Showing papers by "University of California, San Francisco published in 1986"
TL;DR: An all atom potential energy function for the simulation of proteins and nucleic acids and the first general vibrational analysis of all five nucleic acid bases with a molecular mechanics potential approach is presented.
Abstract: We present an all atom potential energy function for the simulation of proteins and nucleic acids. This work is an extension of the CH united atom function recently presented by S.J. Weiner et al. J. Amer. Chem. Soc., 106, 765 (1984). The parameters of our function are based on calculations on ethane, propane, n−butane, dimethyl ether, methyl ethyl ether, tetrahydrofuran, imidazole, indole, deoxyadenosine, base paired dinucleoside phosphates, adenine, guanine, uracil, cytosine, thymine, insulin, and myoglobin. We have also used these parameters to carry out the first general vibrational analysis of all five nucleic acid bases with a molecular mechanics potential approach.
3,291 citations
TL;DR: The cDNA sequence of human c-erb-A indicates that the protein encoded by the gene is related to the steroid hormone receptors, and binding studies show it to be a receptor for thyroid hormones.
Abstract: The cDNA sequence of human c-erb-A, the cellular counterpart of the viral oncogene v-erb-A, indicates that the protein encoded by the gene is related to the steroid hormone receptors. Binding studies with the protein show it to be a receptor for thyroid hormones.
1,433 citations
1,319 citations
TL;DR: The primary structure of the receptor for platelet-derived growth factor (PDGF), determined by means of cloning a cDNA that encodes the murine pre-PDGF receptor, is closely related to that of the v-kit oncogene product and the receptors for macrophage colony stimulating factor (CSF-1).
Abstract: The primary structure of the receptor for platelet-derived growth factor (PDGF), determined by means of cloning a cDNA that encodes the murine pre-PDGF receptor, is closely related to that of the v-kit oncogene product and the receptor for macrophage colony stimulating factor (CSF-1). Common structural features include the presence of long sequences that interrupt the tyrosine-specific protein kinase domains of each molecule. The PDGF and CSF-1 receptors also share a characteristic distribution of extracellular cysteine residues. Ubiquitin is covalently bound to the purified PDGF receptor, the human gene for which is on chromosome 5.
1,144 citations
TL;DR: For both CHD and total mortality, serum cholesterol was similar to diastolic blood pressure in the shape of the risk curve and in the size of the high-risk group, which supports the policy of a moderate fat intake for the general population and intensive treatment for those at high risk.
1,089 citations
TL;DR: In this article, an approach to couple ab initio quantum mechanical geometry optimiuzations with molecular mechanical optimizations is presented, with the added capability to carry out molecular dynamics simulations of the systems to earch for new local minima.
Abstract: We present an approach to couple ab initio quantum mechanical geometry optimiuzations with molecular mechanical optimizations, with the added capability to carry out molecular dynamics simulations of the systems to earch for new local minima. The approach is applied to the aqueous solution CH3Cl + Cl− exchange reaction and the gas phase protonation of polyethers.
1,046 citations
TL;DR: It is shown that replacement of one or both of the twin tyrosines (residues 1162 and 1163) with phenylalanine results in a dramatic reduction in or loss of insulin-activated autophosphorylation and kinase activity in vitro.
1,020 citations
TL;DR: A potential approach to therapy in which autologous CD8 lymphocytes could be administered to individuals to inhibit HIV replication and perhaps progression of disease is suggested.
Abstract: Lymphocytes bearing the CD8 marker were shown to suppress replication of human immunodeficiency virus (HIV) in peripheral blood mononuclear cells. The effect was dose-dependent and most apparent with autologous lymphocytes; it did not appear to be mediated by a cytotoxic response. This suppression of HIV replication could be demonstrated by the addition of CD8+ cells at the initiation of virus production as well as after several weeks of virus replication by cultured cells. The observations suggest a potential approach to therapy in which autologous CD8 lymphocytes could be administered to individuals to inhibit HIV replication and perhaps progression of disease.
1,012 citations
TL;DR: An oligonucleotide probe was designed from the nucleotide sequence of the amino-terminal exon of bovine acidic FGF, taking into account the 55 percent amino acid sequence homology between the two factors.
Abstract: Basic and acidic fibroblast growth factors (FGF's) are potent mitogens for capillary endothelial cells in vitro, stimulate angiogenesis in vivo, and may participate in tissue repair. An oligonucleotide probe for bovine basic FGF was designed from the nucleotide sequence of the amino-terminal exon of bovine acidic FGF, taking into account the 55 percent amino acid sequence homology between the two factors. With this oligonucleotide probe, a full length complementary DNA for basic FGF was isolated from bovine pituitary. Basic FGF in bovine hypothalamus was shown to be encoded by a single 5.0-kilobase messenger RNA; in a human hepatoma cell line, both 4.6- and 2.2-kilobase basic FGF messenger RNA's were present. Both growth factors seem to be synthesized with short amino-terminal extensions that are not found on the isolated forms for which the amino acid sequences have been determined. Neither basic nor acidic FGF has a classic signal peptide.
1,002 citations
TL;DR: Both serotonin and the selective gamma-aminobutyric acidB (GABAB) agonist, baclofen, increase potassium (K+) conductance in hippocampal pyramidal cells, indicating that the two receptors share the same potassium channels.
Abstract: Both serotonin and the selective gamma-aminobutyric acidB (GABAB) agonist, baclofen, increase potassium (K+) conductance in hippocampal pyramidal cells. Although these agonists act on separate receptors, the potassium currents evoked by the agonists are not additive, indicating that the two receptors share the same potassium channels. Experiments with hydrolysis-resistant guanosine triphosphate (GTP) and guanosine diphosphate analogs and pertussis toxin indicate that the opening of the potassium channels by serotonin and GABAB receptors involves a pertussis toxin-sensitive GTP-binding (G) protein, which may directly couple the two receptors to the potassium channel.
862 citations
TL;DR: The primary structure of PrP encoded by the gene of a healthy animal does not differ from that encoded by a cDNA from a scrapie-infected animal, suggesting that the different properties ofPrP from normal and scrapie -infected brains are due to post-translational events.
TL;DR: The ability of heparin or that of hexuronyl hexosaminoglygan sulfate (HHS‐4) to protect basic or acidic fibroblast growth factor (FGF) from acid or heat inactivation has been analyzed and indicates that heparIn and HHS‐4, in addition to protecting FGF from inactivation, also acts at another locus, as yet unidentified.
Abstract: The ability of heparin or that of hexuronyl hexosaminoglycan sulfate (HHS-4) to protect basic or acidic fibroblast growth factor (FGF) from acid or heat inactivation has been analyzed. Both freshly prepared basic and acidic FGF stimulate the growth of baby hamster kidney (BHK-21) cells exposed to medium supplemented with transferrin and insulin. Freshly prepared basic FGF was 10 fold more potent than acidic FGF. The addition of heparin to the medium decreased the potency of basic FGF while it potentiated that of acidic FGF. Upon storage of FGF at -80 degrees C, a decline in potency of both basic and acidic FGF was observed. Heparin, when added to the medium, potentiated their activities, which became similar to that of freshly prepared basic FGF. In order to test whether heparin could protect basic or acidic FGF from inactivation, both mitogens were exposed to acid conditions (1% trifluoroacetic acid, pH 1.08, 2 h) or heat (65 degrees C, 5 min) which inactivate basic or acidic FGF. When exposed to such treatment in the presence of heparin or HHS-4, basic and acidic FGF retained their potency. The effect of heparin and HHS-4 on the bioactivity of basic and acidic FGF is truly of a protective nature, since they had no effect when added after inactivation of the mitogens. Potentiation of the bioactivity of the protected mitogens or of the inactivated one could only be observed when cells were exposed to high heparin or HHS-4 concentrations. This indicates that heparin and HHS-4, in addition to protecting FGF from inactivation, also acts at another locus, as yet unidentified.
TL;DR: The most prominent structural feature of both lamins is an α-helical region of repeating heptads of amino acids that shows striking homology with the entire family of cytoplasmic intermediate filament proteins, suggesting that the nuclear envelope is made up of a network of coiled-coil polymers.
Abstract: The A, B and C lamins are the major proteins of the nuclear envelope. The complete nucleotide sequence of the coding region of the A and C lamins shows that these proteins are identical except for their carboxy termini. The most prominent structural feature of both lamins is an alpha-helical region of repeating heptads of amino acids that shows striking homology with the entire family of cytoplasmic intermediate filament proteins. These features suggest that the nuclear envelope is made up of a network of coiled-coil polymers.
TL;DR: New interactions between the two monokines IL-1 and TNF are revealed and provide a dual role for TNF, as immunomodulator and mediator of monocyte cytotoxicity induced by certain specific lymphokine and monokine molecules.
Abstract: Activated monocytes or macrophages can release soluble cytotoxic molecules capable of lysing tumour cells in vitro and thus represent an important component of the host defence mechanisms against malignancy. The recent availability of pure recombinant or natural human lymphokines and monokines and their respective polyclonal or monoclonal antibodies now makes it possible to dissect the interactions of these factors in the induction and performance of the cytotoxic event by the monocytes. Our studies indicate that pretreatment of monocytes with alpha-IFN or gamma-IFN, and also interleukin (IL)-1 or tumour necrosis factor (TNF) results in enhanced monocyte cytotoxicity. Although all these substances induce the production of IL-1 by monocytes, TNF mediates the enhanced cytotoxicity induced in monocytes by gamma-IFN, IL-1 and, in an autocrine manner, by TNF itself. Neither TNF, IL-1, gamma-IFN nor alpha-IFN mediate spontaneous monocyte cytotoxicity or that induced by alpha-IFN. Our studies thus reveal new interactions between the two monokines IL-1 and TNF and provide a dual role for TNF, as immunomodulator and mediator of monocyte cytotoxicity induced by certain specific lymphokine and monokine molecules.
TL;DR: The cloned receptor protein activates its corresponding enhancers, restoring to the receptor-deficient cells the full capacity for regulated enhancement.
TL;DR: It is found that phorbol esters profoundly potentiate excitatory synaptic transmission in the hippocampus in a manner that appears indistinguishable from LTP, which raises the possibility that, in mammalian brain, PKC plays a role in controlling the release of neurotransmitter and may be involved in the generation of LTP.
Abstract: Protein kinase C (PKC), a calcium-dependent phospholipid-sensitive kinase which is selectively activated by phorbol esters, is thought to play an important role in several cellular processes1,2. In mammalian brain PKC is present in high concentrations1 and has been shown to phosphorylate several substrate phospho-proteins3–6, one of which may be involved in the generation of long-term potentiation (LTP)7,8, a long-lasting increase in synaptic efficacy evoked by brief, high-frequency stimulation. Since the hippocampus contains one of the brain's highest levels of binding sites for phorbol esters9 and is the site where LTP has been most thoroughly characterized, we examined the effects of phorbol esters on hippocampal synaptic transmission and LTP. We found that phorbol esters profoundly potentiate excitatory synaptic transmission in the hippocampus in a manner that appears indistinguishable from LTP. Furthermore, after maximal synaptic enhancement by phorbol esters, LTP can no longer be elicited. Although the site of synaptic enhancement during LTP is not clearly established, phorbol esters appear to potentiate synaptic transmission by acting primarily at a presynaptic locus since changes in the postsynaptic responses to the putative transmitter, glutamate, cannot account for the increased synaptic responses induced by phorbol esters. These findings, in conjunction with previous biochemical studies, raise the possibility that, in mammalian brain, PKC plays a role in controlling the release of neurotransmitter and may be involved in the generation of LTP.
TL;DR: The complete 4,563-amino-acid sequence of apo B-100 precursor (relative molecular mass (Mr) 514,000 (514K)) determined from complementary DNA clones is reported, identifying a domain enriched in basic amino-acid residues as important for the cellular uptake of cholesterol by the LDL receptor pathway.
Abstract: Epidemiological, pathological and genetic studies show a strong positive correlation between elevated plasma concentrations of low-density lipoprotein (LDL) cholesterol and the risk of premature coronary heart disease. Apolipoprotein (apo) B-100 is the sole protein component of LDL and is the ligand responsible for the receptor-mediated uptake and clearance of LDL from the circulation. Apo B-100 is made by the liver and is essential for the assembly of triglyceride-rich very low-density lipoproteins (VLDL) in the cisternae of the endoplasmic reticulum and for their secretion into the plasma. VLDL transports triglyceride to peripheral muscle and adipose tissue, where the triglyceride is hydrolysed by lipoprotein lipase. The resultant particle, relatively enriched in cholesteryl ester, constitutes LDL. LDL delivers cholesterol to peripheral tissues where it is used for membrane and steroid hormone biosynthesis and to the liver, the only organ which can catabolize and excrete cholesterol. Plasma LDL levels are therefore determined by the balance between their rate of production from VLDL and clearance by the hepatic LDL (apo B/E) receptor pathway. Here we report the complete 4,563-amino-acid sequence of apo B-100 precursor (relative molecular mass (Mr) 514,000 (514K] determined from complementary DNA clones. Numerous lipid-binding structures are distributed throughout the extraordinary length of apo B-100 and must underlie its special functions as a nucleus for lipoprotein assembly and maintenance of plasma lipoprotein integrity. A domain enriched in basic amino-acid residues has been identified as important for the cellular uptake of cholesterol by the LDL receptor pathway.
TL;DR: Biochemical and electron microscopic data indicate that the human hepatitis δ viral agent contains a covalently closed circular and single-stranded RNA genome that has certain similarities with viroid-like agents from plants.
Abstract: Biochemical and electron microscopic data indicate that the human hepatitis δ viral agent contains a covalently closed circular and single-stranded RNA genome that has certain similarities with viroid-like agents from plants. The sequence of the viral genome (1,678 nucleotides) has been determined and an open reading frame within the complementary strand has been shown to encode an antigen that binds specifically to antisera from patients with chronic hepatitis δ viral infections.
TL;DR: The role of the T3/antigen receptor complex is summarized by the diagram presented, and for those events occurring after the early events pictured in Figure 4 that result in gene activation, the sequence is a black box.
Abstract: The results of several studies demonstrate that activation of resting T-cells requires two stimuli (1–4). One stimulus is represented by the recognition of antigen in conjunction with MHC gene products by the T-cell antigen receptor. The second stimulus is represented by accessory cells and their products. The delineation of the T-cell receptor for antigen and it’s associated molecules, T3, allows a study of how stimuli transmitted through these molecules signal activation. We present here some of these studies. To perform them, we have used the human T-cell line, Jurkat.
TL;DR: These studies have improved the understanding and application of the chiral interactions of beta-cyclodextrin, and they have demonstrated a means to measure optical purity and to isolate or produce pure enantiomers of drugs.
Abstract: For many drugs, only racemic mixtures are available for clinical use. Because different stereoisomers of drugs often cause different physiological responses, the use of pure isomers could elicit more exact therapeutic effects. Differential complexation of a variety of drug stereoisomers by immobilized beta-cyclodextrin was investigated. Chiral recognition and racemic resolution were observed with a number of compounds from such clinically useful classes as beta-blockers, calcium-channel blockers, sedative hypnotics, antihistamines, anticonvulsants, diuretics, and synthetic opiates. Separation of the diastereomers of the cardioactive and antimalarial cinchona alkaloids and of two antiestrogens was demonstrated as well. Three dimensional projections of beta-cyclodextrin complexes of propanolol, which is resolved by this technique, and warfarin, which is not, are compared. These studies have improved the understanding and application of the chiral interactions of beta-cyclodextrin, and they have demonstrated a means to measure optical purity and to isolate or produce pure enantiomers of drugs. In addition, this highly specific technique could also be used in the pharmacological evaluation of enantiomeric drugs.
TL;DR: The authors obtained the first evidence of a facial expression unique to contempt, which was recognized by people in Estonia S.S.R., Germany, Greece, Hong Kong, Italy, Japan, Scotland, Turkey, United States, and West Sumatra.
Abstract: We obtained the first evidence of a facial expression unique to contempt. Contrary to our prediction, this contempt expression was not culture-specific but was recognized by people in Estonia S.S.R., Germany, Greece, Hong Kong, Italy, Japan, Scotland, Turkey, the United States, and West Sumatra. Pan-cultural agreement about the contempt expression was as high as has been found previously for other emotions.
TL;DR: The partially deleted gene for the common biosynthetic precursor of gonadotropin-releasing hormone and GnRH-associated peptide is transcriptionally active as revealed by in situ hybridization histochemistry of hpg hypothalamic tissue sections, but immunocytochemical analysis failed to show the presence of antigen corresponding to any part of the precursor protein.
Abstract: Hereditary hypogonadism in the hypogonadal (hpg) mouse is caused by a deletional mutation of at least 33.5 kilobases encompassing the distal half of the gene for the common biosynthetic precursor of gonadotropin-releasing hormone (GnRH) and GnRH-associated peptide (GAP). The partially deleted gene is transcriptionally active as revealed by in situ hybridization histochemistry of hpg hypothalamic tissue sections, but immunocytochemical analysis failed to show the presence of antigen corresponding to any part of the precursor protein.
TL;DR: It is suggested that, in vivo, cell fusion involving the CD4 molecule may represent a mechanism whereby uninfected cells can be incorporated into AIDS virus infected syncytia.
Abstract: The formation of multinucleated giant cells with progression to cell death is a characteristic manifestation of the cytopathology induced by the AIDS retrovirus in infected T lymphoid cells. The mechanism of giant cell formation was studied in the CD4 (T4/Leu 3) positive T cell lines JM (Jurkat) and VB and in variants of these lines that are negative for cell surface CD4 antigen. By means of a two-color fluorescent labeling technique, multinucleated giant cells in infected cultures were shown to form through cell fusion. Antibody to CD4 specifically inhibited fusion, and uninfected CD4 negative cells, in contrast to uninfected CD4 positive cells, did not undergo fusion with infected cells, suggesting a direct role for the CD4 antigen in the process of syncytium formation. These results suggest that, in vivo, cell fusion involving the CD4 molecule may represent a mechanism whereby uninfected cells can be incorporated into AIDS virus infected syncytia. Because the giant cells die soon after they are formed, this process may contribute to the depletion of helper/inducer T cells characteristically observed in AIDS.
TL;DR: HIV-1 RNA load testing is sometimes requested to resolve equivocal serologic findings or to facilitate the diagnosis of HIV-1 infection during the acute phase or in a pediatric setting.
Abstract: The human immunodeficiency virus (HIV) is the etiologic agent of AIDS. HIVs are enveloped plus-stranded RNA viruses. The HIV genome is organized similarly to other retroviruses. It contains the gag, pol, and env genes which encode structural proteins, viral enzymes, and envelope glycoproteins, respectively. The major structural proteins which are encoded by the gag gene include p17, p24, p7, and p9. Replication begins with the attachment of virus to the target cell via the interaction of gp120 and the cellular receptor CD4. Both HIV-1 and HIV-2 have the same modes of transmission. The most common mode of HIV infection is sexual transmission at the genital mucosa through direct contact with infected blood fluids, including blood, semen, and vaginal secretions. Serological testing for HIV antibody is used for various purposes, including primary diagnosis, screening of blood products, management of untested persons in labor and delivery, evaluation of occupational exposures to blood/body fluid, and epidemiological surveillance. The first generation of HIV antibody assays relied on the detection of antibody to HIV viral protein lysates. A test using a sandwich-capture format and significantly more blood than other methods was more sensitive in early seroconversion. HIV-1 RNA load testing is sometimes requested to resolve equivocal serologic findings or to facilitate the diagnosis of HIV-1 infection during the acute phase or in a pediatric setting.
TL;DR: Findings show a strong relationship between drug and alcohol use during sex and non-compliance with safe sex techniques to prevent the spread of AIDS.
Abstract: This article describes the association between drug and alcohol use during sexual activity and high-risk sex for AIDS. Data to test this association are drawn from a prospective study of the behavioral changes made by gay men in San Francisco in response to the AIDS epidemic. Findings drawn from the May, 1984 and May 1985 waves of data collection are described. The cross-sectional analysis showed that use of particular drugs during sex, the number of drugs used during such activity, and the frequency of combining drugs and sex are all positively associated with risky sexual activity for AIDS. The retrospective data showed that men who currently abstained from combining drug use with sexual activity were likely to have been at no risk for AIDS over two measurement points during the previous year. The men who currently combined drug use with sex were most likely to have a history of high-risk sexual activity over the previous year. These findings show a strong relationship between drug and alcohol use during sex and non-compliance with safe sex techniques to prevent the spread of AIDS. Implications of this relationship for AIDS health education efforts are discussed.
TL;DR: The crystal structure of the complex between Eco RI endonuclease and the cognate oligonucleotide TCGCGAATTCGCG provides a detailed example of the structural basis of sequence-specific DNA-protein interactions.
Abstract: The crystal structure of the complex between Eco RI endonuclease and the cognate oligonucleotide TCGCGAATTCGCG provides a detailed example of the structural basis of sequence-specific DNA-protein interactions. The structure was determined, to 3 A resolution, by the ISIR (iterative single isomorphous replacement) method with a platinum isomorphous derivative. The complex has twofold symmetry. Each subunit of the endonuclease is organized into an alpha/beta domain consisting a five-stranded beta sheet, alpha helices, and an extension, called the "arm," which wraps around the DNA. The large beta sheet consists of antiparallel and parallel motifs that form the foundations for the loops and alpha helices responsible for DNA strand scission and sequence-specific recognition, respectively. The DNA cleavage site is located in a cleft that binds the DNA backbone in the vicinity of the scissile bond. Sequence specificity is mediated by 12 hydrogen bonds originating from alpha helical recognition modules. Arg200 forms two hydrogen bonds with guanine while Glu144 and Arg145 form four hydrogen bonds to adjacent adenine residues. These interactions discriminate the Eco RI hexanucleotide GAATTC from all other hexanucleotides because any base substitution would require rupture of at least one of these hydrogen bonds.
TL;DR: A single gene (Prn-i) that affects scrapie incubation period in mice has been identified and analysis of DNA from 66 backcross mice indicated PrN-i is tightly linked to Prn-p, the structural gene for PrP.
TL;DR: The existence of opposite fluxes at the kinetochore during metaphase and anaphase suggests that two separate forces are responsible for chromosome congression and anAPHase movement.
TL;DR: Ducts of the lateral prostate (LP), a ventrolateral subdivision of the DLP, initiated branching morphogenesis between 1 to 5 days after birth and the LP grew into and became embedded within the capsule of the VP, which may explain why the ductal architecture of these two lobes are similar.
Abstract: Postnatal growth and development of the glandular architecture of the ventral and dorsolateral lobes of the mouse prostate (VP and DLP) were investigated by microdissection techniques that permitted precise quantification of the numbers of primary ducts emerging from the urethra, the terminal ductal tips, and ductal branchpoints. At birth both the right and left lobe of the VP consisted of 1-3 main ducts that had already undergone secondary and tertiary branching. In contrast, at birth the more complex DLP had 9-12 unbranched main ducts per lobe on both the right and left sides. During the first 15 days after birth, 80.7% of tips and 76.4% of branchpoints of the adult gland formed in the VP, and 70.4% of tips and 53.6% of branch-points formed in the DLP. Ductal branching was completed by 60 to 90 days. The DLP developed in three stages: first, formation of unbranched main ducts (first 10 days); second, distal branching of each main duct resulting in 3-5 terminal branches per main duct (10-15 days after birth); third, elaboration of intraductal mucosal infolding in distal ducts after 30 days of age. Ducts of the lateral prostate (LP), a ventrolateral subdivision of the DLP, initiated branching morphogenesis between I to 5 days after birth. The LP grew into and became embedded within the capsule of the VP, which may explain why the ductal architecture of these two lobes are similar. These heretofore unrecognized differences in the organogenesis and morphology of the mouse VP and DLP and the striking morphological heterogeneity both between and within the lobes of the mouse prostate may be morphological manifestations of functional heterogeneities within the prostate.