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1.
Biochemistry ; 52(26): 4482-91, 2013 Jul 02.
Artículo en Inglés | MEDLINE | ID: mdl-23713611

RESUMEN

Proline utilization A (PutA) from Escherichia coli is a membrane-associated trifunctional flavoenzyme that catalyzes the oxidation of proline to glutamate and moonlights as a transcriptional regulator. As a regulatory protein, PutA represses transcription of the put regulon, which contains the genes encoding PutA and the proline transporter PutP. The binding of proline to the proline dehydrogenase active site and the subsequent reduction of the flavin induce high affinity membrane association of PutA and relieve repression of the put regulon, thereby causing PutA to switch from its regulatory to its enzymatic role. Here, we present evidence suggesting that residues of the ß3-α3 loop of the proline dehydrogenase domain (ßα)8 barrel are involved in proline-mediated allosteric regulation of PutA-membrane binding. Mutation of the conserved residues Asp370 and Glu372 in the ß3-α3 loop abrogates the ability of proline to induce functional membrane association. Both in vitro lipid/membrane binding assays and in vivo cell-based assays demonstrate that mutagenesis of Asp370 (D370N/A) or Glu372 (E372A) dramatically impedes PutA functional switching. The crystal structures of the proline dehydrogenase domain mutants PutA86-630D370N and PutA86-630D370A complexed with the proline analogue l-tetrahydro-2-furoic acid show that the mutations cause only minor perturbations to the active site but no major structural changes, suggesting that the lack of proline response is not due to a failure of the mutated active sites to correctly bind the substrate. Rather, these results suggest that the ß3-α3 loop may be involved in transmitting the status of the proline dehydrogenase active site and flavin redox state to the distal membrane association domain.


Asunto(s)
Proteínas Bacterianas/química , Escherichia coli/enzimología , Proteínas de la Membrana/química , Prolina Oxidasa/química , Prolina/química , Regulación Alostérica , Dominio Catalítico , Membranas/química , Membranas/enzimología , Prolina/metabolismo , Prolina Oxidasa/metabolismo , Unión Proteica , Estructura Terciaria de Proteína
2.
J Biol Chem ; 286(50): 43144-53, 2011 Dec 16.
Artículo en Inglés | MEDLINE | ID: mdl-22013066

RESUMEN

The trifunctional flavoprotein proline utilization A (PutA) links metabolism and gene regulation in Gram-negative bacteria by catalyzing the two-step oxidation of proline to glutamate and repressing transcription of the proline utilization regulon. Small-angle x-ray scattering (SAXS) and domain deletion analysis were used to obtain solution structural information for the 1320-residue PutA from Escherichia coli. Shape reconstructions show that PutA is a symmetric V-shaped dimer having dimensions of 205 × 85 × 55 Å. The particle consists of two large lobes connected by a 30-Å diameter cylinder. Domain deletion analysis shows that the N-terminal DNA-binding domain mediates dimerization. Rigid body modeling was performed using the crystal structure of the DNA-binding domain and a hybrid x-ray/homology model of residues 87-1113. The calculations suggest that the DNA-binding domain is located in the connecting cylinder, whereas residues 87-1113, which contain the two catalytic active sites, reside in the large lobes. The SAXS data and amino acid sequence analysis suggest that the Δ(1)-pyrroline-5-carboxylate dehydrogenase domains lack the conventional oligomerization flap, which is unprecedented for the aldehyde dehydrogenase superfamily. The data also provide insight into the function of the 200-residue C-terminal domain. It is proposed that this domain serves as a lid that covers the internal substrate channeling cavity, thus preventing escape of the catalytic intermediate into the bulk medium. Finally, the SAXS model is consistent with a cloaking mechanism of gene regulation whereby interaction of PutA with the membrane hides the DNA-binding surface from the put regulon thereby activating transcription.


Asunto(s)
Proteínas Bacterianas/química , Proteínas Bacterianas/metabolismo , Escherichia coli/metabolismo , Proteínas de la Membrana/química , Proteínas de la Membrana/metabolismo , Dispersión del Ángulo Pequeño , Rayos X , Multimerización de Proteína , Estructura Terciaria de Proteína
3.
Biochemistry ; 48(5): 951-9, 2009 Feb 10.
Artículo en Inglés | MEDLINE | ID: mdl-19140736

RESUMEN

Proline dehydrogenase (PRODH) catalyzes the oxidation of l-proline to Delta-1-pyrroline-5-carboxylate. PRODHs exhibit a pronounced preference for proline over hydroxyproline (trans-4-hydroxy-l-proline) as the substrate, but the basis for specificity is unknown. The goal of this study, therefore, is to gain insight into the structural determinants of substrate specificity of this class of enzyme, with a focus on understanding how PRODHs discriminate between the two closely related molecules, proline and hydroxyproline. Two site-directed mutants of the PRODH domain of Escherichia coli PutA were created: Y540A and Y540S. Kinetics measurements were performed with both mutants. Crystal structures of Y540S complexed with hydroxyproline, proline, and the proline analogue l-tetrahydro-2-furoic acid were determined at resolutions of 1.75, 1.90, and 1.85 A, respectively. Mutation of Tyr540 increases the catalytic efficiency for hydroxyproline 3-fold and decreases the specificity for proline by factors of 20 (Y540S) and 50 (Y540A). The structures show that removal of the large phenol side chain increases the volume of the substrate-binding pocket, allowing sufficient room for the 4-hydroxyl of hydroxyproline. Furthermore, the introduced serine residue participates in recognition of hydroxyproline by forming a hydrogen bond with the 4-hydroxyl. This result has implications for understanding the substrate specificity of the related enzyme human hydroxyproline dehydrogenase, which has serine in place of tyrosine at this key active site position. The kinetic and structural results suggest that Tyr540 is an important determinant of specificity. Structurally, it serves as a negative filter for hydroxyproline by clashing with the 4-hydroxyl group of this potential substrate.


Asunto(s)
Proteínas Bacterianas/química , Secuencia Conservada , Proteínas de Escherichia coli/química , Hidroxiprolina/química , Proteínas de la Membrana/química , Prolina Oxidasa/química , Prolina/química , Tirosina/química , Secuencia de Aminoácidos , Dominio Catalítico , Cristalografía por Rayos X , Humanos , Hidroxiprolina/genética , Hidroxiprolina/metabolismo , Datos de Secuencia Molecular , Prolina/genética , Prolina/metabolismo , Prolina Oxidasa/genética , Prolina Oxidasa/metabolismo , Especificidad por Sustrato , Tirosina/genética , Tirosina/metabolismo
4.
Protein Sci ; 15(11): 2630-41, 2006 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-17001030

RESUMEN

PutA (proline utilization A) from Escherichia coli is a 1320-amino-acid residue protein that is both a bifunctional proline catabolic enzyme and an autogenous transcriptional repressor. Here, we report the first crystal structure of a PutA DNA-binding domain along with functional analysis of a mutant PutA defective in DNA binding. Crystals were grown using a polypeptide corresponding to residues 1-52 of E. coli PutA (PutA52). The 2.1 Angstrom resolution structure of PutA52 mutant Lys9Met was determined using Se-Met MAD phasing, and the structure of native PutA52 was solved at 1.9 Angstrom resolution using molecular replacement. Residues 3-46 form a ribbon-helix-helix (RHH) substructure, thus establishing PutA as the largest protein to contain an RHH domain. The PutA RHH domain forms the intertwined dimer with tightly packed hydrophobic core that is characteristic of the RHH family. The structures were used to examine the three-dimensional context of residues conserved in PutA RHH domains. Homology modeling suggests that Lys9 and Thr5 contact DNA bases through the major groove, while Arg15, Thr28, and His30 may interact with the phosphate backbone. Lys9 is shown to be essential for specific recognition of put control DNA using gel shift analysis of the Lys9Met mutant of full-length PutA. Lys9 is disordered in the PutA52 structure, which implies an induced-fit binding mechanism in which the side chain of Lys9 becomes ordered through interaction with DNA. These results provide new insights into the structural basis of DNA recognition by PutA and reveal three-dimensional structural details of the PutA dimer interface.


Asunto(s)
Proteínas Bacterianas/química , Cristalografía por Rayos X/métodos , ADN Bacteriano/química , ADN Bacteriano/metabolismo , Proteínas de la Membrana/química , Sitios de Unión , Secuencia Conservada , Proteínas de Unión al ADN/química , Escherichia coli , Proteínas de Escherichia coli/química , Flavoproteínas/química , Modelos Moleculares , Datos de Secuencia Molecular , Prolina/metabolismo , Unión Proteica , Pliegue de Proteína , Estructura Terciaria de Proteína , Análisis de Secuencia de Proteína , Homología de Secuencia de Aminoácido
5.
Artículo en Inglés | MEDLINE | ID: mdl-28113892

RESUMEN

In this paper, the principles of finite-element modeling for the electroacoustic simulation of bulk-acoustic-wave devices will be summarized. We will outline the model setup including governing equations and boundary conditions, as well as its efficient computer implementation. Particular emphasis will be given to tailoring the model dimension to the specific requirements of the desired investigation. As 3-D simulations still require a major effort, it will be illustrated that various aspects of device physics and design can already be addressed by fast and efficient 2-D simulations. Multiple theoretical and experimental evidence will be presented to demonstrate the validity of the modeling concepts. Based on various examples, it will be sketched how to benefit from numerical simulations for understanding fundamental effects, designing devices for actual products, and exploring novel technologies.

6.
Protein Sci ; 11(1): 158-73, 2002 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-11742132

RESUMEN

15N relaxation data for Ca(2+)-bound rat beta-parvalbumin (a.k.a. oncomodulin) were analyzed using the Lipari-Szabo formalism and compared with existing data for rat alpha-parvalbumin. Although the average S(2) values for the two proteins are very similar (0.85 for alpha, 0.84 for beta), residue-by-residue inspection reveals systematic differences. alpha tends to have the lower S(2) value in helical regions; beta tends to have the lower value in the loop regions. Rat beta was also examined in the Ca(2+)-free state. The 59 assigned residues displayed an average order parameter (0.90) significantly greater than the corresponding residues in the Ca(2+)-loaded form. The pentacarboxylate variants of rat beta-S55D and G98D-also were examined in the Ca(2+)-bound state. Although both mutations significantly heighten Ca(2+) affinity, they utilize distinct energetic strategies. S55D improves the Ca(2+)-binding enthalpy; G98D improves the binding entropy. They also show disparate peptide backbone dynamics. Whereas beta G98D displays an average order parameter (0.87) slightly greater than that of the wild-type protein, beta S55D displays an average order parameter (0.82) slightly lower than wild-type beta. Furthermore, whereas just two backbone N-H bonds in beta G98D show internal motion on the 20-200-psec timescale, fully 52 of the 93 residues analyzed in beta S55D show this behavior. These findings suggest that the increased electrostatic repulsion attendant to introduction of an additional carboxylate into the CD site ligand array impedes backbone vibrational motion throughout the molecule.


Asunto(s)
Carbono/química , Parvalbúminas/química , Secuencia de Aminoácidos , Animales , Calcio/química , Ligandos , Espectroscopía de Resonancia Magnética , Modelos Moleculares , Modelos Estadísticos , Datos de Secuencia Molecular , Unión Proteica , Conformación Proteica , Estructura Secundaria de Proteína , Estructura Terciaria de Proteína , Ratas , Homología de Secuencia de Aminoácido , Factores de Tiempo
7.
Hear Res ; 191(1-2): 101-9, 2004 May.
Artículo en Inglés | MEDLINE | ID: mdl-15109709

RESUMEN

OCP1 and OCP2 are the most abundant proteins in the organ of Corti. Their distributions map identically to the epithelial gap-junction system, which unites the supporting cell population. Sequence data imply that OCP1 and OCP2 are subunits of an SCF E3 ubiquitin ligase. Consistent with that hypothesis, electrophoretic mobility-shift assays and pull-down assays with immobilized OCP1 demonstrate the formation of an OCP1-OCP2 complex. Sedimentation equilibrium data indicate that the complex is heterodimeric. The coincidence of the OCP1-OCP2 distribution and the epithelial gap-junction system suggests that one or more connexin isoforms may be targets of an SCF(OCP1) complex. Significantly, immobilized OCP1 binds (35)S-labeled connexin 26 (Cx26) produced by in vitro transcription-translation. Moreover, Cx26 can be co-immunoprecipitated from extracts of the organ of Corti by immobilized anti-OCP1, implying that OCP1 and Cx26 may associate in vivo. Given that lesions in the Cx26 gene (GJB2) are the most common cause of hereditary deafness, the OCP1-Cx26 interaction has substantial biomedical relevance.


Asunto(s)
Conexinas/análisis , Órgano Espiral/metabolismo , Factores de Transcripción/análisis , Animales , Proteínas de Ciclo Celular/metabolismo , Conexina 26 , Conexinas/química , Electroforesis en Gel de Poliacrilamida , Ensayo de Cambio de Movilidad Electroforética , Proteínas F-Box , Cobayas , Humanos , Inmunoprecipitación , Análisis de los Mínimos Cuadrados , Proteínas del Tejido Nervioso , Péptido Sintasas/metabolismo , Proteínas Quinasas Asociadas a Fase-S , Factores de Transcripción/química , Ultracentrifugación
8.
Artículo en Inglés | MEDLINE | ID: mdl-14609067

RESUMEN

A full-field view laser ultrasonic imaging method has been developed that measures acoustic motion at a surface without scanning. Images are recorded at normal video frame rates by using dynamic holography with photorefractive interferometric detection. By extending the approach to ultra high frequencies, an acoustic microscope has been developed that is capable of operation at Gigahertz frequency and micron length scales. Both acoustic amplitude and phase are recorded, allowing full calibration and determination of phases to within a single arbitrary constant. Results are presented of measurements at frequencies of 800-900 MHz, illustrating a multitude of normal mode behavior in electrically driven thin film acoustic resonators. Coupled with microwave electrical impedance measurements, this imaging mode provides an exceptionally fast method for evaluation of electric-to-acoustic coupling of these devices and their performance. Images of 256 x 240 pixels are recorded at 18 fps rates synchronized to obtain both in-phase and quadrature detection of the acoustic motion. Simple averaging provides sensitivity to the subnanometer level at each pixel calibrated over the image using interferometry. Identification of specific acoustic modes and their relationship to electrical impedance characteristics show the advantages and overall high speed of the technique.

9.
Artículo en Inglés | MEDLINE | ID: mdl-18986880

RESUMEN

We discuss the operation of novel coupled-resonator filters with single-layer acoustic couplers. Our analysis employs the physical Mason model for acoustic resonators. Their simpler fabrication process is counterbalanced by the high acoustic attenuation of suitable coupler materials. At high levels of attenuation, both the phase and the acoustic impedance must be treated as complex quantities to accurately predict the filter insertion loss. We demonstrate that the typically poor near-band rejection of coupled resonator filters can be improved at the die level by connecting a small capacitance between the input and output of the filter to produce a pair of tunable transmission minima. We make use of these theoretical findings to fabricate coupled resonators filters operating at 2.45 GHz.


Asunto(s)
Acústica/instrumentación , Diseño Asistido por Computadora , Filtración/instrumentación , Transductores , Simulación por Computador , Diseño de Equipo , Análisis de Falla de Equipo , Modelos Teóricos , Reproducibilidad de los Resultados , Dispersión de Radiación , Sensibilidad y Especificidad
10.
J Mol Biol ; 381(1): 174-88, 2008 Aug 01.
Artículo en Inglés | MEDLINE | ID: mdl-18586269

RESUMEN

The multifunctional Escherichia coli proline utilization A (PutA) flavoprotein functions both as a membrane-associated proline catabolic enzyme and as a transcriptional repressor of the proline utilization genes putA and putP. To better understand the mechanism of transcriptional regulation by PutA, we have mapped the put-regulatory region, determined a crystal structure of the PutA ribbon-helix-helix domain (PutA52, a polypeptide corresponding to residues 1-52 of E. coli PutA) complexed with DNA, and examined the thermodynamics of DNA binding to PutA52. Five operator sites, each containing the sequence motif 5'-GTTGCA-3', were identified using gel-shift analysis. Three of the sites are shown to be critical for repression of putA, whereas the two other sites are important for repression of putP. The 2.25-A-resolution crystal structure of PutA52 bound to one of the operators (operator 2; 21 bp) shows that the protein contacts a 9-bp fragment corresponding to the GTTGCA consensus motif plus three flanking base pairs. Since the operator sequences differ in flanking bases, the structure implies that PutA may have different affinities for the five operators. This hypothesis was explored using isothermal titration calorimetry. The binding of PutA52 to operator 2 is exothermic, with an enthalpy of -1.8 kcal/mol and a dissociation constant of 210 nM. Substitution of the flanking bases of operator 4 into operator 2 results in an unfavorable enthalpy of 0.2 kcal/mol and a 15-fold-lower affinity, showing that base pairs outside of the consensus motif impact binding. Structural and thermodynamic data suggest that hydrogen bonds between Lys9 and bases adjacent to the GTTGCA motif contribute to transcriptional regulation by fine-tuning the affinity of PutA for put control operators.


Asunto(s)
Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Escherichia coli/enzimología , Escherichia coli/genética , Proteínas de la Membrana/genética , Proteínas de la Membrana/metabolismo , Prolina/metabolismo , Regulón/genética , Transcripción Genética/genética , Sistemas de Transporte de Aminoácidos Neutros/genética , Sistemas de Transporte de Aminoácidos Neutros/metabolismo , Proteínas Bacterianas/química , Secuencia de Bases , Sitios de Unión , Calorimetría , Cristalografía por Rayos X , ADN/química , ADN/genética , ADN/metabolismo , Proteínas de Escherichia coli/genética , Proteínas de Escherichia coli/metabolismo , Proteínas de la Membrana/química , Modelos Moleculares , Conformación de Ácido Nucleico , Oxígeno/química , Oxígeno/metabolismo , Prolina/genética , Unión Proteica , Estructura Terciaria de Proteína , Simportadores/genética , Simportadores/metabolismo , Volumetría , beta-Galactosidasa/metabolismo
11.
Biochemistry ; 43(10): 2747-63, 2004 Mar 16.
Artículo en Inglés | MEDLINE | ID: mdl-15005610

RESUMEN

Rat alpha- and beta-parvalbumins have distinct monovalent cation-binding properties [Henzl et al. (2000) Biochemistry 39, 5859-5867]. Beta binds two Na(+) or one K(+), and alpha binds one Na(+) and no K(+). Ca(2+) abolishes these binding events, suggesting that the monovalent ions occupy the EF-hand motifs. This study compares alpha and beta divalent ion affinities in Na(+) and K(+) solutions. Solvent cation identity seriously affects alpha. In Hepes-buffered NaCl, at 5 degrees C, the macroscopic Ca(2+)-binding constants are 2.6 x 10(8) and 6.4 x 10(7) M(-1) and the Mg(2+) constants, 1.8 x 10(4) and 4.3 x 10(3) M(-1). In Hepes-buffered KCl, the Ca(2+) values increase to 2.9 x 10(9) and 6.6 x 10(8) M(-1) and the Mg(2+) values to 2.2 x 10(5) and 3.7 x 10(4) M(-1). Monte Carlo simulation of alpha binding data-employing site-specific constants and explicitly considering Na(+) binding-yields a K(Na) of 630 M(-1) and indicates that divalent ion-binding is positively cooperative. NMR data suggest that the lone Na(+) ion occupies the CD loop. Solvent cation identity has a smaller impact on beta. In Na(+), the Ca(2+) constants for the EF and CD sites are 2.3 x 10(7) and 1.5 x 10(6) M(-1), respectively; the Mg(2+) constants are 9.2 x 10(3) and 1.7 x 10(2) M(-1). In K(+), these values shift to 3.1 x 10(7) and 3.8 x 10(6) M(-1) and the latter to 1.4 x 10(4) and 2.9 x 10(2) M(-1). These data suggest that parvalbumin divalent ion affinity, particularly that of rat alpha, can be significantly attenuated by increased intracellular Na(+) levels.


Asunto(s)
Parvalbúminas/química , Animales , Radioisótopos de Calcio/química , Proteínas de Unión al Calcio/química , Calorimetría , Cationes Bivalentes/química , Cationes Monovalentes/química , Diálisis , Motivos EF Hand , Magnesio/química , Resonancia Magnética Nuclear Biomolecular , Potasio/química , Unión Proteica , Isoformas de Proteínas/química , Ratas , Sodio/química , Soluciones
12.
Biochemistry ; 43(34): 10906-17, 2004 Aug 31.
Artículo en Inglés | MEDLINE | ID: mdl-15323551

RESUMEN

Association of the parvalbumin AB and CD-EF domains was examined in Hepes-buffered saline, pH 7.4, employing fragments from rat alpha and beta. All of the interactions require Ca(2+). In saturating Ca(2+), the alpha AB/alpha CD-EF (alpha/alpha) complex displays an association constant of (7.6 +/- 0.4) x 10(7) M(-1). Ca(2+)-binding data for a mixture of the alpha fragments are compatible with an identical two-site model, yielding an average binding constant of (8.5 +/- 0.2) x 10(5) M(-1). The beta/beta interaction is significantly weaker, exhibiting an association constant of (3.0 +/- 0.6) x 10(6) M(-1). The Ca(2+)-binding constants for beta/beta are likewise diminished, at (1.0 +/- 0.1) x 10(5) and (2.3 +/- 0.2) x 10(4) M(-1). The magnitude of the apparent DeltaDeltaG(degree)' for Ca(2+) binding by alpha/alpha and beta/beta, at 3.4 kcal/mol, approaches that measured for the intact proteins (3.6 kcal/mol) and is substantially larger than the 1.5 kcal/mol value previously measured for the isolated CD-EF domains. This result suggests that the AB domain can modulate the Ca(2+) affinities of the CD and EF sites. Interestingly, the heterologous alpha/beta complex displays a larger association constant [(6.6 +/- 0.4) x 10(6) M(-1)] than the homologous beta/beta complex and heightened Ca(2+) affinity [binding constants of (1.3 +/- 0.1) x 10(6) and (8.8 +/- 0.2) x 10(4) M(-1)]. By contrast, beta/alpha associates more weakly than alpha/alpha and exhibits sharply reduced affinity for Ca(2+). Thus, the interaction between the beta AB domain and beta CD-EF domain may act to attenuate Ca(2+) affinity in the intact protein.


Asunto(s)
Parvalbúminas/química , Parvalbúminas/metabolismo , Fragmentos de Péptidos/química , Fragmentos de Péptidos/metabolismo , Secuencia de Aminoácidos , Animales , Calcio/metabolismo , Proteínas de Unión al Calcio/química , Proteínas de Unión al Calcio/metabolismo , Cationes Bivalentes , Datos de Secuencia Molecular , Unión Proteica , Pliegue de Proteína , Isoformas de Proteínas/química , Isoformas de Proteínas/metabolismo , Estructura Terciaria de Proteína , Ratas , Termodinámica , Ultracentrifugación
13.
Biochemistry ; 42(37): 10886-95, 2003 Sep 23.
Artículo en Inglés | MEDLINE | ID: mdl-12974622

RESUMEN

Despite its higher net charge and reduced opportunities for favorable tertiary interactions, Ca(2+)-free rat beta-parvalbumin is more stable than rat alpha-parvalbumin. Under conditions wherein alpha denatures at 45.8 degrees C, beta denatures at 53.6 degrees. The homologous chicken beta isoform known as CPV3 also exhibits heightened stability-prompting an inquiry into the stabilizing influence of Pro-21 and Pro-26. Individual P21A and P26A mutations lower the T(m) of rat beta by 3.2 degrees, decreasing conformational stability by 0.74 kcal/mol. Simultaneous replacement of Pro-21 and Pro-26 essentially abolishes the excess stability (DeltaT(m) = -7.6 degrees; DeltaDeltaG(conf) = -1.77 kcal/mol). Significantly, the P21A/P26A variant displays Ca(2+) affinity virtually indistinguishable from wild-type beta, implying that structural alterations in the AB domain do not necessarily influence the divalent ion affinity of the CD-EF domain. The consequences of introducing proline at positions 21 and 26 in rat alpha were also examined. Whereas the H26P mutation raises the T(m) by 5.6 degrees (DeltaDeltaG(conf) = 1.25 kcal/mol), A21P lowers the T(m) by 8.5 degrees (DeltaDeltaG(conf) = -1.9 kcal/mol). Replacement of Ala-21 by proline in an alpha AB/beta CD-EF chimera increases the T(m) by 5.8 degrees (DeltaDeltaG(conf) = 0.95 kcal/mol), implying that the destabilization of alpha by Pro-21 results from steric conflict with a residue in the CD-EF domain. Consistent with that hypothesis, the K80S mutation markedly stabilizes alpha A21P, yielding a protein with a T(m) 2.0 degrees higher than wild-type alpha. The observed differences in stability resulting from proline addition/removal are largely consistent with alterations in main-chain and side-chain conformational entropy.


Asunto(s)
Parvalbúminas/química , Prolina/química , Secuencia de Aminoácidos , Animales , Sitios de Unión , Calcio/química , Calcio/metabolismo , Calcio/farmacología , Pollos , Relación Dosis-Respuesta a Droga , Entropía , Datos de Secuencia Molecular , Mutagénesis Sitio-Dirigida , Mutación , Conformación Proteica , Isoformas de Proteínas , Estructura Terciaria de Proteína , Ratas , Temperatura , Termodinámica
14.
Biochemistry ; 43(29): 9307-19, 2004 Jul 27.
Artículo en Inglés | MEDLINE | ID: mdl-15260474

RESUMEN

Introduction of a fifth carboxylate into the ligand array of the CD site (via the combined S55D and E59D mutations) or the EF site (G98D) of rat alpha-parvalbumin substantially increases divalent ion affinity. This behavior, in conflict with that seen in model peptide systems, agrees with existing data for rat beta-parvalbumin [Henzl et al. (1996) Biochemistry 35, 5856-5869]. The complete analysis of the S55D/E59D double variant necessitated characterization of alpha E59D. Whereas the D59E mutation has minimal influence on beta CD site affinity, E59D has a major impact on the alpha CD site, lowering the apparent association constant by a factor of 14. The thermodynamic consequences of exchanging the rat alpha CD and EF site ligand arrays, which differ at the +z and -x coordination positions, were also examined. When the alpha CD array is imported into the EF site, it acquires a low-affinity phenotype, in agreement with previous findings for beta [Henzl et al. (1998) Biochemistry 37, 9101-9111]. However, when the EF ligand array is introduced into the alpha CD binding loop, it retains a high-affinity signature. This result, contrary to that observed in beta, suggests that the influence of the parvalbumin CD site environment supersedes the intrinsic behavior of the ligand array, a conclusion further supported by the disparate impact of the beta D59E and alpha E59D mutations.


Asunto(s)
Ácidos Carboxílicos/química , Parvalbúminas/química , Isoformas de Proteínas/química , Secuencia de Aminoácidos , Animales , Calcio/metabolismo , Magnesio/metabolismo , Datos de Secuencia Molecular , Parvalbúminas/genética , Parvalbúminas/metabolismo , Isoformas de Proteínas/genética , Isoformas de Proteínas/metabolismo , Ratas , Homología de Secuencia de Aminoácido , Termodinámica
15.
Anal Biochem ; 319(2): 216-33, 2003 Aug 15.
Artículo en Inglés | MEDLINE | ID: mdl-12871715

RESUMEN

The use of competitive isothermal titration calorimetry (ITC) to measure high-affinity binding constants has been largely restricted to systems with a single binding site or multiple identical sites. This study demonstrates the extension of this approach to proteins with two nonequivalent EF-hand Ca(2+)-binding sites--rat beta parvalbumin and the S55D/E59D variant of rat alpha parvalbumin. The method involves simultaneous (global) least-squares analysis of titrations with Ca(2+), with Mg(2+), with Ca(2+) in the presence of Mg(2+), and with Ca(2+) or Mg(2+) in the presence of a competitive chelator (EDTA or EGTA). The Ca(2+) and Mg(2+) binding constants obtained for rat beta agree well with estimates obtained by flow dialysis. Although the Ca(2+) affinity of alpha S55D/E59D is too high to measure by flow dialysis, it was amenable to analysis using the ITC-based approach. The combined S55D and E59D mutations increase the Ca(2+) and Mg(2+) affinities of the mutated binding site by factors of 14 and 26, respectively. This behavior is consistent with that seen previously for the rat beta S55D variant.


Asunto(s)
Calcio/química , Magnesio/química , Parvalbúminas/química , Sustitución de Aminoácidos , Animales , Calcio/metabolismo , Calorimetría/métodos , Simulación por Computador , Diálisis/métodos , Ácido Edético/química , Ácido Edético/metabolismo , Ácido Egtácico/química , Ácido Egtácico/metabolismo , Cinética , Análisis de los Mínimos Cuadrados , Magnesio/metabolismo , Método de Montecarlo , Parvalbúminas/metabolismo , Unión Proteica , Ratas , Proteínas Recombinantes/química , Proteínas Recombinantes/metabolismo , Termodinámica , Volumetría/métodos
16.
Biochemistry ; 42(12): 3594-607, 2003 Apr 01.
Artículo en Inglés | MEDLINE | ID: mdl-12653564

RESUMEN

We have examined the metal ion-binding domains from rat alpha and beta parvalbumin. We find that the CD-EF fragments differ markedly in their tendency to self-associate. Whereas Ca(2+)-free alpha CD-EF is monomeric, the Ca(2+)-free beta peptide dimerizes weakly (K(2) = 2400 +/- 200 M(-1)). In buffer containing 1.0 mM Ca(2+), the apparent dimerization constant for beta CD-EF (191,000 +/- 29,000 M(-1)) is more than 50 times that of alpha (3400 +/- 200 M(-1)). Alpha CD-EF binds two Ca(2+) with positive cooperativity. Titration calorimetry data afford binding constants of 3.7(0.1) x 10(3) M(-1) and 8.6(0.2) x 10(4) M(-1). Beta CD-EF also binds two Ca(2+) cooperatively but with lower affinity. Equilibrium dialysis yields Adair constants of 4.2(0.1) x 10(3) and 6.1(0.2) x 10(3) M(-1). Significantly, the difference in Ca(2+) affinity is substantially smaller than that observed for the full-length proteins-suggesting that the AB domain can modulate divalent ion affinity. Analysis of beta calorimetry data requires explicit consideration of the self-association behavior. Data collected at low CD-EF concentration are consistent with preferential occupation of the EF site, dimerization of singly bound monomers, and cooperative filling of the CD sites. At higher concentrations, apo-protein dimerization can apparently precede cooperative occupation of the EF sites. In the presence of Ca(2+), alpha CD-EF exhibits higher thermal stability, consistent with its higher Ca(2+) affinity. However, the beta melting temperature shows greater concentration dependence, consistent with its greater tendency to dimerize. Neither fragment exhibits a sigmoidal melting curve in the Ca(2+)-free state, suggesting that the apo-peptides are disordered.


Asunto(s)
Calcio/metabolismo , Parvalbúminas/química , Parvalbúminas/metabolismo , Animales , Sitios de Unión , Técnicas In Vitro , Cinética , Modelos Biológicos , Parvalbúminas/genética , Fragmentos de Péptidos/química , Fragmentos de Péptidos/genética , Fragmentos de Péptidos/metabolismo , Unión Proteica , Desnaturalización Proteica , Isoformas de Proteínas/química , Isoformas de Proteínas/genética , Isoformas de Proteínas/metabolismo , Estructura Terciaria de Proteína , Ratas , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Terbio/metabolismo , Termodinámica
17.
Biochemistry ; 43(31): 10008-17, 2004 Aug 10.
Artículo en Inglés | MEDLINE | ID: mdl-15287728

RESUMEN

In model peptide systems, Ca2+ affinity is maximized in EF-hand motifs containing four carboxylates positioned on the +x and -x and +z and -z axes; introduction of a fifth carboxylate ligand reduces the affinity. However, in rat beta-parvalbumin, replacement of Ser-55 with aspartate heightens divalent ion affinity [Henzl, M. T., et al. (1996) Biochemistry 35, 5856-5869]. The corresponding alpha-parvalbumin variant (S55D/E59D) likewise exhibits elevated affinity [Henzl, M. T., et al. (2003) Anal. Biochem. 319, 216-233]. To determine whether these mutations produce a variation on the archetypal EF-hand coordination scheme, we have obtained high-resolution X-ray crystallographic data for alpha S55D/E59D. As anticipated, the aspartyl carboxylate replaces the serine hydroxyl at the +z coordination position. Interestingly, the Asp-59 carboxylate abandons the role it plays as an outer sphere ligand in wild-type rat beta, rotating away from the Ca2+ and, instead, forming a hydrogen bond with the amide of Glu-62. Superficially, the coordination sphere in the CD site of alpha S55D/E59D resembles that in the EF site. However, the orientation of the Asp-59 side chain is predicted to stabilize the D-helix, which may contribute to the heightened divalent ion affinity. DSC data indicate that the alpha S55D/E59D variant retains the capacity to bind 1 equiv of Na+. Consistent with this finding, when binding measurements are conducted in K(+)-containing buffer, divalent ion affinity is markedly higher. In 0.15 M KCl and 0.025 M Hepes-KOH (pH 7.4) at 5 degrees C, the macroscopic Ca2+ binding constants are 1.8 x 10(10) and 2.0 x 10(9) M(-1). The corresponding Mg2+ binding constants are 2.7 x 10(6) and 1.2 x 10(5) M(-1).


Asunto(s)
Sustitución de Aminoácidos , Proteínas de Unión al Calcio/química , Parvalbúminas/química , Sustitución de Aminoácidos/genética , Animales , Ácido Aspártico/genética , Sitios de Unión , Calcio/química , Proteínas de Unión al Calcio/genética , Cationes Bivalentes , Cristalización , Cristalografía por Rayos X , Motivos EF Hand , Ácido Glutámico/genética , Magnesio/química , Parvalbúminas/genética , Potasio/química , Unión Proteica , Isoformas de Proteínas/química , Isoformas de Proteínas/genética , Estructura Secundaria de Proteína , Ratas , Serina/genética , Soluciones
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