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Article: Mutation in the Common Docking Domain Affects MAP Kinase ERK2 Catalysis and Stability.

Novak, Leonore / Petrosino, Maria / Pasquo, Alessandra / Chaikuad, Apirat / Chiaraluce, Roberta / Knapp, Stefan / Consalvi, Valerio

Cancers

2023 Volume 15, Issue 11

Abstract: The extracellular-signal-regulated kinase 2 (ERK2), a mitogen-activated protein kinase (MAPK) located downstream of the Ras-Raf-MEK-ERK signal transduction cascade, is involved in the regulation of a large variety of cellular processes. The ERK2, ... ...

Abstract	The extracellular-signal-regulated kinase 2 (ERK2), a mitogen-activated protein kinase (MAPK) located downstream of the Ras-Raf-MEK-ERK signal transduction cascade, is involved in the regulation of a large variety of cellular processes. The ERK2, activated by phosphorylation, is the principal effector of a central signaling cascade that converts extracellular stimuli into cells. Deregulation of the ERK2 signaling pathway is related to many human diseases, including cancer. This study reports a comprehensive biophysical analysis of structural, function, and stability data of pure, recombinant human non-phosphorylated (NP-) and phosphorylated (P-) ERK2 wild-type and missense variants in the common docking site (CD-site) found in cancer tissues. Because the CD-site is involved in interaction with protein substrates and regulators, a biophysical characterization of missense variants adds information about the impact of point mutations on the ERK2 structure-function relationship. Most of the P-ERK2 variants in the CD-site display a reduced catalytic efficiency, and for the P-ERK2 D321E, D321N, D321V and E322K, changes in thermodynamic stability are observed. The thermal stability of NP-ERK2 and P-ERK2 D321E, D321G, and E322K is decreased with respect to the wild-type. In general, a single residue mutation in the CD-site may lead to structural local changes that reflects in alterations in the global ERK2 stability and catalysis.
Language	English
Publishing date	2023-05-26
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2527080-1
ISSN	2072-6694
ISSN	2072-6694
DOI	10.3390/cancers15112938
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Article ; Online: The complex impact of cancer-related missense mutations on the stability and on the biophysical and biochemical properties of MAPK1 and MAPK3 somatic variants.

Petrosino, Maria / Novak, Leonore / Pasquo, Alessandra / Turina, Paola / Capriotti, Emidio / Minicozzi, Velia / Consalvi, Valerio / Chiaraluce, Roberta

Human genomics

2023 Volume 17, Issue 1, Page(s) 95

Abstract: Mitogen-activated protein kinases 1 and 3 (MAPK1 and MAPK3), also called extracellular regulated kinases (ERK2 and ERK1), are serine/threonine kinase activated downstream by the Ras/Raf/MEK/ERK signal transduction cascade that regulates a variety of ... ...

Abstract	Mitogen-activated protein kinases 1 and 3 (MAPK1 and MAPK3), also called extracellular regulated kinases (ERK2 and ERK1), are serine/threonine kinase activated downstream by the Ras/Raf/MEK/ERK signal transduction cascade that regulates a variety of cellular processes. A dysregulation of MAPK cascade is frequently associated to missense mutations on its protein components and may be related to many pathologies, including cancer. In this study we selected from COSMIC database a set of MAPK1 and MAPK3 somatic variants found in cancer tissues carrying missense mutations distributed all over the MAPK1 and MAPK3 sequences. The proteins were expressed as pure recombinant proteins, and their biochemical and biophysical properties have been studied in comparison with the wild type. The missense mutations lead to changes in the tertiary arrangements of all the variants. The thermodynamic stability of the wild type and variants has been investigated in the non-phosphorylated and in the phosphorylated form. Significant differences in the thermal stabilities of most of the variants have been observed, as well as changes in the catalytic efficiencies. The energetics of the catalytic reaction is affected for all the variants for both the MAPK proteins. The stability changes and the variation in the enzyme catalysis observed for most of MAPK1/3 variants suggest that a local change in a residue, distant from the catalytic site, may have long-distance effects that reflect globally on enzyme stability and functions.
MeSH term(s)	Humans ; Mitogen-Activated Protein Kinase 1/metabolism ; Mutation, Missense/genetics ; Neoplasms/genetics ; Neoplasms/metabolism ; Phosphorylation ; Protein Serine-Threonine Kinases/metabolism ; Signal Transduction
Chemical Substances	MAPK1 protein, human (EC 2.7.11.24) ; Mitogen-Activated Protein Kinase 1 (EC 2.7.11.24) ; Protein Serine-Threonine Kinases (EC 2.7.11.1) ; MAPK3 protein, human (EC 2.7.11.24)
Language	English
Publishing date	2023-10-27
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2147618-4
ISSN	1479-7364 ; 1479-7364
ISSN (online)	1479-7364
ISSN	1479-7364
DOI	10.1186/s40246-023-00544-x
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Article ; Online: Analysis and Interpretation of the Impact of Missense Variants in Cancer.

Petrosino, Maria / Novak, Leonore / Pasquo, Alessandra / Chiaraluce, Roberta / Turina, Paola / Capriotti, Emidio / Consalvi, Valerio

International journal of molecular sciences

2021 Volume 22, Issue 11

Abstract: Large scale genome sequencing allowed the identification of a massive number of genetic variations, whose impact on human health is still unknown. In this review we analyze, by an in silico-based strategy, the impact of missense variants on cancer- ... ...

Abstract	Large scale genome sequencing allowed the identification of a massive number of genetic variations, whose impact on human health is still unknown. In this review we analyze, by an in silico-based strategy, the impact of missense variants on cancer-related genes, whose effect on protein stability and function was experimentally determined. We collected a set of 164 variants from 11 proteins to analyze the impact of missense mutations at structural and functional levels, and to assess the performance of state-of-the-art methods (FoldX and Meta-SNP) for predicting protein stability change and pathogenicity. The result of our analysis shows that a combination of experimental data on protein stability and in silico pathogenicity predictions allowed the identification of a subset of variants with a high probability of having a deleterious phenotypic effect, as confirmed by the significant enrichment of the subset in variants annotated in the COSMIC database as putative cancer-driving variants. Our analysis suggests that the integration of experimental and computational approaches may contribute to evaluate the risk for complex disorders and develop more effective treatment strategies.
MeSH term(s)	Computational Biology/methods ; Computer Simulation ; Humans ; Mutation, Missense/genetics ; Neoplasms/genetics ; Protein Stability ; Proteins/genetics
Chemical Substances	Proteins
Language	English
Publishing date	2021-05-21
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms22115416
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Article ; Online: Zn-Induced Interactions Between SARS-CoV-2 orf7a and BST2/Tetherin.

Petrosino, Maria / Stellato, Francesco / Chiaraluce, Roberta / Consalvi, Valerio / La Penna, Giovanni / Pasquo, Alessandra / Proux, Olivier / Rossi, Giancarlo / Morante, Silvia

ChemistryOpen

2021 Volume 10, Issue 11, Page(s) 1133–1141

Abstract: We present in this work a first X-ray Absorption Spectroscopy study of the interactions of Zn with human BST2/tetherin and SARS-CoV-2 orf7a proteins as well as with some of their complexes. The analysis of the XANES region of the measured spectra shows ... ...

Abstract	We present in this work a first X-ray Absorption Spectroscopy study of the interactions of Zn with human BST2/tetherin and SARS-CoV-2 orf7a proteins as well as with some of their complexes. The analysis of the XANES region of the measured spectra shows that Zn binds to BST2, as well as to orf7a, thus resulting in the formation of BST2-orf7a complexes. This structural information confirms the the conjecture, recently put forward by some of the present Authors, according to which the accessory orf7a (and possibly also orf8) viral protein are capable of interfering with the BST2 antiviral activity. Our explanation for this behavior is that, when BST2 gets in contact with Zn bound to the orf7a Cys
MeSH term(s)	Antigens, CD/metabolism ; Cysteine/chemistry ; GPI-Linked Proteins/metabolism ; Histidine/chemistry ; Humans ; Molecular Dynamics Simulation ; Protein Binding ; SARS-CoV-2/chemistry ; Viral Proteins/metabolism ; X-Ray Absorption Spectroscopy ; Zinc/metabolism
Chemical Substances	Antigens, CD ; BST2 protein, human ; GPI-Linked Proteins ; ORF7a protein, SARS-CoV-2 ; Viral Proteins ; Histidine (4QD397987E) ; Zinc (J41CSQ7QDS) ; Cysteine (K848JZ4886)
Language	English
Publishing date	2021-11-18
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2655605-4
ISSN	2191-1363 ; 2191-1363
ISSN (online)	2191-1363
ISSN	2191-1363
DOI	10.1002/open.202100217
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Article ; Online: A Glimpse into the Structural Properties of the Intermediate and Transition State in the Folding of Bromodomain 2 Domain 2 by Φ Value Analysis.

Novak, Leonore / Petrosino, Maria / Santorelli, Daniele / Chiaraluce, Roberta / Consalvi, Valerio / Pasquo, Alessandra / Travaglini-Allocatelli, Carlo

International journal of molecular sciences

2021 Volume 22, Issue 11

Abstract: Bromodomains (BRDs) are small protein interaction modules of about 110 amino acids that selectively recognize acetylated lysine in histones and other proteins. These domains have been identified in a variety of multi-domain proteins involved in ... ...

Abstract	Bromodomains (BRDs) are small protein interaction modules of about 110 amino acids that selectively recognize acetylated lysine in histones and other proteins. These domains have been identified in a variety of multi-domain proteins involved in transcriptional regulation or chromatin remodeling in eukaryotic cells. BRD inhibition is considered an attractive therapeutic approach in epigenetic disorders, particularly in oncology. Here, we present a Φ value analysis to investigate the folding pathway of the second domain of BRD2 (BRD2(2)). Using an extensive mutational analysis based on 25 site-directed mutants, we provide structural information on both the intermediate and late transition state of BRD2(2). The data reveal that the C-terminal region represents part of the initial folding nucleus, while the N-terminal region of the domain consolidates its structure only later in the folding process. Furthermore, only a small number of native-like interactions have been identified, suggesting the presence of a non-compact, partially folded state with scarce native-like characteristics. Taken together, these results indicate that, in BRD2(2), a hierarchical mechanism of protein folding can be described with non-native interactions that play a significant role in folding.
MeSH term(s)	Kinetics ; Protein Domains ; Protein Folding ; Protein Structure, Tertiary ; Protein-Serine-Threonine Kinases/chemistry ; Transcription Factors/chemistry
Chemical Substances	Transcription Factors ; Protein-Serine-Threonine Kinases (EC 2.7.11.1)
Language	English
Publishing date	2021-05-31
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms22115953
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Article ; Online: Dealing with Cu reduction in X-ray absorption spectroscopy experiments.

Stellato, Francesco / Chiaraluce, Roberta / Consalvi, Valerio / De Santis, Emiliano / La Penna, Giovanni / Proux, Olivier / Rossi, Giancarlo / Morante, Silvia

Metallomics : integrated biometal science

2019 Volume 11, Issue 8, Page(s) 1401–1410

Abstract: In this paper we prove in the exemplary case of the amyloid-β peptide in complex with Cu(ii) that at the current low temperatures employed in XAS experiments, the time needed for collecting a good quality XAS spectrum is significantly shorter than the ... ...

Abstract	In this paper we prove in the exemplary case of the amyloid-β peptide in complex with Cu(ii) that at the current low temperatures employed in XAS experiments, the time needed for collecting a good quality XAS spectrum is significantly shorter than the time after which structural damage becomes appreciable. Our method takes advantage of the well-known circumstance that the transition of Cu from the oxidized to the reduced form under ionizing radiation can be quantified by monitoring a characteristic peak in the pre-edge region. We show that there exists a sufficiently large time window in which good XAS spectra can be acquired before the structure around the oxidized Cu(ii) ion reorganizes itself into the reduced Cu(i) "resting" structure. We suggest that similar considerations apply to other cases of biological interest, especially when dealing with macromolecules in complex with transition metal ions.
MeSH term(s)	Algorithms ; Amyloid beta-Peptides/chemistry ; Copper/chemistry ; Humans ; Kinetics ; Ligands ; Models, Molecular ; Oxidation-Reduction ; X-Ray Absorption Spectroscopy/methods
Chemical Substances	Amyloid beta-Peptides ; Ligands ; Copper (789U1901C5)
Language	English
Publishing date	2019-07-03
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2474317-3
ISSN	1756-591X ; 1756-5901
ISSN (online)	1756-591X
ISSN	1756-5901
DOI	10.1039/c9mt00110g
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Article ; Online: The phosphoglycerate kinase 1 variants found in carcinoma cells display different catalytic activity and conformational stability compared to the native enzyme.

Fiorillo, Annarita / Petrosino, Maria / Ilari, Andrea / Pasquo, Alessandra / Cipollone, Alessandra / Maggi, Maristella / Chiaraluce, Roberta / Consalvi, Valerio

PloS one

2018 Volume 13, Issue 7, Page(s) e0199191

Abstract: Cancer cells are able to survive in difficult conditions, reprogramming their metabolism according to their requirements. Under hypoxic conditions they shift from oxidative phosphorylation to aerobic glycolysis, a behavior known as Warburg effect. In the ...

Abstract	Cancer cells are able to survive in difficult conditions, reprogramming their metabolism according to their requirements. Under hypoxic conditions they shift from oxidative phosphorylation to aerobic glycolysis, a behavior known as Warburg effect. In the last years, glycolytic enzymes have been identified as potential targets for alternative anticancer therapies. Recently, phosphoglycerate kinase 1 (PGK1), an ubiquitous enzyme expressed in all somatic cells that catalyzes the seventh step of glycolysis which consists of the reversible phosphotransfer reaction from 1,3-bisphosphoglycerate to ADP, has been discovered to be overexpressed in many cancer types. Moreover, several somatic variants of PGK1 have been identified in tumors. In this study we analyzed the effect of the single nucleotide variants found in cancer tissues on the PGK1 structure and function. Our results clearly show that the variants display a decreased catalytic efficiency and/or thermodynamic stability and an altered local tertiary structure, as shown by the solved X-ray structures. The changes in the catalytic properties and in the stability of the PGK1 variants, mainly due to the local changes evidenced by the X-ray structures, suggest also changes in the functional role of PGK to support the biosynthetic need of the growing and proliferating tumour cells.
MeSH term(s)	Adenosine Diphosphate/chemistry ; Adenosine Diphosphate/metabolism ; Amino Acid Sequence ; Binding Sites ; Cloning, Molecular ; Crystallography, X-Ray ; Enzyme Stability ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Gene Expression ; Genetic Vectors/chemistry ; Genetic Vectors/metabolism ; Glyceric Acids/chemistry ; Glyceric Acids/metabolism ; Humans ; Kinetics ; Models, Molecular ; Mutation ; Neoplasm Proteins/chemistry ; Neoplasm Proteins/genetics ; Neoplasm Proteins/metabolism ; Phosphoglycerate Kinase/chemistry ; Phosphoglycerate Kinase/genetics ; Phosphoglycerate Kinase/metabolism ; Protein Binding ; Protein Conformation, alpha-Helical ; Protein Conformation, beta-Strand ; Protein Interaction Domains and Motifs ; Protein Structure, Tertiary ; Recombinant Proteins/chemistry ; Recombinant Proteins/genetics ; Recombinant Proteins/metabolism ; Sequence Alignment ; Sequence Homology, Amino Acid ; Substrate Specificity ; Thermodynamics
Chemical Substances	Glyceric Acids ; Neoplasm Proteins ; Recombinant Proteins ; Adenosine Diphosphate (61D2G4IYVH) ; 3-phosphoglycerate (820-11-1) ; PGK1 protein, human (EC 2.7.2.3) ; Phosphoglycerate Kinase (EC 2.7.2.3)
Language	English
Publishing date	2018-07-11
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0199191
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Article: Unveiling the folding mechanism of the Bromodomains.

Petrosino, Maria / Bonetti, Daniela / Pasquo, Alessandra / Lori, Laura / Chiaraluce, Roberta / Consalvi, Valerio / Travaglini-Allocatelli, Carlo

Biochemistry and biophysics reports

2017 Volume 11, Page(s) 99–104

Abstract: Bromodomains (BRDs) are small protein domains often present in large multidomain proteins involved in transcriptional regulation in eukaryotic cells. They currently represent valuable targets for the development of inhibitors of aberrant transcriptional ... ...

Abstract	Bromodomains (BRDs) are small protein domains often present in large multidomain proteins involved in transcriptional regulation in eukaryotic cells. They currently represent valuable targets for the development of inhibitors of aberrant transcriptional processes in a variety of human diseases. Here we report urea-induced equilibrium unfolding experiments monitored by circular dichroism (CD) and fluorescence on two structurally similar BRDs: BRD2(2) and BRD4(1), showing that BRD4(1) is more stable than BRD2(2). Moreover, we report a description of their kinetic folding mechanism, as obtained by careful analysis of stopped-flow and temperature-jump data. The presence of a high energy intermediate for both proteins, suggested by the non-linear dependence of the folding rate on denaturant concentration in the millisec time regime, has been experimentally observed by temperature-jump experiments. Quantitative global analysis of all the rate constants obtained over a wide range of urea concentrations, allowed us to propose a common, three-state, folding mechanism for these two BRDs. Interestingly, the intermediate of BRD4(1) appears to be more stable and structurally native-like than that populated by BRD2(2). Our results underscore the role played by structural topology and sequence in determining and tuning the folding mechanism.
Language	English
Publishing date	2017-07-08
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2831046-9
ISSN	2405-5808
ISSN	2405-5808
DOI	10.1016/j.bbrep.2017.06.009
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Article ; Online: Characterization of human frataxin missense variants in cancer tissues.

Petrosino, Maria / Pasquo, Alessandra / Novak, Leonore / Toto, Angelo / Gianni, Stefano / Mantuano, Elide / Veneziano, Liana / Minicozzi, Velia / Pastore, Annalisa / Puglisi, Rita / Capriotti, Emidio / Chiaraluce, Roberta / Consalvi, Valerio

Human mutation

2019 Volume 40, Issue 9, Page(s) 1400–1413

Abstract: Human frataxin is an iron-binding protein involved in the mitochondrial iron-sulfur (Fe-S) clusters assembly, a process fundamental for the functional activity of mitochondrial proteins. Decreased level of frataxin expression is associated with the ... ...

Abstract	Human frataxin is an iron-binding protein involved in the mitochondrial iron-sulfur (Fe-S) clusters assembly, a process fundamental for the functional activity of mitochondrial proteins. Decreased level of frataxin expression is associated with the neurodegenerative disease Friedreich ataxia. Defective function of frataxin may cause defects in mitochondria, leading to increased tumorigenesis. Tumor-initiating cells show higher iron uptake, a decrease in iron storage and a reduced Fe-S clusters synthesis and utilization. In this study, we selected, from COSMIC database, the somatic human frataxin missense variants found in cancer tissues p.D104G, p.A107V, p.F109L, p.Y123S, p.S161I, p.W173C, p.S181F, and p.S202F to analyze the effect of the single amino acid substitutions on frataxin structure, function, and stability. The spectral properties, the thermodynamic and the kinetic stability, as well as the molecular dynamics of the frataxin missense variants found in cancer tissues point to local changes confined to the environment of the mutated residues. The global fold of the variants is not altered by the amino acid substitutions; however, some of the variants show a decreased stability and a decreased functional activity in comparison with that of the wild-type protein.
MeSH term(s)	Amino Acid Substitution ; Databases, Genetic ; Humans ; Iron-Binding Proteins/chemistry ; Iron-Binding Proteins/genetics ; Models, Molecular ; Molecular Dynamics Simulation ; Mutagenesis, Site-Directed ; Mutation, Missense ; Neoplasms/genetics ; Protein Conformation ; Protein Stability ; Frataxin
Chemical Substances	Iron-Binding Proteins
Language	English
Publishing date	2019-06-18
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	1126646-6
ISSN	1098-1004 ; 1059-7794
ISSN (online)	1098-1004
ISSN	1059-7794
DOI	10.1002/humu.23789
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Article ; Online: Effect of BET Missense Mutations on Bromodomain Function, Inhibitor Binding and Stability.

Lori, Laura / Pasquo, Alessandra / Lori, Clorinda / Petrosino, Maria / Chiaraluce, Roberta / Tallant, Cynthia / Knapp, Stefan / Consalvi, Valerio

PloS one

2016 Volume 11, Issue 7, Page(s) e0159180

Abstract: Lysine acetylation is an important epigenetic mark regulating gene transcription and chromatin structure. Acetylated lysine residues are specifically recognized by bromodomains, small protein interaction modules that read these modification in a sequence ...

Abstract	Lysine acetylation is an important epigenetic mark regulating gene transcription and chromatin structure. Acetylated lysine residues are specifically recognized by bromodomains, small protein interaction modules that read these modification in a sequence and acetylation dependent way regulating the recruitment of transcriptional regulators and chromatin remodelling enzymes to acetylated sites in chromatin. Recent studies revealed that bromodomains are highly druggable protein interaction domains resulting in the development of a large number of bromodomain inhibitors. BET bromodomain inhibitors received a lot of attention in the oncology field resulting in the rapid translation of early BET bromodomain inhibitors into clinical studies. Here we investigated the effects of mutations present as polymorphism or found in cancer on BET bromodomain function and stability and the influence of these mutants on inhibitor binding. We found that most BET missense mutations localize to peripheral residues in the two terminal helices. Crystal structures showed that the three dimensional structure is not compromised by these mutations but mutations located in close proximity to the acetyl-lysine binding site modulate acetyl-lysine and inhibitor binding. Most mutations affect significantly protein stability and tertiary structure in solution, suggesting new interactions and an alternative network of protein-protein interconnection as a consequence of single amino acid substitution. To our knowledge this is the first report studying the effect of mutations on bromodomain function and inhibitor binding.
MeSH term(s)	Amino Acid Sequence ; Lysine/chemistry ; Lysine/metabolism ; Models, Molecular ; Mutation, Missense ; Neoplasm Proteins/antagonists & inhibitors ; Neoplasm Proteins/chemistry ; Neoplasm Proteins/genetics ; Neoplasm Proteins/metabolism ; Protein Binding ; Protein Domains ; Protein Stability
Chemical Substances	Neoplasm Proteins ; Lysine (K3Z4F929H6)
Language	English
Publishing date	2016
Publishing country	United States
Document type	Journal Article
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0159180
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