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Zhao J, Liu X, Blayney A, Zhang Y, Gandy L, Mirsky PO, Smith N, Zhang F, Linhardt RJ, Chen J, Baines C, Loh SN, Wang C. Intrinsically Disordered N-terminal Domain (NTD) of p53 Interacts with Mitochondrial PTP Regulator Cyclophilin D. J Mol Biol 2022; 434:167552. [PMID: 35341741 DOI: 10.1016/j.jmb.2022.167552] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 03/11/2022] [Accepted: 03/15/2022] [Indexed: 11/26/2022]
Abstract
Mitochondrial permeability transition pore (mPTP) plays crucial roles in cell death in a variety of diseases, including ischemia/reperfusion injury in heart attack and stroke, neurodegenerative conditions, and cancer. To date, cyclophilin D is the only confirmed component of mPTP. Under stress, p53 can translocate into mitochondria and interact with CypD, triggering necrosis and cell growth arrest. However, the molecular details of p53/CypD interaction are still poorly understood. Previously, several studies reported that p53 interacts with CypD through its DNA-binding domain (DBD). However, using surface plasmon resonance (SPR), we found that both NTD-DBD, NTD and NTD (1-70) bind to CypD at ∼μM KD. In solution NMR, NTD binds CypD with μM affinity and mimics the pattern of FLp53 binding in chemical shift perturbation. In contrast, neither solution NMR nor fluorescence anisotropy detected DBD binding to CypD. Thus, instead of DBD, NTD is the major CypD binding site on p53. NMR titration and MD simulation revealed that NTD binds CypD with broad and dynamic interfaces dominated by electrostatic interactions. NTD 20-70 was further identified as the minimal binding region for CypD interaction, and two NTD fragments, D1 (residues 22-44) and D2 (58-70), can each bind CypD with mM affinity. Our detailed biophysical characterization of the dynamic interface between NTD and CypD provides novel insights on the p53-dependent mPTP opening and drug discovery targeting NTD/CypD interface in diseases.
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Affiliation(s)
- Jing Zhao
- Center for Biotechnology and Interdisciplinary Studies, Troy, NY 12180, United States; Present address: College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Xinyue Liu
- Center for Biotechnology and Interdisciplinary Studies, Troy, NY 12180, United States; Present address: Department of Cell Biology, Harvard Medical School
| | - Alan Blayney
- Department Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, United States
| | - Yumeng Zhang
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, United States
| | - Lauren Gandy
- Center for Biotechnology and Interdisciplinary Studies, Troy, NY 12180, United States; Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY 12180, United States. https://twitter.com/a_science_life
| | | | - Nathan Smith
- Center for Biotechnology and Interdisciplinary Studies, Troy, NY 12180, United States; Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, United States
| | - Fuming Zhang
- Center for Biotechnology and Interdisciplinary Studies, Troy, NY 12180, United States; Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY 12180, United States
| | - Robert J Linhardt
- Center for Biotechnology and Interdisciplinary Studies, Troy, NY 12180, United States; Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY 12180, United States
| | - Jianhan Chen
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, United States
| | - Christopher Baines
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO 65211, USA
| | - Stewart N Loh
- Department Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, United States
| | - Chunyu Wang
- Center for Biotechnology and Interdisciplinary Studies, Troy, NY 12180, United States; Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY 12180, United States; Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, United States.
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Delaunay M, Ha-Duong T. Computational Tools and Strategies to Develop Peptide-Based Inhibitors of Protein-Protein Interactions. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2405:205-230. [PMID: 35298816 DOI: 10.1007/978-1-0716-1855-4_11] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein-protein interactions play crucial and subtle roles in many biological processes and modifications of their fine mechanisms generally result in severe diseases. Peptide derivatives are very promising therapeutic agents for modulating protein-protein associations with sizes and specificities between those of small compounds and antibodies. For the same reasons, rational design of peptide-based inhibitors naturally borrows and combines computational methods from both protein-ligand and protein-protein research fields. In this chapter, we aim to provide an overview of computational tools and approaches used for identifying and optimizing peptides that target protein-protein interfaces with high affinity and specificity. We hope that this review will help to implement appropriate in silico strategies for peptide-based drug design that builds on available information for the systems of interest.
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Affiliation(s)
| | - Tâp Ha-Duong
- Université Paris-Saclay, CNRS, BioCIS, Châtenay-Malabry, France.
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Kumutima J, Yao XQ, Hamelberg D. p53 Is Potentially Regulated by Cyclophilin D in the Triple-Proline Loop of the DNA Binding Domain. Biochemistry 2021; 60:597-606. [PMID: 33591178 DOI: 10.1021/acs.biochem.0c00946] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The multifunctional protein p53 is the central molecular sensor of cellular stresses. The canonical function of p53 is to transcriptionally activate target genes in response to, for example, DNA damage that may trigger apoptosis. Recently, p53 was also found to play a role in the regulation of necrosis, another type of cell death featured by the mitochondrial permeability transition (mPT). In this process, p53 directly interacts with the mPT regulator cyclophilin D, the detailed mechanism of which however remains poorly understood. Here, we report a comprehensive computational investigation of the p53-cyclophilin D interaction using molecular dynamics simulations and associated analyses. We have identified the specific cyclophilin D binding site on p53 that is located at proline 151 in the DNA binding domain. As a peptidyl-prolyl isomerase, cyclophilin D binds p53 and catalyzes the cis-trans isomerization of the peptide bond preceding proline 151. We have also characterized the effect of such an isomerization and found that the p53 domain in the cis state is overall more rigid than the trans state except for the local region around proline 151. Dynamical changes upon isomerization occur in both local and distal regions, indicating an allosteric effect elicited by the isomerization. We present potential allosteric communication pathways between proline 151 and distal sites, including the DNA binding surface. Our work provides, for the first time, a model for how cyclophilin D binds p53 and regulates its activity by switching the configuration of a specific site.
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Cau Y, Fiorillo A, Mori M, Ilari A, Botta M, Lalle M. Molecular Dynamics Simulations and Structural Analysis of Giardia duodenalis 14-3-3 Protein-Protein Interactions. J Chem Inf Model 2015; 55:2611-22. [PMID: 26551337 DOI: 10.1021/acs.jcim.5b00452] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Giardiasis is a gastrointestinal diarrheal illness caused by the protozoan parasite Giardia duodenalis, which affects annually over 200 million people worldwide. The limited antigiardial drug arsenal and the emergence of clinical cases refractory to standard treatments dictate the need for new chemotherapeutics. The 14-3-3 family of regulatory proteins, extensively involved in protein-protein interactions (PPIs) with pSer/pThr clients, represents a highly promising target. Despite homology with human counterparts, the single 14-3-3 of G. duodenalis (g14-3-3) is characterized by a constitutive phosphorylation in a region critical for target binding, thus affecting the function and the conformation of g14-3-3/clients interaction. However, to approach the design of specific small molecule modulators of g14-3-3 PPIs, structural elucidations are required. Here, we present a detailed computational and crystallographic study exploring the implications of g14-3-3 phosphorylation on protein structure and target binding. Self-Guided Langevin Dynamics and classical molecular dynamics simulations show that phosphorylation affects locally and globally g14-3-3 conformation, inducing a structural rearrangement more suitable for target binding. Profitable features for g14-3-3/clients interaction were highlighted using a hydrophobicity-based descriptor to characterize g14-3-3 client peptides. Finally, the X-ray structure of g14-3-3 in complex with a mode-1 prototype phosphopeptide was solved and combined with structure-based simulations to identify molecular features relevant for clients binding to g14-3-3. The data presented herein provide a further and structural understanding of g14-3-3 features and set the basis for drug design studies.
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Affiliation(s)
- Ylenia Cau
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena , via Aldo Moro 2, 53019 Siena, Italy
| | - Annarita Fiorillo
- Dipartimento di Scienze Biochimiche, Sapienza Università di Roma , Piazzale A. Moro 5, 00185 Roma, Italy
| | - Mattia Mori
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena , via Aldo Moro 2, 53019 Siena, Italy.,Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia , Viale Regina Elena 291, 00161 Roma, Italy
| | - Andrea Ilari
- CNR-Institute of Molecular Biology and Pathology (IBPM), c/o Department Biochemical Sciences "A. Rossi Fanelli", University Sapienza , P.le A. Moro 5, 00185 Roma, Italy
| | - Maurizo Botta
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena , via Aldo Moro 2, 53019 Siena, Italy.,Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University , BioLife Science Building, Suite 333, 1900 North 12th Street, Philadelphia, Pennsylvania 19122, United States
| | - Marco Lalle
- Department of Infectious, Parasitic and Immunomediated Diseases, Istituto Superiore di Sanità , Viale Regina Elena 299, 00161 Roma, Italy
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