1
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Hymel HC, Anderson JC, Liu D, Gauthier TJ, Melvin AT. Incorporating a β-hairpin sequence motif to increase intracellular stability of a peptide-based PROTAC. Biochem Eng J 2023; 199:109063. [PMID: 37637833 PMCID: PMC10455042 DOI: 10.1016/j.bej.2023.109063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2023]
Abstract
Proteolysis targeting chimeras (PROTACs) have emerged as a new class of therapeutics that utilize the ubiquitin-proteasome system (UPS) to facilitate proteasomal degradation of "undruggable" targets. Peptide-based PROTACs contain three essential components: a binding motif for the target protein, a short amino acid sequence recognized by an E3 ligase called a degron, and a cell penetrating peptide to facilitate uptake into intact cells. While peptide-based PROTACs have been shown to successfully degrade numerous targets, they have often been found to exhibit low cell permeability and high protease susceptibility. Prior work identified peptides containing a β-hairpin sequence motif that function not only as protecting elements, but also as CPPs and degrons. The goal of this study was to investigate if a β-hairpin sequence could replace commonly used unstructured peptides sequences as the degron and the CPP needed for PROTAC uptake and function. The degradation of the protein Tau was selected as a model system as several published works have identified a Tau binding element that could easily be conjugated to the β-hairpin sequence. A series of time- and concentration-dependent studies confirmed that the βhairpin sequence was an adequate alternative CPP and degron to facilitate the proteasomemediated degradation of Tau. Microscopy studies confirmed the time-dependent uptake of the PROTAC and a degradation assay confirmed that the β-hairpin conjugated PROTAC had a greater lifetime in cells.
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Affiliation(s)
- Hannah C Hymel
- Cain Department of Chemical Engineering, Louisiana State University, Baton Rouge, LA, 70803
| | - Jeffery C Anderson
- Cain Department of Chemical Engineering, Louisiana State University, Baton Rouge, LA, 70803
| | - Dong Liu
- LSU AgCenter Biotechnology Lab, Louisiana State University, Baton Rouge, LA 70803
| | - Ted J Gauthier
- LSU AgCenter Biotechnology Lab, Louisiana State University, Baton Rouge, LA 70803
| | - Adam T Melvin
- Cain Department of Chemical Engineering, Louisiana State University, Baton Rouge, LA, 70803
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2
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Rahnama A, Melvin AT. Fluorometric Characterization of DUB Activity: From Single-Enzyme Reactions to Live Intact Cells. Methods Mol Biol 2023; 2591:25-44. [PMID: 36350541 DOI: 10.1007/978-1-0716-2803-4_3] [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] [Indexed: 06/16/2023]
Abstract
Fluorescently tagged molecular probes capable of time- and concentration-dependent quantification of deubiquitinating enzyme (DUB) activity allow for precise characterization of both enzyme and DUB inhibitor. These probes are compatible with most plate readers allowing for rapid, facile fluorometric analysis of DUB activity. DUB activity can be measured in purified enzyme reactions, in cell lysates, or in intact cells depending upon the choice of the fluorometric probe. This chapter describes protocols and potential analysis tools to investigate DUB activity in these three scenarios.
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Affiliation(s)
- Alireza Rahnama
- Cain Department of Chemical Engineering, Louisiana State University, Baton Rouge, LA, USA
| | - Adam T Melvin
- Cain Department of Chemical Engineering, Louisiana State University, Baton Rouge, LA, USA.
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3
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Hymel HC, Rahnama A, Sanchez OM, Liu D, Gauthier TJ, Melvin AT. How Cargo Identity Alters the Uptake of Cell-Penetrating Peptide (CPP)/Cargo Complexes: A Study on the Effect of Net Cargo Charge and Length. Cells 2022; 11:cells11071195. [PMID: 35406759 PMCID: PMC8997848 DOI: 10.3390/cells11071195] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 03/25/2022] [Accepted: 03/30/2022] [Indexed: 01/27/2023] Open
Abstract
Cell-penetrating peptides (CPPs) have emerged as a powerful tool for the delivery of otherwise impermeable cargoes into intact cells. Recent efforts to improve the delivery capability of peptides have mainly focused on the identity of the CPP; however, there is evidence that the identity of the cargo itself affects the uptake. The goal of this work was to investigate how the characteristics of a peptide cargo, including net charge and length, either enhance or diminish the internalization efficiency of the CPP/cargo complex. A small library of CPP/cargo complexes were synthesized consisting of structured and unstructured CPPs with cargoes of net positive, negative, or neutral charge and lengths of 4 or 8 amino acids. Cargoes with a net positive charge were found to enhance the overall uptake of the complexes while net neutral and negatively charged cargoes diminished uptake. Conversely, the net length of the cargo had no significant effect on uptake of the CPP/cargo complexes. Microcopy images confirmed the increased uptake of the positively charged cargoes; however, an increase in punctate regions with the addition of a cargo was also observed. The effects of the net positively charged cargoes were confirmed with both structured and unstructured CPPs, which demonstrated similar trends of an increase in uptake with the addition of positively charged residues. These findings demonstrate that the net charge of cargoes impacts the uptake of the complex, which can be considered in the future when designing peptide-based reporters or therapeutics.
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Affiliation(s)
- Hannah C. Hymel
- Cain Department of Chemical Engineering, Louisiana State University, Baton Rouge, LA 70803, USA; (H.C.H.); (A.R.); (O.M.S.)
| | - Alireza Rahnama
- Cain Department of Chemical Engineering, Louisiana State University, Baton Rouge, LA 70803, USA; (H.C.H.); (A.R.); (O.M.S.)
| | - Olivia M. Sanchez
- Cain Department of Chemical Engineering, Louisiana State University, Baton Rouge, LA 70803, USA; (H.C.H.); (A.R.); (O.M.S.)
| | - Dong Liu
- LSU AgCenter Biotechnology Laboratory, Louisiana State University, Baton Rouge, LA 70803, USA; (D.L.); (T.J.G.)
| | - Ted J. Gauthier
- LSU AgCenter Biotechnology Laboratory, Louisiana State University, Baton Rouge, LA 70803, USA; (D.L.); (T.J.G.)
| | - Adam T. Melvin
- Cain Department of Chemical Engineering, Louisiana State University, Baton Rouge, LA 70803, USA; (H.C.H.); (A.R.); (O.M.S.)
- Correspondence:
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4
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Pace JR, Lampkin BJ, Abakah C, Moyer A, Miao J, Deprey K, Cerulli RA, Lin YS, Baleja JD, Baker D, Kritzer JA. Stapled β-Hairpins Featuring 4-Mercaptoproline. J Am Chem Soc 2021; 143:15039-15044. [PMID: 34516087 DOI: 10.1021/jacs.1c04378] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Peptides constrained by intramolecular cross-links, especially stapled α-helices, have emerged as versatile scaffolds for drug development. However, there are fewer examples of similarly constrained scaffolds for other secondary structures. Here, we used a novel computational strategy to identify an optimal staple for antiparallel β-strands, and then we incorporated that staple within a β-hairpin peptide. The hairpin uses 4-mercaptoproline as a novel staple component, which contributes to a unique, kinked structure. The stapled hairpins show a high degree of structure in aqueous solution, excellent resistance to degradation in cell lysates, and cytosolic penetration at micromolar concentrations. They also overlay with a unique subset of kinked hairpin motifs at protein-protein interaction interfaces. Thus, these scaffolds represent promising starting points for developing inhibitors of cellular protein-protein interactions.
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Affiliation(s)
- Jennifer R Pace
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Bryan J Lampkin
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Charles Abakah
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Adam Moyer
- Molecular Engineering and Sciences Institute, University of Washington, Seattle Washington 98195, United States
| | - Jiayuan Miao
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Kirsten Deprey
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Robert A Cerulli
- Graduate School of Biomedical Sciences, Tufts University, Boston, Massachusetts 02111, United States
| | - Yu-Shan Lin
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - James D Baleja
- Graduate School of Biomedical Sciences, Tufts University, Boston, Massachusetts 02111, United States
| | - David Baker
- Molecular Engineering and Sciences Institute, University of Washington, Seattle Washington 98195, United States.,Department of Biochemistry, Institute for Protein Design, and Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, United States
| | - Joshua A Kritzer
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
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5
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Wen J, Liao H, Stachowski K, Hempfling JP, Qian Z, Yuan C, Foster MP, Pei D. Rational design of cell-permeable cyclic peptides containing a d-Pro-l-Pro motif. Bioorg Med Chem 2020; 28:115711. [PMID: 33069067 DOI: 10.1016/j.bmc.2020.115711] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 08/12/2020] [Accepted: 08/12/2020] [Indexed: 12/01/2022]
Abstract
Cyclic peptides are capable of binding to challenging targets (e.g., proteins involved in protein-protein interactions) with high affinity and specificity, but generally cannot gain access to intracellular targets because of poor membrane permeability. In this work, we discovered a conformationally constrained cyclic cell-penetrating peptide (CPP) containing a d-Pro-l-Pro motif, cyclo(AFΦrpPRRFQ) (where Φ is l-naphthylalanine, r is d-arginine, and p is d-proline). The structural constraints provided by cyclization and the d-Pro-l-Pro motif permitted the rational design of cell-permeable cyclic peptides of large ring sizes (up to 16 amino acids). This strategy was applied to design a potent, cell-permeable, and biologically active cyclic peptidyl inhibitor, cyclo(YpVNFΦrpPRR) (where Yp is l-phosphotyrosine), against the Grb2 SH2 domain. Multidimensional NMR spectroscopic and circular dichroism analyses revealed that the cyclic CPP as well as the Grb2 SH2 inhibitor assume a predominantly random coil structure but have significant β-hairpin character surrounding the d-Pro-l-Pro motif. These results demonstrate cyclo(AFΦrpPRRFQ) as an effective CPP for endocyclic (insertion of cargo into the CPP ring) or exocyclic delivery of biological cargos (attachment of cargo to the Gln side chain).
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Affiliation(s)
- Jin Wen
- Department of Chemistry and Biochemistry and Ohio State Biochemistry Program, The Ohio State University, 484 West 12(th) Avenue, Columbus, OH 43210, USA
| | - Hui Liao
- Department of Chemistry and Biochemistry and Ohio State Biochemistry Program, The Ohio State University, 484 West 12(th) Avenue, Columbus, OH 43210, USA
| | - Kye Stachowski
- Department of Chemistry and Biochemistry and Ohio State Biochemistry Program, The Ohio State University, 484 West 12(th) Avenue, Columbus, OH 43210, USA
| | - Jordan P Hempfling
- Department of Chemistry and Biochemistry and Ohio State Biochemistry Program, The Ohio State University, 484 West 12(th) Avenue, Columbus, OH 43210, USA
| | - Ziqing Qian
- Department of Chemistry and Biochemistry and Ohio State Biochemistry Program, The Ohio State University, 484 West 12(th) Avenue, Columbus, OH 43210, USA
| | - Chunhua Yuan
- Campus Chemical Instrument Center, The Ohio State University, 460 West 12(th) Avenue, Columbus, OH 43210, USA
| | - Mark P Foster
- Department of Chemistry and Biochemistry and Ohio State Biochemistry Program, The Ohio State University, 484 West 12(th) Avenue, Columbus, OH 43210, USA.
| | - Dehua Pei
- Department of Chemistry and Biochemistry and Ohio State Biochemistry Program, The Ohio State University, 484 West 12(th) Avenue, Columbus, OH 43210, USA.
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6
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Vaithiyanathan M, Hymel HC, Safa N, Sanchez OM, Pettigrew JH, Kirkpatrick CS, Gauthier TJ, Melvin AT. Kinetic analysis of cellular internalization and expulsion of unstructured D‐chirality cell penetrating peptides. AIChE J 2020. [DOI: 10.1002/aic.17087] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
| | - Hannah C. Hymel
- Cain Department of Chemical Engineering Louisiana State University Louisiana USA
| | - Nora Safa
- Cain Department of Chemical Engineering Louisiana State University Louisiana USA
| | - Olivia M. Sanchez
- Cain Department of Chemical Engineering Louisiana State University Louisiana USA
| | - Jacob H. Pettigrew
- Cain Department of Chemical Engineering Louisiana State University Louisiana USA
| | - Cole S. Kirkpatrick
- Cain Department of Chemical Engineering Louisiana State University Louisiana USA
| | - Ted J. Gauthier
- LSU AgCenter Biotechnology Lab Louisiana State University Louisiana USA
| | - Adam T. Melvin
- Cain Department of Chemical Engineering Louisiana State University Louisiana USA
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7
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Cho J, Park J, Kim EE, Song EJ. Assay Systems for Profiling Deubiquitinating Activity. Int J Mol Sci 2020; 21:E5638. [PMID: 32781716 PMCID: PMC7460613 DOI: 10.3390/ijms21165638] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 08/04/2020] [Accepted: 08/04/2020] [Indexed: 01/22/2023] Open
Abstract
Deubiquitinating enzymes regulate various cellular processes, particularly protein degradation, localization, and protein-protein interactions. The dysregulation of deubiquitinating enzyme (DUB) activity has been linked to several diseases; however, the function of many DUBs has not been identified. Therefore, the development of methods to assess DUB activity is important to identify novel DUBs, characterize DUB selectivity, and profile dynamic DUB substrates. Here, we review various methods of evaluating DUB activity using cell lysates or purified DUBs, as well as the types of probes used in these methods. In addition, we introduce some techniques that can deliver DUB probes into the cells and cell-permeable activity-based probes to directly visualize and quantify DUB activity in live cells. This review could contribute to the development of DUB inhibitors by providing important information on the characteristics and applications of various probes used to evaluate and detect DUB activity in vitro and in vivo.
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Affiliation(s)
- Jinhong Cho
- Biomedical Research Institute, Korea Institute of Science and Technology, Seoul 02792, Korea; (J.C.); (E.E.K.)
| | - Jinyoung Park
- Molecular Recognition Research Center, Korea Institute of Science and Technology, Seoul 02792, Korea;
| | - Eunice EunKyeong Kim
- Biomedical Research Institute, Korea Institute of Science and Technology, Seoul 02792, Korea; (J.C.); (E.E.K.)
| | - Eun Joo Song
- Graduate School of Pharmaceutical Sciences and College of Pharmacy, Ewha Womans University, Seoul 03760, Korea
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Miller SE, Schneider JP. The effect of turn residues on the folding and cell-penetrating activity of β-hairpin peptides and applications toward protein delivery. Pept Sci (Hoboken) 2020; 112:e24125. [PMID: 34504991 PMCID: PMC8425381 DOI: 10.1002/pep2.24125] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 05/25/2019] [Indexed: 11/11/2022]
Abstract
Cell-penetrating peptides (CPPs) are useful tools for the delivery of a wide variety of cargo into cells. Our lab has developed two classes of CPPs based on β-hairpin sequences, one that folds at the surface of cell membranes and the other that is intrinsically disordered. Although these peptides can effectively deliver different types of cargo, their use in protein delivery has been hindered due to the presence of non-natural D-proline within the central turn region of both sequences, which prohibits functionalizing proteins with the CPPs via standard expression protocols. In this work, we describe new CPPs that replace the non-natural turn region with natural turn motifs amenable to protein expression. We first investigate how these changes within the turn affect various CPP-related properties in the absence of protein cargo, and then generate protein fusions for intracellular delivery.
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Affiliation(s)
- Stephen E Miller
- Chemical Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, Maryland
| | - Joel P Schneider
- Chemical Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, Maryland
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9
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Safa N, Pettigrew JH, Gauthier TJ, Melvin AT. Direct measurement of deubiquitinating enzyme activity in intact cells using a protease-resistant, cell-permeable, peptide-based reporter. Biochem Eng J 2019; 151. [PMID: 32831622 DOI: 10.1016/j.bej.2019.107320] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Deubiquitinating enzymes (DUBs) regulate the removal of the polyubiquitin chain from proteins targeted for degradation. Current approaches to quantify DUB activity are limited to test tube-based assays that incorporate enzymes or cell lysates, but not intact cells. The goal of this work was to develop a novel peptide-based biosensor of DUB activity that is cell permeable, protease-resilient, fluorescent, and specific to DUBs. The biosensor consists of an N-terminal β-hairpin motif that acts as both a 'protectide' to increase intracellular stability and a cell penetrating peptide (CPP) to facilitate the uptake into intact cells. The β-hairpin was conjugated to a C-terminal substrate consisting of the last four amino acids in ubiquitin (LRGG) to facilitate DUB mediated cleavage of a C-terminal fluorophore (AFC). The kinetics of the peptide reporter were characterized in cell lysates by dose response and inhibition enzymology studies. Inhibition studies with an established DUB inhibitor (PR-619) confirmed the specificity of both reporters to DUBs. Fluorometry and fluorescent microscopy experiments followed by mathematical modeling established the capability of the biosensor to measure DUB activity in intact cells while maintaining cellular integrity. The novel reporter introduced here is compatible with high-throughput single cell analysis platforms such as FACS and droplet microfluidics facilitating direct quantification of DUB activity in single intact cells with direct application in point-of-care cancer diagnostics and drug discovery.
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Affiliation(s)
- Nora Safa
- Cain Department of Chemical Engineering, Louisiana State University, Baton Rouge, LA, 70803
| | - Jacob H Pettigrew
- Cain Department of Chemical Engineering, Louisiana State University, Baton Rouge, LA, 70803
| | - Ted J Gauthier
- LSU AgCenter Biotechnology Lab, Louisiana State University, Baton Rouge, LA, 70803
| | - Adam T Melvin
- Cain Department of Chemical Engineering, Louisiana State University, Baton Rouge, LA, 70803
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10
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Safa N, Vaithiyanathan M, Sombolestani S, Charles S, Melvin AT. Population-based analysis of cell-penetrating peptide uptake using a microfluidic droplet trapping array. Anal Bioanal Chem 2019; 411:2729-2741. [PMID: 30854596 PMCID: PMC6472966 DOI: 10.1007/s00216-019-01713-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 02/19/2019] [Accepted: 02/25/2019] [Indexed: 01/09/2023]
Abstract
Cell-penetrating peptides (CPPs) have garnered significant attention as a method to introduce reporters and therapeutics into intact cells. While numerous studies have been performed identifying new CPP sequences, relatively little is known about their uptake efficiency at the single-cell level. Here, a droplet microfluidic trapping array was used to characterize CPP uptake across a population of single intact cells. The microfluidic device allowed for facile and rapid isolation and analysis of single-cell fluorescence in a 787-member overhead trapping array with > 99% droplet trapping efficiency. The permeability efficiencies of four different CPPs were studied and compared in HeLa cells. Population analysis was performed using linkage hierarchical cluster analysis by R programming to bin cells into subpopulations expressing very low to very high peptide uptake efficiencies. CPP uptake was observed to be heterogeneous across the population of cells with peptide concentration and sequence both playing important roles in the diversity of CPP uptake, the overall peptide uptake efficiency, and the intracellular homogeneity of peptide distribution. This microfluidic-based analytical approach finds application in personalized medicine and provides new insight in the heterogeneity of CPP uptake which has the potential to affect both biosensor and drug internalization in intact cells. Graphical abstract .
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Affiliation(s)
- Nora Safa
- Cain Department of Chemical Engineering, Louisiana State University, Baton Rouge, LA, 70803, USA
| | | | - Shayan Sombolestani
- Craft and Hawkins Department of Petroleum Engineering, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Seleipiri Charles
- Cain Department of Chemical Engineering, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Adam T Melvin
- Cain Department of Chemical Engineering, Louisiana State University, Baton Rouge, LA, 70803, USA.
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