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M A Weiss

Publications and source records attributed to M A Weiss.

At least 73 records · Page 4Linked to original sources
PubMed1994

Molecular basis of mammalian sexual determination: activation of Müllerian inhibiting substance gene expression by SRY.

The pathway of male sexual development in mammals is initiated by SRY, a gene on the short arm of the Y chromosome. Its expression in the differentiating gonadal ridge directs testicular morphogenesis, characterized by elaboration of Müllerian inhibiting substance (MIS) and testosterone. SRY and MIS each belong to conserved gene families that function in the control of growth and differentiation. Structural and biochemical studies of the DNA binding domain of SRY (the HMG box) revealed a protein-DNA interaction consisting of partial side chain intercalation into a widened minor groove. Functional studies of SRY in a cell line from embryonic gonadal ridge demonstrated activation of a gene-regulatory pathway leading to expression of MIS. SRY molecules containing mutations associated with human sex reversal have altered structural interactions with DNA and failed to induce transcription of MIS.

Amino Acid Sequence↗
PubMed1994

Cervical spine injuries in patients 65 and older.

STUDY DESIGN: This study was a retrospective data-base review of patients with cervical injuries admitted to a regional spinal cord injury center over a 9-year period. OBJECTIVES: Patients < 40 and > or = 65 were analyzed separately to determine differences in etiology, neurologic findings, mortality, and neurologic recovery. SUMMARY OF BACKGROUND DATA: Previous studies of cervical injuries in older patients have found a high percentage of falling as an etiology, a high incidence of injuries to C2, and a high mortality rate with spinal cord injury (SCI). METHODS: Three databases containing information on all SCI patients, SCI patients with 1-2 year follow-up, and neurogically intact spinal injury patients were reviewed retrospectively. RESULTS: A higher percentage of older patients had cervical injuries, and this group did not show the typical male predominance seen in young patients (4:1 vs. 1:1). Neurologic deficits were more common in the younger age group. In the older patients, falls were a much more common etiology, and upper cervical injuries, especially odontoid fractures, predominated. Cervical spondylosis and stenosis were more common in the older patients, and the mortality with associated SCI was 60 times higher than in younger patients. Younger patients more commonly had complete neurologic injuries, but had more early functional motor return in incomplete lesions. The older patients did show late functional return in incomplete deficits. CONCLUSIONS: Cervical spine injury commonly occurs with relatively minor trauma in patients > or = 65, with a mortality rate of approximately 26% with associated SCI. Return of functional motor recovery is delayed in older patients with incomplete deficits, but can be expected. C2 injuries, especially odontoid fractures, must be ruled out in older patients with neck pain after even a minor injury.

Aged↗
PubMed1994

Two cases of extramedullary acute promyelocytic leukemia. Cytogenetics, molecular biology, and phenotypic and clinical studies.

BACKGROUND: The extramedullary collection of leukemic cells is an infrequent complication of myeloid leukemias, and extremely uncommon in acute promyelocytic leukemia (APL). METHODS: The case reports of two patients with APL who relapsed with extramedullary disease and a review of the literature are presented. RESULTS: Two patients with cytogenetically and molecularly confirmed APL developed extramedullary relapse in skin and lymph nodes after prior treatment with all-trans retinoic acid. A review of the literature revealed only nine cases of APL complicated by extramedullary disease. However, only one of these previously reported patients was shown to have the cytogenetic abnormality characteristic of APL. CONCLUSIONS: To the authors' knowledge, These two patients represent the first cases of cytogenetically confirmed APL treated with all-trans retinoic acid who developed extramedullary relapse. These events, which were reported infrequently in patients treated only with cytotoxic therapy, may be more common in patients receiving all-trans retinoic acid. In view of the differentiating activity of all-trans retinoic acid, which may increase the migratory capacity of these malignant cells, it is hypothesized that this agent may predispose some patients to unusual forms of relapse.

Adult↗
PubMed1994

Solution structure of a POU-specific homeodomain: 3D-NMR studies of human B-cell transcription factor Oct-2.

The POU DNA-binding motif defines a conserved family of eukaryotic transcription factors involved in regulation of gene expression. This bipartite motif consists of an N-terminal POU-specific domain (POUs), a flexible linker, and a C-terminal POU-specific homeodomain (POUHD). Here we describe the solution structure of a POU-specific homeodomain. An NMR model is obtained from Oct-2, a human B-cell specific transcription factor which participates in the regulation of immunoglobulin genes. A fragment of Oct-2 containing POUHD and an adjoining linker was expressed in Escherichia coli and characterized by three-dimensional nuclear magnetic resonance (3D-NMR) spectroscopy. Complete 1H and 15N resonance assignment of the POUHD moiety is presented. The POUHD solution structure, as calculated by distance geometry and simulated annealing (DG/SA), is similar to that of canonical homeodomains. A salient difference between solution and crystal structures is observed in the C-terminal segment of alpha-helix 3 (the HTH recognition helix), which is not well ordered in solution. Because this segment presumably folds upon specific DNA binding, its flexibility in solution may reduce the intrinsic DNA affinity of POUHD in the absence of POUs.

Amino Acid Sequence↗
PubMed1994

An invariant asparagine in the POU-specific homeodomain regulates the specificity of the Oct-2 POU motif.

The homeodomain defines a family of transcription factors broadly involved in the regulation of gene expression. DNA recognition, as observed in three representative complexes (Engrailed, Antennapedia, and MAT alpha 2), is mediated in the major groove by a helix-turn-helix (HTH) element and in the minor groove by an N-terminal arm. The three complexes share similar overall features, but they also exhibit significant differences in DNA interactions. Because these differences may distinguish the biological activities of different classes of homeodomains, we have investigated the contribution of the Oct-2 POU-specific homeodomain (POUHD) to the specificity of the bipartite POU motif. Comparative studies of variant protein-DNA complexes demonstrate the following. (i) Mutations in an invariant residue in the POUHD HTH (N347; residue 10 of the putative recognition alpha-helix) reduce octamer binding with the relaxation of specificity at one position (5'-ATGCAAAT). The inferred HTH side chain-base interaction, although not observed in the solution structure of the Antennapedia complex, is in accord with homologous contacts in the Engrailed and MAT alpha 2 cocrystal structures. (ii) Comparison of the DNA-binding properties of POU and POUHD demonstrates that POUs and POUHD independently regulate specificity at opposite ends of the DNA site (5'-TATGCAAAT). Both domains contact the two central bases (5'-TATGCAAAT) where coordinate binding of POUS in the major groove overrides the intrinsic specificity of POUHD in the minor groove. (iii) The differential sensitivity of POU and POUHD to 2'-deoxyinosine substitutions (a minor-groove modification) suggests that POUS binding repositions the POUHD N-terminal "arm".(ABSTRACT TRUNCATED AT 250 WORDS)

Adenosine↗
PubMed1994

Mapping critical residues in eukaryotic DNA-binding proteins: a plasmid-based genetic selection strategy with application to the Oct-2 POU motif.

Discrimination between allowed and disallowed amino acid substitutions provides a powerful method for analysis of protein structure and function. Site-directed mutagenesis allows specific hypotheses to be tested, but its systematic application to entire structural motifs is inefficient. This limitation may be overcome by genetic selection, which allows rapid scoring of thousands of randomly (or pseudorandomly) generated mutants. To facilitate structural dissection of DNA-binding proteins, we have designed two generally applicable bacterial selection systems: pPLUS selects for the ability of a protein to bind to a user-defined DNA sequence, whereas pMINUS selects against such binding. Complementary positive and negative selections allow rapid mapping of critical residues. To test and calibrate the systems, we have investigated the bipartite POU domain of the human B-cell-specific transcription factor Oct-2. (i) An invariant residue (Asn347) in the DNA-recognition helix of the POU-specific homeodomain (POUHD) was substituted by each of the 19 other possible amino acids. The mutant proteins each exhibited decreased specific DNA binding as defined in vivo by genetic selection and in vitro by gel retardation; relative affinities correlate with phenotypes in the positive and negative selection systems. An essential role for Asn347 in wild-type POUHD-DNA recognition is consistent with homologous Asn-adenine interactions in cocrystal structures of canonical homeodomains. (ii) Extension of pPLUS/pMINUS selection to the POU-specific subdomain (POUs) is demonstrated by analysis of mutations in its putative helix-turn-helix (HTH) element.(ABSTRACT TRUNCATED AT 250 WORDS)

Base Sequence↗
PubMed1994

An altered-specificity mutation in a human POU domain demonstrates functional analogy between the POU-specific subdomain and phage lambda repressor.

The POU motif, conserved among a family of eukaryotic transcription factors, contains two DNA-binding domains: an N-terminal POU-specific domain (POUS) and a C-terminal homeodomain (POUHD). Surprisingly, POUS is similar in structure to the helix-turn-helix domains of bacteriophage repressor and Cro proteins. Such similarity predicts a common mechanism of DNA recognition. To test this prediction, we have studied the DNA-binding properties of the human Oct-2 POU domain by combined application of chemical synthesis and site-directed mutagenesis. The POUS footprint of DNA contacts, identified by use of modified bases, is analogous to those of bacteriophage repressor-operator complexes. Moreover, a loss-of-contact substitution in the putative POUS recognition alpha-helix leads to relaxed specificity at one position in the DNA target site. The implied side chain-base contact is identical to that of bacteriophage repressor and Cro proteins. These results establish a functional analogy between the POUS and prokaryotic helix-turn-helix elements and suggest that their DNA specificities may be governed by a shared set of rules.

Base Sequence↗
PubMed1994

An altered specificity mutation in the lambda repressor induces global reorganization of the protein-DNA interface.

The lambda repressor exhibits structural characteristics of lock and key complementary through the helix-turn-helix motif, and of induced fit by virtue of DNA-dependent folding of the N-terminal arm. In both cases, molecular recognition is mediated by direct contacts between amino acids and DNA bases. The extent to which such contacts function as discrete elements in a protein-DNA recognition code is not known. Because of the relevance of protein recognition to the broader issue of protein design, and because the lambda system serves as a prototype for gene regulation, we have employed laser Raman and 1H NMR spectroscopy to compare free and operator-bound structures of lambda repressor variants which are known to exhibit altered DNA-binding specificities. Experimental design is based upon a previous biochemical study of mutations in the repressor N-terminal arm (K4Q) and helix-turn-helix motif (G48S) (Nelson, H. C. M., and Sauer, R. T. (1986) J. Mol. Biol. 192, 27-38). These mutations, which were originally isolated by loss of function (K4Q) and second-site reversion (G48S), are of particular interest in light of their complex effects on sequence specificity at multiple positions in the operator site (Benson, N., Adams, C., and Youderian, P. (1992) Genetics 130, 17-26). Laser Raman and 1H NMR spectra of repressor variants carrying one (G48S) or two mutations (K4Q/G48S) are similar to those of the native wild type repressor and are in accord with the x-ray crystal structure. Remarkably, however, the complexes of wild type and mutant repressors exhibit extensive differences both in the global DNA structure and in the environments of key functional groups along the major groove. By demonstrating that single amino acid substitutions can induce global reorganization of a protein-DNA interface, the present results establish that repressor-operator recognition in solution cannot be explained in terms of a simple recognition code.

Amino Acid Sequence↗
PubMed1994

Bipartite DNA recognition by the human Oct-2 POU domain: POUs-specific phosphate contacts are analogous to those of bacteriophage lambda repressor.

The POU motif defines a family of eukaryotic transcription factors broadly involved in tissue-specific gene expression and developmental regulation. The motif contains two DNA-binding domains: an N-terminal POU-specific domain (POUs) and C-terminal homeodomain (POUHD). Surprisingly, POUs has recently been found to be similar in structure to helix-turn-helix (HTH) domains of phage repressor and Cro proteins [Assa-Munt, N., Mortishire-Smith, R., Aurora, R., Herr, W., & Wright, P.E. (1993) Cell 73, 193-205; Dekker, N., Cox, M., Boelens, R., Verrijzer, C.P., van der Vliet, P.C., & Kaptein, R. (1993) Nature 362, 852-855]. Because POUHD and POUs are expected to bind DNA differently, we have used "methylphosphonate interference" to investigate the alignment of their HTH elements in a specific DNA complex. This neutral phosphate analogue, originally developed for applications in antisense drug design [Miller, P. S., & Ts'o, P. O. P. (1987) Anti-Cancer Drug Des. 2, 117-128], is shown to provide a sensitive probe for sites of backbone-specific protein-DNA interaction. Inferred POUs-phosphate contacts are in striking accord with cocrystal structures of bacteriophage repressor and Cro proteins. Alignment of POUHD and POUs in successive major grooves in each case predicts unique HTH-adenine contacts. This prediction is verified using DNA base analogues to effect interchange of AT functional groups by the method of 2'-deoxyinosine/5-methyl-2'-deoxycytosine substitution [McLaughlin, L. W., Benseler, F., Graeser, E., Piel, N., & Scholtissek, S. (1987) Biochemistry 26, 7238-7245]. Our results strongly support the hypothesis that the DNA-binding properties of POUs are analogous to those of bacteriophage lambda repressor.

5-Methylcytosine↗
PubMed1994

Terephthalate 1,2-dioxygenase system from Comamonas testosteroni T-2: purification and some properties of the oxygenase component.

Comamonas testosteroni T-2, grown in terephthalate (TER)-salts medium, synthesizes inducible enzymes that convert TER to (1R,2S)-dihydroxy-3,5-cyclohexadiene-1,4-dicarboxylic acid (DCD) and protocatechuate (PC). Anion-exchange chromatography of cell extracts yielded two sets of fractions, R and Z, that were necessary for oxygenation of TER to DCD; we termed this activity the TER dioxygenase system (TERDOS). An NAD(+)-dependent DCD dehydrogenase, which converted DCD to PC, overlapped all fractions R. No significant purification from fraction R, which contained an NADH-dependent reductase function(s) of TERDOS, was attained. Fraction Z, at the end of the gradient, contained essentially one protein, which was further purified by hydrophobic interaction chromatography. This component, Z, had the UV-visible spectrum and electron paramagnetic resonance characteristics of a Rieske [2Fe-2S] protein and was considered to be the oxygenase. M(r)s of about 126,000 for oxygenase Z under native conditions were observed. Oxygenase Z consisted of two subunits, alpha and beta, with M(r)s of 49,000 and 18,000, respectively, under denaturing conditions. We presume that this oxygenase has an alpha 2 beta 2 structure. The sequences of the N-terminal amino acids of each subunit were determined. The activity of the purified enzyme was enhanced about fivefold by addition of Fe2+. In the presence of O2, NADH, and fraction R, component Z catalyzed the stoichiometric transformation of TER to PC, with the intermediate formation of DCD. The reaction was confirmed as a dioxygenation when we observed incorporation of two oxygen atoms from 18O2 into PC. The substrate range of TERDOS appeared to be narrow; apart from TER, only 2,5-dicarboxypyridine and 1,4-dicarboxynaphthalene (of 11 compounds tested) were converted to a product.

Biodegradation, Environmental↗
PubMed1993

The SRY high-mobility-group box recognizes DNA by partial intercalation in the minor groove: a topological mechanism of sequence specificity.

SRY, a putative transcription factor encoded by the sex-determining region of the human Y chromosome, regulates a genetic switch in male development. Impairment of this switch leads to intersex abnormalities of the newborn and is observed in association with mutations in the SRY DNA-binding domain [the high-mobility-group (HMG) box]. Here we show that the SRY HMG box exhibits a novel mechanism of DNA recognition: partial intercalation of a nonpolar side chain in the DNA minor groove. Base stacking (but not base pairing) is interrupted at the site of insertion. Sequence specificity reflects topological requirements of partial intercalation rather than direct readout of base-specific functional groups. Our results predict that the SRY HMG box inserts an alpha-helix into a widened minor groove at the center of a sharp DNA bend. A similar mechanism may underlie binding of SRY and homologous HMG proteins to four-way junctions (Holliday intermediates) and other noncanonical DNA structures.

Base Composition↗
PubMed1993

Novel zinc finger motif in the basal transcriptional machinery: three-dimensional NMR studies of the nucleic acid binding domain of transcriptional elongation factor TFIIS.

Transcriptional elongation provides a key control point in the regulation of eukaryotic gene expression. Here we describe homonuclear and 15N-heteronuclear 3D NMR studies of the nucleic acid binding domain of human transcriptional elongation factor TFIIS. This domain contains a Cys4 Zn(2+)-binding site with no homology to previously characterized Cys4, Cys6, or Cys2-His2 Zn fingers. Complete 1H and 15N NMR resonance assignment of a 50-residue TFIIS peptide-Zn2+ complex is obtained. Its solution structure, as determined by distance geometry/simulated annealing (DG/SA) calculations, exhibits a novel three-stranded antiparallel beta-sheet (designated the Zn ribbon). Analogous sequence motifs occur in a wide class of proteins involved in RNA or DNA transactions, including human basal transcriptional initiation factor TFIIE. A three-dimensional model of the TFIIE Cys4 domain is obtained by DG-based homology modeling. The role of the TFIIS Zn ribbon in the control of eukaryotic transcriptional elongation is discussed.

Amino Acid Sequence↗
PubMed1993

Structure of a new nucleic-acid-binding motif in eukaryotic transcriptional elongation factor TFIIS.

Transcriptional elongation involves dynamic interactions among RNA polymerase and single-stranded and double-stranded nucleic acids in the ternary complex. In prokaryotes its regulation provides an important mechanism of genetic control. Analogous eukaryotic mechanisms are not well understood, but may control expression of proto-oncogenes and viruses, including the human immunodeficiency virus HIV-1 (ref. 8). The highly conserved eukaryotic transcriptional elongation factor TFIIS enables RNA polymerase II (RNAPII) to read though pause or termination sites, nucleosomes and sequence-specific DNA-binding proteins. Two distinct domains of human TFIIS, which bind RNAPII and nucleic acids, regulate read-through and possibly nascent transcript cleavage. Here we describe the three-dimensional NMR structure of a Cys4 nucleic-acid-binding domain from human TFIIS. Unlike previously characterized zinc modules, which contain an alpha-helix, this structure consists of a three-stranded beta-sheet. Analogous Cys4 structural motifs may occur in other proteins involved in DNA or RNA transactions, including RNAPII itself. This new structure, designated the Zn ribbon, extends the repertoire of Zn-mediated peptide architectures and highlights the growing recognition of the beta-sheet as a motif of nucleic-acid recognition.

Amino Acid Sequence↗
PubMed1993

Role of native disulfide bonds in the structure and activity of insulin-like growth factor 1: genetic models of protein-folding intermediates.

Insulin and insulin-related proteins contain three motif-specific disulfide bonds. Here we examine the role of these disulfide bonds in the folding and function of one family member, human insulin-like growth factor 1 (IGF-1). Analogues containing pariwise Cys-->Ser or Cys-->Ala substitutions were expressed in Escherichia coli, purified, and analyzed with respect to receptor-binding, solution structure, and thermodynamic stability. An analogue lacking all three disulfide bonds (designated des-Cys-IGF-1) is inactive and unfolded. Introduction of the [18-61] disulfide bond, previously shown to occur in an early intermediate in oxidative refolding [Miller, J. A., Owers-Narhi, L., Hua, Q. X., Rosenfeld, R., Arakawa, T., Rohde, M., Prestrelski, S., Lauren, S., S. Stoney, K. S., Tsai, L., & Weiss, M. A. (1993) Biochemistry (preceding paper in this issue)], results in a compact partially folded state with low but significant biological activity. Additional but incomplete structural organization and biological activity are observed following introduction of either the [6-48] or the [47-52] disulfide bonds. Native function, structure, and stability require the presence of all three disulfide bonds. These analogues provide genetic models of IGF-1 protein-folding intermediates. Their characterization suggests that bifurcation of the IGF-1 folding pathway reflects alternative late steps in the folding of a molten-globule intermediate.

Amino Acid Sequence↗
PubMed1993

Comparison of the dynamics of an engineered insulin monomer and dimer by acid-quenched amide proton exchange. Non-local stabilization of interchain hydrogen bonds by dimerization.

Dynamic differences between an engineered insulin monomer and dimer are investigated under physiological conditions by an adaptation of the method of acid-quenched amide proton exchange. Although exchange lifetimes of amide protons involved in intrachain hydrogen bonds are similar in the two analogs, dimerization specifically stabilizes two interchain hydrogen bonds (LeuB6-NH...O = C-CysA6 and CysA11-NH...O = C-GluB4) that are distant from the dimer interface. Such non-local stabilization demonstrates that fluctuations in the tertiary structure of the monomer are damped by dimerization. As the B6-A6 and A11-B4 hydrogen bonds are specific to the crystallographic T-state, their stabilization also indicates that the R-state (an allosteric feature of hexamer assembly) is not significantly populated in an isolated dimer. Our results are discussed in reference to recent hypotheses that crystal structures of insulin depict inactive conformers and that detachment of interchain contacts accompany receptor binding.

Amides↗
PubMed1993

Aromatic-histidine interactions in the zinc finger motif: structural inequivalence of phenylalanine and tyrosine in the hydrophobic core.

The classical Zn finger (Cys-X2,4-Cys-X3-Phe-X5-Leu-X2-His-X3,4-His contains [corrected] an aromatic-histidine interaction (underlined) in its hydrophobic core whose importance is suggested by the marked destabilization of a Phe-->Leu analogue [Mortishire-Smith, R.J., Lee, M.S., Bolinger, L., & Wright, P.E. (1992) FEBS Lett. 1, 11-15]. In some Zn finger sequences the central Phe is replaced [corrected] by Tyr, and when present, this substitution is generally conserved among species. To investigate whether Tyr would participate in an analogous aromatic-histidine interaction, we have determined the solution structure in a Phe-->Tyr mutant domain. Its global fold (the beta beta alpha motif) is similar to that of the Phe domain. Although the variant Tyr maintains edge-to-face packing against the proximal histidine, the phenolic ring is displaced toward solvent. Such displacement increases the solvent accessibility of the Tyr p-OH group and reduces steric overlap (and possible electrostatic repulsion) between the Tyr O zeta and His pi electrons. The Tyr analogue exhibits reduced dynamic stability (as indicated by more rapid exchange of amide protons in D2O) and may alternate in rapid equilibrium between major and minor conformers. Inequivalent Tyr-His and Phe-His interactions are likely to be general features of Zn finger architecture. Molecular modeling based on the Zif268 cocrystal structure [Pavletich, N.P., & Pabo, C.O. (1991) Science 252, 809-817] suggests that the variant Tyr p-OH group may readily be positioned to contribute a novel hydrogen bond to a DNA phosphate.

Amino Acid Sequence↗
PubMed1993

Dynamics of a monomeric insulin analogue: testing the molten-globule hypothesis.

The structure of insulin exhibits local and nonlocal differences among crystal forms and so provides an important model for analysis of protein dynamics. A novel combination of order and disorder has recently been inferred from 2D-NMR studies of the monomeric analogue des-pentapeptide(B26-B30) insulin (DPI) under acidic conditions [the molten-globule hypothesis; Hua, Q.X., Kochoyan, M., & Weiss, M.A. (1992) Proc. Natl. Acad. Sci. U.S.A. 89, 2379-2383]. Distance-geometry structures are similar in general to crystal structures but differ by rigid-body displacements of alpha-helices; the hydrophobic core is not well ordered due to insufficient long-range restraints. To test whether such informational uncertainty may represent physical disorder, we have performed complementary studies of the thermal unfolding of DPI and its interaction with 1-anilino-8-naphthalenesulfonate (ANS). Experimental design is based on a predicted analogy between DPI and A-state models of protein-folding intermediates (the "molten globule"). Unfolding is monitored by five distinct biophysical probes: photochemical dynamic nuclear polarization (photo-CIDNP), differential scanning calorimetry (DSC), circular dichroism (CD), 1H-NMR chemical shifts, and slowly exchanging amide 1H-NMR resonances in D2O solution. The results provide evidence that DPI adopts a compact partially folded state. Because the 2D-NMR spectrum of an engineered insulin monomer under physiological conditions is similar to that of DPI under acidic conditions [Weiss, M.A., Hua, Q.X., Frank, B.H., Lynch, C., & Shoelson, S.E. (1991) Biochemistry 30, 7373-7389], we propose that the functional form of insulin is a molten globule.

Amino Acid Sequence↗