RESUMEN
The CTX-M family of beta lactamases mediate broad-spectrum antibiotic resistance and are present in the majority of drug-resistant Gram-negative bacterial infections worldwide. Allosteric mutations that increase catalytic rates of these drug resistance enzymes have been identified in clinical isolates but are challenging to predict prospectively. We have used molecular dynamics simulations to predict allosteric mutants increasing CTX-M9 drug resistance, experimentally testing top mutants using multiple antibiotics. Purified enzymes show an increase in catalytic rate and efficiency, while mutant crystal structures show no detectable changes from wild-type CTX-M9. We hypothesize that increased drug resistance results from changes in the conformational ensemble of an acyl intermediate in hydrolysis. Machine-learning analyses on the three top mutants identify changes to the binding-pocket conformational ensemble by which these allosteric mutations transmit their effect. These findings show how molecular simulation can predict how allosteric mutations alter active-site conformational equilibria to increase catalytic rates and thus resistance against common clinically used antibiotics.
RESUMEN
TEL is a transcriptional repressor that is a frequent target of chromosomal translocations in a large number of hematalogical malignancies. These rearrangements fuse a potent oligomerization module, the SAM domain of TEL, to a variety of tyrosine kinases or transcriptional regulatory proteins. The self-associating property of TEL-SAM is essential for cell transformation in many, if not all of these diseases. Here we show that the TEL-SAM domain forms a helical, head-to-tail polymeric structure held together by strong intermolecular contacts, providing the first clear demonstration that SAM domains can polymerize. Our results also suggest a mechanism by which SAM domains could mediate the spreading of transcriptional repression complexes along the chromosome.
Asunto(s)
Proteínas de Unión al ADN/química , Polímeros/química , Proteínas Represoras/química , Secuencia de Aminoácidos , Cristalografía por Rayos X , Proteínas de Unión al ADN/biosíntesis , Proteínas de Unión al ADN/genética , Proteínas de Unión al ADN/fisiología , Humanos , Leucemia Mielomonocítica Crónica , Datos de Secuencia Molecular , Estructura Secundaria de Proteína , Estructura Terciaria de Proteína , Proteínas Proto-Oncogénicas c-ets , Proteínas Recombinantes de Fusión/biosíntesis , Proteínas Recombinantes de Fusión/química , Proteínas Recombinantes de Fusión/genética , Proteínas Recombinantes de Fusión/fisiología , Proteínas Represoras/biosíntesis , Proteínas Represoras/genética , Proteínas Represoras/fisiología , Solubilidad , Transcripción Genética , Proteína ETS de Variante de Translocación 6RESUMEN
The sterile alpha motif (SAM) domain is a protein module found in many diverse signaling proteins. SAM domains in some systems have been shown to self-associate. Previous crystal structures of an EphA4-SAM domain dimer (Stapleton, D., Balan, I., Pawson, T., and Sicheri, F. (1999) Nat. Struct. Biol. 6, 44-49) and a possible EphB2-SAM oligomer (Thanos, C. D., Goodwill, K. E., and Bowie, J. U. (1999) Science 283, 833-836) both revealed large interfaces comprising an exchange of N-terminal peptide arms. Within the arm, a conserved hydrophobic residue (Tyr-8 in the EphB2-SAM structure or Phe-910 in the EphA4-SAM structure) is anchored into a hydrophobic cleft on a neighboring molecule. Here we have solved a new crystal form of the human EphB2-SAM domain that has the same overall SAM domain fold yet has no substantial intermolecular contacts. In the new structure, the N-terminal peptide arm of the EphB2-SAM domain protrudes out from the core of the molecule, leaving both the arm (including Tyr-8) and the hydrophobic cleft solvent-exposed. To verify that Tyr-8 is solvent-exposed in solution, we made a Tyr-8 to Ala-8 mutation and found that the EphB2-SAM domain structure and stability were only slightly altered. These results suggest that Tyr-8 is not part of the hydrophobic core of the EphB2-SAM domain and is conserved for functional reasons. Cystallographic evidence suggests a possible role for the N-terminal arm in oligomerization. In the absence of a direct demonstration of biological relevance, however, the functional role of the N-terminal arm remains an open question.
Asunto(s)
Proteínas Tirosina Quinasas Receptoras/química , Secuencias de Aminoácidos , Secuencia de Aminoácidos , Clonación Molecular , Cristalización , Dimerización , Humanos , Datos de Secuencia MolecularRESUMEN
The crystal structure of Ru(2, 2'-bipyridine)2(imidazole)(His83)azurin (RuAz) has been determined to 2.3 A -resolution by X-ray crystallography. The spectroscopic and thermodynamic properties of both the native protein and [Ru(2, 2'-bipyridine)2(imidazole)2]2+ are maintained in the modified protein. Dark-green RuAz crystals grown from PEG 4000, LiNO3, CuCl2 and Tris buffer are monoclinic, belong to the space group C2 and have cell parameters a = 100.6, b = 35.4, c = 74.7 A and beta = 106. 5 degrees. In addition, [Ru(2,2'-bipyridine)2(imidazole)2]SO4 x 10H2O was synthesized, crystallized and structurally characterized by X-ray crystallography. Red-brown crystals of this complex are monoclinic, space group P21/n, unit-cell parameters a = 13.230 (2), b = 18.197 (4), c = 16.126 (4) A, beta = 108.65 (2) degrees. Stereochemical parameters for the refinement of Ru(2, 2'-bipyridine)2(imidazole)(His83) were taken from the atomic coordinates of [Ru(2,2'-bipyridine)2(imidazole)2]2+. The structure of RuAz confirms that His83 is the only site of chemical modification and that the native azurin structure is not perturbed significantly by the ruthenium label.
Asunto(s)
Azurina/química , Compuestos Organometálicos/química , Pseudomonas aeruginosa/química , Rutenio/química , Cristalografía por Rayos X , Espectroscopía de Resonancia por Spin del Electrón , Espectroscopía de Resonancia Magnética , Estructura Molecular , Oxidación-Reducción , Conformación ProteicaRESUMEN
Crystal structures of formaldehyde ferredoxin oxidoreductase (FOR), a tungstopterin-containing protein from the hyperthermophilic archaeon Pyrococcus furiosus, have been determined in the native state and as a complex with the inhibitor glutarate at 1.85 A and 2. 4 A resolution, respectively. The native structure was solved by molecular replacement using the structure of the homologous P. furiosus aldehyde ferredoxin oxidoreductase (AOR) as the initial model. Residues are identified in FOR that may be involved in either the catalytic mechanism or in determining substrate specificity. The binding site on FOR for the physiological electron acceptor, P. furiosus ferredoxin (Fd), has been established from an FOR-Fd cocrystal structure. Based on the arrangement of redox centers in this structure, an electron transfer pathway is proposed that begins at the tungsten center, leads to the (4Fe:4S) cluster of FOR via one of the two pterins that coordinate the tungsten, and ends at the (4Fe:4S) cluster of ferredoxin. This pathway includes two residues that coordinate the (4Fe:4S) clusters, Cys287 of FOR and Asp14 of ferredoxin. Similarities in the active site structures between FOR and the unrelated molybdoenzyme aldehyde oxidoreductase from Desulfovibrio gigas suggest that both enzymes utilize a common mechanism for aldehyde oxidation.
Asunto(s)
Aldehído Oxidorreductasas/química , Pyrococcus furiosus/enzimología , Secuencia de Aminoácidos , Proteínas Arqueales/química , Sitios de Unión , Calcio/metabolismo , Catálisis , Cristalografía por Rayos X , Transporte de Electrón , Ferredoxinas/química , Glutaratos/química , Modelos Moleculares , Datos de Secuencia Molecular , Conformación Proteica , Pliegue de Proteína , Estructura Secundaria de Proteína , Pterinas/química , Alineación de Secuencia , Tungsteno/químicaRESUMEN
Fibroblast growth factors (FGFs) are members of a protein family with a broad range of biological activities. The best characterized FGFs interact with two distinct extracellular receptors--a transmembrane tyrosine kinase FGF receptor (FGFR) and a heparan f1p4ate-related proteoglycan of the extracellular matrix. These components form a FGF-FGFR-proteoglycan complex that activates the FGF-mediated signal transduction process through FGFR dimerization. Recent crystal structure determinations of FGF-heparin complexes have provided insights into both the interactions between these components and the role of heparin-like proteoglycans in FGF function. Future advances in this field will benefit enormously from an ability to specifically prepare homogeneous heparin-based oligosaccharides of defined sequence for use in biochemical and structural studies of FGF and many other systems.
Asunto(s)
Factores de Crecimiento de Fibroblastos/química , Factores de Crecimiento de Fibroblastos/metabolismo , Heparina/química , Heparina/metabolismo , Sitios de Unión , Conformación de Carbohidratos , Secuencia de Carbohidratos , Modelos Moleculares , Datos de Secuencia Molecular , Conformación Proteica , Transducción de SeñalRESUMEN
Crystal structures of heparin-derived tetra- and hexasaccharides complexed with basic fibroblast growth factor (bFGF) were determined at resolutions of 1.9 and 2.2 angstroms, respectively. The heparin structure may be approximated as a helical polymer with a disaccharide rotation of 174 degrees and a translation of 8.6 angstroms along the helix axis. Both molecules bound similarly to a region of the bFGF surface containing residues asparagine-28, arginine-121, lysine-126, and glutamine-135, the hexasaccharide also interacted with an additional binding site formed by lysine-27, asparagine-102, and lysine-136. No significant conformational change in bFGF occurred upon heparin oligosaccharide binding, which suggests that heparin primarily serves to juxtapose components of the FGF signal transduction pathway.
Asunto(s)
Factor 2 de Crecimiento de Fibroblastos/metabolismo , Heparina/química , Sitios de Unión , Conformación de Carbohidratos , Secuencia de Carbohidratos , Cristalización , Cristalografía por Rayos X , Heparina/metabolismo , Enlace de Hidrógeno , Modelos Moleculares , Datos de Secuencia Molecular , Oligosacáridos/química , Oligosacáridos/metabolismo , Conformación ProteicaRESUMEN
Members of the fibroblast growth factor (FGF) family of proteins stimulate the proliferation and differentiation of a variety of cell types through receptor-mediated pathways. The three-dimensional structures of two members of this family, bovine acidic FGF and human basic FGF, have been crystallographically determined. These structures contain 12 antiparallel beta strands organized into a folding pattern with approximate threefold internal symmetry. Topologically equivalent folds have been previously observed for soybean trypsin inhibitor and interleukins-1 beta and -1 alpha. The locations of sequences implicated in receptor and heparin binding by FGF are presented. These sites include beta-sheet strand 10, which is adjacent to the site of an extended sequence insertion in several oncogene proteins of the FGF family, and which shows sequence conservation among the FGF family and interleukin-1 beta.