NDLI: Protein solution structure determination using distances from two-dimensional nuclear Overhauser effect experiments: effect of approximations on the accuracy of derived structures.

Please wait, while we are loading the content...

Year: 2016, Volume: 113

Year: 2015, Volume: 112

Year: 2014, Volume: 111

Year: 2013, Volume: 110

Year: 2012, Volume: 109

Year: 2011, Volume: 109

Year: 2011, Volume: 108

Year: 2010, Volume: 107

Year: 2009, Volume: 106

Year: 2009, Volume: 94

Year: 2008, Volume: 105

Year: 2007, Volume: 104

Year: 2006, Volume: 103

Year: 2005, Volume: 103

Year: 2005, Volume: 102

Year: 2004, Volume: 101

Year: 2003, Volume: 100

Year: 2002, Volume: 99

Year: 2001, Volume: 98

Year: 2000, Volume: 97

Year: 1999, Volume: 96

Year: 1998, Volume: 95

Year: 1997, Volume: 94

Year: 1996, Volume: 93

Year: 1995, Volume: 92

Year: 1994, Volume: 91

Year: 1993, Volume: 90

Year: 1992, Volume: 89

Year: 1991, Volume: 88

Year: 1991, Volume: 88, Issue: 24

Year: 1991, Volume: 88, Issue: 23

Year: 1991, Volume: 88, Issue: 22

Year: 1991, Volume: 88, Issue: 21

Year: 1991, Volume: 88, Issue: 20

Year: 1991, Volume: 88, Issue: 19

Year: 1991, Volume: 88, Issue: 18

Year: 1991, Volume: 88, Issue: 17

Year: 1991, Volume: 88, Issue: 16

Year: 1991, Volume: 88, Issue: 15

Year: 1991, Volume: 88, Issue: 14

Year: 1991, Volume: 88, Issue: 13

Year: 1991, Volume: 88, Issue: 12

Year: 1991, Volume: 88, Issue: 11

Year: 1991, Volume: 88, Issue: 10

Year: 1991, Volume: 88, Issue: 9

Year: 1991, Volume: 88, Issue: 8

Year: 1991, Volume: 88, Issue: 7

Year: 1991, Volume: 88, Issue: 6

Year: 1991, Volume: 88, Issue: 5

Year: 1991, Volume: 88, Issue: 4

Activated protooncogenes in human lung tumors from smokers.

Inhibition of the N-end rule pathway in living cells.

Isolation of an additional member of the fibroblast growth factor receptor family, FGFR-3.

Borrowed proteins in bacterial bioluminescence.

Association of DNA helicase and primase activities with a subassembly of the herpes simplex virus 1 helicase-primase composed of the UL5 and UL52 gene products.

Identification of the intermediate allosteric species in human hemoglobin reveals a molecular code for cooperative switching.

Identification of a protein kinase multigene family of Dictyostelium discoideum: molecular cloning and expression of a cDNA encoding a developmentally regulated protein kinase.

The frequency of meiotic recombination in yeast is independent of the number and position of homologous donor sequences: implications for chromosome pairing.

Positive transcriptional regulation of an iron-regulated virulence gene in Vibrio cholerae.

Evolution of life history variation among female mammals.

Carbohydrate ligands for endothelial-leukocyte adhesion molecule 1.

Single nucleotide primer extension to detect genetic diseases: experimental application to hemophilia B (factor IX) and cystic fibrosis genes.

Reconstitution in vitro of RNase H activity by using purified N-terminal and C-terminal domains of human immunodeficiency virus type 1 reverse transcriptase.

An Escherichia coli tyrosine transfer RNA is a leucine-specific transfer RNA in the yeast Saccharomyces cerevisiae.

Inducible proteins binding to the murine thymidine kinase promoter in late G1/S phase.

The v-src inducible gene 9E3/pCEF4 is regulated by both its promoter upstream sequence and its 3' untranslated region.

Cotranslational autoproteolysis involved in gene expression from a double-stranded RNA genetic element associated with hypovirulence of the chestnut blight fungus.

Isolation and expression of human cytokine synthesis inhibitory factor cDNA clones: homology to Epstein-Barr virus open reading frame BCRFI.

Selective inhibition by a synthetic hirudin peptide of fibrin-dependent thrombosis in baboons.

Sexual transmission of human T-cell leukemia virus type I associated with the presence of anti-Tax antibody.

Tyrosine phosphate hydrolysis of host proteins by an essential Yersinia virulence determinant.

The use of sarkosyl in generating soluble protein after bacterial expression.

Ca2+ current is regulated by cyclic GMP-dependent protein kinase in mammalian cardiac myocytes.

Multilocus genetic structure of ancestral Spanish and colonial Californian populations of Avena barbata.

Genetic diversity and adaptedness in tetraploid Avena barbata and its diploid ancestors Avena hirtula and Avena wiestii.

ATP-dependent partitioning of the DNA template into supercoiled domains by Escherichia coli UvrAB.

Mouse hepatocytes migrate to liver parenchyma and function indefinitely after intrasplenic transplantation.

Sexually dimorphic distribution of substance P in specific anterior pituitary cell populations.

Interleukin 2 induces tyrosine phosphorylation and activation of p72-74 Raf-1 kinase in a T-cell line.

Interleukin 1 beta induces rapid phosphorylation and redistribution of talin: a possible mechanism for modulation of fibroblast focal adhesion.

Protein solution structure determination using distances from two-dimensional nuclear Overhauser effect experiments: effect of approximations on the accuracy of derived structures.

Paired MyoD-binding sites regulate myosin light chain gene expression.

Transposon-facilitated DNA sequencing.

Requirements for bypass of UV-induced lesions in single-stranded DNA of bacteriophage phi X174 in Salmonella typhimurium.

Seismic communication in a blind subterranean mammal: a major somatosensory mechanism in adaptive evolution underground.

Multiple actions of extracellular ATP on calcium currents in cultured bovine chromaffin cells.

Anti-reovirus receptor antibody accelerates expression of the optic nerve oligodendrocyte developmental program.

In vivo mapping of a sequence required for interference with the yeast killer virus.

Dystrophin is transcribed in brain from a distant upstream promoter.

Retrovirus-induced spongiform myeloencephalopathy in mice: regional distribution of infected target cells and neuronal loss occurring in the absence of viral expression in neurons.

Cocaine induces striatal c-fos-immunoreactive proteins via dopaminergic D1 receptors.

Mechanism of glucoregulatory responses to stress and their deficiency in diabetes.

Phased cis-acting promoter elements interact at short distances to direct avian skeletal alpha-actin gene transcription.

Clustered tRNA genes in Schizosaccharomyces pombe centromeric DNA sequence repeats.

Surface immunoglobulin crosslinking activates a tyrosine kinase pathway in B cells that is independent of protein kinase C.

Evidence for separate pathways within the tecto-geniculate projection in the tree shrew.

Atypical prodynorphin gene expression in corticosteroid-producing cells of the rat adrenal gland.

Gene synthesis, expression, and mutagenesis of the blue copper proteins azurin and plastocyanin.

Genetically modified skin fibroblasts persist long after transplantation but gradually inactivate introduced genes.

In vitro peptide binding to the heavy chain of the class I molecule of the major histocompatibility complex molecule HLA-A2.

Activities of human immunodeficiency virus (HIV) integration protein in vitro: specific cleavage and integration of HIV DNA.

Nucleosomes on linear duplex DNA allow homologous pairing but prevent strand exchange promoted by RecA protein.

Myogenin and MyoD join a family of skeletal muscle genes regulated by electrical activity.

Early phenotype expression of cortical neurons: evidence that a subclass of migrating neurons have callosal axons.

Chicken major histocompatibility complex-encoded B-G antigens are found on many cell types that are important for the immune system.

Characterization of lipid domains in erythrocyte membranes.

Multimerization of AAGTGA and GAAAGT generates sequences that mediate virus inducibility by mimicking an interferon promoter element.

In vivo mapping of a DNA adduct at nucleotide resolution: detection of pyrimidine (6-4) pyrimidone photoproducts by ligation-mediated polymerase chain reaction.

Cells that express all five proteins of vesicular stomatitis virus from cloned cDNAs support replication, assembly, and budding of defective interfering particles.

Isolation of cDNA encoding a newly identified major allergenic protein of rye-grass pollen: intracellular targeting to the amyloplast.

Iteron inhibition of plasmid RK2 replication in vitro: evidence for intermolecular coupling of replication origins as a mechanism for RK2 replication control.

scid mutation in mice confers hypersensitivity to ionizing radiation and a deficiency in DNA double-strand break repair.

Pollen-mediated introgression and hybrid speciation in Louisiana irises.

Identification of the ancestral haplotype for apolipoprotein B suggests an African origin of Homo sapiens sapiens and traces their subsequent migration to Europe and the Pacific.

Tissue acylation by the chlorofluorocarbon substitute 2,2-dichloro-1,1,1-trifluoroethane.

Influence of chromosomal integration on glucocorticoid-regulated transcription of growth-stimulating papillomavirus genes E6 and E7 in cervical carcinoma cells.

Human catechol-O-methyltransferase: cloning and expression of the membrane-associated form.

gamma-Aminobutyric acid type A receptor point mutation increases the affinity of compounds for the benzodiazepine site.

Chromostatin, a 20-amino acid peptide derived from chromogranin A, inhibits chromaffin cell secretion.

Demonstration of a pronounced effect of noncovalent binding selectivity on the (+)-CC-1065 DNA alkylation and identification of the pharmacophore of the alkylation subunit.

Rapid accumulation of cyclic GMP near activated vitamin D receptors.

Characterization of anti-peptide antibodies for the localization of D2 dopamine receptors in rat striatum.

Characterization of a variant of human T-lymphotropic virus type I isolated from a healthy member of a remote, recently contacted group in Papua New Guinea.

An antiviral target on reverse transcriptase of human immunodeficiency virus type 1 revealed by tetrahydroimidazo-[4,5,1-jk] [1,4]benzodiazepin-2 (1H)-one and -thione derivatives.

Sequence identity in the nick regions of IncP plasmid transfer origins and T-DNA borders of Agrobacterium Ti plasmids.

Amyloid precursor protein in aged nonhuman primates.

Localization and quantitation of tritiated compounds in tissue sections with a gaseous detector of beta particles: comparison with film autoradiography.

The conserved GTPase center and variable region V9 from Saccharomyces cerevisiae 26S rRNA can be replaced by their equivalents from other prokaryotes or eukaryotes without detectable loss of ribosomal function.

Independently arising macrophage mutants dissociate growth factor-regulated survival and proliferation.

Transcribed sequences of the Escherichia coli btuB gene control its expression and regulation by vitamin B12.

Gene for non-insulin-dependent diabetes mellitus (maturity-onset diabetes of the young subtype) is linked to DNA polymorphism on human chromosome 20q.

In vitro apolipoprotein B mRNA editing: identification of a 27S editing complex.

Interactive effects of neurohypophyseal neuropeptides with receptor antagonists on passive avoidance behavior: mediation by a cerebral neurohypophyseal hormone receptor?

Intracellular metabolism and mechanism of anti-retrovirus action of 9-(2-phosphonylmethoxyethyl)adenine, a potent anti-human immunodeficiency virus compound.

Search for cellular phosphorylation products of D-allose.

Stimulation of cAMP and phosphomonoester production by melanotropin in melanoma cells: 31P NMR studies.

Inducer-dependent conditional-lethal mutant animal viruses.

Epithelial-mesenchymal transformation of embryonic cardiac endothelial cells is inhibited by a modified antisense oligodeoxynucleotide to transforming growth factor beta 3.

Selective targeting of gene products with the megakaryocyte platelet factor 4 promoter.

Mononuclear phagocytes: a major population of effector cells responsible for rejection of allografted tumor cells in mice.

Cloning and expression of human deoxycytidine kinase cDNA.

Very long charge runs in systemic lupus erythematosus-associated autoantigens.

Microglial progenitors with a high proliferative potential in the embryonic and adult mouse brain.

Recombinant Epstein-Barr virus with small RNA (EBER) genes deleted transforms lymphocytes and replicates in vitro.

A spectroscopic and calorimetric study of the melting behaviors of a "bent" and a "normal" DNA duplex: [d(GA4T4C)]2 versus [d(GT4A4C)]2.

Inhibition of dipeptidyl aminopeptidase IV (DP-IV) by Xaa-boroPro dipeptides and use of these inhibitors to examine the role of DP-IV in T-cell function.

cDNA analysis predicts a cornea-specific collagen.

Binding protein BiP is required for translocation of secretory proteins into the endoplasmic reticulum in Saccharomyces cerevisiae.

Resolution of the African hominoid trichotomy by use of a mitochondrial gene sequence.

AIDS epidemiology: inconsistencies with human immunodeficiency virus and with infectious disease.

Photosensitized destruction of human bladder carcinoma cells treated with chlorin e6-conjugated microspheres.

Leukemia initiated by hemopoietic stem cells expressing the v-abl oncogene.

Triton,... electron,... cosmon,...: An infinite regression?

Genomic subtraction for cloning DNA corresponding to deletion mutations

Dynamics of the distribution of cyclic AMP-dependent protein kinase in living cells

Influenza virus hemagglutinin-specific antibodies isolated from a combinatorial expression library are closely related to the immune response of the donor

Cation-dependent mannose 6-phosphate receptor contains two internalization signals in its cytoplasmic domain

Year: 1991, Volume: 88, Issue: 3

Year: 1991, Volume: 88, Issue: 2

Year: 1991, Volume: 88, Issue: 1

Year: 1990, Volume: 87

Year: 1989, Volume: 86

Year: 1988, Volume: 85

Year: 1987, Volume: 84

Year: 1986, Volume: 83

Year: 1985, Volume: 82

Year: 1984, Volume: 81

Year: 1983, Volume: 80

Year: 1982, Volume: 79

Year: 1981, Volume: 78

Year: 1980, Volume: 77

Year: 1979, Volume: 76

Year: 1978, Volume: 75

Year: 1977, Volume: 74

Year: 1976, Volume: 73

Year: 1975, Volume: 72

Year: 1974, Volume: 71

Year: 1973, Volume: 70

Year: 1972, Volume: 69

Year: 1971, Volume: 68

Year: 1970, Volume: 67

Year: 1970, Volume: 66

Year: 1970, Volume: 65

Year: 1969, Volume: 64

Year: 1969, Volume: 63

Year: 1969, Volume: 62

Year: 1968, Volume: 61

Year: 1968, Volume: 60

Year: 1968, Volume: 59

Year: 1967, Volume: 58

Year: 1967, Volume: 57

Year: 1966, Volume: 56

Year: 1966, Volume: 55

Year: 1965, Volume: 54

Year: 1965, Volume: 53

Year: 1964, Volume: 52

Year: 1964, Volume: 51

Year: 1963, Volume: 50

Year: 1963, Volume: 49

Year: 1962, Volume: 48

Year: 1961, Volume: 47

Year: 1960, Volume: 46

Year: 1959, Volume: 45

Year: 1958, Volume: 44

Year: 1957, Volume: 43

Year: 1956, Volume: 42

Year: 1955, Volume: 41

Year: 1954, Volume: 40

Year: 1953, Volume: 39

Year: 1952, Volume: 38

Year: 1951, Volume: 37

Year: 1950, Volume: 36

Year: 1949, Volume: 35

Year: 1948, Volume: 34

Year: 1947, Volume: 33

Year: 1946, Volume: 32

Year: 1945, Volume: 31

Year: 1944, Volume: 30

Year: 1943, Volume: 29

Year: 1942, Volume: 28

Year: 1941, Volume: 27

Year: 1940, Volume: 26

Year: 1939, Volume: 25

Year: 1938, Volume: 24

Year: 1937, Volume: 23

Year: 1936, Volume: 22

Year: 1935, Volume: 21

Year: 1934, Volume: 20

Year: 1933, Volume: 19

Year: 1932, Volume: 18

Year: 1931, Volume: 17

Year: 1930, Volume: 16

Year: 1929, Volume: 15

Year: 1928, Volume: 14

Year: 1927, Volume: 13

Year: 1926, Volume: 12

Year: 1925, Volume: 11

Year: 1924, Volume: 10

Year: 1923, Volume: 9

Year: 1922, Volume: 8

Year: 1921, Volume: 7

Year: 1920, Volume: 6

Year: 1919, Volume: 5

Year: 1918, Volume: 4

Year: 1917, Volume: 3

Year: 1916, Volume: 2

Year: 1915, Volume: 1

Protein solution structure determination using distances from two-dimensional nuclear Overhauser effect experiments: effect of approximations on the accuracy of derived structures.

Content Provider	PubMed Central
Author	Thomas, P. D. James, T. L. Basus, V. J.
Abstract	Solution structures for many proteins have been determined to date utilizing interproton distance constraints estimated from two-dimensional nuclear Overhauser effect (2D NOE) spectra. Although the simple isolated spin pair approximation (ISPA) generally used can result in systematic errors in distances, the large number of constraints enables protein structure to be defined with reasonably high resolution. Effects of these systematic errors on the resulting protein structure are examined. Iterative relaxation matrix calculations, which account for dipolar interactions between all protons in a molecule, can accurately determine internuclear distances with little or no a priori knowledge of the molecular structure. The value of this additional complexity is also addressed. To assess these distance determination methods, hypothetical "experimental" data, including random noise and peak overlap, are calculated for an arbitrary "true" protein structure. Three methods of obtaining distance constraints from 2D NOE peak intensities are examined: one entails a conservative use of ISPA, one assumes the ISPA to be fairly accurate, and one utilizes an iterative relaxation matrix method called MARDIGRAS (matrix analysis of relaxation for discerning the geometry of an aqueous structure), developed in this laboratory. A distance geometry algorithm was used to generate a family of structures for each distance set. The quality of the average structure from each family was good. The root-mean-square deviation of that average structure from the true structure was improved about 2-5% using the more restrictive rather than the more conservative ISPA approach. Use of MARDIGRAS in a conservative fashion--i.e., with a poor initial model--resulted in improvement in the root-mean-square deviation by 8-15%. With a better initial model, MARDIGRAS obtained even more accurate distances. MARDIGRAS also permits analysis of 2D NOE data at longer mixing times, yielding additional distances. Use of more restrictive ISPA distances did, however, result in a few systematically incorrect structural features in local regions of the protein, producing distortions of 2-3 A. Comparison between experimental data and spectra calculated for the structures correlates with root-mean-square deviation, offering a method of structure evaluation. An R factor for evaluating fit between experimental and calculated 2D NOE intensities is proposed.
Starting Page	1237
File Format	PDF
ISSN	10916490
e-ISSN	10916490
Journal	Proceedings of the National Academy of Sciences of the United States of America
Issue Number	4
Volume Number	88
Language	English
Publisher Date	1991-02-15
Access Restriction	Open
Subject Keyword	Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Multidisciplinary

Central Library (ISO-9001:2015 Certified)
Indian Institute of Technology Kharagpur
Kharagpur, West Bengal, India | PIN - 721302

See location in the Map
03222 282435
Mail: support@ndl.gov.in

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in