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1.
Proteins ; 91(10): 1383-1393, 2023 10.
Article in English | MEDLINE | ID: mdl-37163386

ABSTRACT

Cystathionine ß-synthase (CBS) catalyzes the condensation of l-serine and l-homocysteine to give l-cystathionine in the transsulfuration pathway. Recently, a few O-acetylserine (l-OAS)-dependent CBSs (OCBSs) have been found in bacteria that can exclusively function with l-OAS. CBS from Toxoplasma gondii (TgCBS) can efficiently use both l-serine and l-OAS to form l-cystathionine. In this work, a series of site-specific variants substituting S84, Y160, and Y246 with hydrophobic residues found at the same positions in OCBSs was generated to explore the roles of the hydroxyl moieties of these residues as determinants of l-serine/l-OAS preference in TgCBS. We found that the S84A/Y160F/Y246V triple mutant behaved like an OCBS in terms of both substrate requirements, showing ß-replacement activity only with l-OAS, and pH optimum, which is decreased by ~1 pH unit. Formation of a stable aminoacrylate upon reaction with l-serine is prevented by the triple mutation, indicating the importance of the H-bonds between the hydroxyl groups of Y160, Y246, and S84 with l-serine in formation of the intermediate. Analysis of the independent effect of each mutation on TgCBS activity and investigation of the protein-aminoacrylate complex structure allowed for the conclusion that the hydroxyl group of Y246 has a major, but not exclusive, role in controlling the l-serine preference by efficiently stabilizing its leaving group. These studies demonstrate that differences in substrate specificity of CBSs are controlled by natural variations in as few as three residue positions. A better understanding of substrate specificity in TgCBS will facilitate the design of new antimicrobial compounds.


Subject(s)
Cystathionine beta-Synthase , Toxoplasma , Cystathionine beta-Synthase/genetics , Cystathionine beta-Synthase/chemistry , Cystathionine beta-Synthase/metabolism , Cystathionine/chemistry , Cystathionine/metabolism , Catalytic Domain , Toxoplasma/genetics , Toxoplasma/metabolism , Serine/metabolism , Kinetics
2.
Proc Natl Acad Sci U S A ; 117(6): 2948-2956, 2020 02 11.
Article in English | MEDLINE | ID: mdl-31974312

ABSTRACT

The spliceosome consists of five small RNAs and more than 100 proteins. Almost 50% of the human spliceosomal proteins were predicted to be intrinsically disordered or to contain disordered regions, among them the G-patch protein Spp2. The G-patch region of Spp2 binds to the DEAH-box ATPase Prp2, and both proteins together are essential for promoting the transition from the Bact to the catalytically active B* spliceosome. Here we show by circular dichroism and nuclear magnetic resonance (NMR) spectroscopy that Spp2 is intrinsically disordered in solution. Crystal structures of a complex consisting of Prp2-ADP and the G-patch domain of Spp2 demonstrate that the G-patch gains a defined fold when bound to Prp2. While the N-terminal region of the G-patch always folds into an α-helix in five different crystal structures, the C-terminal part is able to adopt two alternative conformations. NMR studies further revealed that the N-terminal part of the Spp2 G-patch, which is the most conserved region in different G-patch proteins, transiently samples helical conformations, possibly facilitating a conformational selection binding mechanism. The structural analysis unveils the role of conserved residues of the G-patch in the dynamic interaction mode of Spp2 with Prp2, which is vital to maintain the binding during the Prp2 domain movements needed for RNA translocation.


Subject(s)
DEAD-box RNA Helicases/metabolism , Saccharomyces cerevisiae Proteins/chemistry , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae/enzymology , Amino Acid Sequence , DEAD-box RNA Helicases/chemistry , DEAD-box RNA Helicases/genetics , Protein Binding , Protein Folding , Saccharomyces cerevisiae/chemistry , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae Proteins/genetics , Sequence Alignment
3.
J Am Chem Soc ; 144(35): 16157-16163, 2022 09 07.
Article in English | MEDLINE | ID: mdl-36018855

ABSTRACT

Liquid-liquid phase separation (LLPS) of intrinsically disordered proteins (IDPs) and the action of molecular chaperones are tightly connected. An important class of molecular chaperones are peptidyl prolyl isomerases, which enhance the cis/trans-isomerization of proline. However, little is known about the impact of peptidyl prolyl isomerases on the LLPS of IDPs, which often contain many prolines. Here, we demonstrate that the most ubiquitous peptidyl prolyl isomerase, peptidyl prolyl isomerase A (PPIA), concentrates inside liquid-like droplets formed by the Alzheimer's disease-associated protein tau, as well as inside RNA-induced coacervates of a proline-arginine dipeptide repeat protein. We further show that the recruitment of PPIA into the IDP droplets triggers their dissolution and return to a single mixed phase. NMR-based binding and proline isomerization studies provide insights into the mechanism of LLPS modulation. Together, the results establish a regulatory role of proline isomerases on the liquid-liquid phase separation of proline-rich IDPs.


Subject(s)
Intrinsically Disordered Proteins , Peptidylprolyl Isomerase , Molecular Chaperones , Peptidylprolyl Isomerase/metabolism , Proline/chemistry , tau Proteins/metabolism
4.
Biochem J ; 478(13): 2571-2587, 2021 07 16.
Article in English | MEDLINE | ID: mdl-34114596

ABSTRACT

Centrins are conserved calcium (Ca2+)-binding proteins typically associated with centrosomes that have been implicated in several biological processes. In Toxoplasma gondii, a parasite that causes toxoplasmosis, three centrin isoforms have been recognized. We have recently characterized the metal binding and structural features of isoform 1 (TgCEN1), demonstrating that it possesses properties consistent with a role as a Ca2+ sensor and displays a Ca2+-dependent tendency to self-assemble. Herein, we expanded our studies, focusing on the self-association and target binding properties of TgCEN1 by combining biophysical techniques including dynamic light scattering, isothermal titration calorimetry, nuclear magnetic resonance, circular dichroism, and fluorescence spectroscopy. We found that the self-assembly process of TgCEN1 depends on different physicochemical factors, including Ca2+ concentration, temperature, and protein concentration, and is mediated by both electrostatic and hydrophobic interactions. The process is completely abolished upon removal of the first 21-residues of the protein and is significantly reduced in the presence of a binding target peptide derived from the human XPC protein (P17-XPC). Titration of P17-XPC to the intact protein and isolated domains showed that TgCEN1 possesses two binding sites with distinct affinities and Ca2+ sensitivity; a high-affinity site in the C-lobe which may be constitutively bound to the peptide and a low-affinity site in the N-lobe which is active only upon Ca2+ stimulus. Overall, our results suggest a specific mechanism of TgCEN1 for Ca2+-modulated target binding and support a N-to-C self-assembly mode, in which the first 21-residues of one molecule likely interact with the C-lobe of the other.


Subject(s)
Calcium-Binding Proteins/metabolism , Cell Cycle Proteins/metabolism , Protozoan Proteins/metabolism , Toxoplasma/metabolism , Amino Acid Sequence , Calcium/metabolism , Calcium-Binding Proteins/chemistry , Calcium-Binding Proteins/genetics , Calorimetry , Cell Cycle Proteins/chemistry , Cell Cycle Proteins/genetics , Circular Dichroism , DNA-Binding Proteins/chemistry , Magnetic Resonance Spectroscopy , Peptides/chemistry , Peptides/metabolism , Protein Binding , Protein Isoforms/chemistry , Protein Isoforms/genetics , Protein Isoforms/metabolism , Protozoan Proteins/chemistry , Protozoan Proteins/genetics , Sequence Homology, Amino Acid , Thermodynamics , Toxoplasma/genetics , Toxoplasma/physiology , Toxoplasmosis/parasitology
5.
Int J Mol Sci ; 23(15)2022 Jul 25.
Article in English | MEDLINE | ID: mdl-35897745

ABSTRACT

Cystathionine beta-synthase (CBS) is a key regulator of homocysteine metabolism. Although eukaryotic CBS have a similar domain architecture with a catalytic core and a C-terminal Bateman module, their regulation varies widely across phyla. In human CBS (HsCBS), the C-terminus has an autoinhibitory effect by acting as a cap that avoids the entry of substrates into the catalytic site. The binding of the allosteric modulator AdoMet to this region alleviates this cap, allowing the protein to progress from a basal toward an activated state. The same activation is obtained by artificial removal or heat-denaturation of the Bateman module. Recently, we reported the crystal structure of CBS from Toxoplasma gondii (TgCBS) showing that the enzyme assembles into basket-like dimers similar to the basal conformers of HsCBS. These findings would suggest a similar lid function for the Bateman module which, as in HsCBS, should relax in the absence of the C-terminal module. However, herein we demonstrate that, in contrast with HsCBS, removal of the Bateman module in TgCBS through deletion mutagenesis, limited proteolysis, or thermal denaturation has no effects on its activity, oligomerization, and thermal stability. This opposite behavior we have now found in TgCBS provides evidence of a novel type of CBS regulation.


Subject(s)
Cystathionine beta-Synthase , Toxoplasma , Catalytic Domain , Humans , S-Adenosylmethionine/metabolism , Toxoplasma/metabolism
6.
Int J Mol Sci ; 22(22)2021 Nov 10.
Article in English | MEDLINE | ID: mdl-34830049

ABSTRACT

Centrins are a family of small, EF hand-containing proteins that are found in all eukaryotes and are often complexed with centrosome-related structures. Since their discovery, centrins have attracted increasing interest due to their multiple, diverse cellular functions. Centrins are similar to calmodulin (CaM) in size, structure and domain organization, although in contrast to CaM, the majority of centrins possess at least one calcium (Ca2+) binding site that is non-functional, thus displaying large variance in Ca2+ sensing abilities that could support their functional versatility. In this review, we summarize current knowledge on centrins from both biophysical and structural perspectives with an emphasis on centrin-target interactions. In-depth analysis of the Ca2+ sensing properties of centrins and structures of centrins complexed with target proteins can provide useful insight into the mechanisms of the different functions of centrins and how these proteins contribute to the complexity of the Ca2+ signaling cascade. Moreover, it can help to better understand the functional redundancy of centrin isoforms and centrin-binding proteins.


Subject(s)
Calcium-Binding Proteins/chemistry , Calcium-Binding Proteins/physiology , Calcium/metabolism , Calcium/chemistry , Calcium-Binding Proteins/metabolism , Cell Cycle Proteins/metabolism , Centrosome/metabolism , DNA Repair , EF Hand Motifs , Humans , Nuclear Proteins/metabolism , Protein Binding , RNA, Messenger/metabolism
7.
PLoS Biol ; 15(6): e2001336, 2017 Jun.
Article in English | MEDLINE | ID: mdl-28654636

ABSTRACT

The accumulation of amyloidogenic proteins is a pathological hallmark of neurodegenerative disorders. The aberrant accumulation of the microtubule associating protein tau (MAPT, tau) into toxic oligomers and amyloid deposits is a primary pathology in tauopathies, the most common of which is Alzheimer's disease (AD). Intrinsically disordered proteins, like tau, are enriched with proline residues that regulate both secondary structure and aggregation propensity. The orientation of proline residues is regulated by cis/trans peptidyl-prolyl isomerases (PPIases). Here we show that cyclophilin 40 (CyP40), a PPIase, dissolves tau amyloids in vitro. Additionally, CyP40 ameliorated silver-positive and oligomeric tau species in a mouse model of tau accumulation, preserving neuronal health and cognition. Nuclear magnetic resonance (NMR) revealed that CyP40 interacts with tau at sites rich in proline residues. CyP40 was also able to interact with and disaggregate other aggregating proteins that contain prolines. Moreover, CyP40 lacking PPIase activity prevented its capacity for disaggregation in vitro. Finally, we describe a unique structural property of CyP40 that may permit disaggregation to occur in an energy-independent manner. This study identifies a novel human protein disaggregase and, for the first time, demonstrates its capacity to dissolve intracellular amyloids.


Subject(s)
Amyloid/metabolism , Cyclophilins/metabolism , Neurodegenerative Diseases/metabolism , alpha-Synuclein/metabolism , tau Proteins/metabolism , Alzheimer Disease/genetics , Alzheimer Disease/metabolism , Amyloid/genetics , Amyloid/ultrastructure , Animals , Blotting, Western , Brain/metabolism , Brain/pathology , Brain/physiopathology , Cognition Disorders/genetics , Cognition Disorders/metabolism , Cognition Disorders/physiopathology , Peptidyl-Prolyl Isomerase F , Cyclophilins/genetics , Cyclosporine/pharmacology , Disease Models, Animal , Female , HEK293 Cells , Humans , Male , Mice, Transgenic , Microscopy, Electron, Transmission , Neurodegenerative Diseases/genetics , Protein Aggregates/drug effects , Protein Aggregation, Pathological , Tauopathies/genetics , Tauopathies/metabolism , alpha-Synuclein/genetics , tau Proteins/genetics
8.
Angew Chem Int Ed Engl ; 59(14): 5643-5646, 2020 03 27.
Article in English | MEDLINE | ID: mdl-31830361

ABSTRACT

Peptidylprolyl isomerases (PPIases) catalyze cis/trans isomerization of prolines. The PPIase CypA colocalizes with the Parkinson's disease (PD)-associated protein α-synuclein in cells and interacts with α-synuclein oligomers. Herein, we describe atomic insights into the molecular details of the α-synuclein/CypA interaction. NMR spectroscopy shows that CypA catalyzes isomerization of proline 128 in the C-terminal domain of α-synuclein. Strikingly, we reveal a second CypA-binding site formed by the hydrophobic sequence 47 GVVHGVATVA56 , termed PreNAC. The 1.38 Šcrystal structure of the CypA/PreNAC complex displays a contact between alanine 53 of α-synuclein and glutamine 111 in the catalytic pocket of CypA. Mutation of alanine 53 to glutamate, as found in patients with early-onset PD, weakens the interaction of α-synuclein with CypA. Our study provides high-resolution insights into the structure of the PD-associated protein α-synuclein in complex with the most abundant cellular cyclophilin.


Subject(s)
Cyclophilin A/metabolism , alpha-Synuclein/metabolism , Amino Acid Sequence , Binding Sites , Biocatalysis , Crystallography, X-Ray , Cyclophilin A/chemistry , Isomerism , Molecular Dynamics Simulation , Mutagenesis, Site-Directed , Nuclear Magnetic Resonance, Biomolecular , Proline/chemistry , Protein Binding , alpha-Synuclein/chemistry , alpha-Synuclein/genetics
9.
Hum Mol Genet ; 25(2): 275-90, 2016 Jan 15.
Article in English | MEDLINE | ID: mdl-26586132

ABSTRACT

Synucleins belong to a family of intrinsically unstructured proteins that includes alpha-synuclein (aSyn), beta-synuclein (bSyn) and gamma-synuclein (gSyn). aSyn is the most studied member of the synuclein family due to its central role in genetic and sporadic forms of Parkinson's disease and other neurodegenerative disorders known as synucleionopathies. In contrast, bSyn and gSyn have been less studied, but recent reports also suggest that, unexpectedly, these proteins may also cause neurotoxicity. Here, we explored the yeast toolbox to investigate the cellular effects of bSyn and gSyn. We found that bSyn is toxic and forms cytosolic inclusions that are similar to those formed by aSyn. Moreover, we found that bSyn shares similar toxicity mechanisms with aSyn, including vesicular trafficking impairment and induction of oxidative stress. We demonstrate that co-expression of aSyn and bSyn exacerbates cytotoxicity, due to increased dosage of toxic synuclein forms, and that they are able to form heterodimers in both yeast and in human cells. In contrast, gSyn is not toxic and does not form inclusions in yeast cells. Altogether, our findings shed light into the question of whether bSyn can exert toxic effects and confirms the occurrence of aSyn/bSyn heterodimers, opening novel perspectives for the development of novel strategies for therapeutic intervention in synucleinopathies.


Subject(s)
Oxidative Stress , alpha-Synuclein/metabolism , beta-Synuclein/metabolism , HEK293 Cells , Humans , Mutation , Protein Multimerization , Protein Transport , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/metabolism , Transgenes , Transport Vesicles , alpha-Synuclein/genetics , beta-Synuclein/genetics
10.
Arch Biochem Biophys ; 606: 99-110, 2016 09 15.
Article in English | MEDLINE | ID: mdl-27457417

ABSTRACT

Macromolecular crowding is a distinctive feature of the cellular interior, influencing the behaviour of biomacromolecules. Despite significant advancements in the description of the effects of crowding on global protein properties, the influence of cellular components on local protein attributes has received limited attention. Here, we describe a residue-level systematic interrogation of the structural, dynamic, and binding properties of the liver fatty acid binding protein (LFABP) in crowded solutions. Two-dimensional NMR spectral fingerprints and relaxation data were collected on LFABP in the presence of polymeric and biomolecular crowders. Non-interacting crowders produced minimal site-specific spectral perturbations on ligand-free and lipid-bound LFABP. Conformational adaptations upon ligand binding reproduced those observed in dilute solution, but a perturbation of the free oleate state resulted in less favorable uptake. When LFABP engaged in direct interactions with background molecules, changes in local chemical environments were detected for residues of the internal binding pocket and of the external surface. Enhanced complexity was introduced by investigating LFABP in cell lysates, and in membrane-bounded compartments. LFABP was able to capture ligands from prokaryotic and eukaryotic cell lysates, and from artificial cells (water-in-oil emulsion droplets). The data suggest that promiscuous interactions are a major factor influencing protein function in the cell.


Subject(s)
Fatty Acid-Binding Proteins/chemistry , Lipids/chemistry , Macromolecular Substances/metabolism , Amino Acids/chemistry , Animals , Binding Sites , Chickens , Egg White , Escherichia coli/metabolism , HeLa Cells , Humans , Hydrodynamics , Ligands , Light , Magnetic Resonance Spectroscopy , Muramidase/chemistry , Polymers/chemistry , Protein Binding , Protein Conformation , Scattering, Radiation , Serum Albumin, Bovine/chemistry
11.
Biochim Biophys Acta ; 1844(7): 1268-78, 2014 Jul.
Article in English | MEDLINE | ID: mdl-24768771

ABSTRACT

Lipids are essential for many biological processes and crucial in the pathogenesis of several diseases. Intracellular lipid-binding proteins (iLBPs) provide mobile hydrophobic binding sites that allow hydrophobic or amphipathic lipid molecules to penetrate into and across aqueous layers. Thus iLBPs mediate the lipid transport within the cell and participate to a spectrum of tissue-specific pathways involved in lipid homeostasis. Structural studies have shown that iLBPs' binding sites are inaccessible from the bulk, implying that substrate binding should involve a conformational change able to produce a ligand entry portal. Many studies have been reported in the last two decades on iLBPs indicating that their dynamics play a pivotal role in regulating ligand binding and targeted release. The ensemble of reported data has not been reviewed until today. This review is thus intended to summarize and possibly generalize the results up to now described, providing a picture which could help to identify the missing notions necessary to improve our understanding of the role of dynamics in iLBPs' molecular recognition. Such notions would clarify the chemistry of lipid binding to iLBPs and set the basis for the development of new drugs.


Subject(s)
Fatty Acid-Binding Proteins/chemistry , Fatty Acid-Binding Proteins/metabolism , Lipids/chemistry , Animals , Humans , Ligands , Protein Conformation
12.
Protein Sci ; 33(10): e5157, 2024 Oct.
Article in English | MEDLINE | ID: mdl-39312281

ABSTRACT

Toxoplasmosis persists as a prevalent disease, facing challenges from parasite resistance and treatment side effects. Consequently, identifying new drugs by exploring novel protein targets is essential for effective intervention. Cyclosporin A (CsA) possesses antiparasitic activity against Toxoplasma gondii, with cyclophilins identified as possible targets. However, CsA immunosuppressive nature hinders its use as an antitoxoplasmosis agent. Here, we evaluate the potential of three CsA derivatives devoid of immunosuppressive activity, namely, NIM811, Alisporivir, and dihydrocyclosporin A to target a previously characterized cyclophilin from Toxoplasma gondii (TgCyp23). We determined the X-ray crystal structures of TgCyp23 in complex with the three analogs and elucidated their binding and inhibitory properties. The high resolution of the structures revealed the precise positioning of ligands within the TgCyp23 binding site and the details of protein-ligand interactions. A comparison with the established ternary structure involving calcineurin indicates that substitutions at position 4 in CsA derivatives prevent calcineurin binding. This finding provides a molecular explanation for why CsA analogs can target Toxoplasma cyclophilins without compromising the human immune response.


Subject(s)
Cyclophilins , Cyclosporine , Toxoplasma , Toxoplasma/drug effects , Cyclophilins/chemistry , Cyclophilins/antagonists & inhibitors , Cyclophilins/metabolism , Crystallography, X-Ray , Cyclosporine/chemistry , Cyclosporine/pharmacology , Protozoan Proteins/chemistry , Protozoan Proteins/metabolism , Protozoan Proteins/antagonists & inhibitors , Protozoan Proteins/genetics , Models, Molecular , Binding Sites , Cyclosporins/chemistry , Cyclosporins/pharmacology
13.
Sci Rep ; 14(1): 9364, 2024 04 23.
Article in English | MEDLINE | ID: mdl-38654065

ABSTRACT

The escalating drug resistance among microorganisms underscores the urgent need for innovative therapeutic strategies and a comprehensive understanding of bacteria's defense mechanisms against oxidative stress and antibiotics. Among the recently discovered barriers, the endogenous production of hydrogen sulfide (H2S) via the reverse transsulfuration pathway, emerges as a noteworthy factor. In this study, we have explored the catalytic capabilities and crystal structure of cystathionine γ-lyase from Pseudomonas aeruginosa (PaCGL), a multidrug-opportunistic pathogen chiefly responsible for nosocomial infections. In addition to a canonical L-cystathionine hydrolysis, PaCGL efficiently catalyzes the production of H2S using L-cysteine and/or L-homocysteine as alternative substrates. Comparative analysis with the human enzyme and counterparts from other pathogens revealed distinct structural features within the primary enzyme cavities. Specifically, a distinctly folded entrance loop could potentially modulate the access of substrates and/or inhibitors to the catalytic site. Our findings offer significant insights into the structural evolution of CGL enzymes across different pathogens and provide novel opportunities for developing specific inhibitors targeting PaCGL.


Subject(s)
Catalytic Domain , Cystathionine gamma-Lyase , Hydrogen Sulfide , Pseudomonas aeruginosa , Pseudomonas aeruginosa/enzymology , Cystathionine gamma-Lyase/metabolism , Cystathionine gamma-Lyase/chemistry , Crystallography, X-Ray , Substrate Specificity , Hydrogen Sulfide/metabolism , Hydrogen Sulfide/chemistry , Models, Molecular , Cysteine/metabolism , Cysteine/chemistry , Protein Conformation , Bacterial Proteins/chemistry , Bacterial Proteins/metabolism , Humans , Homocysteine/metabolism , Homocysteine/chemistry , Catalysis
14.
Biochim Biophys Acta Proteins Proteom ; 1872(4): 141019, 2024 Jul 01.
Article in English | MEDLINE | ID: mdl-38641086

ABSTRACT

The Fragile X messenger ribonucleoprotein (FMRP) is a multi-domain protein involved in interactions with various macromolecules, including proteins and coding/non-coding RNAs. The three KH domains (KH0, KH1 and KH2) within FMRP are recognized for their roles in mRNA binding. In the context of Fragile X syndrome (FXS), over-and-above CGG triplet repeats expansion, three specific point mutations have been identified, each affecting one of the three KH domains (R138QKH0, G266EKH1, and I304NKH2) resulting in the expression of non-functional FMRP. This study aims to elucidate the molecular mechanism underlying the loss of function associated with the G266EKH1 pathological variant. We investigate the conformational and dynamic properties of the isolated KH1 domain and the two KH1 site-directed mutants G266EKH1 and G266AKH1. Employing a combined in vitro and in silico approach, we reveal that the G266EKH1 variant lacks the characteristic features of a folded domain. This observation provides an explanation for functional impairment observed in FMRP carrying the G266E mutation within the KH1 domain, as it renders the domain unable to fold properly. Molecular Dynamics simulations suggest a pivotal role for residue 266 in regulating the structural stability of the KH domains, primarily through stabilizing the α-helices of the domain. Overall, these findings enhance our comprehension of the molecular basis for the dysfunction associated with the G266EKH1 variant in FMRP.


Subject(s)
Fragile X Mental Retardation Protein , Fragile X Syndrome , Fragile X Mental Retardation Protein/genetics , Fragile X Mental Retardation Protein/metabolism , Fragile X Mental Retardation Protein/chemistry , Fragile X Syndrome/genetics , Fragile X Syndrome/metabolism , Humans , Protein Domains , Molecular Dynamics Simulation , Protein Conformation , Mutagenesis, Site-Directed
15.
Chembiochem ; 14(14): 1807-19, 2013 Sep 23.
Article in English | MEDLINE | ID: mdl-23757005

ABSTRACT

Human liver fatty acid binding protein (hL-FABP) has been reported to act as an intracellular shuttle of lipid molecules, thus playing a central role in systemic metabolic homeostasis. The involvement of hL-FABP in the transport of bile salts has been postulated but scarcely investigated. Here we describe a thorough NMR investigation of glycocholate (GCA) binding to hL-FABP. The protein molecule bound a single molecule of GCA, in contrast to the 1:2 stoichiometry observed with fatty acids. GCA was found to occupy the large internal cavity of hL-FABP, without requiring major conformational rearrangement of the protein backbone; rather, this led to increased stability, similar to that estimated for the hL-FABP:oleate complex. Fast-timescale dynamics appeared not to be significantly perturbed in the presence of ligands. Slow motions (unlike for other proteins of the family) were retained or enhanced upon binding, consistent with a requirement for structural plasticity for promiscuous recognition.


Subject(s)
Fatty Acid-Binding Proteins/chemistry , Glycocholic Acid/chemistry , Oleic Acid/chemistry , Binding Sites , Fatty Acid-Binding Proteins/genetics , Fatty Acid-Binding Proteins/metabolism , Glycocholic Acid/metabolism , Humans , Ligands , Nuclear Magnetic Resonance, Biomolecular , Oleic Acid/metabolism , Protein Binding , Protein Structure, Secondary , Protein Structure, Tertiary , Recombinant Proteins/biosynthesis , Recombinant Proteins/chemistry , Recombinant Proteins/genetics
16.
ACS Infect Dis ; 9(2): 365-377, 2023 02 10.
Article in English | MEDLINE | ID: mdl-36653744

ABSTRACT

Cyclosporin (CsA) has antiparasite activity against the human pathogen Toxoplasma gondii. A possible mechanism of action involves CsA binding to T. gondii cyclophilins, although much remains to be understood. Herein, we characterize the functional and structural properties of a conserved (TgCyp23) and a more divergent (TgCyp18.4) cyclophilin isoform from T. gondii. While TgCyp23 is a highly active cis-trans-prolyl isomerase (PPIase) and binds CsA with nanomolar affinity, TgCyp18.4 shows low PPIase activity and is significantly less sensitive to CsA inhibition. The crystal structure of the TgCyp23:CsA complex was solved at the atomic resolution showing the molecular details of CsA recognition by the protein. Computational and structural studies revealed relevant differences at the CsA-binding site between TgCyp18.4 and TgCyp23, suggesting that the two cyclophilins might have distinct functions in the parasite. These studies highlight the extensive diversification of TgCyps and pave the way for antiparasite interventions based on selective targeting of cyclophilins.


Subject(s)
Cyclophilins , Toxoplasma , Binding Sites , Cyclophilins/chemistry , Cyclophilins/metabolism , Cyclosporine/pharmacology , Cyclosporine/metabolism , Protein Isoforms
17.
Plant Physiol Biochem ; 203: 108003, 2023 Oct.
Article in English | MEDLINE | ID: mdl-37717348

ABSTRACT

Plasma membrane-associated Cation-binding Protein 1 (PCaP1) belongs to the plant-unique DREPP protein family with largely unknown biological functions but ascertained roles in plant development and calcium (Ca2+) signaling. PCaP1 is anchored to the plasma membrane via N-myristoylation and a polybasic cluster, and its N-terminal region can bind Ca2+/calmodulin (CaM). However, the molecular determinants of PCaP1-Ca2+-CaM interaction and the functional impact of myristoylation in the complex formation and Ca2+ sensitivity of CaM remained to be elucidated. Herein, we investigated the direct interaction between Arabidopsis PCaP1 (AtPCaP1) and CaM1 (AtCaM1) using both myristoylated and non-myristoylated peptides corresponding to the N-terminal region of AtPCaP1. ITC analysis showed that AtCaM1 forms a high affinity 1:1 complex with AtPCaP1 peptides and the interaction is strictly Ca2+-dependent. Spectroscopic and kinetic Ca2+ binding studies showed that the myristoylated peptide dramatically increased the Ca2+-binding affinity of AtCaM1 and slowed the Ca2+ dissociation rates from both the C- and N-lobes, thus suggesting that the myristoylation modulates the mechanism of AtPCaP1 recognition by AtCaM1. Furthermore, NMR and CD spectroscopy revealed that the structure of both the N- and C-lobes of Ca2+-AtCaM1 changes markedly in the presence of the myristoylated AtPCaP1 peptide, which assumes a helical structure in the final complex. Overall, our results indicate that AtPCaP1 biological function is strictly related to the presence of multiple ligands, i.e., the myristoyl moiety, Ca2+ ions and AtCaM1 and only a full characterization of their equilibria will allow for a complete molecular understanding of the putative role of PCaP1 as signal protein.

18.
Protein Sci ; 32(4): e4619, 2023 04.
Article in English | MEDLINE | ID: mdl-36883335

ABSTRACT

Cystathionine γ-lyase (CGL) is a PLP-dependent enzyme that catalyzes the last step of the reverse transsulfuration route for endogenous cysteine biosynthesis. The canonical CGL-catalyzed process consists of an α,γ-elimination reaction that breaks down cystathionine into cysteine, α-ketobutyrate, and ammonia. In some species, the enzyme can alternatively use cysteine as a substrate, resulting in the production of hydrogen sulfide (H2 S). Importantly, inhibition of the enzyme and consequently of its H2 S production activity, makes multiresistant bacteria considerably more susceptible to antibiotics. Other organisms, such as Toxoplasma gondii, the causative agent of toxoplasmosis, encode a CGL enzyme (TgCGL) that almost exclusively catalyzes the canonical process, with only minor reactivity to cysteine. Interestingly, the substitution of N360 by a serine (the equivalent amino acid residue in the human enzyme) at the active site changes the specificity of TgCGL for the catalysis of cystathionine, resulting in an enzyme that can cleave both the CγS and the CßS bond of cystathionine. Based on these findings and to deepen the molecular basis underlying the enzyme-substrate specificity, we have elucidated the crystal structures of native TgCGL and the variant TgCGL-N360S from crystals grown in the presence of cystathionine, cysteine, and the inhibitor d,l-propargylglycine (PPG). Our structures reveal the binding mode of each molecule within the catalytic cavity and help explain the inhibitory behavior of cysteine and PPG. A specific inhibitory mechanism of TgCGL by PPG is proposed.


Subject(s)
Cystathionine gamma-Lyase , Toxoplasma , Humans , Cystathionine gamma-Lyase/chemistry , Cystathionine gamma-Lyase/metabolism , Cysteine , Toxoplasma/metabolism , Cystathionine/metabolism
19.
Biomolecules ; 12(8)2022 08 13.
Article in English | MEDLINE | ID: mdl-36009009

ABSTRACT

Centrins are calcium (Ca2+)-binding proteins that are involved in many cellular functions including centrosome regulation. A known cellular target of centrins is SFI1, a large centrosomal protein containing multiple repeats that represent centrin-binding motifs. Recently, a protein homologous to yeast and mammalian SFI1, denominated TgSFI1, which shares SFI1-repeat organization, was shown to colocalize at centrosomes with centrin 1 from Toxoplasma gondii (TgCEN1). However, the molecular details of the interaction between TgCEN1 and TgSFI1 remain largely unknown. Herein, combining different biophysical methods, including isothermal titration calorimetry, nuclear magnetic resonance, circular dichroism, and fluorescence spectroscopy, we determined the binding properties of TgCEN1 and its individual N- and C-terminal domains to synthetic peptides derived from distinct repeats of TgSFI1. Overall, our data indicate that the repeats in TgSFI1 constitute binding sites for TgCEN1, but the binding modes of TgCEN1 to the repeats differ appreciably in terms of binding affinity, Ca2+ sensitivity, and lobe-specific interaction. These results suggest that TgCEN1 displays remarkable conformational plasticity, allowing for the distinct repeats in TgSFI1 to possess precise modes of TgCEN1 binding and regulation during Ca2+ sensing, which appears to be crucial for the dynamic association of TgCEN1 with TgSFI1 in the centrosome architecture.


Subject(s)
Saccharomyces cerevisiae Proteins , Toxoplasma , Amino Acid Sequence , Animals , Calcium/metabolism , Calcium-Binding Proteins/metabolism , Cell Cycle Proteins/metabolism , Mammals/metabolism , Protein Binding , Protein Conformation , Repressor Proteins/metabolism , Saccharomyces cerevisiae/metabolism , Saccharomyces cerevisiae Proteins/metabolism , Toxoplasma/metabolism
20.
Protein Sci ; 30(7): 1326-1336, 2021 07.
Article in English | MEDLINE | ID: mdl-33452693

ABSTRACT

In Parkinson's disease with dementia, up to 50% of patients develop a high number of tau-containing neurofibrillary tangles. Tau-based pathologies may thus act synergistically with the α-synuclein pathology to confer a worse prognosis. A better understanding of the relationship between the two distinct pathologies is therefore required. Liquid-liquid phase separation (LLPS) of proteins has recently been shown to be important for protein aggregation involved in amyotrophic lateral sclerosis, whereas tau phase separation has been linked to Alzheimer's disease. We therefore investigated the interaction of α-synuclein with tau and its consequences on tau LLPS. We find α-synuclein to have a low propensity for both, self-coacervation and RNA-mediated LLPS at pH 7.4. However, full-length but not carboxy-terminally truncated α-synuclein efficiently partitions into tau/RNA droplets. We further demonstrate that Cdk2-phosphorylation promotes the concentration of tau into RNA-induced droplets, but at the same time decreases the amount of α-synuclein inside the droplets. NMR spectroscopy reveals that the interaction of the carboxy-terminal domain of α-synuclein with the proline-rich region P2 of tau is required for the recruitment of α-synuclein into tau droplets. The combined data suggest that the concentration of α-synuclein into tau-associated condensates can contribute to synergistic aSyn/tau pathologies.


Subject(s)
alpha-Synuclein/chemistry , alpha-Synuclein/isolation & purification , tau Proteins/chemistry , tau Proteins/isolation & purification , Alzheimer Disease/metabolism , Amyotrophic Lateral Sclerosis/metabolism , Humans , Recombinant Proteins/chemistry , Recombinant Proteins/isolation & purification , Recombinant Proteins/metabolism , alpha-Synuclein/metabolism , tau Proteins/metabolism
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