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1.
Proc Natl Acad Sci U S A ; 119(15): e2116097119, 2022 04 12.
Artículo en Inglés | MEDLINE | ID: mdl-35377786

RESUMEN

Confining the activity of a designed protein to a specific microenvironment would have broad-ranging applications, such as enabling cell type-specific therapeutic action by enzymes while avoiding off-target effects. While many natural enzymes are synthesized as inactive zymogens that can be activated by proteolysis, it has been challenging to redesign any chosen enzyme to be similarly stimulus responsive. Here, we develop a massively parallel computational design, screening, and next-generation sequencing-based approach for proenzyme design. For a model system, we employ carboxypeptidase G2 (CPG2), a clinically approved enzyme that has applications in both the treatment of cancer and controlling drug toxicity. Detailed kinetic characterization of the most effectively designed variants shows that they are inhibited by ∼80% compared to the unmodified protein, and their activity is fully restored following incubation with site-specific proteases. Introducing disulfide bonds between the pro- and catalytic domains based on the design models increases the degree of inhibition to 98% but decreases the degree of restoration of activity by proteolysis. A selected disulfide-containing proenzyme exhibits significantly lower activity relative to the fully activated enzyme when evaluated in cell culture. Structural and thermodynamic characterization provides detailed insights into the prodomain binding and inhibition mechanisms. The described methodology is general and could enable the design of a variety of proproteins with precise spatial regulation.


Asunto(s)
Diseño Asistido por Computadora , Diseño de Fármacos , Precursores Enzimáticos , Ingeniería de Proteínas , gamma-Glutamil Hidrolasa , Dominio Catalítico , Diseño de Fármacos/métodos , Precursores Enzimáticos/química , Precursores Enzimáticos/farmacología , Humanos , Células PC-3 , Ingeniería de Proteínas/métodos , gamma-Glutamil Hidrolasa/química , gamma-Glutamil Hidrolasa/farmacología
2.
Structure ; 26(8): 1080-1090.e5, 2018 08 07.
Artículo en Inglés | MEDLINE | ID: mdl-29937357

RESUMEN

Integrin receptors bind collagen via metal-mediated interactions that are modulated by magnesium (Mg2+) levels in the extracellular matrix. Nuclear magnetic resonance-based relaxation experiments, isothermal titration calorimetry, and adhesion assays reveal that Mg2+ functions as both a structural anchor and dynamic switch of the α1ß1 integrin I domain (α1I). Specifically, Mg2+ binding activates micro- to millisecond timescale motions of residues distal to the binding site, particularly those surrounding the salt bridge at helix 7 and near the metal ion-dependent adhesion site. Mutagenesis of these residues impacts α1I functional activity, thereby suggesting that Mg-bound α1I dynamics are important for collagen binding and consequent allosteric rearrangement of the low-affinity closed to high-affinity open conformation. We propose a multistep recognition mechanism for α1I-Mg-collagen interactions involving both conformational selection and induced-fit processes. Our findings unravel the multifaceted role of Mg2+ in integrin-collagen recognition and assist in elucidating the molecular mechanisms by which metals regulate protein-protein interactions.


Asunto(s)
Sustitución de Aminoácidos , Aminoácidos/química , Colágeno Tipo I/química , Integrina alfa1beta1/química , Magnesio/química , Aminoácidos/metabolismo , Animales , Sitios de Unión , Cationes Bivalentes , Clonación Molecular , Colágeno Tipo I/genética , Colágeno Tipo I/metabolismo , Escherichia coli/genética , Escherichia coli/metabolismo , Matriz Extracelular/química , Expresión Génica , Vectores Genéticos/química , Vectores Genéticos/metabolismo , Humanos , Integrina alfa1beta1/genética , Integrina alfa1beta1/metabolismo , Cinética , Magnesio/metabolismo , Modelos Moleculares , Mutación , Resonancia Magnética Nuclear Biomolecular , Unión Proteica , Conformación Proteica en Hélice alfa , Conformación Proteica en Lámina beta , Dominios y Motivos de Interacción de Proteínas , Ratas , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo
3.
J Biol Chem ; 291(36): 18620-31, 2016 09 02.
Artículo en Inglés | MEDLINE | ID: mdl-27402847

RESUMEN

To accomplish its crucial role, mitochondria require proteins that are produced in the cytosol, delivered by cytosolic Hsp90, and translocated to its interior by the translocase outer membrane (TOM) complex. Hsp90 is a dimeric molecular chaperone and its function is modulated by its interaction with a large variety of co-chaperones expressed within the cell. An important family of co-chaperones is characterized by the presence of one TPR (tetratricopeptide repeat) domain, which binds to the C-terminal MEEVD motif of Hsp90. These include Tom70, an important component of the TOM complex. Despite a wealth of studies conducted on the relevance of Tom70·Hsp90 complex formation, there is a dearth of information regarding the exact molecular mode of interaction. To help fill this void, we have employed a combined experimental strategy consisting of cross-linking/mass spectrometry to investigate binding of the C-terminal Hsp90 domain to the cytosolic domain of Tom70. This approach has identified a novel region of contact between C-Hsp90 and Tom70, a finding that is confirmed by probing the corresponding peptides derived from cross-linking experiments via isothermal titration calorimetry and mitochondrial import assays. The data generated in this study are combined to input constraints for a molecular model of the Hsp90/Tom70 interaction, which has been validated by small angle x-ray scattering, hydrogen/deuterium exchange, and mass spectrometry. The resultant model suggests that only one of the MEEVD motifs within dimeric Hsp90 contacts Tom70. Collectively, our findings provide significant insight on the mechanisms by which preproteins interact with Hsp90 and are translocated via Tom70 to the mitochondria.


Asunto(s)
Proteínas Portadoras/metabolismo , Proteínas HSP90 de Choque Térmico/metabolismo , Proteínas Mitocondriales/metabolismo , Neurospora crassa/metabolismo , Proteínas Protozoarias/metabolismo , Secuencias de Aminoácidos , Animales , Proteínas Portadoras/química , Proteínas Portadoras/genética , Bovinos , Proteínas HSP90 de Choque Térmico/química , Proteínas HSP90 de Choque Térmico/genética , Proteínas del Complejo de Importación de Proteínas Precursoras Mitocondriales , Proteínas Mitocondriales/química , Proteínas Mitocondriales/genética , Neurospora crassa/química , Neurospora crassa/genética , Dominios Proteicos , Proteínas Protozoarias/química , Proteínas Protozoarias/genética
4.
Protein Sci ; 25(9): 1672-81, 2016 09.
Artículo en Inglés | MEDLINE | ID: mdl-27342747

RESUMEN

Integrin-collagen interactions play a critical role in a myriad of cellular functions that include immune response, and cell development and differentiation, yet their mechanism of binding is poorly understood. There is increasing evidence that conformational flexibility assumes a central role in the molecular mechanisms of protein-protein interactions and here we employ NMR hydrogen-deuterium exchange (HDX) experiments to explore the impact of slower timescale dynamic events. To gain insight into the mechanisms underlying collagen-induced conformational switches, we have undertaken a comparative study between the wild type integrin α1 I and a gain-of-function E317A mutant. NMR HDX results suggest a relationship between regions exhibiting a reduced local stability in the unbound I domain and those that undergo significant conformational changes upon binding. Specifically, the αC and α7 helices within the C-terminus are at the center of such major perturbations and present reduced local stabilities in the unbound state relative to other structural elements. Complementary isothermal titration calorimetry experiments have been performed to derive complete thermodynamic binding profiles for association of the collagen-like triple-helical peptide with wild type α1 I and E317A mutant. The differential energetics observed for E317A are consistent with the HDX experiments and support a model in which intrinsically destabilized regions predispose conformational rearrangement in the integrin I domain. This study highlights the importance of exploring different timescales to delineate allosteric and binding events.


Asunto(s)
Colágeno/química , Integrina alfa1/química , Sustitución de Aminoácidos , Colágeno/genética , Colágeno/metabolismo , Humanos , Integrina alfa1/genética , Integrina alfa1/metabolismo , Mutación Missense , Resonancia Magnética Nuclear Biomolecular , Dominios Proteicos , Estabilidad Proteica , Estructura Secundaria de Proteína
5.
Biopolymers ; 103(9): 491-508, 2015 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-25991500

RESUMEN

The magnitude and nature of lesion-induced energetic perturbations empirically correlate with mutagenicity/cytotoxicity profiles and can be predictive of lesion outcomes during polymerase-mediated replication in vitro. In this study, we assess the sequence and counterbase-dependent energetic impact of the Thymine glycol (Tg) lesion on a family of deoxyoligonucleotide duplexes. Tg damage arises from thymine and methyl-cytosine exposure to oxidizing agents or radiation-generated free-radicals. The Tg lesion blocks polymerase-mediated DNA replication in vitro and the unrepaired site elicits cytotoxic lethal consequences in vivo. Our combined calorimetric and spectroscopic characterization correlates Tg -induced energetic perturbations with biological and structural properties. Specifically, we incorporate a 5R-Tg isomer centered within the tridecanucleotide sequence 5'-GCGTACXCATGCG-3' (X = Tg or T) which is hybridized with the corresponding complementary sequence 5'-CGCATGNGTACGC-3' (N = A, G, T, C) to generate families of Tg -damaged (Tg ·N) and lesion-free (T·N) duplexes. We demonstrate that the magnitude and nature of the Tg destabilizing impact is dependent on counterbase identity (i.e., A ∼ G < T < C). The observation that a Tg lesion is less destabilizing when positioned opposite purines suggests that favorable counterbase stacking interactions may partially compensate lesion-induced perturbations. Moreover, the destabilizing energies of Tg ·N duplexes parallel their respective lesion-free T·N mismatch counterparts (i.e., G < T < C). Elucidation of Tg-induced destabilization relative to the corresponding undamaged mismatch energetics allows resolution of lesion-specific and sequence-dependent impacts. The Tg-induced energetic perturbations are consistent with its replication blocking properties and may serve as differential recognition elements for discrimination by the cellular repair machinery.


Asunto(s)
ADN/química , Timina/análogos & derivados , Rastreo Diferencial de Calorimetría , Dicroismo Circular , Daño del ADN/genética , Conformación de Ácido Nucleico , Termodinámica , Timina/química
6.
Biochemistry ; 53(17): 2815-7, 2014 May 06.
Artículo en Inglés | MEDLINE | ID: mdl-24739028

RESUMEN

α-Synuclein (αS) is an amyloidogenic intrinsically disordered protein implicated in Parkinson's disease, for which copper-mediated pathways of neurodegeneration have been suggested. We have employed nuclear magnetic resonance, circular dichroism, electrospray ionization mass spectrometry, and thioflavin T fluorescence to characterize interactions of Cu(2+) with the physiological acetylated form (Ac-αS). Significantly, N-terminal acetylation abolishes Cu(2+) binding at the high-affinity M1-D2 site present in the nonacetylated protein and maintains Cu(2+) interactions around H50/D121. Fibrillation enhancement observed at an equimolar Cu(2+) stoichiometry with the nonacetylated model does not occur with Ac-αS. These findings open new avenues of investigation into Cu(2+)-mediated neurodegenerative pathology suggested in vivo.


Asunto(s)
Cobre/química , Cobre/metabolismo , alfa-Sinucleína/química , alfa-Sinucleína/metabolismo , Acetilación , Amiloide/biosíntesis , Sitios de Unión , Dicroismo Circular , Humanos , Manganeso/química , Resonancia Magnética Nuclear Biomolecular , Enfermedad de Parkinson/metabolismo
7.
Cell Rep ; 3(3): 709-15, 2013 Mar 28.
Artículo en Inglés | MEDLINE | ID: mdl-23523349

RESUMEN

The targeting of type III secretion (TTS) proteins at the injectisome is an important process in bacterial virulence. Nevertheless, how the injectisome specifically recognizes TTS substrates among all bacterial proteins is unknown. A TTS peripheral membrane ATPase protein located at the base of the injectisome has been implicated in the targeting process. We have investigated the targeting of the EspA filament protein and its cognate chaperone, CesAB, to the EscN ATPase of the enteropathogenic E. coli (EPEC). We show that EscN selectively engages the EspA-loaded CesAB but not the unliganded CesAB. Structure analysis revealed that the targeting signal is encoded in a disorder-order structural transition in CesAB that is elicited only upon the binding of its physiological substrate, EspA. Abrogation of the interaction between the CesAB-EspA complex and EscN resulted in severe secretion and infection defects. Additionally, we show that the targeting and secretion signals are distinct and that the two processes are likely regulated by different mechanisms.


Asunto(s)
Proteínas de Escherichia coli/química , Escherichia coli/metabolismo , Chaperonas Moleculares/química , Señales de Clasificación de Proteína , Adenosina Trifosfatasas/química , Adenosina Trifosfatasas/metabolismo , Secuencia de Aminoácidos , Escherichia coli/química , Proteínas de Escherichia coli/metabolismo , Chaperonas Moleculares/metabolismo , Simulación del Acoplamiento Molecular , Datos de Secuencia Molecular , Unión Proteica , Estructura Terciaria de Proteína , Transporte de Proteínas
8.
Mol Cell ; 44(5): 734-44, 2011 Dec 09.
Artículo en Inglés | MEDLINE | ID: mdl-22152477

RESUMEN

Protein-protein interactions mediate a vast number of cellular processes. Here, we present a regulatory mechanism in protein-protein interactions mediated by finely tuned structural instability and coupled with molecular mimicry. We show that a set of type III secretion (TTS) autoinhibited homodimeric chaperones adopt a molten globule-like state that transiently exposes the substrate binding site as a means to become rapidly poised for binding to their cognate protein substrates. Packing defects at the homodimeric interface stimulate binding, whereas correction of these defects results in less labile chaperones that give rise to nonfunctional biological systems. The protein substrates use structural mimicry to offset the weak spots in the chaperones and to counteract their autoinhibitory conformation. This regulatory mechanism of protein activity is evolutionarily conserved among several TSS systems and presents a lucid example of functional advantage conferred upon a biological system by finely tuned structural instability.


Asunto(s)
Proteínas/química , Proteínas/metabolismo , Proteínas de Escherichia coli/antagonistas & inhibidores , Proteínas de Escherichia coli/química , Proteínas de Escherichia coli/metabolismo , Evolución Molecular , Modelos Moleculares , Chaperonas Moleculares/antagonistas & inhibidores , Chaperonas Moleculares/química , Chaperonas Moleculares/metabolismo , Imitación Molecular , Unión Proteica , Conformación Proteica , Pliegue de Proteína , Multimerización de Proteína , Estabilidad Proteica
9.
Nucleic Acids Res ; 39(13): 5776-89, 2011 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-21415012

RESUMEN

Accumulation of damaged guanine nucleobases within genomic DNA, including the imidazole ring opened N(6)-(2-Deoxy-α,ß-D-erythro-pentafuranosyl)-2,6-diamino-4-hydroxy-5-formylamidopyrimidine (Fapy-dG), is associated with progression of age-related diseases and cancer. To evaluate the impact of this mutagenic lesion on DNA structure and energetics, we have developed a novel synthetic strategy to incorporate cognate Fapy-dG site-specifically within any oligodeoxynucleotide sequence. The scheme involves the synthesis of an oligonucleotide precursor containing a 5-nitropyrimidine moiety at the desired lesion site via standard solid-phase procedures. Following deprotection and isolation, the Fapy-dG lesion is generated by catalytic hydrogenation and subsequent formylation. NMR assignment of the Fapy-dG lesion (X) embedded within a TXT trimer reveals the presence of rotameric and anomeric species. The latter have been characterized by synthesizing the tridecamer oligodeoxynucleotide d(GCGTACXCATGCG) harboring Fapy-dG as the central residue and developing a protocol to resolve the isomeric components. Hybridization of the chromatographically isolated fractions with their complementary d(CGCATGCGTACGC) counterpart yields two Fapy-dG·C duplexes that are differentially destabilized relative to the canonical G·C parent. The resultant duplexes exhibit distinct thermal and thermodynamic profiles that are characteristic of α- and ß-anomers, the former more destabilizing than the latter. These anomer-specific impacts are discussed in terms of differential repair enzyme recognition, processing and translesion synthesis.


Asunto(s)
Daño del ADN , Formamidas/química , Furanos/química , Oligodesoxirribonucleótidos/química , Pirimidinas/química , Cromatografía por Intercambio Iónico , ADN/química , ADN de Cadena Simple/química , Isomerismo , Mutágenos/química , Conformación de Ácido Nucleico , Oligodesoxirribonucleótidos/síntesis química , Oligodesoxirribonucleótidos/aislamiento & purificación , Termodinámica
10.
Nucleic Acids Res ; 38(1): 97-116, 2010 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-19946018

RESUMEN

DNA bulges are biologically consequential defects that can arise from template-primer misalignments during replication and pose challenges to the cellular DNA repair machinery. Calorimetric and spectroscopic characterizations of defect-containing duplexes reveal systematic patterns of sequence-context dependent bulge-induced destabilizations. These distinguishing energetic signatures are manifest in three coupled characteristics, namely: the magnitude of the bulge-induced duplex destabilization (DeltaDeltaG(Bulge)); the thermodynamic origins of DeltaDeltaG(Bulge) (i.e. enthalpic versus entropic); and, the cooperativity of the duplex melting transition (i.e. two-state versus non-two state). We find moderately destabilized duplexes undergo two-state dissociation and exhibit DeltaDeltaG(Bulge) values consistent with localized, nearest neighbor perturbations arising from unfavorable entropic contributions. Conversely, strongly destabilized duplexes melt in a non-two-state manner and exhibit DeltaDeltaG(Bulge) values consistent with perturbations exceeding nearest-neighbor expectations that are enthalpic in origin. Significantly, our data reveal an intriguing correlation in which the energetic impact of a single bulge base centered in one strand portends the impact of the corresponding complementary bulge base embedded in the opposite strand. We discuss potential correlations between these bulge-specific differential energetic profiles and their overall biological implications in terms of DNA recognition, repair and replication.


Asunto(s)
ADN/química , Termodinámica , Rastreo Diferencial de Calorimetría , Reparación del ADN , Replicación del ADN , Modelos Genéticos , Conformación de Ácido Nucleico , Purinas/química , Pirimidinas/química
11.
Biopolymers ; 93(4): 370-82, 2010 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-19937758

RESUMEN

Acrolein is an alpha,beta-unsaturated aldehyde that is a major environmental pollutant, as well as a product of cellular metabolism. DNA bases react with acrolein to form two regioisomeric exocyclic guanine adducts, namely gamma-hydroxy-propanodeoxyguanosine (gamma-OH-PdG) and its positional isomer alpha-hydroxy-propanodeoxyguanosine (alpha-OH-PdG). The gamma-OH-PdG isomer adopts a ring-opened conformation with minimal structural perturbation of the DNA host duplex. Conversely, the alpha-OH-PdG isomer assumes a ring-closed conformation that significantly disrupts Watson-Crick base-pair alignments within the immediate vicinity of the damaged site. We have employed a combination of calorimetric and spectroscopic techniques to characterize the thermodynamic origins of these lesion-induced structural alterations. Specifically, we have assessed the energetic impact of alpha-OH-PdG centered within an 11-mer duplex by hybridizing the adduct-containing oligonucleotide with its complementary strand harboring a central base N [where N = C or A], yielding a pair of duplexes containing the nascent lesion (alpha-OH-PdG.C) or mismatched adduct (alpha-OH-PdG.A), respectively. Our data reveal that the nascent lesion is highly destabilizing, whereas its mismatched counterpart partially ameliorates alpha-OH-PdG-induced destabilization. Collectively, our data provide energetic characterizations of the driving forces that modulate error-free versus error-prone DNA translesion synthesis. The biological implications of our findings are discussed in terms of energetically probing acrolein-mediated mutagenicity versus adduct-induced genotoxicity.


Asunto(s)
Aductos de ADN/química , Daño del ADN , ADN/química , Guanina/análogos & derivados , Guanina/química , Mutagénesis , Acroleína/química , Acroleína/toxicidad , Rastreo Diferencial de Calorimetría , Dicroismo Circular , Oligonucleótidos/química , Termodinámica
12.
Proc Natl Acad Sci U S A ; 105(1): 70-5, 2008 Jan 08.
Artículo en Inglés | MEDLINE | ID: mdl-18172202

RESUMEN

We report a continuous hyperchromicity assay (CHA) for monitoring and characterizing enzyme activities associated with DNA processing. We use this assay to determine kinetic and thermodynamic parameters for a repair enzyme that targets nucleic acid substrates containing a specific base lesion. This optically based kinetics assay exploits the free-energy differences between a lesion-containing DNA duplex substrate and the enzyme-catalyzed, lesion-excised product, which contains at least one hydrolyzed phosphodiester bond. We apply the assay to the bifunctional formamidopyrimidine glycosylase (Fpg) repair enzyme (E) that recognizes an 8-oxodG lesion within a 13-mer duplex substrate (S). Base excision/elimination yields a gapped duplex product (P) that dissociates to produce the diagnostic hyperchromicity signal. Analysis of the kinetic data at 25 degrees C yields a K(m) of 46.6 nM for the E.S interaction, and a k(cat) of 1.65 min(-1) for conversion of the ES complex into P. The temperature dependence reveals a free energy (DeltaG(b)) of -10.0 kcal.mol(-1) for the binding step (E + S <--> ES) that is enthalpy-driven (DeltaH(b) = -16.4 kcal.mol(-1)). The activation barrier (DeltaG) of 19.6 kcal.mol(-1) for the chemical step (ES <--> P) also is enthalpic in nature (DeltaH = 19.2 kcal.mol(-1)). Formation of the transition state complex from the reactants (E + S <--> ES), a pathway that reflects Fpg catalytic specificity (k(cat)/K(m)) toward excision of the 8-oxodG lesion, exhibits an overall activation free energy (DeltaG(T)) of 9.6 kcal.mol(-1). These parameters characterize the driving forces that dictate Fpg enzyme efficiency and specificity and elucidate the energy landscape for lesion recognition and repair.


Asunto(s)
Reparación del ADN , ADN-Formamidopirimidina Glicosilasa/química , ADN/química , Termodinámica , Catálisis , Daño del ADN , ADN-Formamidopirimidina Glicosilasa/metabolismo , Escherichia coli/metabolismo , Ésteres/química , Hidrólisis , Cinética , Modelos Químicos , Conformación de Ácido Nucleico , Nucleótidos/química , Reproducibilidad de los Resultados , Temperatura , Factores de Tiempo
13.
J Mol Biol ; 365(1): 1-9, 2007 Jan 05.
Artículo en Inglés | MEDLINE | ID: mdl-17055530

RESUMEN

The energetic profiles of a significant number of protein-DNA systems at 20 degrees C reveal that, despite comparable Gibbs free energies, association with the major groove is primarily an enthalpy-driven process, whereas binding to the minor groove is characterized by an unfavorable enthalpy that is compensated by favorable entropic contributions. These distinct energetic signatures for major versus minor groove binding are irrespective of the magnitude of DNA bending and/or the extent of binding-induced protein refolding. The primary determinants of their different energetic profiles appear to be the distinct hydration properties of the major and minor grooves; namely, that the water in the A+T-rich minor groove is in a highly ordered state and its removal results in a substantial positive contribution to the binding entropy. Since the entropic forces driving protein binding into the minor groove are a consequence of displacing water ordered by the regular arrangement of polar contacts, they cannot be regarded as hydrophobic.


Asunto(s)
Proteínas de Unión al ADN/química , Proteínas de Unión al ADN/metabolismo , ADN/química , ADN/metabolismo , Composición de Base , Sitios de Unión , Entropía , Modelos Químicos , Modelos Moleculares , Conformación de Ácido Nucleico , Unión Proteica , Pliegue de Proteína , Electricidad Estática , Termodinámica
14.
Arch Biochem Biophys ; 453(1): 32-53, 2006 Sep 01.
Artículo en Inglés | MEDLINE | ID: mdl-16712771

RESUMEN

The critical role of membrane proteins in a myriad of biological and physiological functions has spawned numerous investigations over the past several decades with the long-term goal of identifying the molecular origins and energetic forces that stabilize these proteins within the membrane. Parallel structural and thermodynamics studies on several systems have provided significant insight regarding the driving forces governing folding, assembly, insertion, and translocation of membrane proteins. The present review surveys families of membrane-associated proteins including alpha-helical and beta-barrel structures, viral surface receptors, and pore-forming toxins, citing representative proteins within each of these classes for further scrutiny in terms of structure-function relationships and global conformational stability. This overview presents seminal findings from pioneering studies on the energetics of membrane protein folding and stability to modern techniques that are exploiting the use of molecular genetics and single molecule studies. An overall consensus regarding the molecular origins of membrane protein stability is that a number of intrinsic properties resemble features of soluble proteins, yet there are distinct energetic differences arising from specific intra- and intermolecular interactions within the membrane. The combined efforts from structural, energetics, and dynamics approaches offer unique insights and improve our fundamental understanding of the driving forces dictating membrane protein folding and stability.


Asunto(s)
Transferencia Lineal de Energía , Proteínas de la Membrana/química , Proteínas de la Membrana/metabolismo , Modelos Químicos , Modelos Moleculares , Pliegue de Proteína , Proteínas de la Membrana/ultraestructura , Conformación Proteica , Termodinámica
15.
Proteins ; 57(1): 15-26, 2004 Oct 01.
Artículo en Inglés | MEDLINE | ID: mdl-15326591

RESUMEN

Reverse transcriptase is an essential retroviral enzyme that replicates the single-stranded RNA genome of the retrovirus producing a double-stranded DNA copy, which is subsequently integrated into the host's genome. We have previously reported that processive DNA synthesis of Moloney murine leukemia virus reverse transcriptase (MMLV RT) is severely compromised by substitution of an Ala for the fingers domain residue Arg 116. In order to further investigate the role of Arg 116 in interactions of MMLV RT with nucleic acids, we have determined the crystal structure of the R116A N-terminal fragment and characterized the binding of two self-complementary DNA duplexes [d(CATGCATG)2 and d(CGCGCGCG)2] to both the wild-type and R116A fragments by isothermal titration calorimetry. The resultant thermodynamic profiles extrapolated to 25 degrees C reveal that binding of the wild-type N-terminal fragment to both DNA duplexes is enthalpy-driven and characterized by an unfavorable entropy. Although the temperature dependence of the respective protein-DNA binding enthalpies is markedly different reflecting distinct heat capacity changes, the binding free energies are nearly identical and relatively invariant to temperature (DeltaG approximately -6.0 kcal x mol(-1)). In contrast to the wild-type fragment, the R116A fragment exhibits no measurable affinity for either DNA duplex, yet its crystal structure reveals no significant changes when compared to the wild-type structures. We suggest that hydrogen-bonding interactions involving the fingers domain residue Arg 116 are critical for DNA binding as well as processive DNA synthesis by MMLV RT.


Asunto(s)
ADN/metabolismo , Virus de la Leucemia Murina de Moloney/enzimología , ADN Polimerasa Dirigida por ARN/metabolismo , Sustitución de Aminoácidos , Sitios de Unión , Calorimetría , Dominio Catalítico , Cristalografía , Enlace de Hidrógeno , Modelos Moleculares , Mutación , Oligodesoxirribonucleótidos/metabolismo , Fragmentos de Péptidos/metabolismo , Unión Proteica , Estructura Secundaria de Proteína , ADN Polimerasa Dirigida por ARN/química , Termodinámica
16.
Proc Natl Acad Sci U S A ; 100(25): 14719-24, 2003 Dec 09.
Artículo en Inglés | MEDLINE | ID: mdl-14623953

RESUMEN

We used stopped-flow calorimetry to measure the overall enthalpy change associated with template-directed nucleotide insertion and DNA extension. Specifically, we used families of hairpin self-priming templates in conjunction with an exonuclease-free DNA polymerase to study primer extension by one or more dA or dT residues. Our results reveal exothermic heats between -9.8 and -16.0 kcal/bp for template-directed enzymatic polymerization. These extension enthalpies depend on the identity of the inserting base, the primer terminus, and/or the preceding base. Despite the complexity of the overall process, the sign, magnitude, and sequence dependence of these insertion and extension enthalpies are consistent with nearest-neighbor data derived from DNA melting studies. We recognize that the overall process studied here involves contributions from a multitude of events, including dNTP to dNMP hydrolysis, phosphodiester bond formation, and enzyme conformational changes. It is therefore noteworthy that the overall enthalpic driving force per base pair is of a magnitude similar to that expected for addition of one base pair or base stack per insertion event, rather than that associated with the rupture and/or formation of covalent bonds, as occurs during this catalytic process. Our data suggest a constant sequence-independent background of compensating enthalpic contributions to the overall process of DNA synthesis, with discrimination expressed by differences in noncovalent interactions at the template-primer level. Such enthalpic discrimination underscores a model in which complex biological events are regulated by relatively modest energy balances involving weak interactions, thereby allowing subtle mechanisms of regulation.


Asunto(s)
ADN Polimerasa Dirigida por ADN/química , ADN/biosíntesis , Secuencia de Bases , Calorimetría , ADN/química , Entropía , Escherichia coli/enzimología , Hidrólisis , Cinética , Datos de Secuencia Molecular , Oligonucleótidos/química , Temperatura , Moldes Genéticos , Termodinámica , Rayos Ultravioleta
17.
J Mol Biol ; 328(5): 1047-60, 2003 May 16.
Artículo en Inglés | MEDLINE | ID: mdl-12729740

RESUMEN

As part of an overall effort to map the energetic landscape of the base excision repair pathway, we report the first thermodynamic characterization of repair enzyme binding to lesion-containing duplexes. Isothermal titration calorimetry (ITC) in conjunction with spectroscopic measurements and protease protection assays have been employed to characterize the binding of Escherichia coli formamidopyrimidine-glycosylase (Fpg), a bifunctional repair enzyme, to a series of 13-mer DNA duplexes. To resolve energetically the binding and the catalytic events, several of these duplexes are constructed with non-hydrolyzable lesion analogs that mimic the natural 8-oxo-dG substrate and the abasic-like intermediates. Specifically, one of the duplexes contains a central, non-hydrolyzable, tetrahydrofuran (THF) abasic site analog, while another duplex contains a central, carbocyclic substrate analog (carba-8-oxo-dG). ITC-binding studies conducted between 5.0 degrees C and 15.0 degrees C reveal that Fpg association with the THF-containing duplex is characterized by binding free energies that are relatively invariant to temperature (deltaG approximately -9.5 kcalmol(-1)), in contrast to both the reaction enthalpy and entropy that are strongly temperature-dependent. Complex formation between Fpg and the THF-containing duplex at 15 degrees C exhibits an unfavorable association enthalpy (deltaH=+7.5 kcalmol(-1)) that is compensated by a favorable association entropy (TdeltaS=+17.0 kcalmol(-1)). The entropic nature of the binding interaction, coupled with the large negative heat capacity (deltaC(p)=-0.67 kcaldeg(-1)mol(-1)), is consistent with Fpg complexation to the THF-containing duplex involving significant burial of non-polar surface areas. By contrast, under the high ionic strength buffer conditions employed herein (200 mM NaCl), no appreciable Fpg affinity for the carba-8-oxo-dG substrate analog is detected. Our results suggest that initial Fpg recognition of a damaged DNA site is predominantly electrostatic in nature, and does not involve large contact interfaces. Subsequent base excision presumably facilitates accommodation of the resulting lesion site into the binding pocket, as the enzyme interaction with the THF-containing duplex is characterized by high affinity and a large negative heat capacity change. Our data are consistent with a pathway in which Fpg glycosylase activity renders the base excision product a preferred ligand relative to the natural substrate, thereby ensuring the fidelity of removing highly reactive and potentially mutagenic abasic-like intermediates through catalytic elimination reactions.


Asunto(s)
Daño del ADN , Reparación del ADN/fisiología , Proteínas de Escherichia coli , N-Glicosil Hidrolasas/metabolismo , Secuencia de Bases , Sitios de Unión , Calorimetría , Dicroismo Circular , ADN-Formamidopirimidina Glicosilasa , Metabolismo Energético , Escherichia coli/enzimología , N-Glicosil Hidrolasas/química , Oligodesoxirribonucleótidos/química , Oligodesoxirribonucleótidos/metabolismo , Especificidad por Sustrato , Termodinámica
18.
Biochemistry ; 41(6): 2044-54, 2002 Feb 12.
Artículo en Inglés | MEDLINE | ID: mdl-11827552

RESUMEN

The conformational and thermal stability of full-length hemagglutinin (HA) of influenza virus (strain X31) has been investigated using a combination of differential scanning calorimetry (DSC), analytical ultracentrifugation, fluorescence, and circular dichroism (CD) spectroscopy as a function of pH. HA sediments as a rosette comprised of 5-6 trimers (31-35 S) over the pH range of 7.4-5.4. The DSC profile of HA in the native state at pH 7.4 is characterized by a single cooperative endotherm with a transition temperature (Tm) of 66 degrees C and unfolding enthalpy (DeltaH(cal)) of 800 kcal x (mol of trimer)(-1). Upon acidification to pH 5.4, there is a significant decrease in the transition temperature (from 66 to 45 degrees C), unfolding enthalpy [from 800 to 260 kcal x (mol of trimer)(-1)], and DeltaH(cal)/DeltaH(vH) ratio (from 3.0 to approximately 1.3). Whereas the far- and near-UV ellipticities are maintained over this pH range, there is an acid-induced increase in surface hydrophobicity and decrease in intrinsic tryptophanyl fluorescence. The major contribution to the DSC endotherm arises from unfolding HA1 domains. The relationship between acid-induced changes in thermal stability and the fusion activity of HA has been examined by evaluating the kinetics and extent of fusion of influenza virus with erythrocytes over the temperature and pH range of the DSC measurements. Surprisingly, X31 influenza virus retains its fusion activity at acidic pH and temperatures significantly below the unfolding transition of HA. This finding is consistent with the notion that the fusion activity of influenza virus may involve structural changes of only a small fraction of HA molecules.


Asunto(s)
Glicoproteínas Hemaglutininas del Virus de la Influenza/química , Ácidos , Dicroismo Circular , Estabilidad de Medicamentos , Membrana Eritrocítica , Glicoproteínas Hemaglutininas del Virus de la Influenza/fisiología , Humanos , Concentración de Iones de Hidrógeno , Técnicas In Vitro , Fusión de Membrana/fisiología , Orthomyxoviridae/patogenicidad , Orthomyxoviridae/fisiología , Conformación Proteica , Desnaturalización Proteica , Estructura Secundaria de Proteína , Estructura Terciaria de Proteína , Espectrometría de Fluorescencia , Temperatura , Triptófano/química
19.
Arq. bras. endocrinol. metab ; 30(2): 40-3, jun. 1986. tab, graf
Artículo en Inglés | LILACS | ID: lil-208694

RESUMEN

The effects of streptozotocin diabetes on the male reproductive tract were studied in young rats in different ages (25 to 60 days old). The data showed that diabetes caused atrophy of pituitary, testes and sexual accessory glands as well as testicular and pituitary functions, as evaluated by the circulating levels of LH and testosterone. In addition, an impairment of thyroidal function was detected since thyroxine serum levels were decreased. It is also seen that prolactin levels were reduced as a consequence of streptozotocin treated rats. Since younger animals were more drasticaly affected, we conclude that hypothyroidism that follows after the onset of diabetes could contribute to the picture on the basis of the importance of thyroidal function in the developing animal. Also it seems that reduction of prolactin levels due to hypothalamic TRH impairment would bring about a lack of the so important sinergistic action of this hormone and androgens in maintenance of androgen targetorgans.


Asunto(s)
Masculino , Ratas , Animales , Vértebra Cervical Axis/metabolismo , Diabetes Mellitus Experimental/metabolismo , Glándula Tiroides/metabolismo , Maduración Sexual/fisiología , Sistema Hipotálamo-Hipofisario/metabolismo , Glándula Tiroides , Ratas Wistar , Sistema Hipotálamo-Hipofisario , Estreptozocina/farmacología
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