Abstract:
:Restriction endonucleases such as EcoRI bind and cleave DNA with great specificity and represent a paradigm for protein-DNA interactions and molecular recognition. Using osmotic pressure to induce water release, we demonstrate the participation of bound waters in the sequence discrimination of substrate DNA by EcoRI. Changes in solvation can play a critical role in directing sequence-specific DNA binding by EcoRI and are also crucial in assisting site discrimination during catalysis. By measuring the volume change for complex formation, we show that at the cognate sequence (GAATTC) EcoRI binding releases about 70 fewer water molecules than binding at an alternate DNA sequence (TAATTC), which differs by a single base pair. EcoRI complexation with nonspecific DNA releases substantially less water than either of these specific complexes. In cognate substrates (GAATTC) kcat decreases as osmotic pressure is increased, indicating the binding of about 30 water molecules accompanies the cleavage reaction. For the alternate substrate (TAATTC), release of about 40 water molecules accompanies the reaction, indicated by a dramatic acceleration of the rate when osmotic pressure is raised. These large differences in solvation effects demonstrate that water molecules can be key players in the molecular recognition process during both association and catalytic phases of the EcoRI reaction, acting to change the specificity of the enzyme. For both the protein-DNA complex and the transition state, there may be substantial conformational differences between cognate and alternate sites, accompanied by significant alterations in hydration and solvent accessibility.
journal_name
Proc Natl Acad Sci U S Aauthors
Robinson CR,Sligar SGdoi
10.1073/pnas.95.5.2186subject
Has Abstractpub_date
1998-03-03 00:00:00pages
2186-91issue
5eissn
0027-8424issn
1091-6490journal_volume
95pub_type
杂志文章abstract::Comparisons were made of the T1 ribonuclease digests of 32P-labeled nucleolar 45S RNA of intact Novikoff hepatoma cells and the RNA synthesized in vitro by isolated nucleoli. Approximately 200 oligonucleotide spots were found in the two-dimensional chromatogram of 45S nucleolar RNA labeled in vivo, which includes frag...
journal_title:Proceedings of the National Academy of Sciences of the United States of America
pub_type: 杂志文章
doi:10.1073/pnas.74.6.2446
更新日期:1977-06-01 00:00:00
abstract::The electrical transport through self-assembled monolayers of alkanedithiols was studied in large-area molecular junctions and described by the Simmons model [Simmons JG (1963) J Appl Phys 34:1793-1803 and 2581-2590] for tunneling through a practical barrier, i.e., a rectangular barrier with the image potential includ...
journal_title:Proceedings of the National Academy of Sciences of the United States of America
pub_type: 杂志文章,评审
doi:10.1073/pnas.0701472104
更新日期:2007-07-03 00:00:00
abstract::Postnatal development and adult function of the central nervous system are dependent on the capacity of neurons to effect long-term changes of specific properties in response to neural activity. This neuronal response has been demonstrated to be tightly correlated with the expression of a set of regulatory genes which...
journal_title:Proceedings of the National Academy of Sciences of the United States of America
pub_type: 杂志文章
doi:10.1073/pnas.93.6.2317
更新日期:1996-03-19 00:00:00
abstract::The rat mammary cell line Rama 25 [Bennett, D.C., Peachey, L.A., Durbin, H. & Rudland, P.S. (1978) Cell 15, 283--298] differentiates morphologically in vitro from a cuboidal form to a fusiform cell resembling myoepithelial cells. This differentiation occurs in all clonal isolates of the line. By using three different ...
journal_title:Proceedings of the National Academy of Sciences of the United States of America
pub_type: 杂志文章
doi:10.1073/pnas.75.12.6093
更新日期:1978-12-01 00:00:00
abstract::The nucleotide sequence of intracellular 26S mRNA of Sindbis virus has been determined by direct sequence analysis of the cDNA made to this RNA with reverse transcriptase. From this, the amino acid sequences of the encoded virus structural proteins, which include a basic capsid protein and two integral membrane glycop...
journal_title:Proceedings of the National Academy of Sciences of the United States of America
pub_type: 杂志文章
doi:10.1073/pnas.78.4.2062
更新日期:1981-04-01 00:00:00
abstract::The oligopeptide permease of Escherichia coli has been characterized by Payne, Gilvarg, and their colleagues. We have confirmed its existence in Salmonella typhimurium, and have isolated a series of mutants lacking the permease. We use this transport system for smuggling a histidine biosynthetic intermediate, histidin...
journal_title:Proceedings of the National Academy of Sciences of the United States of America
pub_type: 杂志文章
doi:10.1073/pnas.70.2.456
更新日期:1973-02-01 00:00:00
abstract::Oil spills can lead to irreversible environmental degradation and are a potential hazard to human health. We study how onshore oil spills affect neonatal and infant mortality by combining spatial data from the Nigerian Oil Spill Monitor with Demographic and Health Surveys. To identify a causal effect, we compare sibli...
journal_title:Proceedings of the National Academy of Sciences of the United States of America
pub_type: 杂志文章
doi:10.1073/pnas.1818303116
更新日期:2019-03-19 00:00:00
abstract::The nature of color categories in the world's languages is contested. One major view holds that color categories are organized around universal focal colors, whereas an opposing view holds instead that categories are defined at their boundaries by linguistic convention. Both of these standardly opposed views are chall...
journal_title:Proceedings of the National Academy of Sciences of the United States of America
pub_type: 杂志文章
doi:10.1073/pnas.0610341104
更新日期:2007-01-23 00:00:00
abstract::The clonal rat pituitary cell line GH4C1 expresses the genes for several voltage-dependent potassium channels including Kv1.5 and Kv1.4. Dexamethasone, a glucocorticoid agonist, induces a slowly inactivating potassium current in these cells but does not alter the amplitude of a rapidly inactivating component of potass...
journal_title:Proceedings of the National Academy of Sciences of the United States of America
pub_type: 杂志文章
doi:10.1073/pnas.92.13.5955
更新日期:1995-06-20 00:00:00
abstract::The Fbw7 (F-box/WD repeat-containing protein 7) ubiquitin ligase targets multiple oncoproteins for degradation and is commonly mutated in cancers. Like other pleiotropic tumor suppressors, Fbw7's complex biology has impeded our understanding of how Fbw7 mutations promote tumorigenesis and hindered the development of t...
journal_title:Proceedings of the National Academy of Sciences of the United States of America
pub_type: 杂志文章
doi:10.1073/pnas.1718338115
更新日期:2018-05-22 00:00:00
abstract::Formamide is one of the important compounds from which prebiotic molecules can be synthesized, provided that its concentration is sufficiently high. For nucleotides and short DNA strands, it has been shown that a high degree of accumulation in hydrothermal pores occurs, so that temperature gradients might play a role ...
journal_title:Proceedings of the National Academy of Sciences of the United States of America
pub_type: 杂志文章
doi:10.1073/pnas.1600275113
更新日期:2016-04-19 00:00:00
abstract::DNA sequences in Neurospora crassa that code for ribosomal RNA have been isolated in a highly purified state by DNA-RNA hybridization. About 100 separate ribosomal RNA genes exist in each nucleus. These genes are composed of repeated sequences that are present about 100 times per nucleus. The individual members of thi...
journal_title:Proceedings of the National Academy of Sciences of the United States of America
pub_type: 杂志文章
doi:10.1073/pnas.69.11.3256
更新日期:1972-11-01 00:00:00
abstract::Type C retroviruses are endogenous in most vertebrate species. These viruses generally are of low pathogenicity in their natural hosts. Variants that contain cell-derived transforming genes have been isolated infrequently in the past upon continued passage in vivo. We report here a procedure that allows the isolation ...
journal_title:Proceedings of the National Academy of Sciences of the United States of America
pub_type: 杂志文章
doi:10.1073/pnas.77.1.624
更新日期:1980-01-01 00:00:00
abstract::Converging TGF-beta and insulin-like neuroendocrine signaling pathways regulate whether Caenorhabditis elegans develops reproductively or arrests at the dauer larval stage. We examined whether neurotransmitters act in the dauer entry or recovery pathways. Muscarinic agonists promote recovery from dauer arrest induced ...
journal_title:Proceedings of the National Academy of Sciences of the United States of America
pub_type: 杂志文章
doi:10.1073/pnas.97.1.460
更新日期:2000-01-04 00:00:00
abstract::The L-A double-stranded RNA virus of Saccharomyces cerevisiae makes a gag-pol fusion protein by a -1 ribosomal frameshift. The pol amino acid sequence includes consensus patterns typical of the RNA-dependent RNA polymerases (EC 2.7.7.48) of (+) strand and double-stranded RNA viruses of animals and plants. We have carr...
journal_title:Proceedings of the National Academy of Sciences of the United States of America
pub_type: 杂志文章
doi:10.1073/pnas.89.6.2185
更新日期:1992-03-15 00:00:00
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journal_title:Proceedings of the National Academy of Sciences of the United States of America
pub_type: 杂志文章
doi:10.1073/pnas.251526398
更新日期:2001-12-04 00:00:00
abstract::During the developmental process of the Gram-negative soil bacterium Myxococcus xanthus, vegetatively growing rod cells differentiate to ultimately become metabolically quiescent and environmentally resistant myxospores encased within fruiting bodies. This program, initiated by nutrient deprivation, is propagated by b...
journal_title:Proceedings of the National Academy of Sciences of the United States of America
pub_type: 杂志文章
doi:10.1073/pnas.0506969102
更新日期:2005-10-04 00:00:00
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journal_title:Proceedings of the National Academy of Sciences of the United States of America
pub_type: 杂志文章
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更新日期:2016-12-20 00:00:00
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journal_title:Proceedings of the National Academy of Sciences of the United States of America
pub_type: 杂志文章
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更新日期:2010-10-19 00:00:00
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journal_title:Proceedings of the National Academy of Sciences of the United States of America
pub_type: 杂志文章
doi:10.1073/pnas.77.10.5884
更新日期:1980-10-01 00:00:00
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journal_title:Proceedings of the National Academy of Sciences of the United States of America
pub_type: 杂志文章
doi:10.1073/pnas.1717082115
更新日期:2018-04-10 00:00:00
abstract::Development of type 1 diabetes in the nonobese diabetic (NOD) mouse is preceded by an immune cell infiltrate in the pancreatic islets. The exact role of the attracted cells is still poorly understood. Chemokine CCL2/MCP-1 is known to attract CCR2(+) monocytes and dendritic cells (DCs). We have previously shown that tr...
journal_title:Proceedings of the National Academy of Sciences of the United States of America
pub_type: 杂志文章
doi:10.1073/pnas.1115308109
更新日期:2012-02-28 00:00:00
abstract::In this note the Weierstrass integral J is taken as L, the Riemann integral of length. Here M(n), n > 1, is a compact, connected manifold of class C(infinity) with a positive definite Riemann structure. Presentations (phi, U(phi)) in M(n) and geodesics (with the aid of the Euler-Riemann equations) are defined in Morse...
journal_title:Proceedings of the National Academy of Sciences of the United States of America
pub_type: 杂志文章
doi:10.1073/pnas.74.6.2209
更新日期:1977-06-01 00:00:00
abstract::A major challenge of the 21st century is to produce more food for a growing population without increasing humanity's agricultural footprint. Urban food production may help to solve this challenge; however, little research has examined the productivity of urban farming systems. We investigated inputs and produce yields...
journal_title:Proceedings of the National Academy of Sciences of the United States of America
pub_type: 杂志文章
doi:10.1073/pnas.1809707115
更新日期:2019-01-02 00:00:00
abstract::Nonresolving chronic inflammation at the neoplastic site is consistently associated with promoting tumor progression and poor patient outcomes. However, many aspects behind the mechanisms that establish this tumor-promoting inflammatory microenvironment remain undefined. Using bladder cancer (BC) as a model, we found ...
journal_title:Proceedings of the National Academy of Sciences of the United States of America
pub_type: 杂志文章
doi:10.1073/pnas.1424795112
更新日期:2015-04-14 00:00:00
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journal_title:Proceedings of the National Academy of Sciences of the United States of America
pub_type: 杂志文章
doi:10.1073/pnas.92.25.11642
更新日期:1995-12-05 00:00:00
abstract::The candidate phylum TM7 is globally distributed and often associated with human inflammatory mucosal diseases. Despite its prevalence, the TM7 phylum remains recalcitrant to cultivation, making it one of the most enigmatic phyla known. In this study, we cultivated a TM7 phylotype (TM7x) from the human oral cavity. Th...
journal_title:Proceedings of the National Academy of Sciences of the United States of America
pub_type: 杂志文章
doi:10.1073/pnas.1419038112
更新日期:2015-01-06 00:00:00
abstract::Hydrogenases catalyze the reversible reaction 2H(+) + 2e(-) ↔ H(2) with an equilibrium constant that is dependent on the reducing potential of electrons carried by their redox partner. To examine the possibility of increasing the photobiological production of hydrogen within cyanobacterial cultures, we expressed the [...
journal_title:Proceedings of the National Academy of Sciences of the United States of America
pub_type: 杂志文章
doi:10.1073/pnas.1016026108
更新日期:2011-03-08 00:00:00
abstract::Using tunicamycin, we have investigated the role of glycoproteins in membrane transport. Tunicamycin is a glucosamine-containing antibiotic that specifically inhibits dolichol pyrophosphate-mediated glycosylation of asparaginyl residues of glycoproteins. Inhibition of protein glycosylation in chick embryo fibroblasts ...
journal_title:Proceedings of the National Academy of Sciences of the United States of America
pub_type: 杂志文章
doi:10.1073/pnas.76.2.791
更新日期:1979-02-01 00:00:00
abstract::The effects of systemic PD134308 [0.1-3 mg/kg; an antagonist of the cholecystokinin (CCK) type B receptor], morphine, and intrathecal (i.t.) galanin (GAL) on the excitability of the spinal nociceptive flexor reflex and in the hot plate test were examined in rats. PD134308 caused a weak naloxone-reversible depression o...
journal_title:Proceedings of the National Academy of Sciences of the United States of America
pub_type: 杂志文章
doi:10.1073/pnas.87.18.7105
更新日期:1990-09-01 00:00:00