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Emperador A. Accurate Description of Protein-Protein Recognition and Protein Aggregation with the Implicit-Solvent-Based PACSAB Protein Model. Polymers (Basel) 2021; 13:polym13234172. [PMID: 34883675 PMCID: PMC8659885 DOI: 10.3390/polym13234172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/12/2021] [Accepted: 11/18/2021] [Indexed: 02/01/2023] Open
Abstract
We used the PACSAB protein model, based on the implicit solvation approach, to simulate protein–protein recognition and study the effect of helical structure on the association of aggregating peptides. After optimization, the PACSAB force field was able to reproduce correctly both the correct binding interface in ubiquitin dimerization and the conformational ensemble of the disordered protein activator for hormone and retinoid receptor (ACTR). The PACSAB model allowed us to predict the native binding of ACTR with its binding partner, reproducing the refolding upon binding mechanism of the disordered protein.
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Affiliation(s)
- Agustí Emperador
- Department of Physics, Universitat Politècnica de Catalunya, B4-B5 Campus Nord, Jordi Girona 1-3, 08034 Barcelona, Spain
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Linker Dependence of Avidity in Multivalent Interactions Between Disordered Proteins. J Mol Biol 2019; 431:4784-4795. [DOI: 10.1016/j.jmb.2019.09.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 08/13/2019] [Accepted: 09/04/2019] [Indexed: 11/21/2022]
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Hadži S, Mernik A, Podlipnik Č, Loris R, Lah J. The Thermodynamic Basis of the Fuzzy Interaction of an Intrinsically Disordered Protein. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201707853] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- San Hadži
- Faculty of Chemistry and Chemical Technology; University of Ljubljana; Večna pot 113 Ljubljana Slovenia
| | - Andrej Mernik
- Faculty of Chemistry and Chemical Technology; University of Ljubljana; Večna pot 113 Ljubljana Slovenia
| | - Črtomir Podlipnik
- Faculty of Chemistry and Chemical Technology; University of Ljubljana; Večna pot 113 Ljubljana Slovenia
| | - Remy Loris
- Structural Biology Brussels; Department of Biotechnology; Vrije Universiteit Brussel and Center for Structural Biology; Vlaams Instituut voor Biotechnologie; Pleinlaan 2 1050 Brussel Belgium
| | - Jurij Lah
- Faculty of Chemistry and Chemical Technology; University of Ljubljana; Večna pot 113 Ljubljana Slovenia
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Hadži S, Mernik A, Podlipnik Č, Loris R, Lah J. The Thermodynamic Basis of the Fuzzy Interaction of an Intrinsically Disordered Protein. Angew Chem Int Ed Engl 2017; 56:14494-14497. [DOI: 10.1002/anie.201707853] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Indexed: 12/22/2022]
Affiliation(s)
- San Hadži
- Faculty of Chemistry and Chemical Technology; University of Ljubljana; Večna pot 113 Ljubljana Slovenia
| | - Andrej Mernik
- Faculty of Chemistry and Chemical Technology; University of Ljubljana; Večna pot 113 Ljubljana Slovenia
| | - Črtomir Podlipnik
- Faculty of Chemistry and Chemical Technology; University of Ljubljana; Večna pot 113 Ljubljana Slovenia
| | - Remy Loris
- Structural Biology Brussels; Department of Biotechnology; Vrije Universiteit Brussel and Center for Structural Biology; Vlaams Instituut voor Biotechnologie; Pleinlaan 2 1050 Brussel Belgium
| | - Jurij Lah
- Faculty of Chemistry and Chemical Technology; University of Ljubljana; Večna pot 113 Ljubljana Slovenia
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Kim D, Lee C, Lee S, Kim K, Han JJ, Cha E, Lim J, Cho Y, Hong S, Han K. The Mechanism of p53 Rescue by SUSP4. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201607819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Do‐Hyoung Kim
- Genome Editing Research Center Korea Research Institute of Bioscience and Biotechnology 125, Gwahak-ro, Yuseong-gu Daejeon 34141 Korea
| | - Chewook Lee
- Genome Editing Research Center Korea Research Institute of Bioscience and Biotechnology 125, Gwahak-ro, Yuseong-gu Daejeon 34141 Korea
| | - Si‐Hyung Lee
- Genome Editing Research Center Korea Research Institute of Bioscience and Biotechnology 125, Gwahak-ro, Yuseong-gu Daejeon 34141 Korea
| | - Kyung‐Tae Kim
- Molecular Epidemology Branch Research Institute National Cancer Center 323 Ilsandong-gu, Goyang-si Gyeonggi-do 10408 Korea
| | - Joan J. Han
- Genome Editing Research Center Korea Research Institute of Bioscience and Biotechnology 125, Gwahak-ro, Yuseong-gu Daejeon 34141 Korea
- College of Human Medicine Michigan State University East Lansing MI 48824 USA
| | - Eun‐Ji Cha
- Genome Editing Research Center Korea Research Institute of Bioscience and Biotechnology 125, Gwahak-ro, Yuseong-gu Daejeon 34141 Korea
| | - Ji‐Eun Lim
- Genome Editing Research Center Korea Research Institute of Bioscience and Biotechnology 125, Gwahak-ro, Yuseong-gu Daejeon 34141 Korea
| | - Ye‐Jin Cho
- Genome Editing Research Center Korea Research Institute of Bioscience and Biotechnology 125, Gwahak-ro, Yuseong-gu Daejeon 34141 Korea
- Department of Bioinformatics University of Science and Technology 217, Gajeong-ro, Yuseong-gu Daejoen 34113 Korea
| | - Seung‐Hee Hong
- Division of Food Science and Culinary Art, Food and Nutrition Major Shinhan University 95 Hoam-ro, Uijeongbu-si Gyeonggi-do 11644 Korea
| | - Kyou‐Hoon Han
- Genome Editing Research Center Korea Research Institute of Bioscience and Biotechnology 125, Gwahak-ro, Yuseong-gu Daejeon 34141 Korea
- Department of Bioinformatics University of Science and Technology 217, Gajeong-ro, Yuseong-gu Daejoen 34113 Korea
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Kim D, Lee C, Lee S, Kim K, Han JJ, Cha E, Lim J, Cho Y, Hong S, Han K. The Mechanism of p53 Rescue by SUSP4. Angew Chem Int Ed Engl 2016; 56:1278-1282. [DOI: 10.1002/anie.201607819] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 09/25/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Do‐Hyoung Kim
- Genome Editing Research Center Korea Research Institute of Bioscience and Biotechnology 125, Gwahak-ro, Yuseong-gu Daejeon 34141 Korea
| | - Chewook Lee
- Genome Editing Research Center Korea Research Institute of Bioscience and Biotechnology 125, Gwahak-ro, Yuseong-gu Daejeon 34141 Korea
| | - Si‐Hyung Lee
- Genome Editing Research Center Korea Research Institute of Bioscience and Biotechnology 125, Gwahak-ro, Yuseong-gu Daejeon 34141 Korea
| | - Kyung‐Tae Kim
- Molecular Epidemology Branch Research Institute National Cancer Center 323 Ilsandong-gu, Goyang-si Gyeonggi-do 10408 Korea
| | - Joan J. Han
- Genome Editing Research Center Korea Research Institute of Bioscience and Biotechnology 125, Gwahak-ro, Yuseong-gu Daejeon 34141 Korea
- College of Human Medicine Michigan State University East Lansing MI 48824 USA
| | - Eun‐Ji Cha
- Genome Editing Research Center Korea Research Institute of Bioscience and Biotechnology 125, Gwahak-ro, Yuseong-gu Daejeon 34141 Korea
| | - Ji‐Eun Lim
- Genome Editing Research Center Korea Research Institute of Bioscience and Biotechnology 125, Gwahak-ro, Yuseong-gu Daejeon 34141 Korea
| | - Ye‐Jin Cho
- Genome Editing Research Center Korea Research Institute of Bioscience and Biotechnology 125, Gwahak-ro, Yuseong-gu Daejeon 34141 Korea
- Department of Bioinformatics University of Science and Technology 217, Gajeong-ro, Yuseong-gu Daejoen 34113 Korea
| | - Seung‐Hee Hong
- Division of Food Science and Culinary Art, Food and Nutrition Major Shinhan University 95 Hoam-ro, Uijeongbu-si Gyeonggi-do 11644 Korea
| | - Kyou‐Hoon Han
- Genome Editing Research Center Korea Research Institute of Bioscience and Biotechnology 125, Gwahak-ro, Yuseong-gu Daejeon 34141 Korea
- Department of Bioinformatics University of Science and Technology 217, Gajeong-ro, Yuseong-gu Daejoen 34113 Korea
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Medina SH, Miller SE, Keim AI, Gorka AP, Schnermann MJ, Schneider JP. An Intrinsically Disordered Peptide Facilitates Non-Endosomal Cell Entry. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201510518] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Scott H. Medina
- Chemical Biology Laboratory; National Cancer Institute; National Institutes of Health Fort Detrick; 376 Boyle Street Frederick MD 21702-1201 USA
| | - Stephen E. Miller
- Chemical Biology Laboratory; National Cancer Institute; National Institutes of Health Fort Detrick; 376 Boyle Street Frederick MD 21702-1201 USA
| | - Allison I. Keim
- Chemical Biology Laboratory; National Cancer Institute; National Institutes of Health Fort Detrick; 376 Boyle Street Frederick MD 21702-1201 USA
| | - Alexander P. Gorka
- Chemical Biology Laboratory; National Cancer Institute; National Institutes of Health Fort Detrick; 376 Boyle Street Frederick MD 21702-1201 USA
| | - Martin J. Schnermann
- Chemical Biology Laboratory; National Cancer Institute; National Institutes of Health Fort Detrick; 376 Boyle Street Frederick MD 21702-1201 USA
| | - Joel P. Schneider
- Chemical Biology Laboratory; National Cancer Institute; National Institutes of Health Fort Detrick; 376 Boyle Street Frederick MD 21702-1201 USA
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Medina SH, Miller SE, Keim AI, Gorka AP, Schnermann MJ, Schneider JP. An Intrinsically Disordered Peptide Facilitates Non-Endosomal Cell Entry. Angew Chem Int Ed Engl 2016; 55:3369-72. [PMID: 26835878 DOI: 10.1002/anie.201510518] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 12/14/2015] [Indexed: 01/03/2023]
Abstract
Many cell-penetrating peptides (CPPs) fold at cell surfaces, adopting α- or β-structure that enable their intracellular transport. However, the same structural folds that facilitate cellular entry can also elicit potent membrane-lytic activity, limiting their use in delivery applications. Further, a distinct CPP can enter cells through many mechanisms, often leading to endosomal entrapment. Herein, we describe an intrinsically disordered peptide (CLIP6) that exclusively employs non-endosomal mechanisms to cross cellular membranes, while being remarkably biocompatible and serum-stable. We show that a single anionic glutamate residue is responsible for maintaining the disordered bioactive state of the peptide, defines its mechanism of cellular entry, and is central to its biocompatibility. CLIP6 can deliver membrane-impermeable cargo directly to the cytoplasm of cells, suggesting its broad utility for delivery of drug candidates limited by poor cell permeability and endosomal degradation.
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Affiliation(s)
- Scott H Medina
- Chemical Biology Laboratory, National Cancer Institute, National Institutes of Health Fort Detrick, 376 Boyle Street, Frederick, MD, 21702-1201, USA
| | - Stephen E Miller
- Chemical Biology Laboratory, National Cancer Institute, National Institutes of Health Fort Detrick, 376 Boyle Street, Frederick, MD, 21702-1201, USA
| | - Allison I Keim
- Chemical Biology Laboratory, National Cancer Institute, National Institutes of Health Fort Detrick, 376 Boyle Street, Frederick, MD, 21702-1201, USA
| | - Alexander P Gorka
- Chemical Biology Laboratory, National Cancer Institute, National Institutes of Health Fort Detrick, 376 Boyle Street, Frederick, MD, 21702-1201, USA
| | - Martin J Schnermann
- Chemical Biology Laboratory, National Cancer Institute, National Institutes of Health Fort Detrick, 376 Boyle Street, Frederick, MD, 21702-1201, USA
| | - Joel P Schneider
- Chemical Biology Laboratory, National Cancer Institute, National Institutes of Health Fort Detrick, 376 Boyle Street, Frederick, MD, 21702-1201, USA.
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