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Fagnani E, Cocomazzi P, Pellegrino S, Tedeschi G, Scalvini FG, Cossu F, Da Vela S, Aliverti A, Mastrangelo E, Milani M. CHCHD4 binding affects the active site of apoptosis inducing factor (AIF): Structural determinants for allosteric regulation. Structure 2024; 32:594-602.e4. [PMID: 38460521 DOI: 10.1016/j.str.2024.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 01/08/2024] [Accepted: 02/13/2024] [Indexed: 03/11/2024]
Abstract
Apoptosis-inducing factor (AIF), which is confined to mitochondria of normal healthy cells, is the first identified caspase-independent cell death effector. Moreover, AIF is required for the optimal functioning of the respiratory chain machinery. Recent findings have revealed that AIF fulfills its pro-survival function by interacting with CHCHD4, a soluble mitochondrial protein which promotes the entrance and the oxidative folding of different proteins in the inner membrane space. Here, we report the crystal structure of the ternary complex involving the N-terminal 27-mer peptide of CHCHD4, NAD+, and AIF harboring its FAD (flavin adenine dinucleotide) prosthetic group in oxidized form. Combining this information with biophysical and biochemical data on the CHCHD4/AIF complex, we provide a detailed structural description of the interaction between the two proteins, validated by both chemical cross-linking mass spectrometry analysis and site-directed mutagenesis.
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Affiliation(s)
- Elisa Fagnani
- Biophysics Institute, CNR-IBF, Via Corti 12, 20133 Milan, Italy; Department of Bioscience, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy
| | - Paolo Cocomazzi
- Biophysics Institute, CNR-IBF, Via Corti 12, 20133 Milan, Italy; Department of Bioscience, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy
| | - Sara Pellegrino
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, Via Golgi 19, 20133 Milan, Italy
| | - Gabriella Tedeschi
- Department of Veterinary Medicine and Animal Science (DIVAS), Università degli Studi di Milano, Via dell'Università 6, 26900 Lodi, Italy; Cimaina, Università degli Studi di Milano, Milan, Italy
| | - Francesca Grassi Scalvini
- Department of Veterinary Medicine and Animal Science (DIVAS), Università degli Studi di Milano, Via dell'Università 6, 26900 Lodi, Italy
| | - Federica Cossu
- Biophysics Institute, CNR-IBF, Via Corti 12, 20133 Milan, Italy; Department of Bioscience, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy
| | - Stefano Da Vela
- Hochschule Bremerhaven, Karlstadt 8, 27568 Bremerhaven, Germany
| | - Alessandro Aliverti
- Department of Bioscience, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy.
| | - Eloise Mastrangelo
- Biophysics Institute, CNR-IBF, Via Corti 12, 20133 Milan, Italy; Department of Bioscience, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy.
| | - Mario Milani
- Biophysics Institute, CNR-IBF, Via Corti 12, 20133 Milan, Italy; Department of Bioscience, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy.
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Double approaches for obtaining an asymmetric one-pot addition/reduction reaction. MOLECULAR CATALYSIS 2022. [DOI: 10.1016/j.mcat.2022.112716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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3
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Van Stappen C, Deng Y, Liu Y, Heidari H, Wang JX, Zhou Y, Ledray AP, Lu Y. Designing Artificial Metalloenzymes by Tuning of the Environment beyond the Primary Coordination Sphere. Chem Rev 2022; 122:11974-12045. [PMID: 35816578 DOI: 10.1021/acs.chemrev.2c00106] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Metalloenzymes catalyze a variety of reactions using a limited number of natural amino acids and metallocofactors. Therefore, the environment beyond the primary coordination sphere must play an important role in both conferring and tuning their phenomenal catalytic properties, enabling active sites with otherwise similar primary coordination environments to perform a diverse array of biological functions. However, since the interactions beyond the primary coordination sphere are numerous and weak, it has been difficult to pinpoint structural features responsible for the tuning of activities of native enzymes. Designing artificial metalloenzymes (ArMs) offers an excellent basis to elucidate the roles of these interactions and to further develop practical biological catalysts. In this review, we highlight how the secondary coordination spheres of ArMs influence metal binding and catalysis, with particular focus on the use of native protein scaffolds as templates for the design of ArMs by either rational design aided by computational modeling, directed evolution, or a combination of both approaches. In describing successes in designing heme, nonheme Fe, and Cu metalloenzymes, heteronuclear metalloenzymes containing heme, and those ArMs containing other metal centers (including those with non-native metal ions and metallocofactors), we have summarized insights gained on how careful controls of the interactions in the secondary coordination sphere, including hydrophobic and hydrogen bonding interactions, allow the generation and tuning of these respective systems to approach, rival, and, in a few cases, exceed those of native enzymes. We have also provided an outlook on the remaining challenges in the field and future directions that will allow for a deeper understanding of the secondary coordination sphere a deeper understanding of the secondary coordintion sphere to be gained, and in turn to guide the design of a broader and more efficient variety of ArMs.
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Affiliation(s)
- Casey Van Stappen
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yunling Deng
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yiwei Liu
- Department of Chemistry, University of Illinois, Urbana-Champaign, 505 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Hirbod Heidari
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Jing-Xiang Wang
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yu Zhou
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Aaron P Ledray
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yi Lu
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States.,Department of Chemistry, University of Illinois, Urbana-Champaign, 505 South Mathews Avenue, Urbana, Illinois 61801, United States
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Bucci R, Vaghi F, Di Lorenzo D, Anastasi F, Broggini G, Lo Presti L, Contini A, Gelmi ML. A Non‐coded β2,2‐Amino Acid with Isoxazoline Core Able to Stabilize Peptides Folding Through an Unprecedented Hydrogen Bond. European J Org Chem 2022. [DOI: 10.1002/ejoc.202200601] [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)
- Raffaella Bucci
- Università degli Studi di Milano: Universita degli Studi di Milano Dipartimento di Scienze Farmaceutiche ITALY
| | - Francesco Vaghi
- Università degli Studi di Milano: Universita degli Studi di Milano Dipartimento di Scienze Farmaceutiche ITALY
| | - Davide Di Lorenzo
- Università degli Studi di Milano: Universita degli Studi di Milano Dipartimento di Scienze Farmaceutiche ITALY
| | - Francesco Anastasi
- Università degli Studi di Milano: Universita degli Studi di Milano Dipartimento di Scienze Farmaceutiche ITALY
| | - Gianluigi Broggini
- Università degli Studi dell'Insubria Dipartimento di Scienza e Alta Tecnologia ITALY
| | - Leonardo Lo Presti
- Università degli Studi di Milano: Universita degli Studi di Milano Dipartimento di Chimica ITALY
| | - Alessandro Contini
- Università degli Studi di Milano: Universita degli Studi di Milano Dipartimento di Scienze Farmaceutiche ITALY
| | - Maria Luisa Gelmi
- Universita degli Studi di Milano DISFARM, Sezione di Chimica Generale e Organica “A. Marchesini” Via Venezian 21 20133 Milano ITALY
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Hybrid Catalysts from Copper Biosorbing Bacterial Strains and Their Recycling for Catalytic Application in the Asymmetric Addition Reaction of B2(pin)2 on α,β-Unsaturated Chalcones. Catalysts 2022. [DOI: 10.3390/catal12040433] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The recycling of heavy metal contaminants from wastewater as a source of valuable products perfectly fits with the principles of a Circular Economy system in view of restoring pollutants back into the system endowed with new social and economic benefits. Heavy metals are often present in such a low concentration that it makes the removal efficiency difficult to realize through the conventional physicochemical methods with high selectivity. Biosorption, conversely, by EPSs (extracellular polymeric substances) produced by several bacterial cells’ strains, is gaining a great deal of attention as an economic, efficient and sustainable depolluting process of wastewater from metal cations such as copper. Metal coordination to EPS components was thus deeply investigated by 1H NMR titration experiments. The 1,10–Phenanthroline–copper complex was exploited for quantifying the ability of different strains to sequester copper by a practical UV-Vis spectrophotometric method. The obtained data distinguished Serratia plymuthica strain SC5II as the bacterial strain displaying copper-adsorbing properties higher than any other, with Stenotrophomonas sp. strain 13a resulting in the worst one. Different analytical techniques, i.e., Dynamic Light Scattering (DLS), FT-IR analysis and SEM spectroscopy were thus employed to rationalize these results. Finally, the obtained copper chelates were successfully employed as hybrid catalysts in the asymmetric boron addition to α,β-unsaturated chalcones for the synthesis of valuable pharmaceutical intermediates, thus placing waste management in a new circular perspective.
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Bucci R, Maggioni D, Locarno S, Ferretti AM, Gelmi ML, Pellegrino S. Exploiting Ultrashort α,β-Peptides in the Colloidal Stabilization of Gold Nanoparticles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:11365-11373. [PMID: 34533956 DOI: 10.1021/acs.langmuir.1c01981] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Colloidal gold nanoparticles (GNPs) have found wide-ranging applications in nanomedicine due to their unique optical properties, ease of preparation, and functionalization. To avoid the formation of GNP aggregates in the physiological environment, molecules such as lipids, polysaccharides, or polymers are employed as GNP coatings. Here, we present the colloidal stabilization of GNPs using ultrashort α,β-peptides containing the repeating unit of a diaryl β2,3-amino acid and characterized by an extended conformation. Differently functionalized GNPs have been characterized by ultraviolet, dynamic light scattering, and transmission electron microscopy analysis, allowing us to define the best candidate that inhibits the aggregation of GNPs not only in water but also in mouse serum. In particular, a short tripeptide was found to be able to stabilize GNPs in physiological media over 3 months. This new system has been further capped with albumin, obtaining a material with even more colloidal stability and ability to prevent the formation of a thick protein corona in physiological media.
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Affiliation(s)
- Raffaella Bucci
- DISFARM-Dipartimento di Scienze Farmaceutiche, Sezione Chimica Generale e Organica "A. Marchesini", Università degli Studi di Milano, Via Venezian 21, 20133 Milano, Italy
| | - Daniela Maggioni
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi 19, 20133 Milano, Italy
| | - Silvia Locarno
- Dipartimento di Fisica "Aldo Pontremoli", Università degli Studi di Milano, Via Celoria 16, 20133 Milano, Italy
| | - Anna Maria Ferretti
- Istituto di Scienze e Tecnologie Chimiche ″Giulio Natta″, Consiglio Nazionale Delle Ricerche (SCITEC-CNR), Via G. Fantoli 16/15, 20138 Milano, Italy
| | - Maria Luisa Gelmi
- DISFARM-Dipartimento di Scienze Farmaceutiche, Sezione Chimica Generale e Organica "A. Marchesini", Università degli Studi di Milano, Via Venezian 21, 20133 Milano, Italy
| | - Sara Pellegrino
- DISFARM-Dipartimento di Scienze Farmaceutiche, Sezione Chimica Generale e Organica "A. Marchesini", Università degli Studi di Milano, Via Venezian 21, 20133 Milano, Italy
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Facchetti G, Fusè M, Pecoraro T, Nava D, Rimoldi I. New sp 3 diphosphine-based rhodium catalysts for the asymmetric conjugate addition of aryl boronic acids to 3-azaarylpropenones. NEW J CHEM 2021. [DOI: 10.1039/d1nj03634c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The new diphosphine (R,R)-EPHOS featuring a stereogenic sp3 carbon combined with a C2 axial chirality was applied to the Rh-catalyzed asymmetric 1,4 addition of aryl boronic acids to 3-azaarylpropenones, affording the product with e.e. up to 94%.
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Affiliation(s)
- Giorgio Facchetti
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, Via Venezian 21, 20133 Milano, Italy
| | - Marco Fusè
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Tania Pecoraro
- Department of Molecular Biochemistry and Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, 20156, Italy
| | - Donatella Nava
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, Via Venezian 21, 20133 Milano, Italy
| | - Isabella Rimoldi
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, Via Venezian 21, 20133 Milano, Italy
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