrial-scale application of biocatalysts is still quite modest in comparison with that of traditional chemical catalysts. A critical issue is that the catalytic performance of enzymes, the sophisticated and vulnerable catalytic machineries, strongly depends on their intracellular working environment; however the working circumstances provided by the support matrix are radically different from those in cells. This often leads to various adverse consequences on enzyme conformation and dynamic properties, consequently decreasing the overall performance of immobilized enzymes with regard to their activity, selectivity and stability. Engineering enzyme catalysis in support nanopores by mimicking the physiological milieu of enzymes in vivo and investigating how the interior microenvironment of nanopores imposes an influence on enzyme behaviors in vitro are of paramount significance to modify and improve the catalytic functions of immobilized enzymes. In this feature article, we have summarized the recent advances in mimicking the working environment and working patterns of intracellular enzymes in nanopores of mesoporous silica-based supports. Especially, we have demonstrated that incorporation of polymers into silica nanopores could be a valuable approach to create the biomimetic microenvironment for enzymes in the immobilized state.
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Affiliation(s)
- Jia Liu
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
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Wu E, Coppens MO, Garde S. Role of arginine in mediating protein-carbon nanotube interactions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:1683-1692. [PMID: 25575129 DOI: 10.1021/la5043553] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Arginine-rich proteins (e.g., lysozyme) or poly-L-arginine peptides have been suggested as solvating and dispersing agents for single-wall carbon nanotubes (CNTs) in water. In addition, protein structure-function in porous and hydrophobic materials is of broad interest. The amino acid residue, arginine (Arg(+)), has been implicated as an important mediator of protein/peptide-CNT interactions. To understand the structural and thermodynamic aspects of this interaction at the molecular level, we employ molecular dynamics (MD) simulations of the protein lysozyme in the interior of a CNT, as well as of free solutions of Arg(+) in the presence of a CNT. To dissect the Arg(+)-CNT interaction further, we also perform simulations of aqueous solutions of the guanidinium ion (Gdm(+)) and the norvaline (Nva) residue in the presence of a CNT. We show that the interactions of lysozyme with the CNT are mediated by the surface Arg(+) residues. The strong interaction of Arg(+) residue with the CNT is primarily driven by the favorable interactions of the Gdm(+) group with the CNT wall. The Gdm(+) group is not as well-hydrated on its flat sides, which binds to the CNT wall. This is consistent with a similar binding of Gdm(+) ions to a hydrophobic polymer. In contrast, the Nva residue, which lacks the Gdm(+) group, binds to the CNT weakly. We present details of the free energy of binding, molecular structure, and dynamics of these solutes on the CNT surface. Our results highlight the important role of Arg(+) residues in protein-CNT or protein-carbon-based material interactions. Such interactions could be manipulated precisely through protein engineering, thereby offering control over protein orientation and structure on CNTs, graphene, or other hydrophobic interfaces.
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Affiliation(s)
- Eugene Wu
- Howard P. Isermann Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
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Grimaldi J, Radhakrishna M, Kumar SK, Belfort G. Stability of proteins on hydrophilic surfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:1005-1010. [PMID: 25533285 DOI: 10.1021/la503865b] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The physical and chemical properties of solid substrates or surfaces critically influence the stability and activity of immobilized proteins such as enzymes. Reports of increased stability and activity of enzymes near/on surfaces as compared with those in solution abound; however, a mechanistic understanding is wanting. Simulations and experiments are used here to provide details toward such a mechanistic understanding. Experiments demonstrate increased activity of alcohol dehydrogenase (ADH) inside moderate hydrophilic mesopourous silica (SBA-15) pores but drastically decreased activity inside very hydrophilic NH2-SBA-15 surfaces as compared with that in solution. Also, the temperature stability of ADH was increased over that in solution when immobilized in a cavity with a mildly hydrophilic surface. Simulations confirm these experimental findings. Simulations calculated in the framework of a hydrophobic-polar (H-P) lattice model show increased thermal stability of a model 64-mer peptide on positive and zero curvature surfaces over that in solution. Peptides immobilized inside negative curvature cavities (concave) with hydrophilic surfaces exhibit increased stability only inside pores that are only 3-4 nm larger than the hydrodynamic radius of the peptide. Peptides are destabilized, however, when the surface hydrophilic character inside very small cavities/pores becomes large.
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Affiliation(s)
- Joseph Grimaldi
- Howard P. Isermann Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute , Troy, New York 12180-3590, United States
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Yoshimoto M, Kozono R, Tsubomura N. Liposomes as chaperone mimics with controllable affinity toward heat-denatured formate dehydrogenase from Candida boidinii. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:762-770. [PMID: 25513889 DOI: 10.1021/la504126b] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Chaperone machinery in living systems can catch denatured enzymes and induce their reactivation. Chaperone mimics are beneficial for applying enzymatic reactions in vitro. In this work, the affinity between liposomes and thermally denatured enzymes was controlled to stabilize the enzyme activity. The model enzyme is formate dehydrogenase from Candida boidinii (CbFDH) which is a homodimer and negatively charged in the phosphate buffer solution (pH 7.2) used. The activity of free CbFDH readily decreased at 58 °C following the first-order kinetics with the half-life t1/2 of 27 min. The turbidity measurements showed that the denatured enzyme molecules formed aggregates. The liposomes composed of zwitterionic phosphatidylcholines (PCs) stabilized the CbFDH activity at 58 °C, as revealed with six different PCs. The PC liposomes were indicated to bind to the aggregate-prone enzyme molecules, allowing reactivation at 25 °C. The cofactor β-reduced nicotinamide adenine dinucleotide (NADH) also stabilized the enzyme activity. The affinity between liposomes and denatured CbFDH could be modulated by incorporating cationic 1,2-dioleoyloxy-3-trimethylammonium propane chloride (DOTAP) in PC membranes. The t1/2 values significantly increased in the presence of liposomes ([lipid] = 1.5 mM) composed of PC and DOTAP at the mole fraction f(D) of 0.1. On the other hand, the DOTAP-rich liposomes (f(D) ≥ 0.7) showed strong affinity toward denatured CbFDH, accelerating its deactivation. The liposomes with low charge density function as chaperone mimics that can efficiently catch the denatured enzymes without interfering with their intramolecular interaction for reactivation.
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Affiliation(s)
- Makoto Yoshimoto
- Department of Applied Molecular Bioscience, Yamaguchi University , 2-16-1 Tokiwadai, Ube 755-8611, Japan
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Kuznetsova IM, Zaslavsky BY, Breydo L, Turoverov KK, Uversky VN. Beyond the excluded volume effects: mechanistic complexity of the crowded milieu. Molecules 2015; 20:1377-409. [PMID: 25594347 PMCID: PMC6272634 DOI: 10.3390/molecules20011377] [Citation(s) in RCA: 135] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 01/09/2015] [Indexed: 11/16/2022] Open
Abstract
Macromolecular crowding is known to affect protein folding, binding of small molecules, interaction with nucleic acids, enzymatic activity, protein-protein interactions, and protein aggregation. Although for a long time it was believed that the major mechanism of the action of crowded environments on structure, folding, thermodynamics, and function of a protein can be described in terms of the excluded volume effects, it is getting clear now that other factors originating from the presence of high concentrations of “inert” macromolecules in crowded solution should definitely be taken into account to draw a more complete picture of a protein in a crowded milieu. This review shows that in addition to the excluded volume effects important players of the crowded environments are viscosity, perturbed diffusion, direct physical interactions between the crowding agents and proteins, soft interactions, and, most importantly, the effects of crowders on solvent properties.
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Affiliation(s)
- Irina M. Kuznetsova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Ave., St. Petersburg 194064, Russia; E-Mails: (I.M.K.); (K.K.T.)
- St. Petersburg State Polytechnical University, 29 Polytechnicheskaya st., St. Petersburg 195251, Russia
| | - Boris Y. Zaslavsky
- Cleveland Diagnostics, 3615 Superior Ave., Suite 4407B, Cleveland, OH 44114, USA; E-Mail:
| | - Leonid Breydo
- Department of Molecular Medicine and USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd. MDC07, Tampa, FL 33612, USA; E-Mails:
| | - Konstantin K. Turoverov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Ave., St. Petersburg 194064, Russia; E-Mails: (I.M.K.); (K.K.T.)
- St. Petersburg State Polytechnical University, 29 Polytechnicheskaya st., St. Petersburg 195251, Russia
| | - Vladimir N. Uversky
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Ave., St. Petersburg 194064, Russia; E-Mails: (I.M.K.); (K.K.T.)
- Department of Molecular Medicine and USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd. MDC07, Tampa, FL 33612, USA; E-Mails:
- Biology Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-813-974-5816; Fax: +1-813-974-7357
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Siefker J, Karande P, Coppens MO. Packaging biological cargoes in mesoporous materials: opportunities for drug delivery. Expert Opin Drug Deliv 2014; 11:1781-93. [PMID: 25016923 PMCID: PMC4245185 DOI: 10.1517/17425247.2014.938636] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
INTRODUCTION Confinement of biomolecules in structured nanoporous materials offers several desirable features ranging from chemical and thermal stability, to resistance to degradation from the external environment. A new generation of mesoporous materials presents exciting new possibilities for the formulation and controlled release of biological agents. Such materials address niche applications in enteral and parenteral delivery of biologics, such as peptides, polypeptides, enzymes and proteins for use as therapeutics, imaging agents, biosensors, and adjuvants. AREAS COVERED Mesoporous silica Santa Barbara Amorphous-15 (SBA-15), with its unique, tunable pore diameter, and easily functionalized surface, provides a representative example of this new generation of materials. Here, we review recent advances in the design and synthesis of nanostructured mesoporous materials, focusing on SBA-15, and highlight opportunities for the delivery of biological agents to various organ and tissue compartments. EXPERT OPINION The SBA-15 platform provides a delivery carrier that is inherently separated from the active biologic due to distinct intra and extra-particle environments. This permits the SBA-15 platform to not require direct modification of the active biological therapeutic. Additionally, this makes the platform universal and allows for its application independent of the desired methods of discovery and development. The SBA-15 platform also directly addresses issues of targeted delivery and controlled release, although future challenges in the implementation of this platform reside in particle design, biocompatibility, and the tunability of the internal and external material properties. Examples illustrating the flexibility in the application of the SBA-15 platform are also discussed.
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Affiliation(s)
- Justin Siefker
- University College London, Department of Chemical Engineering and EPSRC Frontier Engineering Centre for Nature Inspired Engineering,
Torrington Place, London, WC1E 7JE, UK
| | - Pankaj Karande
- Rensselaer Polytechnic Institute, Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies,
110 Eighth Street, Troy, NY 12180, USA+1 518 276 4459;
| | - Marc-Olivier Coppens
- University College London, Department of Chemical Engineering and EPSRC Frontier Engineering Centre for Nature Inspired Engineering,
Torrington Place, London, WC1E 7JE, UK+44 20 7679 7369; +44 20 7383 2348;
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Radhakrishna M, Kumar SK. Surface-mediated protein disaggregation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:3507-3512. [PMID: 24588096 DOI: 10.1021/la5000155] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Preventing protein aggregation is of both biological and industrial importance. Interprotein interactions between the hydrophobic residues of the protein are known to be the major driving force for protein aggregation. In this article, we show how surface chemistry and curvature can be tuned to mitigate these interprotein interactions. Our results calculated in the framework of the Hydrophobic-Polar (HP) lattice model show that interprotein interactions can be drastically reduced by increasing the surface hydrophobicity to a critical value corresponding to the adsorption transition of the protein. At this value of surface hydrophobicity, proteins lose interprotein contacts to gain surface contacts, and thus the surface helps to reduce the interprotein interactions. Furthermore, we show that the adsorption of the proteins inside hydrophobic pores of optimal sizes are most efficient at both reducing interprotein contacts and simultaneously retaining most of the native contacts probably as a result of confinement-induced stabilization.
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Affiliation(s)
- Mithun Radhakrishna
- Department of Chemical Engineering, Columbia University , New York, New York 10027, United States
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