Abstract:
:Prediction of the native tertiary structure of a globular protein from the primary sequence will require a potential energy model that can discriminate all nonnative structures from the native structure(s). A successful model must distinguish not only alternate structures that are very nonnative but also alternate structures that are compact and near-native. We describe here a method, based on molecular dynamics simulation, that allows generation of hundreds of compact alternate structures that are arbitrarily close to the native structure. In this way, a significant amount of conformational space in the neighborhood of the native structure can be sampled and these alternate structures can be used as a stringent test of protein folding models. We have used two sets of these alternate structures generated for six crystallographically characterized small globular proteins (1200 alternate structures in all) to test eight empirical energy models for their ability to discriminate alternate from native structures. Seven of the models fail to correctly identify at least some of the alternate structures as nonnative. An atomic solvation model is presented that succeeds in discriminating all 1200 alternate structures from native.
journal_name
Proc Natl Acad Sci U S Aauthors
Wang Y,Zhang H,Li W,Scott RAdoi
10.1073/pnas.92.3.709subject
Has Abstractpub_date
1995-01-31 00:00:00pages
709-13issue
3eissn
0027-8424issn
1091-6490journal_volume
92pub_type
杂志文章abstract::In order to study the mutagenic effects of site-specific, covalent modifications of biologically active DNA, we need host cells that are permissive for any type of mutation that might be produced in vivo from the modified DNA. Specifically, we require a general, in vivo complementation system for the bacteriophage phi...
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:1978-02-01 00:00:00
abstract::To test the hypothesis that the pubertal increase in luteinizing hormone-releasing hormone (LHRH) release is withheld by a dominant inhibitory neuronal system, the role of gamma-aminobutyric acid (GABA), a known inhibitory neurotransmitter, in the control of LHRH release was examined in conscious female monkeys at the...
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:1994-01-04 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:2003-06-24 00:00:00
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journal_title:Proceedings of the National Academy of Sciences of the United States of America
pub_type: 历史文章,杂志文章
doi:10.1073/pnas.0813117106
更新日期:2009-03-17 00:00:00
abstract::The mammalian innate immune system uses several sensors of double-stranded RNA (dsRNA) to develop the interferon response. Among these sensors are dsRNA-activated oligoadenylate synthetases (OAS), which produce signaling 2',5'-linked RNA molecules (2-5A) that activate regulated RNA decay in mammalian tissues. Differen...
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.1419409112
更新日期:2015-03-31 00:00:00
abstract::A comparison of the monoclinic and orthorhombic crystal structures of the uncomplexed double-stranded, antiparallel, left-handed beta-helix (5.6 amino acid residues per turn) (increases decreases beta 5.6) conformers of gramicidin A reveals marked differences in the tryptophan side-chain orientations and the degree of...
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.88.12.5345
更新日期:1991-06-15 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.1605886113
更新日期:2016-05-24 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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journal_title:Proceedings of the National Academy of Sciences of the United States of America
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更新日期:1988-01-01 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.0800466105
更新日期:2008-12-02 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:2010-04-06 00:00:00
abstract::Kruppel-like factor 4 (KLF4) is involved in self-renewal of embryonic stem cells and reprogramming of somatic cells to pluripotency. However, its role in lineage-committed stem cells remains largely unknown. Here, we show that KLF4 is expressed in neural stem cells (NSCs) and is down-regulated during neuronal differen...
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:2011-12-27 00:00:00
abstract::The activity of Drosophila melanogaster DNA polymerase alpha on DNA-primed single-stranded DNA templates has been examined. The DNA templates contain a 1471-nucleotide sequence from the heavy-strand origin region of mouse mtDNA inserted into the single-stranded bacteriophage vector M13Gori1. Preferred sites for pausin...
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:1982-02-01 00:00:00
abstract::We describe the preparation and structural analysis of ordered tubular arrays of the actin-DNase I complex. These structures consist of helically stacked rings; each ring is 73 A thick, has a 240 A outer and a 120 A inner diameter, and has 7-fold rotational symmetry. The actin-DNase I complex forms tubes under conditi...
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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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:1993-03-01 00:00:00
abstract::We carried out a large-scale screen to identify interactions between integral membrane proteins of Saccharomyces cerevisiae by using a modified split-ubiquitin technique. Among 705 proteins annotated as integral membrane, we identified 1,985 putative interactions involving 536 proteins. To ascribe confidence levels to...
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.0505482102
更新日期:2005-08-23 00:00:00
abstract::Plants can defend themselves from herbivorous insects by emitting volatile chemical signals that attract natural enemies of the herbivore. For example, maize seedlings attacked by beet armyworm larvae (Spodoptera exigua) produce a mixture of terpenoid and indole volatiles that serve to attract parasitic wasps. A key s...
journal_title:Proceedings of the National Academy of Sciences of the United States of America
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journal_title:Proceedings of the National Academy of Sciences of the United States of America
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journal_title:Proceedings of the National Academy of Sciences of the United States of America
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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:2010-03-23 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:1994-10-25 00:00:00
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journal_title:Proceedings of the National Academy of Sciences of the United States of America
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更新日期:1980-07-01 00:00:00
abstract::We have evaluated two synthetic epothilone analogues lacking the 12,13-epoxide functionality, 12,13-desoxyepothilone B (dEpoB), and 12,13-desoxyepothilone F (dEpoF). The concentrations required for 50% growth inhibition (IC(50)) for a variety of anticancer agents were measured in CCRF-CEM/VBL1000 cells (2,048-fold res...
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:2001-07-03 00:00:00
abstract::Astrogenesis is repressed in the early embryonic period and occurs in the late embryonic period. A variety of external and internal signals contribute to the sequential differentiation of neural stem cells. Here, we discovered that immune-related CD93 plays a critical negative role in the regulation of astrogenesis in...
journal_title:Proceedings of the National Academy of Sciences of the United States of America
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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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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:1999-03-30 00:00:00
abstract::The O(2)-reaction chemistry of 1:1 mixtures of (F(8))Fe(II) (1; F(8) = tetrakis(2,6-diflurorophenyl)porphyrinate) and [(L(Me(2))N)Cu(I)](+) (2; L(Me(2))N = N,N-bis(2-[2-(N',N'-4-dimethylamino)pyridyl]ethyl)methylamine) is described, to model aspects of the chemistry occurring in cytochrome c oxidase. Spectroscopic inv...
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.0737180100
更新日期:2003-04-01 00:00:00
abstract::Chemical cross-linking mass spectrometry (CXMS) is being increasingly used to study protein assemblies and complex protein interaction networks. Existing CXMS chemical cross-linkers target only Lys, Cys, Glu, and Asp residues, limiting the information measurable. Here we report a "plant-and-cast" cross-linking strateg...
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:2018-10-30 00:00:00
abstract::The assembly and composition of human excision nuclease were investigated by electrophoretic mobility shift assay and DNase I footprinting. Individual repair factors or any combination of up to four repair factors failed to form DNA-protein complexes of high specificity and stability. A stable complex of high specific...
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.95.12.6669
更新日期:1998-06-09 00:00:00