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Article ; Online: Structural analysis of the transferrin receptor multifaceted ligand(s) interface.

Testi, Claudia / Boffi, Alberto / Montemiglio, Linda Celeste

2019 Volume 254, Page(s) 106242

Abstract: The transferrin receptor 1 (TfR1) is one of the key regulators of iron homeostasis for most higher organisms. It mediates cellular iron import through a constitutive clathrin-dependent endocytosis mechanism and by recruiting iron- regulator proteins as ... ...

Abstract	The transferrin receptor 1 (TfR1) is one of the key regulators of iron homeostasis for most higher organisms. It mediates cellular iron import through a constitutive clathrin-dependent endocytosis mechanism and by recruiting iron- regulator proteins as transferrin, Hereditary Hemochromatosis factor (HFE) and serum ferritin in response to cellular demand. The receptor is also opportunistically exploited by several viruses and the malaria parasite as a preferential door for cell invasion. In this review, we analyze the structural information available for TfR1 and all its functional complexes to figure out how structural signals in a single receptor can guide the recognition of multiple ligands and how the conservation of key residues in TfR1 might have a role in iron uptake and cell infection.
MeSH term(s)	Animals ; Binding Sites ; Humans ; Iron/chemistry ; Iron/metabolism ; Ligands ; Protein Binding ; Protein Conformation, alpha-Helical ; Receptors, Transferrin/chemistry ; Receptors, Transferrin/metabolism
Chemical Substances	Ligands ; Receptors, Transferrin ; Iron (E1UOL152H7)
Language	English
Publishing date	2019-08-01
Publishing country	Netherlands
Document type	Journal Article ; Review
ZDB-ID	185052-0
ISSN	1873-4200 ; 0301-4622
ISSN (online)	1873-4200
ISSN	0301-4622
DOI	10.1016/j.bpc.2019.106242
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Article ; Online: Effect of Salts on the Conformational Dynamics of the Cytochrome P450 OleP.

De Sciscio, Maria Laura / Nardi, Alessandro Nicola / Parisi, Giacomo / Bulfaro, Giovanni / Costanzo, Antonella / Gugole, Elena / Exertier, Cécile / Freda, Ida / Savino, Carmelinda / Vallone, Beatrice / Montemiglio, Linda Celeste / D'Abramo, Marco

Molecules (Basel, Switzerland)

2023 Volume 28, Issue 2

Abstract: Cytochrome P450 OleP catalytic activity is strongly influenced by its structural dynamic conformational behavior. Here, we combine equilibrium-binding experiments with all-atom molecular dynamics simulations to clarify how different environments affect ... ...

Abstract	Cytochrome P450 OleP catalytic activity is strongly influenced by its structural dynamic conformational behavior. Here, we combine equilibrium-binding experiments with all-atom molecular dynamics simulations to clarify how different environments affect OleP conformational equilibrium between the open and the closed-catalytic competent-forms. Our data clearly show that at high-ionic strength conditions, the closed form is favored, and, very interestingly, different mechanisms, depending on the chemistry of the cations, can be used to rationalize such an effect.
MeSH term(s)	Salts ; Cytochrome P-450 Enzyme System/metabolism ; Protein Conformation ; Molecular Dynamics Simulation
Chemical Substances	Salts ; Cytochrome P-450 Enzyme System (9035-51-2)
Language	English
Publishing date	2023-01-13
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	1413402-0
ISSN	1420-3049 ; 1431-5165 ; 1420-3049
ISSN (online)	1420-3049
ISSN	1431-5165 ; 1420-3049
DOI	10.3390/molecules28020832
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Article: A novel strategy for molecular interfaces optimization: The case of Ferritin-Transferrin receptor interaction

Di Rienzo, Lorenzo / Milanetti, Edoardo / Testi, Claudia / Montemiglio, Linda Celeste / Baiocco, Paola / Boffi, Alberto / Ruocco, Giancarlo

Computational and Structural Biotechnology Journal. 2020, v. 18

2020

Abstract: Protein-protein interactions regulate almost all cellular functions and rely on a fine tune of surface amino acids properties involved on both molecular partners. The disruption of a molecular association can be caused even by a single residue mutation, ... ...

Abstract	Protein-protein interactions regulate almost all cellular functions and rely on a fine tune of surface amino acids properties involved on both molecular partners. The disruption of a molecular association can be caused even by a single residue mutation, often leading to a pathological modification of a biochemical pathway. Therefore the evaluation of the effects of amino acid substitutions on binding, and the ad hoc design of protein-protein interfaces, is one of the biggest challenges in computational biology. Here, we present a novel strategy for computational mutation and optimization of protein-protein interfaces. Modeling the interaction surface properties using the Zernike polynomials, we describe the shape and electrostatics of binding sites with an ordered set of descriptors, making possible the evaluation of complementarity between interacting surfaces. With a Monte Carlo approach, we obtain protein mutants with controlled molecular complementarities. Applying this strategy to the relevant case of the interaction between Ferritin and Transferrin Receptor, we obtain a set of Ferritin mutants with increased or decreased complementarity. The extensive molecular dynamics validation of the method results confirms its efficacy, showing that this strategy represents a very promising approach in designing correct molecular interfaces.
Keywords	amino acids ; biochemical pathways ; bioinformatics ; biotechnology ; ferritin ; molecular dynamics ; transferrin receptors
Language	English
Size	p. 2678-2686.
Publishing place	Elsevier B.V.
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	2694435-2
ISSN	2001-0370
ISSN	2001-0370
DOI	10.1016/j.csbj.2020.09.020
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Article: Lack of orientation selectivity of the heme insertion in murine neuroglobin revealed by resonance Raman spectroscopy

Milazzo, Lisa / Exertier, Cécile / Becucci, Maurizio / Freda, Ida / Montemiglio, Linda Celeste / Savino, Carmelinda / Vallone, Beatrice / Smulevich, Giulietta

FEBS journal. 2020 Sept., v. 287, no. 18

2020

Abstract: Different murine neuroglobin variants showing structural and dynamic alterations that are associated with perturbation of ligand binding have been studied: the CD loop mutants characterized by an enhanced flexibility (Gly‐loop⁴⁰–⁴⁸ and Gly‐loop⁴⁴–⁴⁷), ... ...

Abstract	Different murine neuroglobin variants showing structural and dynamic alterations that are associated with perturbation of ligand binding have been studied: the CD loop mutants characterized by an enhanced flexibility (Gly‐loop⁴⁰–⁴⁸ and Gly‐loop⁴⁴–⁴⁷), the F106A mutant, and the double Gly‐loop⁴⁴–⁴⁷/F106A mutant. Their ferric resonance Raman spectra in solution and in crystals are almost identical. In the high‐frequency region, the identification of a double set of core size marker bands indicates the presence of two 6‐coordinate low spin species. The resonance Raman data, together with the corresponding crystal structures, indicate the presence of two neuroglobin conformers with a reversed (A conformer) or a canonical (B conformer) heme insertion orientation. With the identification of the marker bands corresponding to each conformer, the data indicate that the B conformer increases at the expense of the A form, predominantly in the Gly‐loop⁴⁴–⁴⁷/F106A double mutant, as confirmed by X‐ray crystallography. This is the first time that a reversed heme insertion has been identified by resonance Raman in a native 6‐coordinate low‐spin heme protein. This diagnostic tool could be extended to other heme proteins in order to detect heme orientational disorder, which are likely to be correlated to functionally relevant heme dynamics. DATABASE: Crystallographic structure: structural data are deposited in the Protein Data Bank under the 6RA6 PDB entry.
Keywords	Raman spectroscopy ; X-ray diffraction ; databases ; diagnostic techniques ; heme ; heme proteins ; ligands ; mice ; mutants
Language	English
Dates of publication	2020-09
Size	p. 4082-4097.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	NAL-AP-2-clean ; JOURNAL ARTICLE
ZDB-ID	2173655-8
ISSN	1742-4658 ; 1742-464X
ISSN (online)	1742-4658
ISSN	1742-464X
DOI	10.1111/febs.15241
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Article ; Online: Neuroglobin, clues to function and mechanism.

Exertier, Cécile / Montemiglio, Linda Celeste / Freda, Ida / Gugole, Elena / Parisi, Giacomo / Savino, Carmelinda / Vallone, Beatrice

Molecular aspects of medicine

2021 Volume 84, Page(s) 101055

Abstract: Neuroglobin is expressed in vertebrate brain and belongs to a branch of the globin family that diverged early in evolution. Sequence conservation and presence in nervous cells of several taxa suggests a relevant role in the nervous system, with tight ... ...

Abstract	Neuroglobin is expressed in vertebrate brain and belongs to a branch of the globin family that diverged early in evolution. Sequence conservation and presence in nervous cells of several taxa suggests a relevant role in the nervous system, with tight structural restraints. Twenty years after its discovery, a rich scientific literature provides convincing evidence of the involvement of neuroglobin in sustaining neuron viability in physiological and pathological conditions however, a full and conclusive picture of its specific function, or set of functions is still lacking. The difficulty of unambiguously assigning a precise mechanism and biochemical role to neuroglobin might arise from the participation to one or more cell mechanism that redundantly guarantee the functioning of the highly specialized and metabolically demanding central nervous system of vertebrates. Here we collect findings and hypotheses arising from recent biochemical, biophysical, structural, in cell and in vivo experimental work on neuroglobin, aiming at providing an overview of the most recent literature. Proteins are said to have jobs and hobbies, it is possible that, in the case of neuroglobin, evolution has selected for it more than one job, and support to cover for its occasional failings. Disentangling the mechanisms and roles of neuroglobin is thus a challenging task that might be achieved by considering data from different disciplines and experimental approaches.
MeSH term(s)	Animals ; Brain/metabolism ; Globins/chemistry ; Globins/genetics ; Humans ; Nerve Tissue Proteins/chemistry ; Nerve Tissue Proteins/genetics ; Neuroglobin/metabolism ; Neurons/metabolism
Chemical Substances	Nerve Tissue Proteins ; Neuroglobin ; Globins (9004-22-2)
Language	English
Publishing date	2021-12-06
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	197640-0
ISSN	1872-9452 ; 0098-2997
ISSN (online)	1872-9452
ISSN	0098-2997
DOI	10.1016/j.mam.2021.101055
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Zs.A 1189: Show issues

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Article ; Online: Structural insights into the DNA recognition mechanism by the bacterial transcription factor PdxR.

Freda, Ida / Exertier, Cécile / Barile, Anna / Chaves-Sanjuan, Antonio / Vega, Mirella Vivoli / Isupov, Michail N / Harmer, Nicholas J / Gugole, Elena / Swuec, Paolo / Bolognesi, Martino / Scipioni, Anita / Savino, Carmelinda / Di Salvo, Martino Luigi / Contestabile, Roberto / Vallone, Beatrice / Tramonti, Angela / Montemiglio, Linda Celeste

Nucleic acids research

2023 Volume 51, Issue 15, Page(s) 8237–8254

Abstract: Specificity in protein-DNA recognition arises from the synergy of several factors that stem from the structural and chemical signatures encoded within the targeted DNA molecule. Here, we deciphered the nature of the interactions driving DNA recognition ... ...

Abstract	Specificity in protein-DNA recognition arises from the synergy of several factors that stem from the structural and chemical signatures encoded within the targeted DNA molecule. Here, we deciphered the nature of the interactions driving DNA recognition and binding by the bacterial transcription factor PdxR, a member of the MocR family responsible for the regulation of pyridoxal 5'-phosphate (PLP) biosynthesis. Single particle cryo-EM performed on the PLP-PdxR bound to its target DNA enabled the isolation of three conformers of the complex, which may be considered as snapshots of the binding process. Moreover, the resolution of an apo-PdxR crystallographic structure provided a detailed description of the transition of the effector domain to the holo-PdxR form triggered by the binding of the PLP effector molecule. Binding analyses of mutated DNA sequences using both wild type and PdxR variants revealed a central role of electrostatic interactions and of the intrinsic asymmetric bending of the DNA in allosterically guiding the holo-PdxR-DNA recognition process, from the first encounter through the fully bound state. Our results detail the structure and dynamics of the PdxR-DNA complex, clarifying the mechanism governing the DNA-binding mode of the holo-PdxR and the regulation features of the MocR family of transcription factors.
MeSH term(s)	Bacteria/genetics ; Bacterial Proteins/metabolism ; DNA/metabolism ; Protein Binding ; Pyridoxal Phosphate/metabolism ; Transcription Factors/metabolism ; Bacillus clausii/genetics
Chemical Substances	Bacterial Proteins ; DNA (9007-49-2) ; Pyridoxal Phosphate (5V5IOJ8338) ; Transcription Factors
Language	English
Publishing date	2023-08-17
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkad552
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Zs.A 1067: Show issues

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Article: A novel strategy for molecular interfaces optimization: The case of Ferritin-Transferrin receptor interaction.

Di Rienzo, Lorenzo / Milanetti, Edoardo / Testi, Claudia / Montemiglio, Linda Celeste / Baiocco, Paola / Boffi, Alberto / Ruocco, Giancarlo

Computational and structural biotechnology journal

2020 Volume 18, Page(s) 2678–2686

Abstract	Protein-protein interactions regulate almost all cellular functions and rely on a fine tune of surface amino acids properties involved on both molecular partners. The disruption of a molecular association can be caused even by a single residue mutation, often leading to a pathological modification of a biochemical pathway. Therefore the evaluation of the effects of amino acid substitutions on binding, and the
Language	English
Publishing date	2020-09-24
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2694435-2
ISSN	2001-0370
ISSN	2001-0370
DOI	10.1016/j.csbj.2020.09.020
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Article ; Online: Lack of orientation selectivity of the heme insertion in murine neuroglobin revealed by resonance Raman spectroscopy.

Milazzo, Lisa / Exertier, Cécile / Becucci, Maurizio / Freda, Ida / Montemiglio, Linda Celeste / Savino, Carmelinda / Vallone, Beatrice / Smulevich, Giulietta

The FEBS journal

2020 Volume 287, Issue 18, Page(s) 4082–4097

Abstract	Different murine neuroglobin variants showing structural and dynamic alterations that are associated with perturbation of ligand binding have been studied: the CD loop mutants characterized by an enhanced flexibility (Gly-loop
MeSH term(s)	Amino Acid Sequence ; Animals ; Crystallography, X-Ray ; Heme/chemistry ; Heme/metabolism ; Mice ; Neuroglobin/chemistry ; Neuroglobin/genetics ; Neuroglobin/metabolism ; Protein Binding ; Protein Conformation ; Recombinant Proteins/chemistry ; Recombinant Proteins/metabolism ; Sequence Homology, Amino Acid ; Spectrum Analysis, Raman/methods
Chemical Substances	Neuroglobin ; Recombinant Proteins ; Heme (42VZT0U6YR)
Language	English
Publishing date	2020-02-27
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2173655-8
ISSN	1742-4658 ; 1742-464X
ISSN (online)	1742-4658
ISSN	1742-464X
DOI	10.1111/febs.15241
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Zs.A 260: Show issues

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Article: Crystal structure and functional characterization of an oligosaccharide dehydrogenase from Pycnoporus cinnabarinus provides insights into fungal breakdown of lignocellulose

Cerutti, Gabriele / Gugole, Elena / Montemiglio, Linda Celeste / Turbé-Doan, Annick / Chena, Dehbia / Navarro, David / Lomascolo, Anne / Piumi, François / Exertier, Cécile / Freda, Ida / Vallone, Beatrice / Record, Eric / Savino, Carmelinda / Sciara, Giuliano

Biotechnology for biofuels. 2021 Dec., v. 14, no. 1

2021

Abstract: BACKGROUND: Fungal glucose dehydrogenases (GDHs) are FAD-dependent enzymes belonging to the glucose-methanol-choline oxidoreductase superfamily. These enzymes are classified in the “Auxiliary Activity” family 3 (AA3) of the Carbohydrate-Active enZymes ... ...

Abstract	BACKGROUND: Fungal glucose dehydrogenases (GDHs) are FAD-dependent enzymes belonging to the glucose-methanol-choline oxidoreductase superfamily. These enzymes are classified in the “Auxiliary Activity” family 3 (AA3) of the Carbohydrate-Active enZymes database, and more specifically in subfamily AA3_2, that also includes the closely related flavoenzymes aryl-alcohol oxidase and glucose 1-oxidase. Based on sequence similarity to known fungal GDHs, an AA3_2 enzyme active on glucose was identified in the genome of Pycnoporus cinnabarinus, a model Basidiomycete able to completely degrade lignin. RESULTS: In our work, substrate screening and functional characterization showed an unexpected preferential activity of this enzyme toward oligosaccharides containing a β(1→3) glycosidic bond, with the highest efficiency observed for the disaccharide laminaribiose. Despite its sequence similarity to GDHs, we defined a novel enzymatic activity, namely oligosaccharide dehydrogenase (ODH), for this enzyme. The crystallographic structures of ODH in the sugar-free form and in complex with glucose and laminaribiose unveiled a peculiar saccharide recognition mechanism which is not shared with previously characterized AA3 oxidoreductases and accounts for ODH preferential activity toward oligosaccharides. The sugar molecules in the active site of ODH are mainly stabilized through CH-π interactions with aromatic residues rather than through hydrogen bonds with highly conserved residues, as observed instead for the fungal glucose dehydrogenases and oxidases characterized to date. Finally, three sugar-binding sites were identified on ODH external surface, which were not previously observed and might be of importance in the physiological scenario. CONCLUSIONS: Structure–function analysis of ODH is consistent with its role as an auxiliary enzyme in lignocellulose degradation and unveils yet another enzymatic function within the AA3 family of the Carbohydrate-Active enZymes database. Our findings allow deciphering the molecular determinants of substrate binding and provide insight into the physiological role of ODH, opening new perspectives to exploit biodiversity for lignocellulose transformation into fuels and chemicals.
Keywords	Pycnoporus ; active sites ; aryl-alcohol oxidase ; biodiversity ; biofuels ; biotechnology ; crystal structure ; databases ; enzyme activity ; fungi ; genome ; glucose ; glycosidic linkages ; hydrogen ; lignin ; lignocellulose ; oligosaccharides ; sequence homology
Language	English
Dates of publication	2021-12
Size	p. 161.
Publishing place	BioMed Central
Document type	Article
ZDB-ID	2421351-2
ISSN	1754-6834
ISSN	1754-6834
DOI	10.1186/s13068-021-02003-y
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Article: Functional analysis and crystallographic structure of clotrimazole bound OleP, a cytochrome P450 epoxidase from Streptomyces antibioticus involved in oleandomycin biosynthesis

Montemiglio, Linda Celeste / Antonella Scaglione / Beatrice Vallone / Carmelinda Savino / Giacomo Parisi / Giuliano Sciara

Biochimica et biophysica acta. 2016 Mar., v. 1860, no. 3

2016

Abstract: OleP is a cyt P450 from Streptomyces antibioticus carrying out epoxigenation of the antibiotic oleandomycin during its biosynthesis. The timing of its reaction has not been fully clarified, doubts remain regarding its substrate and catalytic mechanism ... ...

Abstract	OleP is a cyt P450 from Streptomyces antibioticus carrying out epoxigenation of the antibiotic oleandomycin during its biosynthesis. The timing of its reaction has not been fully clarified, doubts remain regarding its substrate and catalytic mechanism.The crystal structure of OleP in complex with clotrimazole, an inhibitor of P450s used in therapy, was solved and the complex formation dynamics was characterized by equilibrium and kinetic binding studies and compared to ketoconazole, another azole differing for the N1-substituent.Clotrimazole coordinates the heme and occupies the active site. Most of the residues interacting with clotrimazole are conserved and involved in substrate binding in MycG, the P450 epoxigenase with the highest homology with OleP. Kinetic characterization of inhibitor binding revealed OleP to follow a simple bimolecular reaction, without detectable intermediates.Clotrimazole-bound OleP adopts an open form, held by a π-π stacking chain that fastens helices F and G and the FG loop. Affinity is affected by the interactions of the N1 substituent within the active site, given the one order of magnitude difference of the off-rate constants between clotrimazole and ketoconazole. Based on structural similarities with MycG, we propose a binding mode for both oleandomycin intermediates, that are the candidate substrates of OleP.Among P450 epoxigenases OleP is the only one that introduces an epoxide on a non-activated C–C bond. The data here presented are necessary to understand the rare chemistry carried out by OleP, to engineer it and to design more selective and potent P450-targeted drugs.
Keywords	active sites ; biosynthesis ; chemical bonding ; clotrimazole ; crystal structure ; cytochrome P-450 ; drugs ; heme ; ketoconazole ; oleandomycin ; Streptomyces antibioticus ; therapeutics
Language	English
Dates of publication	2016-03
Size	p. 465-475.
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	840755-1
ISSN	0304-4165
ISSN	0304-4165
DOI	10.1016/j.bbagen.2015.10.009
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