NDLI: Structure-based design of mutant Methanococcus jannaschii tyrosyl-tRNA synthetase for incorporation of O-methyl-L-tyrosine.

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

Year: 2017 Volume: 114

Year: 2016 Volume: 113

Year: 2015 Volume: 112

Year: 2014 Volume: 111

Year: 2013 Volume: 110

Year: 2012 Volume: 109

Year: 2011 Volume: 108

Year: 2010 Volume: 107

Year: 2009 Volume: 106

Year: 2008 Volume: 105

Year: 2007 Volume: 104

Year: 2006 Volume: 103

Year: 2005 Volume: 102

Year: 2004 Volume: 101

Year: 2003 Volume: 100

Year: 2002 Volume: 99

Year: 2002 Volume: 99 Issue: 26

Year: 2002 Volume: 99 Issue: 25

Year: 2002 Volume: 99 Issue: 24

Year: 2002 Volume: 99 Issue: 23

Year: 2002 Volume: 99 Issue: 22

Year: 2002 Volume: 99 Issue: 21

Year: 2002 Volume: 99 Issue: 20

Year: 2002 Volume: 99 Issue: 19

Year: 2002 Volume: 99 Issue: 18

Year: 2002 Volume: 99 Issue: 17

Year: 2002 Volume: 99 Issue: 16

Year: 2002 Volume: 99 Issue: 15

Year: 2002 Volume: 99 Issue: 14

Year: 2002 Volume: 99 Issue: 13

Year: 2002 Volume: 99 Issue: 12

Year: 2002 Volume: 99 Issue: 11

Year: 2002 Volume: 99 Issue: 10

Drying-induced hydrophobic polymer collapse.

Complete pathway for protein disulfide bond formation encoded by poxviruses.

Abnormal development of the hippocampal dentate gyrus in mice lacking the CXCR4 chemokine receptor.

Collaborative signaling by mixed chemoreceptor teams in Escherichia coli.

Epidermolysis bullosa and embryonic lethality in mice lacking the multi-PDZ domain protein GRIP1.

Aldosterone signaling pathway across the nuclear envelope.

Global changes in gene expression by human polymorphonuclear leukocytes during receptor-mediated phagocytosis: cell fate is regulated at the level of gene expression.

Key role of proline L209 in connecting the distant quinone pockets in the reaction center of Rhodobacter sphaeroides.

Mutations associated with base excision repair deficiency and methylation-induced genotoxic stress.

The genetics of maternal care: direct and indirect genetic effects on phenotype in the dung beetle Onthophagus taurus.

Molecular dynamics simulations of protein folding from the transition state

Repression of photosynthesis gene expression by formation of a disulfide bond in CrtJ.

ATP6S1 elicits potent humoral responses associated with immune-mediated tumor destruction.

Dynamic assembly of MinD on phospholipid vesicles regulated by ATP and MinE.

Selection bias in gene extraction on the basis of microarray gene-expression data.

Base-specific fragmentation of amplified 16S rRNA genes analyzed by mass spectrometry: a tool for rapid bacterial identification.

Laurasian migration explains Gondwanan disjunctions: evidence from Malpighiaceae.

The OhrR repressor senses organic hydroperoxides by reversible formation of a cysteine-sulfenic acid derivative.

beta-Catenin stabilization dysregulates mesenchymal cell proliferation, motility, and invasiveness and causes aggressive fibromatosis and hyperplastic cutaneous wounds.

Iris hypoplasia in mice that lack the alternatively spliced Pax6(5a) isoform.

FRS2 alpha attenuates FGF receptor signaling by Grb2-mediated recruitment of the ubiquitin ligase Cbl.

The lethal and edema factors of anthrax toxin bind only to oligomeric forms of the protective antigen

Microrheometry of semiflexible actin networks through enforced single-filament reptation: frictional coupling and heterogeneities in entangled networks.

Mapping the lethal factor and edema factor binding sites on oligomeric anthrax protective antigen.

A peptide-based fluorescence resonance energy transfer assay for Bacillus anthracis lethal factor protease.

Single-molecule height measurements on microsomal cytochrome P450 in nanometer-scale phospholipid bilayer disks.

Siderophore-mediated signaling regulates virulence factor production in Pseudomonasaeruginosa.

Noninvasive imaging of protein-protein interactions in living animals.

Diketo acid inhibitor mechanism and HIV-1 integrase: implications for metal binding in the active site of phosphotransferase enzymes.

Refined molecular hinge between allosteric and catalytic domain determines allosteric regulation and stability of fungal chorismate mutase.

Endosomal localization and function of sorting nexin 1

The delta subunit of AP-3 is required for efficient transport of VSV-G from the trans-Golgi network to the cell surface.

Rescue of a pathogenic Marek's disease virus with overlapping cosmid DNAs: use of a pp38 mutant to validate the technology for the study of gene function.

Carbocyclic fatty acids in plants: biochemical and molecular genetic characterization of cyclopropane fatty acid synthesis of Sterculiafoetida.

The intranuclear prolactin/cyclophilin B complex as a transcriptional inducer.

CFTR is a pattern recognition molecule that extracts Pseudomonas aeruginosa LPS from the outer membrane into epithelial cells and activates NF-kappa B translocation.

Antitumor activity of cytotoxic T lymphocytes engineered to target vascular endothelial growth factor receptors.

Identification of in vivo expressed vaccine candidate antigens from Staphylococcus aureus.

Sex-ratio conflicts, kin selection, and the evolution of altruism.

Neonatal hepatic steatosis by disruption of the adenosine kinase gene.

Elevated mutation rates in the germ line of first- and second-generation offspring of irradiated male mice.

Telomerase recognizes its template by using an adjacent RNA motif.

Genome-wide screening for trait conferring genes using DNA microarrays.

Segregation distortion induced by wild-type RanGAP in Drosophila.

Centripetal and centrifugal reorganizations of frequency map of auditory cortex in gerbils.

Mayolenes: labile defensive lipids from the glandular hairs of a caterpillar (Pieris rapae).

Toward development of a screen to identify randomly encoded, foldable sequences.

The iscS gene is essential for the biosynthesis of 2-selenouridine in tRNA and the selenocysteine-containing formate dehydrogenase H.

Broadly cross-reactive HIV-1-neutralizing human monoclonal Fab selected for binding to gp120-CD4-CCR5 complexes.

Reproductive skew in the polygynandrous acorn woodpecker.

Dynamin-dependent and dynamin-independent processes contribute to the regulation of single vesicle release kinetics and quantal size

Energetics of glycerol conduction through aquaglyceroporin GlpF.

Smooth muscle-selective deletion of guanylyl cyclase-A prevents the acute but not chronic effects of ANP on blood pressure.

Reversible cardiac fibrosis and heart failure induced by conditional expression of an antisense mRNA of the mineralocorticoid receptor in cardiomyocytes.

Structure of 2C-methyl-d-erythritol 2,4- cyclodiphosphate synthase: An essential enzyme for isoprenoid biosynthesis and target for antimicrobial drug development

The TOR-controlled transcription activators GLN3, RTG1, and RTG3 are regulated in response to intracellular levels of glutamine.

Specific aneusomies in Chinese hamster cells at different stages of neoplastic transformation, initiated by nitrosomethylurea.

Systemic wound signaling in plants: a new perception.

Push or pull? Teams of motor proteins have it both ways.

Sea level is rising: do we know why?

Progress in rapid screening of Bacillus anthracis lethal factor activity.

Cooperativity between bacterial chemotaxis receptors.

Gaussian fluctuations and linear response in an electron transfer protein.

Twentieth century sea level: an enigma.

Origin of supposedly biogenic magnetite in the Martian meteorite Allan Hills 84001

Diagnosis of multiple cancer types by shrunken centroids of gene expression.

Structure-based design of mutant Methanococcus jannaschii tyrosyl-tRNA synthetase for incorporation of O-methyl-L-tyrosine.

Directed evolution of novel polymerase activities: mutation of a DNA polymerase into an efficient RNA polymerase.

The 1.9-Å crystal structure of the noncollagenous (NC1) domain of human placenta collagen IV shows stabilization via a novel type of covalent Met-Lys cross-link

Changing the lactose permease of Escherichia coli into a galactose-specific symporter.

Looped out and perpendicular: deformation of Watson-Crick base pair associated with actinomycin D binding.

Headpiece domain of dematin is required for the stability of the erythrocyte membrane.

Inhibition of mitochondrial protein synthesis results in increased endothelial cell susceptibility to nitric oxide-induced apoptosis.

The c-Myc target gene PRDX3 is required for mitochondrial homeostasis and neoplastic transformation.

The aflatoxin $B_{1}$ formamidopyrimidine adduct plays a major role in causing the types of mutations observed in human hepatocellular carcinoma

Preferential binding of ATR protein to UV-damaged DNA.

Bidirectional cooperative motion of molecular motors.

CLOUDS, a protocol for deriving a molecular proton density via NMR.

Protein structure elucidation from NMR proton densities.

Identification of beta-cell-specific insulin gene transcription factor RIPE3b1 as mammalian MafA.

A flagellar $K^{+}-dependent$ $Na^{+}/Ca^{2+}$ exchanger keeps $Ca^{2+}$ low in sea urchin spermatozoa

Identification of four candidate cGMP targets in Dictyostelium.

Inositol hexakisphosphate promotes dynamin I- mediated endocytosis.

Clara cell impact in air-side activation of CFTR in small pulmonary airways.

Genome-wide identification of tissue-specific enhancers in the Ciona tadpole.

BORIS, a novel male germ-line-specific protein associated with epigenetic reprogramming events, shares the same 11-zinc-finger domain with CTCF, the insulator protein involved in reading imprinting marks in the soma.

The development of immunity in a social insect: evidence for the group facilitation of disease resistance.

The root of the angiosperms revisited.

Anatomical and ecological constraints on Phanerozoic animal diversity in the marine realm.

Cyclin D3 activates Caspase 2, connecting cell proliferation with cell death.

Position-effect protection and enhancer blocking by the chicken beta-globin insulator are separable activities.

ARGONAUTE1 is required for efficient RNA interference in Drosophila embryos.

Mnd1p: an evolutionarily conserved protein required for meiotic recombination.

Siva-1 binds to and inhibits BCL-X(L)-mediated protection against UV radiation-induced apoptosis.

Negative selection of thymocytes expressing the D10 TCR.

Positive selection of self-MHC-reactive T cells by individual peptide-MHC class II complexes.

The cholesterol-regulated StarD4 gene encodes a StAR-related lipid transfer protein with two closely related homologues, StarD5 and StarD6.

Crystal structure of the Mus musculus cholesterol-regulated START protein 4 (StarD4) containing a StAR-related lipid transfer domain.

Human chronic lymphocytic leukemia modeled in mouse by targeted TCL1 expression.

Initiating oncogenic event determines gene-expression patterns of human breast cancer models.

Transmissibility of systemic amyloidosis by a prion-like mechanism.

Paracrine in vivo inhibitory effects of hepatitis B virus X protein (HBx) on liver cell proliferation: an alternative mechanism of HBx-related pathogenesis.

MRP9, an unusual truncated member of the ABC transporter superfamily, is highly expressed in breast cancer.

AID-GFP chimeric protein increases hypermutation of Ig genes with no evidence of nuclear localization.

Persistent HIV-1 infection of natural killer cells in patients receiving highly active antiretroviral therapy.

Hypoxia alters gene expression in human neuroblastoma cells toward an immature and neural crest-like phenotype.

Mailborne transmission of anthrax: Modeling and implications.

Identification of a protein secretory pathway for the secretion of heat-labile enterotoxin by an enterotoxigenic strain of Escherichia coli.

mu-Opioid receptors and limbic responses to aversive emotional stimuli.

Differential roles for NSF and GRIP/ABP in AMPA receptor cycling.

The gamma-secretase-generated intracellular domain of beta-amyloid precursor protein binds Numb and inhibits Notch signaling.

Coupling asymmetry of heterotypic connexin 45/ connexin 43-EGFP gap junctions: properties of fast and slow gating mechanisms.

Growth hormone induces age-dependent alteration in the expression of hippocampal growth hormone receptor and N-methyl-D-aspartate receptor subunits gene transcripts in male rats.

Determinants of the cellular specificity of acetaminophen as an inhibitor of prostaglandin $H_{2}$ synthases

Anticonvulsant activity of a nonpeptide galanin receptor agonist.

Corticotropin-releasing hormone: an autocrine hormone that promotes lipogenesis in human sebocytes.

The starch-related R1 protein is an α-glucan, water dikinase

Year: 2002 Volume: 99 Issue: 9

Year: 2002 Volume: 99 Issue: 8

Year: 2002 Volume: 99 Issue: 7

Year: 2002 Volume: 99 Issue: 6

Year: 2002 Volume: 99 Issue: 5

Year: 2002 Volume: 99 Issue: 4

Year: 2002 Volume: 99 Issue: Suppl 4

Year: 2002 Volume: 99 Issue: 3

Year: 2002 Volume: 99 Issue: Suppl 3

Year: 2002 Volume: 99 Issue: 2

Year: 2002 Volume: 99 Issue: Suppl 2

Year: 2002 Volume: 99 Issue: 1

Year: 2002 Volume: 99 Issue: Suppl 1

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: 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

Structure-based design of mutant Methanococcus jannaschii tyrosyl-tRNA synthetase for incorporation of O-methyl-L-tyrosine.

Content Provider	World Health Organization (WHO)-Global Index Medicus
Author	Goddard, William A. Vaidehi, Nagarajan Debe, Derek Danzer, Joseph F. Zhang, Deqiang
Description	Author Affiliation: Zhang D ( Materials and Process Simulation Center, Beckman Institute, California Institute of Technology, Pasadena, CA 91125);
Abstract	Although incorporation of amino acid analogs provides a powerful means of producing new protein structures with interesting functions, many amino acid analogs cannot be incorporated easily by using the wild-type aminoacyl-tRNA synthetase (aaRS). To be able to incorporate specific amino acid analogs site-specifically, it is useful to build a mutant aaRS that preferentially activates the analog compared with the natural amino acids. Experimental combinatorial studies to find such mutant aaRSs have been successful but can easily become costly and time-consuming. In this article, we describe the clash opportunity progressive (COP) computational method for designing a mutant aaRS to preferentially take up the analog compared with the natural amino acids. To illustrate this COP procedure, we apply it to the design of mutant Methanococcus jannaschii tyrosyl-tRNA synthetase (M.jann-TyrRS). Because the three-dimensional structure for M.jann-TyrRS was not available, we used the STRUCTFAST homology modeling procedure plus molecular dynamics with continuum solvent forces to predict the structure of wild-type M.jann-TyrRS. We validate this structure by predicting the binding site for tyrosine and calculating the binding energies of the 20 natural amino acids, which shows that tyrosine binds the strongest. With the COP design algorithm we then designed a mutant tyrosyl tRNA synthetase to activate O-methyl-l-tyrosine preferentially compared with l-tyrosine. This mutant [Y32Q, D158A] is similar to the mutant designed with combinatorial experiments, [Y32Q, D158A, E107T, L162P], by Wang et al. [Wang, L., Brock, A., Herberich, B. & Schultz, P. G. (2001) Science 292, 498-500]. We predict that the new one will have much greater activity while retaining significant discrimination between O-methyl-l-tyrosine and tyrosine.
ISSN	00278424
e-ISSN	10916490
Journal	Proceedings of the National Academy of Sciences of the United States of America
Issue Number	10
Volume Number	99
Language	English
Publisher	National Academy of Sciences
Publisher Date	2002-05-01
Publisher Place	United States
Access Restriction	Open
Subject Keyword	Methanococcus Enzymology Methyltyrosines Chemistry Tyrosine-tRNA Ligase Amino Acids Crystallography, X-Ray Models, Molecular Mutagenesis Protein Structure, Tertiary Genetics Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. Research Support, U.S. Gov't, P.H.S. Multidisciplinary
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