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D A Matthews

Publications and source records attributed to D A Matthews.

10 recordsLinked to original sources
PubMed1979

Proton magnetic resonance studies on Escherichia coli dihydrofolate reductase. Assignment of histidine C-2 protons in binary complexes with folates on the basis of the crystal structure with methotrexate and on chemical modifications.

The effects of pH upon the C-2 resonances of the 5 histidine residues of Escherichia coli MB 1428 dihydrofolate reductase in binary complexes with methotrexate, aminopterin, folate, methopterin, and trimethoprim were studied by 300-MHz 1H nmr spectroscopy. Three of the five histidine residues, labeled 1, 2, and 3, exhibited similar pK' values and chemical shifts for their C-2 protons in the five binary complexes. One histidine, 4, was quite different in the folate complex and the last histidine, 5 was quite different in the trimethoprim complex. For all five binary complexes, each histidine had a pK' which was significantly different from the other 4 histidines of that complex. Titration of the binary methotrexate complex of a 5,5'-dithiobis(2-nitrobenzoate)-modified enzyme showed that 2 histidines were not perturbed by this modification of Cys 152, and that the alkaline form of histidine 2, the acid form of histidine 4, and, to a lesser extent, the acid form of histidine 3 were slightly perturbed. Titration of the binary methotrexate complex of a N-bromosuccinimide-modified enzyme demonstrated that this modification slightly affected all of the histidines and drastically affected histidine 5. Histidines 3 and 5 of the binary methotrexate complex reacted rapidly with the histidine-specific reagent, ethoxyformic anhydride, while histidines 2 and 4 reacted at a moderate rate and histidine 1 reacted slowly if at all. The local electrostatic environments of the 5 histidine residues as deduced from the crystal structure of the binary complex of the enzyme with methotrexate (Matthews, D.A., Alden, R.A., Bolin, J.T., Freer, S.T., Hamlin, R., Xuong, N., Kraut, J., Poe, M., Williams, M.N., and Hoogsteen, K. (1977) Science 197, 594-597) were used as the basis for proposed assignments of the five histidine C-2 nmr resonances. The assignments were: 1, pK' 7.9 to 8.2, His 124; 2, pK' 7.2 to 7.4, His 141; 3, pK' 6.5 to 6.7, His 149; 4, pK' 5.7 to 6.3, His 114; and 5, pK' 5.2 to 5.9, His 45. The effect of the chemical modifications upon the enzyme's histidine residues were consistent with the assignments, but no direct chemical evidence in support of the assignments was obtained. It was proposed that, since the crystallographic data provided consistent assignments of the histidine nmr data for both native and chemically modified enzyme, the local environment of each of the 5 histidine residues was similar in the crystal and in solution.

Binding Sites↗
PubMed1979

Dihydrofolate reductase from Lactobacillus casei. Stereochemistry of NADPH binding.

The NADPH molecule binds to dihydrofolate reductase in an extended conformation. Several of the individual dihedral angles, especially in the adenine mononucleotide portion of the coenzyme, differ from their minimum energy conformations. The ribose phosphate portions of the coenzyme are involved in numerous specific hydrogen-bonded and charge-charge interactions. The adenine ring resides in an apparently nonspecific hydrophobic cleft and the nicotinamide ring is bound within an intricately constructed cavity, one wall of which includes the pyrazine ring of bound methotrexate. Two rather extended loops (residues 10 to 24 and 117 to 135) connecting beta A to alpha B and beta F to beta G, respectively, move 2 to 3 A when NADPH binds to dihydrofolate reductase. No overall structural homology is evident between the dinucleotide binding domains of dihydrofolate reductase on the one hand and the four NAD+-dependent dehydrogenases of known structure on the other. However, binding does occur in both cases at the carboxyl edge of a region of parallel beta sheet flanked by a pair of alpha helices.

Binding Sites↗
PubMed1979

Interpretation of nuclear magnetic resonance spectra for Lactobacillus casei dihydrofolate reductase based on the X-ray structure of the enzyme-methotrexate-NADPH complex.

The three-dimensional molecular structure of Lactobacillus casei dihydrofolate reductase complexed with NADPH and methotrexate has been used to interpret published magnetic resonance spectra for this enzyme. Proton resonances from histidine residues and 19F resonances from fluorine-labeled fluorotyrosine and fluorotryptophan dihydrofolate reductase have been assigned in several cases to specific amino acids in the primary sequence. Furthermore, the 31P signals from the pyrophosphate moiety of bound NADPH have been assigned and the large upfield shift for 13C-labeled (at the carboxamide carbon) NADP+ upon binding to the reductase has been explained in terms of desolvation effects.

Lacticaseibacillus casei↗
PubMed1977

Dihydrofolate reductase: x-ray structure of the binary complex with methotrexate.

A central eight-stranded beta-pleated sheet is the main feature of the polypeptide backbone folding in dihydrofolate reductase. The innermost four strands and two bridging helices are geometrically similar to but are connected in a different way from those in the dinucleotide binding domains found in nicotinamide-adenine dinucleotide-linked dehydrogenases. Methotrexate is bound in a 15-angstrom-deep cavity with the pteridine ring buried in a primarily hydrophobic pocket, although a strong interaction occurs between the side chain of aspartic acid 27 and N(1), N(8), and the 2-amino group of methotrexate.

Binding Sites↗
PubMed1977

Genetically-associated variations in the development of hippocampal pyramidal neurons may produce differences in mossy fiber connectivity.

The neuronal generation patterns of hippocampal pyramids were analyzed in two inbred strains of house mice (SM/J and BALB/cJ) using triated thymidine radioautography. These two strains of mice possess markedly different patterns of mossy fiber synapses upon pyramidal neurons within a specific segment of regio inferior. The results of this study show that this same segment of regio inferior also displays markedly different patterns of pyramidal neuron generation in the two strains. Specifically, the pyramids of this segment of regio inferior are generated according to the typical "inside-out" sequence in SM/J mice, but this pattern is reversed into an "outside-in" sequence in BALB/cJ mice. Remaining segment of regio inferior, and all of regio superior, is formed in an inside-out sequence in both strains. These results strongly suggest that altered temporal patterns of pyramidal neuron generation may play a major role in determining mossy fiber connectivity patterns.

Animals↗
PubMed1976

An electron microscopic study of lesion-induced synaptogenesis in the dentate gyrus of the adult rat. I. Magnitude and time course of degeneration.

Synapses in the rat dentate gyrus are rapidly lost after removal of the primary input from the entorhinal cortex. In this paper we describe the extent and time course of degeneration and in the subsequent paper the nature of the reinnervation processes. They synapses of entorhinal afferents are remarkably concentrated in their zone of termination. Unilateral removal of the rat entorhinal cortex results in the loss of about 86% of all synapses in the outer three-fourths of the molecular layer of the epsilateral dentate gyrus. Entorhinal synapses are all asymmetric (Gray type I) and terminate on dendritic spines. Analysis of the degeneration reaction provides a means to examine the characteristics of the loss of a relatively homogeneous afferent on a single cell type. The morphological characteristics of the the degenerating terminals showed some heterogeneity; both the electron lucent and electron dense types of degenerating terminals were identified. The electron lucent type was observed only at short survival times. The time course of the loss of degenerating terminals was resolvable into two components, each of which followed first order decay kinetics. Thus degenerating entorhinal terminals behaved as a population which disappeared randomly at a rate dependent on the fraction of terminals present at any time. The loss of degenerating terminals was accompanied by the loss of postsynaptic sites. At short survival times the majority of postsynaptic sites (defined by the presence of a postsynaptic density) had disappeared. There was also a loss of complex spines and some shrinkage of the molecular layer.

Animals↗
PubMed1976

An electron microscopic study of lesion-induced synaptogenesis in the dentate gyrus of the adult rat. II. Reappearance of morphologically normal synaptic contacts.

Intact synapses in the denervated area of the rat dentate gyrus are reduced to 14% of those normally present 2-4 days following a unilateral entorhinal lesion. By 160-240 days after lesion, the former entorhinal terminal zone is repopulated with new synapses. In all, there is more than a 5-fold increase in the density of intact synapses in the denervated zone between 2 and 240 days post-lesion, and the denervated zone of the molecular layer is restored to 80% of control values. The synapses are Gray type I and are formed on simple and complex spines which closely resemble those normally present. A few boutons have an abnormally large number of synaptic junctions. Reinnervation seems to progress at differential rates. Synapses are rapidly regained up to 30 days after operation, but thereafter the reacquisition of synaptic connections is much slower. Reinnervation is more rapid in the portion of the denervated zone nearest the granule cells, where the maximal densities are attained within 30 days. The time course of reinnervation differed from that of degeneration. A portion of the new synapses in the reinnervated molecular layer appear to arise by the assembly of new synaptic junctions. Over time, the number of post-synaptic contact sites along a given length of dendritic surface recovers, suggesting the formation of new synaptic sites. Our data indicate that granule cells retain a capacity even into adulthood to manufacture, position and assemble postsynaptic components of a synapse and, in concert with reactive afferents, form normal-appearing synapses.

Animals↗
PubMed1975

X-ray crystallographic study of boronic acid adducts with subtilisin BPN' (Novo). A model for the catalytic transition state.

We have studied the structures of adducts formed between subtilisin BPN' and both benzeneboronic acid and 2-phenylethaneboronic acid by x-ray diffraction techniques. Electron density and difference maps at 2.5 A resolution were computed with phases calculated from a partially refined structure of the native enzyme (R = 0.23 at 2.0 A). Both adducts contain a covalent bond between Ogamma of the catalytic Ser-221 and the inhibitor boron atom. The boron atom is coordinated tetrahedrally, with one of the two additional boronic acid oxygen atoms lying in the "oxyanion hole" and the other at the leaving group site identified in previous studies (ROBERTUS, J.D., Kraut, J. ALDEN, R.A., and BIRKTOFT, J.J. (1972) Biochemistry 11, 4293-4303). Moreover, the previously postulated structure of the tetrahedral intermediate for substrate hydrolysis is isosteric with these boronic acid adducts, which can therefore be considered good models for the transition state complex (KOEHLER, K.K., and LIENHARD, G.E. (1972) Biochemistry 10, 2477-2483). These observations further support the suggestion that an important contribution to stabilization of this transition state complex, relative to both the Michaelis complex and the acyl intermediate, occurs as a consequence of hydrogen bond donation to the substrate carbonyl oxygen atom from the side chain amido group of Asn-155 and from the backbone amido group of Ser-221.

Binding Sites↗