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Article: Faster and sensitive zymographic detection of oxidases generating hydrogen peroxide. The case of diamine oxidase

Chomdom Kounga, Paul / Tchoumi Neree, Armelle / Pietrangeli, Paola / Marcocci, Lucia / Mateescu, Mircea Alexandru

Analytical biochemistry. 2022 Mar. 26,

2022

Abstract: The existing zymography method for the detection of diamine oxidase (DAO) activity has been improved by a new staining procedure with the aim to ameliorate its sensitivity. Both procedures used SDS-PAGE gels containing uniformly distributed entrapped ... ...

Abstract	The existing zymography method for the detection of diamine oxidase (DAO) activity has been improved by a new staining procedure with the aim to ameliorate its sensitivity. Both procedures used SDS-PAGE gels containing uniformly distributed entrapped peroxidase (that wouldn't migrate during electrophoresis). The new approach with 3,5-dichloro-2-hydroxybenzenesulfonate (DCHBS) as peroxidase substrate and with 4-amino-antipyrine as color stabilizer allows a more sensitive detection of DAO when compared to the previously reported o-phenylenediamine (o-PDA) as peroxidase substrate. The newly improved method appears faster, simple and environmentally friendly. It can be used for most of oxidases releasing hydrogen peroxide as reaction product.
Keywords	color ; diamine oxidase ; hydrogen peroxide ; peroxidase ; polyacrylamide gel electrophoresis ; stabilizers
Language	English
Dates of publication	2022-0326
Publishing place	Elsevier Inc.
Document type	Article
Note	Pre-press version
ZDB-ID	1110-1
ISSN	1096-0309 ; 0003-2697
ISSN (online)	1096-0309
ISSN	0003-2697
DOI	10.1016/j.ab.2022.114676
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Article ; Online: Faster and sensitive zymographic detection of oxidases generating hydrogen peroxide. The case of diamine oxidase.

Chomdom Kounga, Paul / Tchoumi Neree, Armelle / Pietrangeli, Paola / Marcocci, Lucia / Mateescu, Mircea Alexandru

Analytical biochemistry

2022 Volume 648, Page(s) 114676

Abstract	The existing zymography method for the detection of diamine oxidase (DAO) activity has been improved by a new staining procedure with the aim to ameliorate its sensitivity. Both procedures used SDS-PAGE gels containing uniformly distributed entrapped peroxidase (that wouldn't migrate during electrophoresis). The new approach with 3,5-dichloro-2-hydroxybenzenesulfonate (DCHBS) as peroxidase substrate and with 4-amino-antipyrine as color stabilizer allows a more sensitive detection of DAO when compared to the previously reported o-phenylenediamine (o-PDA) as peroxidase substrate. The newly improved method appears faster, simple and environmentally friendly. It can be used for most of oxidases releasing hydrogen peroxide as reaction product.
MeSH term(s)	Amine Oxidase (Copper-Containing) ; Coloring Agents ; Electrophoresis, Polyacrylamide Gel ; Hydrogen Peroxide ; Oxidoreductases ; Peroxidase ; Peroxidases
Chemical Substances	Coloring Agents ; Hydrogen Peroxide (BBX060AN9V) ; Oxidoreductases (EC 1.-) ; Peroxidases (EC 1.11.1.-) ; Peroxidase (EC 1.11.1.7) ; Amine Oxidase (Copper-Containing) (EC 1.4.3.21)
Language	English
Publishing date	2022-03-29
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1110-1
ISSN	1096-0309 ; 0003-2697
ISSN (online)	1096-0309
ISSN	0003-2697
DOI	10.1016/j.ab.2022.114676
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Article ; Online: Understanding the molecular basis of folding cooperativity through a comparative analysis of a multidomain protein and its isolated domains.

Santorelli, Daniele / Marcocci, Lucia / Pennacchietti, Valeria / Nardella, Caterina / Diop, Awa / Pietrangeli, Paola / Pagano, Livia / Toto, Angelo / Malagrinò, Francesca / Gianni, Stefano

The Journal of biological chemistry

2023 Volume 299, Issue 3, Page(s) 102983

Abstract: Although cooperativity is a well-established and general property of folding, our current understanding of this feature in multidomain folding is still relatively limited. In fact, there are contrasting results indicating that the constituent domains of ... ...

Abstract	Although cooperativity is a well-established and general property of folding, our current understanding of this feature in multidomain folding is still relatively limited. In fact, there are contrasting results indicating that the constituent domains of a multidomain protein may either fold independently on each other or exhibit interdependent supradomain phenomena. To address this issue, here we present the comparative analysis of the folding of a tandem repeat protein, comprising two contiguous PDZ domains, in comparison to that of its isolated constituent domains. By analyzing in detail the equilibrium and kinetics of folding at different experimental conditions, we demonstrate that despite each of the PDZ domains in isolation being capable of independent folding, at variance with previously characterized PDZ tandem repeats, the full-length construct folds and unfolds as a single cooperative unit. By exploiting quantitatively, the comparison of the folding of the tandem repeat to those observed for its constituent domains, as well as by characterizing a truncated variant lacking a short autoinhibitory segment, we successfully rationalize the molecular basis of the observed cooperativity and attempt to infer some general conclusions for multidomain systems.
MeSH term(s)	Kinetics ; Models, Molecular ; Protein Folding ; Proteins/chemistry ; Protein Conformation ; Protein Domains
Chemical Substances	Proteins
Language	English
Publishing date	2023-02-03
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1016/j.jbc.2023.102983
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Article ; Online: Characterization of the folding and binding properties of the PTB domain of FRS2 with phosphorylated and unphosphorylated ligands

Pennacchietti, Valeria / Pagano, Livia / Malagrinò, Francesca / Diop, Awa / Di Felice, Mariana / Di Matteo, Sara / Marcocci, Lucia / Pietrangeli, Paola / Toto, Angelo / Gianni, Stefano

Archives of Biochemistry and Biophysics. 2023 Sept., v. 745 p.109703-

2023

Abstract: PTB (PhosphoTyrosine Binding) domains are protein domains that exert their function by binding phosphotyrosine residues on other proteins. They are commonly found in a variety of signaling proteins and are important for mediating protein-protein ... ...

Abstract	PTB (PhosphoTyrosine Binding) domains are protein domains that exert their function by binding phosphotyrosine residues on other proteins. They are commonly found in a variety of signaling proteins and are important for mediating protein-protein interactions in numerous cellular processes. PTB domains can also exhibit binding to unphosphorylated ligands, suggesting that they have additional binding specificities beyond phosphotyrosine recognition. Structural studies have reported that the PTB domain from FRS2 possesses this peculiar feature, allowing it to interact with both phosphorylated and unphosphorylated ligands, such as TrkB and FGFR1, through different topologies and orientations. In an effort to elucidate the dynamic and functional properties of these protein-protein interactions, we provide a complete characterization of the folding mechanism of the PTB domain of FRS2 and the binding process to peptides mimicking specific regions of TrkB and FGFR1. By analyzing the equilibrium and kinetics of PTB folding, we propose a mechanism implying the presence of an intermediate along the folding pathway. Kinetic binding experiments performed at different ionic strengths highlighted the electrostatic nature of the interaction with both peptides. The specific role of single amino acids in early and late events of binding was pinpointed by site-directed mutagenesis. These results are discussed in light of previous experimental works on these protein systems.
Keywords	biophysics ; fibroblast growth factor receptor 1 ; ligands ; peptides ; site-directed mutagenesis ; Protein-protein interactions ; Stopped-flow ; TrkB ; FGFR1
Language	English
Dates of publication	2023-09
Publishing place	Elsevier Inc.
Document type	Article ; Online
ZDB-ID	523-x
ISSN	1096-0384 ; 0003-9861
ISSN (online)	1096-0384
ISSN	0003-9861
DOI	10.1016/j.abb.2023.109703
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Article ; Online: The binding selectivity of the C-terminal SH3 domain of Grb2, but not its folding pathway, is dictated by its contiguous SH2 domain.

Di Felice, Mariana / Pagano, Livia / Pennacchietti, Valeria / Diop, Awa / Pietrangeli, Paola / Marcocci, Lucia / Di Matteo, Sara / Malagrinò, Francesca / Toto, Angelo / Gianni, Stefano

The Journal of biological chemistry

2024 Volume 300, Issue 4, Page(s) 107129

Abstract: The adaptor protein Grb2, or growth factor receptor-bound protein 2, possesses a pivotal role in the transmission of fundamental molecular signals in the cell. Despite lacking enzymatic activity, Grb2 functions as a dynamic assembly platform, ... ...

Abstract	The adaptor protein Grb2, or growth factor receptor-bound protein 2, possesses a pivotal role in the transmission of fundamental molecular signals in the cell. Despite lacking enzymatic activity, Grb2 functions as a dynamic assembly platform, orchestrating intracellular signals through its modular structure. This study delves into the energetic communication of Grb2 domains, focusing on the folding and binding properties of the C-SH3 domain linked to its neighboring SH2 domain. Surprisingly, while the folding and stability of C-SH3 remain robust and unaffected by SH2 presence, significant differences emerge in the binding properties when considered within the tandem context compared with isolated C-SH3. Through a double mutant cycle analysis, we highlighted a subset of residues, located at the interface with the SH2 domain and far from the binding site, finely regulating the binding of a peptide mimicking a physiological ligand of the C-SH3 domain. Our results have mechanistic implications about the mechanisms of specificity of the C-SH3 domain, indicating that the presence of the SH2 domain optimizes binding to its physiological target, and emphasizing the general importance of considering supramodular multidomain protein structures to understand the functional intricacies of protein-protein interaction domains.
MeSH term(s)	GRB2 Adaptor Protein/metabolism ; GRB2 Adaptor Protein/chemistry ; GRB2 Adaptor Protein/genetics ; src Homology Domains ; Humans ; Protein Folding ; Protein Binding ; Binding Sites
Chemical Substances	GRB2 Adaptor Protein ; GRB2 protein, human
Language	English
Publishing date	2024-03-01
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1016/j.jbc.2024.107129
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Article ; Online: The Mechanism of Folding of Human Frataxin in Comparison to the Yeast Homologue - Broad Energy Barriers and the General Properties of the Transition State.

Pietrangeli, Paola / Marcocci, Lucia / Pennacchietti, Valeria / Diop, Awa / Di Felice, Mariana / Pagano, Livia / Malagrinò, Francesca / Toto, Angelo / Brunori, Maurizio / Gianni, Stefano

Journal of molecular biology

2024 Volume 436, Issue 10, Page(s) 168555

Abstract: The funneled energy landscape theory suggests that the folding pathway of homologous proteins should converge at the late stages of folding. In this respect, proteins displaying a broad energy landscape for folding are particularly instructive, allowing ... ...

Abstract	The funneled energy landscape theory suggests that the folding pathway of homologous proteins should converge at the late stages of folding. In this respect, proteins displaying a broad energy landscape for folding are particularly instructive, allowing inferring both the early, intermediate and late stages of folding. In this paper we explore the folding mechanisms of human frataxin, an essential mitochondrial protein linked to the neurodegenerative disorder Friedreich's ataxia. Building upon previous studies on the yeast homologue, the folding pathway of human frataxin is thoroughly examined, revealing a mechanism implying the presence of a broad energy barrier, reminiscent of the yeast counterpart. Through an extensive site-directed mutagenesis, we employed a Φ -value analysis to map native-like contacts in the folding transition state. The presence of a broad energy barrier facilitated the exploration of such contacts in both early and late folding events. We compared results from yeast and human frataxin providing insights into the impact of native topology on the folding mechanism and elucidating the properties of the underlying free energy landscape. The findings are discussed in the context of the funneled energy landscape theory of protein folding.
MeSH term(s)	Frataxin ; Iron-Binding Proteins/chemistry ; Iron-Binding Proteins/metabolism ; Iron-Binding Proteins/genetics ; Protein Folding ; Humans ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae/genetics ; Thermodynamics ; Models, Molecular ; Protein Conformation ; Saccharomyces cerevisiae Proteins/chemistry ; Saccharomyces cerevisiae Proteins/metabolism ; Saccharomyces cerevisiae Proteins/genetics ; Mutagenesis, Site-Directed ; Kinetics
Chemical Substances	Frataxin ; Iron-Binding Proteins ; Saccharomyces cerevisiae Proteins
Language	English
Publishing date	2024-03-27
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2024.168555
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Article ; Online: Copper‑containing amine oxidase purified from Lathyrus sativus as a modulator of human neutrophil functions.

Pietrangeli, Paola / Capuozzo, Elisabetta / Mateescu, Mircea Alexandru / Marcocci, Lucia

International journal of molecular medicine

2020 Volume 45, Issue 5, Page(s) 1583–1590

Abstract: Over the last few decades, copper‑containing amine oxidase (Cu‑AO) from vegetal sources, and belonging to the class of diamine oxidase, has been documented to exhibit beneficial effects in both in vivo and ex vivo animal models of inflammatory or ... ...

Abstract	Over the last few decades, copper‑containing amine oxidase (Cu‑AO) from vegetal sources, and belonging to the class of diamine oxidase, has been documented to exhibit beneficial effects in both in vivo and ex vivo animal models of inflammatory or allergic conditions, including asthma‑like reaction and myocardial or intestinal ischemia‑reperfusion injuries. The aim of the present study was to assess the potential of vegetal Cu‑AO as an anti‑inflammatory and an antiallergic agent and to clarify its antioxidant properties. In cell‑free systems, the reactive oxygen species and reactive nitrogen species scavenging properties of Cu‑AO that is purified from Lathyrus sativus were investigated. Its effect on the formyl‑methionyl‑leucyl‑phenylalanine peptide (fMLP)‑activated cellular functions of human neutrophils were subsequently analyzed. The obtained results demonstrated that Cu‑AO is not a scavenger of superoxide or nitric oxide, and does not decompose hydrogen peroxide. However, it inhibits the fMLP‑dependent superoxide generation, elastase release and cell migration, and interferes with the process of calcium flux, supporting the idea that plant Cu‑AO can interact with human neutrophils to modulate their inflammatory function. Therefore, the importance of these properties on the possible use of vegetal Cu‑AO to control inflammatory conditions, particularly intestinal inflammation, is discussed in the current study.
MeSH term(s)	Adolescent ; Adult ; Aged ; Amine Oxidase (Copper-Containing)/chemistry ; Amine Oxidase (Copper-Containing)/pharmacology ; Female ; Humans ; Hydrogen Peroxide/metabolism ; Inflammation/metabolism ; Lathyrus/chemistry ; Male ; Middle Aged ; Neutrophils/drug effects ; Nitric Oxide/metabolism ; Plant Proteins/metabolism ; Superoxides/metabolism ; Young Adult
Chemical Substances	Plant Proteins ; Superoxides (11062-77-4) ; Nitric Oxide (31C4KY9ESH) ; Hydrogen Peroxide (BBX060AN9V) ; Amine Oxidase (Copper-Containing) (EC 1.4.3.21)
Language	English
Publishing date	2020-03-11
Publishing country	Greece
Document type	Journal Article
ZDB-ID	1444428-8
ISSN	1791-244X ; 1107-3756
ISSN (online)	1791-244X
ISSN	1107-3756
DOI	10.3892/ijmm.2020.4535
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Article ; Online: Folding and Binding Mechanisms of the SH2 Domain from Crkl.

Nardella, Caterina / Toto, Angelo / Santorelli, Daniele / Pagano, Livia / Diop, Awa / Pennacchietti, Valeria / Pietrangeli, Paola / Marcocci, Lucia / Malagrinò, Francesca / Gianni, Stefano

Biomolecules

2022 Volume 12, Issue 8

Abstract: SH2 domains are structural modules specialized in the recognition and binding of target sequences containing a phosphorylated tyrosine residue. They are mostly incorporated in the 3D structure of scaffolding proteins that represent fundamental regulators ...

Abstract	SH2 domains are structural modules specialized in the recognition and binding of target sequences containing a phosphorylated tyrosine residue. They are mostly incorporated in the 3D structure of scaffolding proteins that represent fundamental regulators of several signaling pathways. Among those, Crkl plays key roles in cell physiology by mediating signals from a wide range of stimuli, and its overexpression is associated with several types of cancers. In myeloid cells expressing the oncogene BCR/ABL, one interactor of Crkl-SH2 is the focal adhesion protein Paxillin, and this interaction is crucial in leukemic transformation. In this work, we analyze both the folding pathway of Crkl-SH2 and its binding reaction with a peptide mimicking Paxillin, under different ionic strength and pH conditions, by using means of fluorescence spectroscopy. From a folding perspective, we demonstrate the presence of an intermediate along the reaction. Moreover, we underline the importance of the electrostatic interactions in the early event of recognition, occurring between the phosphorylated tyrosine of the Paxillin peptide and the charge residues of Crkl-SH2. Finally, we highlight a pivotal role of a highly conserved histidine residue in the stabilization of the binding complex. The experimental results are discussed in light of previous works on other SH2 domains.
MeSH term(s)	Nuclear Proteins/metabolism ; Oncogenes ; Paxillin ; Phosphorylation ; Protein Binding ; Tyrosine/metabolism ; src Homology Domains/physiology
Chemical Substances	Nuclear Proteins ; Paxillin ; Tyrosine (42HK56048U)
Language	English
Publishing date	2022-07-22
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2701262-1
ISSN	2218-273X ; 2218-273X
ISSN (online)	2218-273X
ISSN	2218-273X
DOI	10.3390/biom12081014
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Article ; Online: SH2 Domains: Folding, Binding and Therapeutical Approaches.

Diop, Awa / Santorelli, Daniele / Malagrinò, Francesca / Nardella, Caterina / Pennacchietti, Valeria / Pagano, Livia / Marcocci, Lucia / Pietrangeli, Paola / Gianni, Stefano / Toto, Angelo

International journal of molecular sciences

2022 Volume 23, Issue 24

Abstract: SH2 (Src Homology 2) domains are among the best characterized and most studied protein-protein interaction (PPIs) modules able to bind and recognize sequences presenting a phosphorylated tyrosine. This post-translational modification is a key regulator ... ...

Abstract	SH2 (Src Homology 2) domains are among the best characterized and most studied protein-protein interaction (PPIs) modules able to bind and recognize sequences presenting a phosphorylated tyrosine. This post-translational modification is a key regulator of a plethora of physiological and molecular pathways in the eukaryotic cell, so SH2 domains possess a fundamental role in cell signaling. Consequently, several pathologies arise from the dysregulation of such SH2-domains mediated PPIs. In this review, we recapitulate the current knowledge about the structural, folding stability, and binding properties of SH2 domains and their roles in molecular pathways and pathogenesis. Moreover, we focus attention on the different strategies employed to modulate/inhibit SH2 domains binding. Altogether, the information gathered points to evidence that pharmacological interest in SH2 domains is highly strategic to developing new therapeutics. Moreover, a deeper understanding of the molecular determinants of the thermodynamic stability as well as of the binding properties of SH2 domains appears to be fundamental in order to improve the possibility of preventing their dysregulated interactions.
Language	English
Publishing date	2022-12-15
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/ijms232415944
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Article ; Online: Exploring the effect of tethered domains on the folding of Grb2 protein.

Pagano, Livia / Pennacchietti, Valeria / Diop, Awa / Santorelli, Daniele / Pietrangeli, Paola / Marcocci, Lucia / Nardella, Caterina / Malagrinò, Francesca / Toto, Angelo / Gianni, Stefano

Archives of biochemistry and biophysics

2022 Volume 731, Page(s) 109444

Abstract: Two thirds of eukaryotic proteins have evolved as multidomain constructs, and in vivo, domains fold within a polypeptide chain, with inter-domain interactions possibly crucial for correct folding. However, to date, most of the experimental folding ... ...

Abstract	Two thirds of eukaryotic proteins have evolved as multidomain constructs, and in vivo, domains fold within a polypeptide chain, with inter-domain interactions possibly crucial for correct folding. However, to date, most of the experimental folding studies are based on domains in isolation. In an effort to better understand multidomain folding, in this work we analyzed, through equilibrium and kinetic folding experiments, the folding properties of the Growth factor receptor-bound protein 2 (Grb2), composed by one SRC homology 2 domain flanked by two SRC homology 3 domains. In particular we compared the kinetic features of the multidomain construct with the domains expressed in isolation. By performing single and double mixing folding experiments, we demonstrated that the folding of the SH2 domain is kinetically trapped in a misfolded intermediate when tethered to the C-SH3. Importantly, within the multidomain construct, misfolding occurred independently if refolding is started with C-SH3 in its unfolded or native state. Interestingly, our data reported a peculiar scenario, in which SH2 and C-SH3 domain reciprocally and transiently interact during folding. Altogether, the analysis of kinetic folding data provided a quantitative description of the multidomain folding of Grb2 protein, discussed under the light of previous works on multidomain folding.
MeSH term(s)	src Homology Domains ; Kinetics ; Peptides/chemistry ; Protein Folding
Chemical Substances	Peptides
Language	English
Publishing date	2022-10-18
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	523-x
ISSN	1096-0384 ; 0003-9861
ISSN (online)	1096-0384
ISSN	0003-9861
DOI	10.1016/j.abb.2022.109444
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