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Papers by João M. C. Teixeira

The N-terminal regulatory region of c-Src including the SH4, Unique and SH3 domains adopts a comp... more The N-terminal regulatory region of c-Src including the SH4, Unique and SH3 domains adopts a compact, yet highly dynamic, structure that can be described as an intramolecular fuzzy complex. Most of the long-range interactions within the Unique domain are also observed in constructs lacking the structured SH3, indicating a considerable degree of preorganization of the disordered Unique domain. Here we report that members of the Src family of kinases (SFK) share well-conserved sequence features involving aromatic residues in their Unique domains. This observation contrasts with the supposed lack of sequence homology implied by the name of these domains and suggests that the other members of SFK also have a regulatory region involving their Unique domains. We argue that the Unique domain of each SFK is sensitive to specific input signals, encoded by each specific sequence, but the entire family shares a common mechanism for connecting the disordered and structured domains.

We report the synthesis of a cyclen-based ligand (4,10-bis[(1-oxidopyridin-2-yl)methyl]-1,4,7,10-... more We report the synthesis of a cyclen-based ligand (4,10-bis[(1-oxidopyridin-2-yl)methyl]-1,4,7,10-tetraazacyclododecane-1,7-diacetic acid=L1) containing two acetate and two 2-methylpyridine N-oxide arms anchored on the nitrogen atoms of the cyclen platform, which has been designed for stable complexation of lanthanide(III) ions in aqueous solution. Relaxometric studies suggest that the thermodynamic stability and kinetic inertness of the Gd(III) complex may be sufficient for biological applications. A detailed structural study of the complexes by (1) H NMR spectroscopy and DFT calculations indicates that they adopt an anti-$\Delta$($\lambda$$\lambda$$\lambda$$\lambda$) conformation in aqueous solution, that is, an anti-square antiprismatic (anti-SAP) isomeric form, as demonstrated by analysis of the (1) H NMR paramagnetic shifts induced by Yb(III) . The water-exchange rate of the Gd(III) complex is {\$}{\{}k{\{}{\{}298\backslashhfill \backslashatop {\{}\backslashrm ex{\}}\backslashhfill{\}}{\}}{\}}{\$}=6.7×10(6) s(-1) , about a quarter of that for the mono-oxidopyridine analogue, but still about 50 {\%} higher than the {\$}{\{}k{\{}{\{}298\backslashhfill \backslashatop {\{}\backslashrm ex{\}}\backslashhfill{\}}{\}}{\}}{\$} of GdDOTA (DOTA=1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid). The 2-methylpyridine N-oxide chromophores can be used to sensitize a wide range of Ln(III) ions emitting in both the visible (Eu(III) and Tb(III) ) and NIR (Pr(III) , Nd(III) , Ho(III) , Yb(III) ) spectral regions. The emission quantum yield determined for the Yb(III) complex ({\$}{\{}Q{\{}{\{}{\{}\backslashrm L{\}}\backslashhfill \backslashatop {\{}\backslashrm Yb{\}}\backslashhfill{\}}{\}}{\}}{\$}=7.3(1)×10(-3) ) is among the highest ever reported for complexes of this metal ion in aqueous solution. The sensitization ability of the ligand, together with the spectroscopic and relaxometric properties of its complexes, constitute a useful step forward on the way to efficient dual probes for optical imaging (OI) and MRI.

Catalysis of collagen degradation by matrix metalloproteinase 1 (MMP-1) has been proposed to crit... more Catalysis of collagen degradation by matrix metalloproteinase 1 (MMP-1) has been proposed to critically rely on flexibility between the catalytic (CAT) and hemopexin-like (HPX) domains. A rigorous assessment of the most readily accessed conformations in solution is required to explain the onset of substrate recognition and collagenolysis. The present study utilized paramagnetic NMR spectroscopy and small angle x-ray scattering (SAXS) to calculate the maximum occurrence (MO) of MMP-1 conformations. The MMP-1 conformations with large MO values (up to 47{\%}) are restricted into a relatively small conformational region. All conformations with high MO values differ largely from the closed MMP-1 structures obtained by x-ray crystallography. The MO of the latter is ∼20{\%}, which represents the upper limit for the presence of this conformation in the ensemble sampled by the protein in solution. In all the high MO conformations, the CAT and HPX domains are not in tight contact, and the residues of the HPX domain reported to be responsible for the binding to the collagen triple-helix are solvent exposed. Thus, overall analysis of the highest MO conformations indicated that MMP-1 in solution was poised to interact with collagen and then could readily proceed along the steps of collagenolysis.

Journal of Biomolecular NMR, May 18, 2018

We present Farseer-NMR (https://git.io/vAueU), a software package to treat, evaluate and combine ... more We present Farseer-NMR (https://git.io/vAueU), a software package to treat, evaluate and combine NMR spectroscopic data from sets of protein-derived peaklists covering a range of experimental conditions. The combined advances in NMR and molecular biology enable the study of complex biomolecular systems such as flexible proteins or large multibody complexes, which display a strong and functionally relevant response to their environmental conditions, e.g. the presence of ligands, site-directed mutations, post translational modifications, molecular crowders or the chemical composition of the solution. These advances have created a growing need to analyse those systems’ responses to multiple variables. The combined analysis of NMR peaklists from large and multivariable datasets has become a new bottleneck in the NMR analysis pipeline, whereby information-rich NMR-derived parameters have to be manually generated, which can be tedious, repetitive and prone to human error, or even unfeasible for very large datasets. There is a persistent gap in the development and distribution of software focused on peaklist treatment, analysis and representation, and specifically able to handle large multivariable datasets, which are becoming more commonplace. In this regard, Farseer-NMR aims to close this longstanding gap in the automated NMR user pipeline and, altogether, reduce the time burden of analysis of large sets of peaklists from days/weeks to seconds/minutes. We have implemented some of the most common, as well as new, routines for calculation of NMR parameters and several publication-quality plotting templates to improve NMR data representation. Farseer-NMR has been written entirely in Python and its modular code base enables facile extension.

Febs Letters, 2012

I. Bertini). FEBS Letters 586 (2012) 557-567 j o u r n a l h o m e p a g e : w w w . F E B S L e ... more I. Bertini). FEBS Letters 586 (2012) 557-567 j o u r n a l h o m e p a g e : w w w . F E B S L e t t e r s . o r g

Journal of Biological Inorganic Chemistry, 2011

The study of ligand-receptor interactions using high resolution NMR techniques, namely the Satura... more The study of ligand-receptor interactions using high resolution NMR techniques, namely the Saturation Transfer Difference (STD), is presented for the recognition process between La(III) complexes of DOTA mono(amide) and DTPA bis(amide) glycoconjugates and the galactose specific lectin Ricinus Communis agglutinin (RCA 120 ). This new class of Gd(III)-based potential targeted MRI contrast agents (CAs), bearing one or two terminal sugar (galactosyl or lactosyl) moieties, has been designed for in vivo binding to ASGPR (the asialoglycoprotein receptor), which is specifically expressed at the surface of liver hepatocytes, with the aim of leading to a new possible diagnosis of liver pathologies. The in vitro affinity constants of the divalent La(III)-glycoconjugate complexes to RCA 120 , used as a simple, water soluble receptor model, were higher than those of the monovalent analogues. The combination of the experimental data obtained from the STD NMR experiments with molecular modelling protocols (Autodock 4.1) allowed us to predict the binding mode of mono and divalent forms of these CAs to the galactose 1 binding sites of RCA 120 . The atomic details of the molecular interactions allowed corroborating and supporting the interaction of both the sugar moieties and the linkers with the surface of the protein and thus, their contribution to the observed interaction stabilities.

The N-terminal regulatory region of c-Src including the SH4, Unique and SH3 domains adopts a comp... more The N-terminal regulatory region of c-Src including the SH4, Unique and SH3 domains adopts a compact, yet highly dynamic, structure that can be described as an intramolecular fuzzy complex. Most of the long-range interactions within the Unique domain are also observed in constructs lacking the structured SH3, indicating a considerable degree of preorganization of the disordered Unique domain. Here we report that members of the Src family of kinases (SFK) share well-conserved sequence features involving aromatic residues in their Unique domains. This observation contrasts with the supposed lack of sequence homology implied by the name of these domains and suggests that the other members of SFK also have a regulatory region involving their Unique domains. We argue that the Unique domain of each SFK is sensitive to specific input signals, encoded by each specific sequence, but the entire family shares a common mechanism for connecting the disordered and structured domains.

We report the synthesis of a cyclen-based ligand (4,10-bis[(1-oxidopyridin-2-yl)methyl]-1,4,7,10-... more We report the synthesis of a cyclen-based ligand (4,10-bis[(1-oxidopyridin-2-yl)methyl]-1,4,7,10-tetraazacyclododecane-1,7-diacetic acid=L1) containing two acetate and two 2-methylpyridine N-oxide arms anchored on the nitrogen atoms of the cyclen platform, which has been designed for stable complexation of lanthanide(III) ions in aqueous solution. Relaxometric studies suggest that the thermodynamic stability and kinetic inertness of the Gd(III) complex may be sufficient for biological applications. A detailed structural study of the complexes by (1) H NMR spectroscopy and DFT calculations indicates that they adopt an anti-$\Delta$($\lambda$$\lambda$$\lambda$$\lambda$) conformation in aqueous solution, that is, an anti-square antiprismatic (anti-SAP) isomeric form, as demonstrated by analysis of the (1) H NMR paramagnetic shifts induced by Yb(III) . The water-exchange rate of the Gd(III) complex is {\$}{\{}k{\{}{\{}298\backslashhfill \backslashatop {\{}\backslashrm ex{\}}\backslashhfill{\}}{\}}{\}}{\$}=6.7×10(6) s(-1) , about a quarter of that for the mono-oxidopyridine analogue, but still about 50 {\%} higher than the {\$}{\{}k{\{}{\{}298\backslashhfill \backslashatop {\{}\backslashrm ex{\}}\backslashhfill{\}}{\}}{\}}{\$} of GdDOTA (DOTA=1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid). The 2-methylpyridine N-oxide chromophores can be used to sensitize a wide range of Ln(III) ions emitting in both the visible (Eu(III) and Tb(III) ) and NIR (Pr(III) , Nd(III) , Ho(III) , Yb(III) ) spectral regions. The emission quantum yield determined for the Yb(III) complex ({\$}{\{}Q{\{}{\{}{\{}\backslashrm L{\}}\backslashhfill \backslashatop {\{}\backslashrm Yb{\}}\backslashhfill{\}}{\}}{\}}{\$}=7.3(1)×10(-3) ) is among the highest ever reported for complexes of this metal ion in aqueous solution. The sensitization ability of the ligand, together with the spectroscopic and relaxometric properties of its complexes, constitute a useful step forward on the way to efficient dual probes for optical imaging (OI) and MRI.

Catalysis of collagen degradation by matrix metalloproteinase 1 (MMP-1) has been proposed to crit... more Catalysis of collagen degradation by matrix metalloproteinase 1 (MMP-1) has been proposed to critically rely on flexibility between the catalytic (CAT) and hemopexin-like (HPX) domains. A rigorous assessment of the most readily accessed conformations in solution is required to explain the onset of substrate recognition and collagenolysis. The present study utilized paramagnetic NMR spectroscopy and small angle x-ray scattering (SAXS) to calculate the maximum occurrence (MO) of MMP-1 conformations. The MMP-1 conformations with large MO values (up to 47{\%}) are restricted into a relatively small conformational region. All conformations with high MO values differ largely from the closed MMP-1 structures obtained by x-ray crystallography. The MO of the latter is ∼20{\%}, which represents the upper limit for the presence of this conformation in the ensemble sampled by the protein in solution. In all the high MO conformations, the CAT and HPX domains are not in tight contact, and the residues of the HPX domain reported to be responsible for the binding to the collagen triple-helix are solvent exposed. Thus, overall analysis of the highest MO conformations indicated that MMP-1 in solution was poised to interact with collagen and then could readily proceed along the steps of collagenolysis.

Journal of Biomolecular NMR, May 18, 2018

We present Farseer-NMR (https://git.io/vAueU), a software package to treat, evaluate and combine ... more We present Farseer-NMR (https://git.io/vAueU), a software package to treat, evaluate and combine NMR spectroscopic data from sets of protein-derived peaklists covering a range of experimental conditions. The combined advances in NMR and molecular biology enable the study of complex biomolecular systems such as flexible proteins or large multibody complexes, which display a strong and functionally relevant response to their environmental conditions, e.g. the presence of ligands, site-directed mutations, post translational modifications, molecular crowders or the chemical composition of the solution. These advances have created a growing need to analyse those systems’ responses to multiple variables. The combined analysis of NMR peaklists from large and multivariable datasets has become a new bottleneck in the NMR analysis pipeline, whereby information-rich NMR-derived parameters have to be manually generated, which can be tedious, repetitive and prone to human error, or even unfeasible for very large datasets. There is a persistent gap in the development and distribution of software focused on peaklist treatment, analysis and representation, and specifically able to handle large multivariable datasets, which are becoming more commonplace. In this regard, Farseer-NMR aims to close this longstanding gap in the automated NMR user pipeline and, altogether, reduce the time burden of analysis of large sets of peaklists from days/weeks to seconds/minutes. We have implemented some of the most common, as well as new, routines for calculation of NMR parameters and several publication-quality plotting templates to improve NMR data representation. Farseer-NMR has been written entirely in Python and its modular code base enables facile extension.

Febs Letters, 2012

I. Bertini). FEBS Letters 586 (2012) 557-567 j o u r n a l h o m e p a g e : w w w . F E B S L e ... more I. Bertini). FEBS Letters 586 (2012) 557-567 j o u r n a l h o m e p a g e : w w w . F E B S L e t t e r s . o r g

Journal of Biological Inorganic Chemistry, 2011

The study of ligand-receptor interactions using high resolution NMR techniques, namely the Satura... more The study of ligand-receptor interactions using high resolution NMR techniques, namely the Saturation Transfer Difference (STD), is presented for the recognition process between La(III) complexes of DOTA mono(amide) and DTPA bis(amide) glycoconjugates and the galactose specific lectin Ricinus Communis agglutinin (RCA 120 ). This new class of Gd(III)-based potential targeted MRI contrast agents (CAs), bearing one or two terminal sugar (galactosyl or lactosyl) moieties, has been designed for in vivo binding to ASGPR (the asialoglycoprotein receptor), which is specifically expressed at the surface of liver hepatocytes, with the aim of leading to a new possible diagnosis of liver pathologies. The in vitro affinity constants of the divalent La(III)-glycoconjugate complexes to RCA 120 , used as a simple, water soluble receptor model, were higher than those of the monovalent analogues. The combination of the experimental data obtained from the STD NMR experiments with molecular modelling protocols (Autodock 4.1) allowed us to predict the binding mode of mono and divalent forms of these CAs to the galactose 1 binding sites of RCA 120 . The atomic details of the molecular interactions allowed corroborating and supporting the interaction of both the sugar moieties and the linkers with the surface of the protein and thus, their contribution to the observed interaction stabilities.