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1.
Physiol Behav ; 273: 114413, 2024 Jan 01.
Article in English | MEDLINE | ID: mdl-37989448

ABSTRACT

Vulnerable patients are at risk for neuroinflammation-mediated post-operative complications, including depression (POD) and cognitive dysfunction (POCD). Zucker rats, expressing multiple risk factors for post-operative complications in humans, may provide a clinically relevant model to study pathophysiology and explore potential interventions. J147, a newly developed anti-dementia drug, was shown to prevent POCD in young healthy rats, and improved early post-surgical recovery in Zucker rats. Aim of the present study was to investigate POCD and the therapeutic potential of J147 in male Zucker rats. Risk factors in the Zucker rat strain were evaluated by comparison with lean littermates. Zucker rats were subjected to major abdominal surgery. Acute J147 treatment was provided by a single iv injection (10 mg/kg) at the start of surgery, while chronic J147 treatment was provided in the food (aimed at 30 mg/kg/day), starting one week before surgery and up to end of protocol. Effects on behavior were assessed, and plasma, urine and brain tissue were collected and processed for immunohistochemistry and molecular analyses. Indeed, Zucker rats displayed increased risk factors for POCD, including obesity, high plasma triglycerides, low grade systemic inflammation, impaired spatial learning and decreased neurogenesis. Surgery in Zucker rats reduced exploration and increased anxiety in the Open Field test, impaired short-term spatial memory, induced a shift in circadian rhythm and increased plasma neutrophil gelatinase-associated lipocalin (NGAL), microglia activity in the CA1 and blood brain barrier leakage. Chronic, but not acute J147 treatment reduced anxiety in the Open Field test and protected against the spatial memory decline. Moreover, chronic J147 increased glucose sensitivity. Acute J147 treatment improved long-term spatial memory and reversed the circadian rhythm shift. No anti-inflammatory effects were seen for J147. Although Zucker rats displayed risk factors, surgery did not induce extensive POCD. However, increased anxiety may indicate POD. Treatment with J147 showed positive effects on behavioral and metabolic parameters, but did not affect (neuro)inflammation. The mixed effect of acute and chronic treatment may suggest a combination for optimal treatment.


Subject(s)
Cognition Disorders , Humans , Rats , Male , Animals , Cognition Disorders/etiology , Rats, Zucker , Rats, Wistar , Cognition , Postoperative Complications/etiology , Postoperative Complications/psychology , Anxiety/etiology , Inflammation/complications
2.
Structure ; 7(3): 319-30, 1999 Mar 15.
Article in English | MEDLINE | ID: mdl-10368301

ABSTRACT

BACKGROUND: Angiogenesis is involved in tumor growth, macular degeneration, retinopathy and other diseases. Vascular endothelial growth factor (VEGF) stimulates angiogenesis by binding to specific receptors (VEGFRs) on the surface of vascular endothelial cells. VEGFRs are receptor tyrosine kinases that, like the platelet-derived growth factor receptors (PDGFRs), contain a large insert within the kinase domain. RESULTS: We report here the generation, kinetic characterization, and 2.4 A crystal structure of the catalytic kinase domain of VEGF receptor 2 (VEGFR2). This protein construct, which lacks 50 central residues of the 68-residue kinase insert domain (KID), has comparable kinase activity to constructs containing the entire KID. The crystal structure, determined in an unliganded phosphorylated state, reveals an overall fold and catalytic residue positions similar to those observed in other tyrosine-kinase structures. The kinase activation loop, autophosphorylated on Y1059 prior to crystallization, is mostly disordered; however, a portion of it occupies a position inhibitory to substrate binding. The ends of the KID form a beta-like structure, not observed in other known tyrosine kinase structures, that packs near to the kinase C terminus. CONCLUSIONS: The majority of the VEGFR2 KID residues are not necessary for kinase activity. The unique structure observed for the ends of the KID may also occur in other PDGFR family members and may serve to properly orient the KID for signal transduction. This VEGFR2 kinase structure provides a target for design of selective anti-angiogenic therapeutic agents.


Subject(s)
Neovascularization, Physiologic , Protein Conformation , Receptor Protein-Tyrosine Kinases/chemistry , Receptors, Growth Factor/chemistry , Adenosine Triphosphate/metabolism , Amino Acid Sequence , Binding Sites , Catalytic Domain , Crystallography, X-Ray , Growth Substances/chemistry , Humans , Kinetics , Models, Molecular , Molecular Sequence Data , Multigene Family , Mutagenesis, Site-Directed , Peptide Fragments/chemistry , Protein Folding , Protein Structure, Secondary , Protein-Tyrosine Kinases/chemistry , Receptor Protein-Tyrosine Kinases/genetics , Receptor Protein-Tyrosine Kinases/physiology , Receptors, Growth Factor/genetics , Receptors, Growth Factor/physiology , Receptors, Vascular Endothelial Growth Factor , Recombinant Fusion Proteins/chemistry , Sequence Alignment , Sequence Homology, Amino Acid , Structure-Activity Relationship , Substrate Specificity
3.
Pac Symp Biocomput ; : 437-48, 1998.
Article in English | MEDLINE | ID: mdl-9697202

ABSTRACT

Neural network predictors of protein disorder using primary sequence information were developed and applied to the Swiss Protein Database. More than 15,000 proteins were predicted to contain disordered regions of at least 40 consecutive amino acids, with more than 1,000 having especially high scores indicating disorder. These results support proposals that consideration of structure-activity relationships in proteins need to be broadened to include unfolded or disordered protein.


Subject(s)
Amino Acid Sequence , Databases, Factual , Proteins/chemistry , Animals , Calcineurin/chemistry , False Positive Reactions , Humans , Internet , Reproducibility of Results , Sequence Alignment , Sequence Homology, Amino Acid , Software , Structure-Activity Relationship
4.
Pac Symp Biocomput ; : 473-84, 1998.
Article in English | MEDLINE | ID: mdl-9697205

ABSTRACT

Observations going back more than 20 years show that regions in proteins with disordered backbones can play roles in their binding to other molecules; typically, the disordered regions become ordered upon complex formation. Thought-experiments with Schulz Diagrams, which are defined herein, suggest that disorder-to-order transitions are required for natural selection to operate separately on affinity and specificity. Separation of affinity and specificity may be essential for fine-tuning the molecular interaction networks that comprise the living state. For low affinity, high specificity interactions, our analysis suggests that natural selection would parse the amino acids conferring flexibility in the unbound state from those conferring specificity in the bound state. For high affinity, low specificity or for high affinity, multiple specificity interactions, our analysis suggests that the disorder-to-order transitions enable alternative packing interactions between side chains to accommodate the different binding targets. Disorder-to-order transitions upon binding also have significant kinetic implications as well, by having complex effects on both on- and off-rates. Current data are insufficient to decide on these proposals, but sequence and structure analysis on two examples support further investigations of the role of disorder-to-order transitions upon binding.


Subject(s)
Evolution, Molecular , Protein Conformation , Proteins/chemistry , Software , Algorithms , Amino Acid Sequence , Binding Sites , Calmodulin/chemistry , Macromolecular Substances , Protein Structure, Secondary , Proteins/genetics , Selection, Genetic , Sequence Alignment , Sequence Homology, Amino Acid
5.
Biochemistry ; 36(14): 4212-22, 1997 Apr 08.
Article in English | MEDLINE | ID: mdl-9100016

ABSTRACT

We have determined kinetic and thermodynamic constants governing binding of substrates and products to thymidylate synthase from Escherichia coli (TS) sufficient to describe the kinetic scheme for this enzyme. (1) The catalytic mechanism is ordered in the following manner, TS + dUMP --> TS x dUMP + (6R)-5,10-CH2-H4folate --> TS x dUMP x (6R)-5,10-CH2H4folate --> TS x dTMP x H2folate --> TS x dTMP --> TS as predicted previously by others from steady-state measurements. (2) When substrates are saturating, the overall reaction rate is governed by the slow conversion of enzyme-bound substrates to bound products as demonstrated by (i) large primary and secondary isotope effects on k(cat) and (ii) high rates of product dissociation compared to k(cat). (3) Stopped-flow studies measuring the binding of 10-propargyl-5,8-dideazafolate, an analog of (6R)-5,10-CH2H4folate, with the active site mutant C146A or the C-terminus-truncated mutant P261Am enabled us to identify physical events corresponding to spectral changes which are observed with the wild-type enzyme during initiation of catalysis. A kinetically identifiable reaction step, TS x dUMP x (6R)-5,10-CH2H4folate --> (TS x dUMP x (6R)-5,10-CH2H4folate)*, likely represents reorientation of the C-terminus of the enzyme over the catalytic site. This seals the substrates into a relatively nonaqueous environment in which catalysis can occur. (4) Although TS is a dimer of identical subunits, catalysis is probably confined to only one subunit at a time. (5) The "high-resolution" kinetic scheme described herein provides a framework for the interpretation of the kinetics of catalysis by mutant ecTS chosen to provide insights into the relationship between structure and function.


Subject(s)
Escherichia coli/enzymology , Folic Acid/metabolism , Tetrahydrofolates/metabolism , Thymidylate Synthase/metabolism , Catalysis , Deoxyuracil Nucleotides/metabolism , Folic Acid/analogs & derivatives , Folic Acid/pharmacology , Folic Acid Antagonists/pharmacology , Kinetics , Ligands , Molecular Structure , Mutagenesis, Site-Directed/genetics , Protein Binding , Protein Conformation , Quinazolines/pharmacology , Spectrometry, Fluorescence , Spectrophotometry , Thermodynamics , Thymidine Monophosphate/metabolism , Thymidylate Synthase/chemistry
6.
Curr Opin Biotechnol ; 7(4): 397-402, 1996 Aug.
Article in English | MEDLINE | ID: mdl-8768897

ABSTRACT

In the past year, the three-dimensional structures of two serine/threonine phosphatases, protein phosphatase-1 and protein phosphatase-2b (calcineurin), have been determined. The new information puts previous sequence comparisons and mutagenesis studies into a detailed structural perspective. The active-site structure and catalytic mechanism appear to be common to a variety of phosphoesterase enzymes.


Subject(s)
Phosphoprotein Phosphatases/chemistry , Phosphoprotein Phosphatases/physiology , Amino Acid Sequence , Calcineurin , Calmodulin-Binding Proteins/chemistry , Calmodulin-Binding Proteins/genetics , Crystallography, X-Ray , Models, Molecular , Molecular Sequence Data , Phosphoprotein Phosphatases/classification , Phosphoprotein Phosphatases/genetics , Protein Conformation , Protein Engineering , Protein Phosphatase 1 , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Serine/metabolism , Threonine/metabolism
7.
J Med Chem ; 39(9): 1872-84, 1996 Apr 26.
Article in English | MEDLINE | ID: mdl-8627611

ABSTRACT

The structure-based design and subsequent chemical synthesis of novel, urea-containing FKBP12 inhibitors are described. These compounds are shown to disrupt the cis-trans peptidylprolyl isomerase activity of FKBP12 with inhibition constants (Ki,app) approaching 0.10 microM. Analyses of several X-ray crystal structures of FKBP12-urea complexes demonstrate that the urea-containing inhibitors associate with FKBP12 in a manner that is similar to, but significantly different from, that observed for the natural product FK506.


Subject(s)
Carrier Proteins/antagonists & inhibitors , DNA-Binding Proteins/antagonists & inhibitors , Drug Design , Heat-Shock Proteins/antagonists & inhibitors , Urea/analysis , Amino Acid Isomerases/antagonists & inhibitors , Amino Acid Sequence , Carrier Proteins/chemistry , Crystallography, X-Ray , DNA-Binding Proteins/chemistry , Heat-Shock Proteins/chemistry , Humans , Magnetic Resonance Spectroscopy , Molecular Sequence Data , Peptidylprolyl Isomerase , Structure-Activity Relationship , Tacrolimus/chemistry , Tacrolimus Binding Proteins
8.
J Med Chem ; 39(4): 904-17, 1996 Feb 16.
Article in English | MEDLINE | ID: mdl-8632414

ABSTRACT

To develop novel lipophilic thymidylate synthase (TS) inhibitors, the X-ray structure of Escherichia coli TS in ternary complex with FdUMP and the inhibitor 10-propargyl-5,8-dideazafolic acid (CB3717) was used as a basis for structure-based design. A total of 31 novel lipophilic TS inhibitors, lacking a glutamate residue, were synthesized; 26 of them had in common a N-((3,4-dihydro-2-methyl-6-quinazolinyl)methyl)-N-prop-2-ynylaniline+ ++ structure in which the aniline was appropriately substituted with simple lipophilic substituents either in position 3 or 4, or in both. Compounds were tested for their inhibition of E. coli TS and human TS and also for their inhibition of the growth in tissue culture of a murine leukemia, a human leukemia, and a thymidine kinase-deficient human adenocarcinoma. The crystal structures of five inhibitors complexed with E. coli TS were determined. Five main conclusions are drawn from this study. (i) A 3-substituent such as CF(3), iodo, or ethynyl enhances binding by up to 1 order of magnitude and in the case of CF(3) was proven to fill a nearby pocket in the enzyme. (ii) A simple strongly electron-withdrawing substituent such as NO(2) or CF(3)SO(2) in the 4-position enhances binding by 2 orders of magnitude; it is hypothesized that the transannular dipole so induced interacts favorably with the protein. (iii) Attempts to combine the enhancements of i and ii in the same molecule were generally unsuccessful (iv) A 4-C(6)H(5)SO(2) substituent provided both electron withdrawal and a van der Waal's interaction of the phenyl group with a hydrophobic surface at the mouth of the active site. The inhibition (K(is) = 12 nM) of human TS by this compound, 7n, showed that C(6)H(5)SO(2) provided virtually as much binding affinity as the CO-glutamate which it had replaced. (v) The series of compounds were poorly water soluble, and also the potent TS inhibition shown by several of them did not translate into good cytotoxicity. Compounds with large cyclic groups linked to position 4 by an SO or SO(2) group did, however, have IC(50)'s in the range 1-5 microM. Of these, 4-(N-((3,4-dihydro-2-methyl-6-quinazolinyl)methyl)-N-prop-2-ynylamino )phenyl phenyl sulfone, 7n, had IC(50)'s of about 1 microM and was chosen for further elaboration.


Subject(s)
Antineoplastic Agents/chemical synthesis , Enzyme Inhibitors/chemical synthesis , Folic Acid Antagonists/chemical synthesis , Quinazolines/chemical synthesis , Thymidylate Synthase/antagonists & inhibitors , Adenocarcinoma , Animals , Antineoplastic Agents/chemistry , Antineoplastic Agents/toxicity , Binding Sites , Cell Line , Crystallography, X-Ray , Drug Design , Enzyme Inhibitors/chemistry , Enzyme Inhibitors/pharmacology , Escherichia coli/enzymology , Folic Acid Antagonists/chemistry , Folic Acid Antagonists/pharmacology , Humans , Leukemia , Leukemia L1210 , Mice , Models, Molecular , Molecular Conformation , Molecular Structure , Protein Conformation , Quinazolines/chemistry , Quinazolines/pharmacology , Structure-Activity Relationship , Thymidylate Synthase/chemistry , Tumor Cells, Cultured
9.
Protein Eng ; 8(7): 677-91, 1995 Jul.
Article in English | MEDLINE | ID: mdl-8577696

ABSTRACT

The steadily increasing number of high-resolution human immunodeficiency virus (HIV) 1 protease complexes has been the impetus for the elaboration of knowledge-based mean field ligand-protein interaction potentials. These potentials have been linked with the hydrophobicity and conformational entropy scales developed originally to explain protein folding and stability. Empirical free energy calculations of a diverse set of HIV-1 protease crystallographic complexes have enabled a detailed analysis of binding thermodynamics. The thermodynamic consequences of conformational changes that HIV-1 protease undergoes upon binding to all inhibitors, and a substantial concomitant loss of conformational entropy by the part of HIV-1 protease that forms the ligand-protein interface, have been examined. The quantitative breakdown of the entropy-driven changes occurring during ligand-protein association, such as the hydrophobic contribution, the conformational entropy term and the entropy loss due to a reduction of rotational and translational degrees of freedom, of a system composed to ligand, protein and crystallographic water molecules at the ligand-protein interface has been carried out. The proposed approach provides reasonable estimates of distinctions in binding affinity and gives an insight into the nature of enthalpyentropy compensation factors detected in the binding process.


Subject(s)
HIV Protease/metabolism , Crystallization , HIV Protease/chemistry , HIV Protease Inhibitors/chemistry , Humans , Ligands , Models, Chemical , Oligopeptides/chemistry , Protein Binding , Substrate Specificity , Thermodynamics , Water/chemistry
10.
Biochemistry ; 34(23): 7678-85, 1995 Jun 13.
Article in English | MEDLINE | ID: mdl-7779814

ABSTRACT

Resonance Raman (RR) spectra are reported for the ternary complex of Escherichia coli thymidylate synthase with the cofactor 5,10-methylenetetrahydrofolate (CH2-H4-folate) and the inhibitor 5-fluoro-2'-deoxyuridylate, excited at 337 or 356 nm, in resonance with perturbed absorption bands of the p-aminobenzoylglutamate (PABA-Glu) portion of the cofactor. For comparison, RR spectra were obtained with 260 nm excitation for PABA-Glu in various solvents, and for CH2H4-folate and H4-folate in aqueous solution. These reference spectra are assigned to modes of PABA-Glu in its benzenoid form. The ternary complex RR spectra are very different, however, and are assigned, with the aid of isotopic data, to the PABA-Glu in a predominantly quinoid form. Similar spectra were obtained for the ternary complexes of the E58Q and K48Q mutants, indicating that neither Glu58 nor Lys48 are essential for maintaining the quinoid structure, even though their side chains complement the dipolar charge distribution of the quinoid form of PABA-Glu. Since these are the only charged residues in the PABA-Glu vicinity, electrostatic stabilization is not essential to maintenance of the quinoid structure. It is proposed that quinoid formation results from steric forces, probably resulting from the protein conformation change known to accompany cofactor binding, which enforce coplanarity of the PABA-Glu ring and substituents. This stereoelectronic change activates the cofactor by opening the methylene bridge. A second RR spectrum of the ternary complex, previously proposed to reflect an alternate structure, is shown to result instead from irreversible formation of a laser-induced photoproduct.


Subject(s)
Tetrahydrofolates/chemistry , Thymidylate Synthase/metabolism , Escherichia coli/enzymology , Spectrum Analysis, Raman
11.
Biochemistry ; 34(23): 7686-93, 1995 Jun 13.
Article in English | MEDLINE | ID: mdl-7779815

ABSTRACT

Resonance Raman (RR) spectra are reported for the binary complex of Escherichia coli thymidylate synthase (TS) with the substrate analog inhibitor 5-nitrodeoxyuridylate (NDU). The TS/NDU binary complex RR spectrum shows many similarities to the RR spectra of thiol adducts of NDU or of 5-nitro-1-methyluracil formed in solution, providing strong evidence in support of the formation of a covalent link between Cys146 of TS and C6 of NDU. Spectral differences between the model compounds and the binary complex reflect the consequences of fixing the conformations of the uracil and ribose rings at the enzyme active site. The RR spectra of the ternary complexes of TS/NDU with either tetrahydrofolate (H4-folate) or the cofactor 5,10-methylenetetrahydrofolate (CH2H4-folate) show that a covalent link is not formed between C11 of CH2H4-folate and C5 of NDU. Neither does the methylene bridge of CH2H4-folate remain intact in the ternary complex; either CH2H4-folate is present as the N5 iminium cation species or the methylene group is lost as formaldehyde. A shift in the NO2 symmetric stretching frequency in the ternary complex indicates expulsion of water molecules from the region of the NO2 group by the cofactor.


Subject(s)
Deoxyuracil Nucleotides/chemistry , Thymidylate Synthase/chemistry , Escherichia coli/enzymology , Spectrophotometry, Ultraviolet , Spectrum Analysis, Raman
12.
Cell ; 77(5): 761-71, 1994 Jun 03.
Article in English | MEDLINE | ID: mdl-7515772

ABSTRACT

The structure of human rhinovirus-14 3C protease (3Cpro) has been determined at 2.3 A resolution and refined to an R factor of 0.22. This cysteine protease folds into two topologically equivalent six-stranded beta barrels and in this sense is similar to trypsin-like serine proteases. However, there are differences in the lengths and positioning of individual beta strands as well as in loops connecting elements of secondary structure. The catalytic residues Cys-146, His-40, and Glu-71 are positioned as in serine proteases, but the oxyanion hole is moved 1-1.2 A away. Residues that bind to the 5' noncoding region of rhinovirus genomic RNA are located on the opposite side of the molecule from the active site. Interactions between individual 3Cpro molecules in the crystal lattice suggest a model for intermolecular proteolytic cleavage of the 3CD polyprotein.


Subject(s)
Cysteine Endopeptidases/chemistry , Rhinovirus/enzymology , 3C Viral Proteases , Amino Acid Sequence , Animals , Binding Sites , Cattle , Cysteine Endopeptidases/genetics , Cysteine Endopeptidases/metabolism , Humans , Models, Molecular , Molecular Sequence Data , Molecular Structure , Protein Folding , RNA/metabolism , Sequence Homology, Amino Acid , Substrate Specificity , Trypsin/chemistry , Viral Proteins/metabolism
13.
Biochemistry ; 32(41): 10950-9, 1993 Oct 19.
Article in English | MEDLINE | ID: mdl-8218161

ABSTRACT

Antibodies with bound metal-chelate haptens provide new means for exploiting the diverse properties of metallic elements. The murine monoclonal antibody CHA255 (IgG1 lambda) binds the metal-chelate hapten indium (III)-4-[N'-(2-hydroxyethyl)thioureido]-L-benzyl-EDTA (designated In-EOTUBE) with high affinity (K(a) = 1.1 x 10(10) M-1). Antibody binding is highly specific for the indium chelate; the affinity decreases as much as 10(4) with other metals, even those having ionic radii close to indium. To better understand this selectivity, the crystal structure of the antigen-binding fragment (Fab') of CHA255 complexed with its hapten, In(III)-EOTUBE, was determined by molecular replacement and refined at 2.2-A resolution. The structure of CHA255 Fab' complexed with Fe(III)-EOTUBE was also determined and refined at 2.8-A resolution. In both structures, the hapten's EDTA moiety is half-buried near the center of the complementarity-determining regions (CDR's). Five of the six CDR's on the Fab' interact with the hapten through protein side-chain atoms (but not main-chain atoms). A novel feature of the In-EOTUBE/Fab' complex is coordination of the indium by N epsilon of one histidine from the heavy chain's third CDR (distance = 2.4 A). The histidine coordination is not observed in the Fe-EOTUBE/Fab' complex, due mainly to a slightly different hapten conformation that reduces metal accessibility; this may partially explain the 20-fold lower affinity of CHA255 for iron hapten. An unexpected feature of the Fab' overall is an elbow angle of 193 degrees (the angle between the pseudodyad axes of the Fab's constant and variable domains).


Subject(s)
Antibodies, Monoclonal/chemistry , Antibody Specificity , Antigens/immunology , Chelating Agents/metabolism , Haptens/metabolism , Immunoglobulin Fab Fragments/chemistry , Metals/immunology , Amino Acid Sequence , Antibodies, Monoclonal/immunology , Binding Sites, Antibody , Chelating Agents/chemistry , Crystallography, X-Ray , Edetic Acid/analogs & derivatives , Edetic Acid/chemistry , Edetic Acid/metabolism , Haptens/chemistry , Indium/immunology , Indium/metabolism , Iron/immunology , Iron/metabolism , Models, Molecular , Molecular Sequence Data , Molecular Structure , Protein Conformation
14.
Biochemistry ; 32(36): 9274-81, 1993 Sep 14.
Article in English | MEDLINE | ID: mdl-8103678

ABSTRACT

The recent determination of the crystal structure of Escherichia coli thymidylate synthase (TS) [Matthews et al. (1989) J. Mol. Biol. 205, 449-454] has implicated the glutamic acid residue at position 58 in a mechanistic role which could involve the interaction of its gamma-carboxyl side chain with the nucleotide substrate and/or the folate cofactor. The site-specific mutagenesis of Glu-58 to Gln-58 in E. coli TS provided the opportunity to explore its functional role in activity and binding. When profiled by the spectrophotometric and tritium release assays, the 370- and 760-fold decreases, respectively, in kcat and the elevated Km values for the Gln-58 mutant enzyme indicated a significant involvement of Glu-58 in substrate binding and turnover. The apparent dissociation constant for the covalent FdUMP-enzyme binary complex was 30 microM, which is 5-fold higher than that found for the wild-type enzyme, while the inhibitory ternary complex apparent dissociation constants for FdUMP and CH2H4folate for the Gln-58 enzyme were 10- and 60-fold higher, respectively, than those for the wild-type enzyme under saturating conditions. The extent of covalent FdUMP binding to the Gln-58 enzyme was reduced from 1.5 to 0.7 per dimer in the inhibitory ternary complex but only from 0.7 to 0.5 per dimer in the binary complex of the Gln-58 enzyme. The usual 2.1-fold enhancement of FdUMP binding to wild-type TS in the presence of CH2H4folate was not observed for the Gln-58 enzyme.(ABSTRACT TRUNCATED AT 250 WORDS)


Subject(s)
Escherichia coli/enzymology , Glutamates/metabolism , Glutamine/metabolism , Thymidylate Synthase/metabolism , Binding Sites , Catalysis , Glutamic Acid , Kinetics , Ligands , Magnetic Resonance Spectroscopy , Mutagenesis, Site-Directed , Thymidylate Synthase/genetics , Thymidylate Synthase/isolation & purification
16.
Biochemistry ; 31(40): 9813-22, 1992 Oct 13.
Article in English | MEDLINE | ID: mdl-1356437

ABSTRACT

Using site-specific mutagenesis, we have constructed two mutants of Escherichia coli dihydrofolate reductase (ecDHFR) to investigate further the function of a weakly acidic side chain at position 27 in substrate protonation: Asp27-->Glu (D27E) and Asp27-->Cys (D27C). The crystal structure of D27E ecDHFR in a binary complex with methotrexate shows that the side-chain oxygen atoms of Glu27 are in almost precisely the same location as those of Asp27 in the wild-type enzyme. Kinetic evidence indicates that Glu27 can indeed function efficiently in the proton relay to dihydrofolate. Even though vertebrate DHFRs all have a glutamic acid at the structurally equivalent position, the kinetic properties of Glu27 ecDHFR more closely resemble those of wild-type bacterial DHFRs than of vertebrate DHFRs. The D27C mutation produced an enzyme still capable of relaying a proton to dihydrofolate, but with the intrinsic pKa in its pH-activity profiles shifted upward to values characteristic of the more basic thiolate group. The crystal structure of the binary complex with methotrexate reveals two unexpected features: (1) the Cys27 sulfhydryl group does not point toward the pteridine-binding site, but the side chain of this residue is instead rotated 120 degrees to interact with a tyrosine side chain projecting from a neighboring beta-strand; (2) a bound ethanol molecule occupies a cavity adjacent to methotrexate. Ethanol is a component of the crystallization medium.


Subject(s)
Tetrahydrofolate Dehydrogenase/metabolism , Asparagine/metabolism , Binding Sites , Crystallography , Escherichia coli/enzymology , Glutamates/metabolism , Glutamic Acid , Humans , Hydrogen-Ion Concentration , Kinetics , Methotrexate/metabolism , Mutagenesis, Site-Directed , Protons , Pteridines/metabolism , Spectrophotometry, Ultraviolet , Tetrahydrofolate Dehydrogenase/chemistry , Tetrahydrofolate Dehydrogenase/genetics
17.
Biochemistry ; 30(46): 11073-80, 1991 Nov 19.
Article in English | MEDLINE | ID: mdl-1932030

ABSTRACT

Replacement of methionine (Met) residues by selenomethionine (SeMet) was recently shown to facilitate the crystallographic analysis of protein structure through the application of multi-wavelength anomalous diffraction techniques [Yang et al. (1990) Science (Washington, D.C.) 249, 1398-1405]. The availability of SeMet-containing proteins provides an excellent opportunity to evaluate the effects of the complete replacement of Met by SeMet. We chose to compare the properties of selenomethionyl thymidylate synthase isolated from Escherichia coli DL41 (a methionine auxotroph) and wild-type (wt) enzyme obtained from E. coli Rue10. An improved purification procedure for thymidylate synthase was developed which permitted the isolation of 25 mg of pure protein from 2 g of E. coli in 90% yield in no more than 8 h. The pure wt and SeMet enzymes exhibited specific activities 40% higher than published values. Thermal stability studies at 30 degrees C in degassed buffer showed that the SeMet enzyme (t1/2 67 h) was 8-fold less stable than wt enzyme (t1/2 557 h). The half-lives for the latter enzymes in nondegassed buffers at 30 degrees C were decreased by 2-fold, thus indicating the sensitivity of the enzyme to dissolved oxygen. Both enzymes exhibited essentially the same kinetic and binding properties, including Km(dUMP) (1.2 x 10(-6) M), specificity constant (1.6 x 10(6) s-1 M-1), and Kd for 5-fluorodeoxyuridylate binding (1.2 nM) in covalent inhibitory ternary complexes. In addition, X-ray crystallographic analysis by difference Fourier synthesis showed there was no significant difference in conformation between the SeMet enzyme and the wt enzyme.


Subject(s)
Escherichia coli/enzymology , Selenomethionine/analogs & derivatives , Thymidylate Synthase/isolation & purification , Amino Acid Sequence , Amino Acids/chemistry , Binding Sites , Buffers , Enzyme Stability , Escherichia coli/growth & development , Hydrogen-Ion Concentration , Kinetics , Protein Conformation , Selenium/chemistry , Temperature , Thymidylate Synthase/antagonists & inhibitors , Thymidylate Synthase/chemistry , X-Ray Diffraction
18.
J Mol Biol ; 214(4): 937-48, 1990 Aug 20.
Article in English | MEDLINE | ID: mdl-2201779

ABSTRACT

The structure of the Escherichia coli thymidylate synthase (TS) covalent inhibitory ternary complex consisting of enzyme, 5-fluoro-2'-deoxyuridylate (FdUMP) and 5,10-methylene tetrahydrofolate (CH2-H4PteGlu) has been determined at 2.5 A resolution using difference Fourier methods. This complex is believed to be a stable structural analog of a true catalytic intermediate. Knowledge of its three-dimensional structure and that for the apo enzyme, also reported here, suggests for the first time how TS may activate dUMP and CH2-H4PteGlu leading to formation of the intermediate and offers additional support for the hypothesis that the substrate and cofactor are linked by a methylene bridge between C-5 of the substrate nucleotide and N-5 of the cofactor. By correlating these structural results with the known stereospecificity of the TS-catalyzed reaction it can be inferred that the catalytic intermediate, once formed, must undergo a conformational isomerization before eliminating across the bond linking C-5 of dUMP to C-11 of the cofactor. The elimination itself may be catalyzed by proton transfer to the cofactor's 5 nitrogen from invariant Asp169 buried deep in the TS active site. The juxtaposition of Asp169 and bound tetrahydrofolate in TS is remarkably reminiscent of binding geometry found in dihydrofolate reductase where a similarly conserved carboxyl group serves as a general acid for protonating the corresponding pyrazine ring nitrogen of dihydrofolate.


Subject(s)
Deoxyuracil Nucleotides/metabolism , Fluorodeoxyuridylate/metabolism , Folic Acid Antagonists/metabolism , Tetrahydrofolates/metabolism , Thymidylate Synthase/metabolism , Binding Sites , Escherichia coli/enzymology , Fluorodeoxyuridylate/pharmacology , Hydrogen Bonding , Ligands , Models, Molecular , Protein Conformation , Tetrahydrofolates/pharmacology , Thymidylate Synthase/antagonists & inhibitors , X-Ray Diffraction/methods
19.
Biochemistry ; 26(26): 8591-8, 1987 Dec 29.
Article in English | MEDLINE | ID: mdl-2894842

ABSTRACT

We have explored the substrate protonation mechanism of Escherichia coli dihydrofolate reductase by changing the location of the proton donor. A double mutant was constructed in which the proton donor of the wild-type enzyme, aspartic acid-27, has been changed to serine and simultaneously an alternative proton donor, glutamic acid, has replaced threonine at position 113. The active site of the resulting variant enzyme molecule should therefore somewhat resemble that proposed for the R67 plasmid-encoded dihydrofolate reductase [Matthews, D. A., Smith, S. L., Baccanari, D. P., Burchall, J. J., Oatley, S. J., & Kraut, J. (1986) Biochemistry 25, 4194]. At pH 7, the double-mutant enzyme has a 3-fold greater kcat and an unchanged Km(dihydrofolate) as compared with the single-mutant Asp-27----Ser enzyme described previously [Howell, E. E., Villafranca, J. E., Warren, M. S., Oatley, S. J., & Kraut, J. (1986) Science (Washington, D.C.) 231, 1123]. Additionally, its activity vs pH profiles together with observed deuterium isotope effects, suggest that catalysis depends on an acidic group with a pKa of 8. It is concluded that the dihydropteridine ring of a bound substrate molecule can indeed be protonated by a glutamic acid side chain at position 113 (instead of an aspartic acid side chain at position 27), but with greatly decreased efficiency: at pH 7, the double mutant still has a 25-fold lower kcat (1.2 s-1) and a 2900-fold lower kcat/km(dihydrofolate) (8.6 X 10(3) s-1 M-1) than the wild-type enzyme.


Subject(s)
Escherichia coli/enzymology , Tetrahydrofolate Dehydrogenase/metabolism , Escherichia coli/genetics , Genes , Genes, Bacterial , Glutamates , Glutamic Acid , Hydrogen-Ion Concentration , Kinetics , Mathematics , Methotrexate/metabolism , Mutation , Protein Binding , Protons , Serine , Tetrahydrofolate Dehydrogenase/genetics
20.
J Biol Chem ; 262(11): 5398-403, 1987 Apr 15.
Article in English | MEDLINE | ID: mdl-3558397

ABSTRACT

The x-ray crystallographic structure of the heterodimeric plant toxin ricin has been determined at 2.8-A resolution. The A chain enzyme is a globular protein with extensive secondary structure and a reasonably prominent cleft assumed to be the active site. The B chain lectin folds into two topologically similar domains, each binding lactose in a shallow cleft. In each site a glutamine residue forms a hydrogen bond to the OH-4 of galactose, accounting for the epimerimic specificity of binding. The interface between the A and B chains shows some hydrophobic contacts in which proline and phenylalanine side chains play a prominent role.


Subject(s)
Ricin , Galactose/metabolism , Macromolecular Substances , Models, Molecular , X-Ray Diffraction
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