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1.
Nat Commun ; 14(1): 7511, 2023 11 18.
Artículo en Inglés | MEDLINE | ID: mdl-37980423

RESUMEN

Sodium-dependent glucose transporters (SGLTs) couple a downhill Na+ ion gradient to actively transport sugars. Here, we investigate the impact of the membrane potential on vSGLT structure and function using sugar uptake assays, double electron-electron resonance (DEER), electrostatic calculations, and kinetic modeling. Negative membrane potentials, as present in all cell types, shift the conformational equilibrium of vSGLT towards an outward-facing conformation, leading to increased sugar transport rates. Electrostatic calculations identify gating charge residues responsible for this conformational shift that when mutated reduce galactose transport and eliminate the response of vSGLT to potential. Based on these findings, we propose a comprehensive framework for sugar transport via vSGLT, where the cellular membrane potential facilitates resetting of the transporter after cargo release. This framework holds significance not only for SGLTs but also for other transporters and channels.


Asunto(s)
Simportadores , Simportadores/metabolismo , Azúcares , Glucosa , Potenciales de la Membrana , Galactosa/metabolismo , Espectroscopía de Resonancia por Spin del Electrón , Proteínas de Transporte de Sodio-Glucosa/genética , Proteínas de Transporte de Sodio-Glucosa/química , Proteínas de Transporte de Sodio-Glucosa/metabolismo , Sodio/metabolismo , Conformación Proteica
2.
PLoS One ; 18(4): e0280975, 2023.
Artículo en Inglés | MEDLINE | ID: mdl-37079572

RESUMEN

Nucleotide Sugar Transporters (NSTs) belong to the SLC35 family (human solute carrier) of membrane transport proteins and are crucial components of the glycosylation machinery. NSTs are localized in the ER and Golgi apparatus membranes, where they accumulate nucleotide sugars from the cytosol for subsequent polysaccharide biosynthesis. Loss of NST function impacts the glycosylation of cell surface molecules. Mutations in NSTs cause several developmental disorders, immune disorders, and increased susceptibility to infection. Atomic resolution structures of three NSTs have provided a blueprint for a detailed molecular interpretation of their biochemical properties. In this work, we have identified, cloned, and expressed 18 members of the SLC35 family from various eukaryotic organisms in Saccharomyces cerevisiae. Out of 18 clones, we determined Vrg4 from Chaetomium thermophilum (CtVrg4) is a GDP-mannose transporter with an enhanced melting point temperature (Tm) of 56.9°C, which increases with the addition of substrates, GMP and GDP-mannose. In addition, we report-for the first time-that the CtVrg4 shows an affinity to bind to phosphatidylinositol lipids.


Asunto(s)
Proteínas Portadoras , Proteínas de Saccharomyces cerevisiae , Humanos , Proteínas Portadoras/metabolismo , Transporte Biológico , Saccharomyces cerevisiae/genética , Glicosilación , Nucleótidos/metabolismo , Aparato de Golgi/metabolismo , Proteínas de Transporte de Membrana/metabolismo , Proteínas de Saccharomyces cerevisiae/metabolismo
3.
J Am Chem Soc ; 144(32): 14564-14577, 2022 08 17.
Artículo en Inglés | MEDLINE | ID: mdl-35925797

RESUMEN

The voltage-dependent anion channel (VDAC) is a ß-barrel channel of the mitochondrial outer membrane (MOM) that passively transports ions, metabolites, polypeptides, and single-stranded DNA. VDAC responds to a transmembrane potential by "gating," i.e. transitioning to one of a variety of low-conducting states of unknown structure. The gated state results in nearly complete suppression of multivalent mitochondrial metabolite (such as ATP and ADP) transport, while enhancing calcium transport. Voltage gating is a universal property of ß-barrel channels, but VDAC gating is anomalously sensitive to transmembrane potential. Here, we show that a single residue in the pore interior, K12, is responsible for most of VDAC's voltage sensitivity. Using the analysis of over 40 µs of atomistic molecular dynamics (MD) simulations, we explore correlations between motions of charged residues inside the VDAC pore and geometric deformations of the ß-barrel. Residue K12 is bistable; its motions between two widely separated positions along the pore axis enhance the fluctuations of the ß-barrel and augment the likelihood of gating. Single channel electrophysiology of various K12 mutants reveals a dramatic reduction of the voltage-induced gating transitions. The crystal structure of the K12E mutant at a resolution of 2.6 Å indicates a similar architecture of the K12E mutant to the wild type; however, 60 µs of atomistic MD simulations using the K12E mutant show restricted motion of residue 12, due to enhanced connectivity with neighboring residues, and diminished amplitude of barrel motions. We conclude that ß-barrel fluctuations, governed particularly by residue K12, drive VDAC gating transitions.


Asunto(s)
Membranas Mitocondriales , Canales Aniónicos Dependientes del Voltaje , Potenciales de la Membrana , Mitocondrias/metabolismo , Membranas Mitocondriales/metabolismo , Simulación de Dinámica Molecular , Canales Aniónicos Dependientes del Voltaje/metabolismo
4.
PLoS Genet ; 17(7): e1009651, 2021 07.
Artículo en Inglés | MEDLINE | ID: mdl-34197453

RESUMEN

Smith-Kingsmore syndrome (SKS) is a rare neurodevelopmental disorder characterized by macrocephaly/megalencephaly, developmental delay, intellectual disability, hypotonia, and seizures. It is caused by dominant missense mutations in MTOR. The pathogenicity of novel variants in MTOR in patients with neurodevelopmental disorders can be difficult to determine and the mechanism by which variants cause disease remains poorly understood. We report 7 patients with SKS with 4 novel MTOR variants and describe their phenotypes. We perform in vitro functional analyses to confirm MTOR activation and interrogate disease mechanisms. We complete structural analyses to understand the 3D properties of pathogenic variants. We examine the accuracy of relative accessible surface area, a quantitative measure of amino acid side-chain accessibility, as a predictor of MTOR variant pathogenicity. We describe novel clinical features of patients with SKS. We confirm MTOR Complex 1 activation and identify MTOR Complex 2 activation as a new potential mechanism of disease in SKS. We find that pathogenic MTOR variants disproportionately cluster in hotspots in the core of the protein, where they disrupt alpha helix packing due to the insertion of bulky amino acid side chains. We find that relative accessible surface area is significantly lower for SKS-associated variants compared to benign variants. We expand the phenotype of SKS and demonstrate that additional pathways of activation may contribute to disease. Incorporating 3D properties of MTOR variants may help in pathogenicity classification. We hope these findings may contribute to improving the precision of care and therapeutic development for individuals with SKS.


Asunto(s)
Trastornos del Neurodesarrollo/genética , Serina-Treonina Quinasas TOR/genética , Adulto , Preescolar , Discapacidades del Desarrollo/genética , Femenino , Humanos , Discapacidad Intelectual/genética , Masculino , Megalencefalia/genética , Persona de Mediana Edad , Mutación , Mutación Missense , Trastornos del Neurodesarrollo/fisiopatología , Fenotipo , Serina-Treonina Quinasas TOR/metabolismo
5.
Genome Med ; 13(1): 90, 2021 05 21.
Artículo en Inglés | MEDLINE | ID: mdl-34020708

RESUMEN

BACKGROUND: We aimed to define the clinical and variant spectrum and to provide novel molecular insights into the DHX30-associated neurodevelopmental disorder. METHODS: Clinical and genetic data from affected individuals were collected through Facebook-based family support group, GeneMatcher, and our network of collaborators. We investigated the impact of novel missense variants with respect to ATPase and helicase activity, stress granule (SG) formation, global translation, and their effect on embryonic development in zebrafish. SG formation was additionally analyzed in CRISPR/Cas9-mediated DHX30-deficient HEK293T and zebrafish models, along with in vivo behavioral assays. RESULTS: We identified 25 previously unreported individuals, ten of whom carry novel variants, two of which are recurrent, and provide evidence of gonadal mosaicism in one family. All 19 individuals harboring heterozygous missense variants within helicase core motifs (HCMs) have global developmental delay, intellectual disability, severe speech impairment, and gait abnormalities. These variants impair the ATPase and helicase activity of DHX30, trigger SG formation, interfere with global translation, and cause developmental defects in a zebrafish model. Notably, 4 individuals harboring heterozygous variants resulting either in haploinsufficiency or truncated proteins presented with a milder clinical course, similar to an individual harboring a de novo mosaic HCM missense variant. Functionally, we established DHX30 as an ATP-dependent RNA helicase and as an evolutionary conserved factor in SG assembly. Based on the clinical course, the variant location, and type we establish two distinct clinical subtypes. DHX30 loss-of-function variants cause a milder phenotype whereas a severe phenotype is caused by HCM missense variants that, in addition to the loss of ATPase and helicase activity, lead to a detrimental gain-of-function with respect to SG formation. Behavioral characterization of dhx30-deficient zebrafish revealed altered sleep-wake activity and social interaction, partially resembling the human phenotype. CONCLUSIONS: Our study highlights the usefulness of social media to define novel Mendelian disorders and exemplifies how functional analyses accompanied by clinical and genetic findings can define clinically distinct subtypes for ultra-rare disorders. Such approaches require close interdisciplinary collaboration between families/legal representatives of the affected individuals, clinicians, molecular genetics diagnostic laboratories, and research laboratories.


Asunto(s)
Estudios de Asociación Genética , Predisposición Genética a la Enfermedad , Trastornos del Neurodesarrollo/diagnóstico , Trastornos del Neurodesarrollo/genética , ARN Helicasas/genética , Animales , Biomarcadores , Expresión Génica , Técnicas de Silenciamiento del Gen , Estudios de Asociación Genética/métodos , Mutación de Línea Germinal , Células HEK293 , Humanos , Inmunohistoquímica , Mutación , Fenotipo , ARN Helicasas/química , ARN Helicasas/metabolismo , Pez Cebra
6.
Sci Transl Med ; 13(594)2021 05 19.
Artículo en Inglés | MEDLINE | ID: mdl-34011630

RESUMEN

Although the role of hydrophilic antioxidants in the development of hepatic insulin resistance and nonalcoholic fatty liver disease has been well studied, the role of lipophilic antioxidants remains poorly characterized. A known lipophilic hydrogen peroxide scavenger is bilirubin, which can be oxidized to biliverdin and then reduced back to bilirubin by cytosolic biliverdin reductase. Oxidation of bilirubin to biliverdin inside mitochondria must be followed by the export of biliverdin to the cytosol, where biliverdin is reduced back to bilirubin. Thus, the putative mitochondrial exporter of biliverdin is expected to be a major determinant of bilirubin regeneration and intracellular hydrogen peroxide scavenging. Here, we identified ABCB10 as a mitochondrial biliverdin exporter. ABCB10 reconstituted into liposomes transported biliverdin, and ABCB10 deletion caused accumulation of biliverdin inside mitochondria. Obesity with insulin resistance up-regulated hepatic ABCB10 expression in mice and elevated cytosolic and mitochondrial bilirubin content in an ABCB10-dependent manner. Revealing a maladaptive role of ABCB10-driven bilirubin synthesis, hepatic ABCB10 deletion protected diet-induced obese mice from steatosis and hyperglycemia, improving insulin-mediated suppression of glucose production and decreasing lipogenic SREBP-1c expression. Protection was concurrent with enhanced mitochondrial function and increased inactivation of PTP1B, a phosphatase disrupting insulin signaling and elevating SREBP-1c expression. Restoration of cellular bilirubin content in ABCB10 KO hepatocytes reversed the improvements in mitochondrial function and PTP1B inactivation, demonstrating that bilirubin was the maladaptive effector linked to ABCB10 function. Thus, we identified a fundamental transport process that amplifies intracellular bilirubin redox actions, which can exacerbate insulin resistance and steatosis in obesity.


Asunto(s)
Biliverdina , Mitocondrias , Animales , Antioxidantes , Bilirrubina , Hígado , Ratones , Obesidad
7.
Int J Mol Sci ; 22(7)2021 Mar 30.
Artículo en Inglés | MEDLINE | ID: mdl-33808202

RESUMEN

Active transport of sugars into bacteria occurs through symporters driven by ion gradients. LacY is the most well-studied proton sugar symporter, whereas vSGLT is the most characterized sodium sugar symporter. These are members of the major facilitator (MFS) and the amino acid-Polyamine organocation (APS) transporter superfamilies. While there is no structural homology between these transporters, they operate by a similar mechanism. They are nano-machines driven by their respective ion electrochemical potential gradients across the membrane. LacY has 12 transmembrane helices (TMs) organized in two 6-TM bundles, each containing two 3-helix TM repeats. vSGLT has a core structure of 10 TM helices organized in two inverted repeats (TM 1-5 and TM 6-10). In each case, a single sugar is bound in a central cavity and sugar selectivity is determined by hydrogen- and hydrophobic- bonding with side chains in the binding site. In vSGLT, the sodium-binding site is formed through coordination with carbonyl- and hydroxyl-oxygens from neighboring side chains, whereas in LacY the proton (H3O+) site is thought to be a single glutamate residue (Glu325). The remaining challenge for both transporters is to determine how ion electrochemical potential gradients drive uphill sugar transport.


Asunto(s)
Proteínas de Transporte de Membrana/química , Proteínas de Transporte de Membrana/metabolismo , Proteínas de Transporte de Sodio-Glucosa/química , Proteínas de Transporte de Sodio-Glucosa/metabolismo , Sitios de Unión , Transporte Biológico Activo , Proteínas de Escherichia coli/química , Proteínas de Escherichia coli/metabolismo , Glucosa/metabolismo , Lactosa/metabolismo , Modelos Moleculares , Proteínas de Transporte de Monosacáridos/química , Proteínas de Transporte de Monosacáridos/metabolismo , Conformación Proteica , Azúcares/metabolismo , Simportadores/química , Simportadores/metabolismo
8.
Proc Natl Acad Sci U S A ; 117(51): 32380-32385, 2020 12 22.
Artículo en Inglés | MEDLINE | ID: mdl-33293416

RESUMEN

A structure of the murine voltage-dependent anion channel (VDAC) was determined by microcrystal electron diffraction (MicroED). Microcrystals of an essential mutant of VDAC grew in a viscous bicelle suspension, making it unsuitable for conventional X-ray crystallography. Thin, plate-like crystals were identified using scanning-electron microscopy (SEM). Crystals were milled into thin lamellae using a focused-ion beam (FIB). MicroED data were collected from three crystal lamellae and merged for completeness. The refined structure revealed unmodeled densities between protein monomers, indicative of lipids that likely mediate contacts between the proteins in the crystal. This body of work demonstrates the effectiveness of milling membrane protein microcrystals grown in viscous media using a focused ion beam for subsequent structure determination by MicroED. This approach is well suited for samples that are intractable by X-ray crystallography. To our knowledge, the presented structure is a previously undescribed mutant of the membrane protein VDAC, crystallized in a lipid bicelle matrix and solved by MicroED.


Asunto(s)
Canales Aniónicos Dependientes del Voltaje/química , Animales , Microscopía por Crioelectrón/métodos , Cristalización , Lípidos/química , Ratones , Microscopía Electrónica de Rastreo/métodos , Microscopía Electrónica de Transmisión , Proteínas Mitocondriales/química , Conformación Proteica
9.
Anal Chem ; 92(9): 6622-6630, 2020 05 05.
Artículo en Inglés | MEDLINE | ID: mdl-32250604

RESUMEN

Native mass spectrometry (MS) provides the capacity to monitor membrane protein complexes and noncovalent binding of ligands and lipids to membrane proteins. The charge states produced by native MS of membrane proteins often result in gas-phase protein unfolding or loss of noncovalent interactions. In an effort to reduce the charge of membrane proteins, we examined the utility of alkali metal salts as a charge-reducing agent. Low concentrations of alkali metal salts caused marked charge reduction in the membrane protein, Erwinia ligand-gated ion channel (ELIC). The charge-reducing effect only occurred for membrane proteins and was detergent-dependent, being most pronounced in long polyethylene glycol (PEG)-based detergents such as C10E5 and C12E8. On the basis of these results, we propose a mechanism for alkali metal charge reduction of membrane proteins. Addition of low concentrations of alkali metals may provide an advantageous approach for charge reduction of detergent-solubilized membrane proteins by native MS.


Asunto(s)
Acetatos/química , Glutamato Deshidrogenasa/química , Proteínas de la Membrana/química , Metales Alcalinos/química , Piruvato Quinasa/química , Animales , Bovinos , Detergentes/química , Glutamato Deshidrogenasa/metabolismo , Espectrometría de Masas , Proteínas de la Membrana/metabolismo , Oxidación-Reducción , Piruvato Quinasa/metabolismo , Conejos , Sales (Química)/química , Solubilidad
11.
J Gen Physiol ; 152(2)2020 02 03.
Artículo en Inglés | MEDLINE | ID: mdl-31935282

RESUMEN

Voltage-dependent anion channel (VDAC) is the major pathway for the transport of ions and metabolites across the mitochondrial outer membrane. Among the three known mammalian VDAC isoforms, VDAC3 is the least characterized, but unique functional roles have been proposed in cellular and animal models. Yet, a high-sequence similarity between VDAC1 and VDAC3 is indicative of a similar pore-forming structure. Here, we conclusively show that VDAC3 forms stable, highly conductive voltage-gated channels that, much like VDAC1, are weakly anion selective and facilitate metabolite exchange, but exhibit unique properties when interacting with the cytosolic proteins α-synuclein and tubulin. These two proteins are known to be potent regulators of VDAC1 and induce similar characteristic blockages (on the millisecond time scale) of VDAC3, but with 10- to 100-fold reduced on-rates and altered α-synuclein blocking times, indicative of an isoform-specific function. Through cysteine scanning mutagenesis, we found that VDAC3's cysteine residues regulate its interaction with α-synuclein, demonstrating VDAC3-unique functional properties and further highlighting a general molecular mechanism for VDAC isoform-specific regulation of mitochondrial bioenergetics.


Asunto(s)
Citosol/metabolismo , Mitocondrias/metabolismo , Proteínas de Transporte de Membrana Mitocondrial/metabolismo , Proteínas Mitocondriales/metabolismo , Isoformas de Proteínas/metabolismo , Canales Aniónicos Dependientes del Voltaje/metabolismo , Animales , Biología/métodos , Cisteína/metabolismo , Humanos , Ratones , Sinucleínas/metabolismo , Canal Aniónico 1 Dependiente del Voltaje/metabolismo
12.
Biochim Biophys Acta Mol Cell Biol Lipids ; 1864(10): 1269-1279, 2019 10.
Artículo en Inglés | MEDLINE | ID: mdl-31176038

RESUMEN

Voltage-dependent anion channel-1 (VDAC1) is a mitochondrial porin that is implicated in cellular metabolism and apoptosis, and modulated by numerous small molecules including lipids. VDAC1 binds sterols, including cholesterol and neurosteroids such as allopregnanolone. Biochemical and computational studies suggest that VDAC1 binds multiple cholesterol molecules, but photolabeling studies have identified only a single cholesterol and neurosteroid binding site at E73. To identify all the binding sites of neurosteroids in VDAC1, we apply photo-affinity labeling using two sterol-based photolabeling reagents with complementary photochemistry: 5α-6-AziP which contains an aliphatic diazirine, and KK200 which contains a trifluoromethyl-phenyldiazirine (TPD) group. 5α-6-AziP and KK200 photolabel multiple residues within an E73 pocket confirming the presence of this site and mapping sterol orientation within this pocket. In addition, KK200 photolabels four other sites consistent with the finding that VDAC1 co-purifies with five cholesterol molecules. Both allopregnanolone and cholesterol competitively prevent photolabeling at E73 and three other sites indicating that these are common sterol binding sites shared by both neurosteroids and cholesterol. Binding at the functionally important residue E73 suggests a possible role for sterols in regulating VDAC1 signaling and interaction with partner proteins.


Asunto(s)
Colesterol/metabolismo , Neuroesteroides/metabolismo , Canal Aniónico 1 Dependiente del Voltaje/metabolismo , Secuencia de Aminoácidos , Animales , Sitios de Unión , Ratones , Modelos Moleculares , Unión Proteica , Canal Aniónico 1 Dependiente del Voltaje/química
13.
Biochim Biophys Acta Bioenerg ; 1860(1): 22-29, 2019 01.
Artículo en Inglés | MEDLINE | ID: mdl-30412693

RESUMEN

The voltage-dependent anion channel (VDAC) is the most abundant protein of the mitochondrial outer membrane (MOM) where it regulates transport of ions and metabolites in and out of the organelle. VDAC function is extensively studied in a lipid bilayer system that allows conductance monitoring of reconstituted channels under applied voltage. The process of switching from a high-conductance state, open to metabolites, to a variety of low-conducting states, which excludes metabolite transport, is termed voltage gating and the mechanism remains poorly understood. Recent studies have implicated the involvement of the membrane-solvated residue E73 in the gating process through ß-barrel destabilization. However, there has been no direct experimental evidence of E73 involvement in VDAC1 voltage gating. Here, using electrophysiology measurements, we exclude the involvement of E73 in murine VDAC1 (mVDAC1) voltage gating process. With an established protocol of assessing voltage gating of VDACs reconstituted into planar lipid membranes, we definitively show that mVDAC1 gating properties do not change when E73 is replaced by either a glutamine or an alanine. We further demonstrate that cholesterol has no effect on mVDAC1 gating characteristics, though it was shown that E73 is coordinating residue in the cholesterol binding site. In contrast, we found a pronounced gating effect based on the charge of the phospholipid headgroup, where the positive charge stimulates and negative charge suppresses gating. These findings call for critical evaluation of the existing models of VDAC gating and contribute to our understanding of VDAC's role in control of MOM permeability and regulation of mitochondrial respiration and metabolism.


Asunto(s)
Ácido Glutámico/fisiología , Activación del Canal Iónico , Canal Aniónico 1 Dependiente del Voltaje/química , Sustitución de Aminoácidos , Animales , Lípidos de la Membrana/química , Lípidos de la Membrana/metabolismo , Ratones , Mitocondrias/metabolismo , Membranas Mitocondriales/metabolismo , Permeabilidad
14.
Nat Commun ; 9(1): 4738, 2018 11 09.
Artículo en Inglés | MEDLINE | ID: mdl-30413716

RESUMEN

Proteins possess a complex and dynamic structure, which is influenced by external signals and may change as they perform their biological functions. We present an optical approach, distance-encoding photoinduced electron transfer (DEPET), capable of the simultaneous study of protein structure and function. An alternative to FRET-based methods, DEPET is based on the quenching of small conjugated fluorophores by photoinduced electron transfer: a reaction that requires contact of the excited fluorophore with a suitable electron donor. This property allows DEPET to exhibit exceptional spatial and temporal resolution capabilities in the range pertinent to protein conformational change. We report the first implementation of DEPET on human large-conductance K+ (BK) channels under voltage clamp. We describe conformational rearrangements underpinning BK channel sensitivity to electrical excitation, in conducting channels expressed in living cells. Finally, we validate DEPET in synthetic peptide length standards, to evaluate its accuracy in measuring sub- and near-nanometer intramolecular distances.


Asunto(s)
Electrones , Canales de Potasio de Gran Conductancia Activados por el Calcio/química , Luz , Óptica y Fotónica/métodos , Proteínas/química , Animales , Aplysia , Colorantes Fluorescentes/química , Humanos , Activación del Canal Iónico , Canales de Potasio de Gran Conductancia Activados por el Calcio/metabolismo , Potenciales de la Membrana , Péptidos/metabolismo , Rodaminas/química , Triptófano/química
15.
Nat Commun ; 9(1): 1753, 2018 05 01.
Artículo en Inglés | MEDLINE | ID: mdl-29717135

RESUMEN

Many pathogenic bacteria utilise sialic acids as an energy source or use them as an external coating to evade immune detection. As such, bacteria that colonise sialylated environments deploy specific transporters to mediate import of scavenged sialic acids. Here, we report a substrate-bound 1.95 Å resolution structure and subsequent characterisation of SiaT, a sialic acid transporter from Proteus mirabilis. SiaT is a secondary active transporter of the sodium solute symporter (SSS) family, which use Na+ gradients to drive the uptake of extracellular substrates. SiaT adopts the LeuT-fold and is in an outward-open conformation in complex with the sialic acid N-acetylneuraminic acid and two Na+ ions. One Na+ binds to the conserved Na2 site, while the second Na+ binds to a new position, termed Na3, which is conserved in many SSS family members. Functional and molecular dynamics studies validate the substrate-binding site and demonstrate that both Na+ sites regulate N-acetylneuraminic acid transport.


Asunto(s)
Transportadores de Anión Orgánico/metabolismo , Sodio/metabolismo , Simportadores/metabolismo , Secuencia de Aminoácidos , Ácido N-Acetilneuramínico/metabolismo , Transportadores de Anión Orgánico/química , Pliegue de Proteína , Homología de Secuencia de Aminoácido , Especificidad por Sustrato , Simportadores/química
16.
Proc Natl Acad Sci U S A ; 115(12): E2742-E2751, 2018 03 20.
Artículo en Inglés | MEDLINE | ID: mdl-29507231

RESUMEN

Sodium-dependent transporters couple the flow of Na+ ions down their electrochemical potential gradient to the uphill transport of various ligands. Many of these transporters share a common core structure composed of a five-helix inverted repeat and deliver their cargo utilizing an alternating-access mechanism. A detailed characterization of inward-facing conformations of the Na+-dependent sugar transporter from Vibrio parahaemolyticus (vSGLT) has previously been reported, but structural details on additional conformations and on how Na+ and ligand influence the equilibrium between other states remains unknown. Here, double electron-electron resonance spectroscopy, structural modeling, and molecular dynamics are utilized to deduce ligand-dependent equilibria shifts of vSGLT in micelles. In the absence and presence of saturating amounts of Na+, vSGLT favors an inward-facing conformation. Upon binding both Na+ and sugar, the equilibrium shifts toward either an outward-facing or occluded conformation. While Na+ alone does not stabilize the outward-facing state, gating charge calculations together with a kinetic model of transport suggest that the resting negative membrane potential of the cell, absent in detergent-solubilized samples, may stabilize vSGLT in an outward-open conformation where it is poised for binding external sugars. In total, these findings provide insights into ligand-induced conformational selection and delineate the transport cycle of vSGLT.


Asunto(s)
Proteínas de Transporte de Sodio-Glucosa/química , Proteínas de Transporte de Sodio-Glucosa/metabolismo , Proteínas Bacterianas/química , Proteínas Bacterianas/metabolismo , Transporte Biológico Activo , Cisteína/genética , Espectroscopía de Resonancia por Spin del Electrón/métodos , Galactosa/metabolismo , Lípidos de la Membrana/química , Lípidos de la Membrana/metabolismo , Micelas , Modelos Moleculares , Simulación de Dinámica Molecular , Mutación , Conformación Proteica , Sodio/metabolismo , Vibrio parahaemolyticus/química
17.
Proc Natl Acad Sci U S A ; 115(2): E172-E179, 2018 01 09.
Artículo en Inglés | MEDLINE | ID: mdl-29279396

RESUMEN

The voltage-dependent anion channel (VDAC) is the most abundant protein in the outer mitochondrial membrane and constitutes the primary pathway for the exchange of ions and metabolites between the cytosol and the mitochondria. There is accumulating evidence supporting VDAC's role in mitochondrial metabolic regulation and apoptosis, where VDAC oligomerization has been implicated with these processes. Herein, we report a specific pH-dependent dimerization of murine VDAC1 (mVDAC1) identified by double electron-electron resonance and native mass spectrometry. Intermolecular distances on four singly spin-labeled mVDAC1 mutants were used to generate a model of the low-pH dimer, establishing the presence of residue E73 at the interface. This dimer arrangement is different from any oligomeric state previously described, and it forms as a steep function of pH with an apparent pKa of 7.4. Moreover, the monomer-dimer equilibrium affinity constant was determined using native MS, revealing a nearly eightfold enhancement in dimerization affinity at low pH. Mutation of E73 to either alanine or glutamine severely reduces oligomerization, demonstrating the role of protonated E73 in enhancing dimer formation. Based on these results, and the known importance of E73 in VDAC physiology, VDAC dimerization likely plays a significant role in mitochondrial metabolic regulation and apoptosis in response to cytosolic acidification during cellular stress.


Asunto(s)
Glutamatos/química , Multimerización de Proteína , Protones , Canal Aniónico 1 Dependiente del Voltaje/química , Algoritmos , Animales , Glutamatos/genética , Glutamatos/metabolismo , Concentración de Iones de Hidrógeno , Cinética , Ratones , Modelos Moleculares , Mutación , Conformación Proteica , Canal Aniónico 1 Dependiente del Voltaje/genética , Canal Aniónico 1 Dependiente del Voltaje/metabolismo
18.
J Biol Chem ; 292(22): 9294-9304, 2017 06 02.
Artículo en Inglés | MEDLINE | ID: mdl-28396346

RESUMEN

Voltage-dependent anion channel-1 (VDAC1) is a highly regulated ß-barrel membrane protein that mediates transport of ions and metabolites between the mitochondria and cytosol of the cell. VDAC1 co-purifies with cholesterol and is functionally regulated by cholesterol, among other endogenous lipids. Molecular modeling studies based on NMR observations have suggested five cholesterol-binding sites in VDAC1, but direct experimental evidence for these sites is lacking. Here, to determine the sites of cholesterol binding, we photolabeled purified mouse VDAC1 (mVDAC1) with photoactivatable cholesterol analogues and analyzed the photolabeled sites with both top-down mass spectrometry (MS), and bottom-up MS paired with a clickable, stable isotope-labeled tag, FLI-tag. Using cholesterol analogues with a diazirine in either the 7 position of the steroid ring (LKM38) or the aliphatic tail (KK174), we mapped a binding pocket in mVDAC1 localized to Thr83 and Glu73, respectively. When Glu73 was mutated to a glutamine, KK174 no longer photolabeled this residue, but instead labeled the nearby Tyr62 within this same binding pocket. The combination of analytical strategies employed in this work permits detailed molecular mapping of a cholesterol-binding site in a protein, including an orientation of the sterol within the site. Our work raises the interesting possibility that cholesterol-mediated regulation of VDAC1 may be facilitated through a specific binding site at the functionally important Glu73 residue.


Asunto(s)
Colesterol/química , Canal Aniónico 1 Dependiente del Voltaje/química , Marcadores de Afinidad , Animales , Sitios de Unión , Ratones , Resonancia Magnética Nuclear Biomolecular , Canal Aniónico 1 Dependiente del Voltaje/genética
19.
Proc Natl Acad Sci U S A ; 114(18): E3622-E3631, 2017 05 02.
Artículo en Inglés | MEDLINE | ID: mdl-28420794

RESUMEN

Dimeric tubulin, an abundant water-soluble cytosolic protein known primarily for its role in the cytoskeleton, is routinely found to be associated with mitochondrial outer membranes, although the structure and physiological role of mitochondria-bound tubulin are still unknown. There is also no consensus on whether tubulin is a peripheral membrane protein or is integrated into the outer mitochondrial membrane. Here the results of five independent techniques-surface plasmon resonance, electrochemical impedance spectroscopy, bilayer overtone analysis, neutron reflectometry, and molecular dynamics simulations-suggest that α-tubulin's amphipathic helix H10 is responsible for peripheral binding of dimeric tubulin to biomimetic "mitochondrial" membranes in a manner that differentiates between the two primary lipid headgroups found in mitochondrial membranes, phosphatidylethanolamine and phosphatidylcholine. The identification of the tubulin dimer orientation and membrane-binding domain represents an essential step toward our understanding of the complex mechanisms by which tubulin interacts with integral proteins of the mitochondrial outer membrane and is important for the structure-inspired design of tubulin-targeting agents.


Asunto(s)
Materiales Biomiméticos/química , Membranas Mitocondriales/química , Tubulina (Proteína)/química , Animales , Materiales Biomiméticos/metabolismo , Bovinos , Membranas Mitocondriales/metabolismo , Unión Proteica , Dominios Proteicos , Tubulina (Proteína)/metabolismo
20.
Anal Chem ; 89(4): 2636-2644, 2017 02 21.
Artículo en Inglés | MEDLINE | ID: mdl-28194953

RESUMEN

Identifying sites of protein-ligand interaction is important for structure-based drug discovery and understanding protein structure-function relationships. Mass spectrometry (MS) has emerged as a useful tool for identifying residues covalently modified by ligands. Current methods use database searches that are dependent on acquiring interpretable fragmentation spectra (MS2) of peptide-ligand adducts. This is problematic for identifying sites of hydrophobic ligand incorporation in integral membrane proteins (IMPs), where poor aqueous solubility and ionization of peptide-ligand adducts and collision-induced adduct loss hinder the acquisition of quality MS2 spectra. To address these issues, we developed a fast ligand identification (FLI) tag that can be attached to any alkyne-containing ligand via Cu(I)-catalyzed cycloaddition. The FLI tag adds charge to increase solubility and ionization, and utilizes stable isotope labeling for MS1 level identification of hydrophobic peptide-ligand adducts. The FLI tag was coupled to an alkyne-containing neurosteroid photolabeling reagent and used to identify peptide-steroid adducts in MS1 spectra via the stable heavy isotope pair. Peptide-steroid adducts were not identified in MS2-based database searches because collision-induced adduct loss was the dominant feature of collision-induced dissociation (CID) fragmentation, but targeted analysis of MS1 pairs using electron transfer dissociation (ETD) markedly reduced adduct loss. Using the FLI tag and ETD, we identified Glu73 as the site of photoincorporation of our neurosteroid ligand in the IMP, mouse voltage-dependent anion channel-1 (mVDAC1), and top-down MS confirmed a single site of photolabeling.


Asunto(s)
Ligandos , Péptidos/química , Espectrometría de Masas en Tándem , Canal Aniónico 1 Dependiente del Voltaje/metabolismo , Alquinos/química , Secuencia de Aminoácidos , Animales , Cromatografía Líquida de Alta Presión , Química Clic , Interacciones Hidrofóbicas e Hidrofílicas , Marcaje Isotópico , Ratones , Péptidos/metabolismo , Solubilidad , Rayos Ultravioleta , Canal Aniónico 1 Dependiente del Voltaje/química
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