Energetics-based discovery of protein-ligand interactions on a proteomic scale.

Abstract:

:Biochemical functions of proteins in cells frequently involve interactions with various ligands. Proteomic methods for the identification of proteins that interact with specific ligands such as metabolites, signaling molecules, and drugs are valuable in investigating the regulatory mechanisms of cellular metabolism, annotating proteins with unknown functions, and elucidating pharmacological mechanisms. Here we report an energetics-based target identification method in which target proteins in a cell lysate are identified by exploiting the effect of ligand binding on their stabilities. Urea-induced unfolding of proteins in cell lysates is probed by a short pulse of proteolysis, and the effect of a ligand on the amount of folded protein remaining is monitored on a proteomic scale. As proof of principle, we identified proteins that interact with ATP in the Escherichia coli proteome. Literature and database mining confirmed that a majority of the identified proteins are indeed ATP-binding proteins. Four identified proteins that were previously not known to interact with ATP were cloned and expressed to validate the result. Except for one protein, the effects of ATP on urea-induced unfolding were confirmed. Analyses of the protein sequences and structure models were also employed to predict potential ATP binding sites in the identified proteins. Our results demonstrate that this energetics-based target identification approach is a facile method to identify proteins that interact with specific ligands on a proteomic scale.

journal_name

J Mol Biol

authors

Liu PF,Kihara D,Park C

doi

10.1016/j.jmb.2011.02.026

subject

Has Abstract

pub_date

2011-04-22 00:00:00

pages

147-62

issue

1

eissn

0022-2836

issn

1089-8638

pii

S0022-2836(11)00171-9

journal_volume

408

pub_type

杂志文章
  • Synthesis and activity of piperazine-containing antirhinoviral agents and crystal structure of SDZ 880-061 bound to human rhinovirus 14.

    abstract::A series of antipicornaviral agents containing piperazinyl moieties was synthesized with the objective of obtaining a compound with a broad spectrum of antirhinovirus activity, high potency (< or = 0.003 microgram/ml), and low cytotoxicity (> or = 30 micrograms/ml). Five compounds of this series were evaluated in deta...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1996.0307

    authors: Oren DA,Zhang A,Nesvadba H,Rosenwirth B,Arnold E

    更新日期:1996-05-31 00:00:00

  • Plasminogen activator inhibitor-2 is highly tolerant to P8 residue substitution--implications for serpin mechanistic model and prediction of nsSNP activities.

    abstract::The serine protease inhibitor (serpin) superfamily is involved in a wide range of cellular processes including fibrinolysis, angiogenesis, apoptosis, inflammation, metastasis and viral pathogenesis. Here, we investigate the unique mousetrap inhibition mechanism of serpins through saturation mutagenesis of the P8 resid...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2005.09.008

    authors: Di Giusto DA,Sutherland AP,Jankova L,Harrop SJ,Curmi PM,King GC

    更新日期:2005-11-11 00:00:00

  • Evolution of an interloop disulfide bond in high-affinity antibody mimics based on fibronectin type III domain and selected by yeast surface display: molecular convergence with single-domain camelid and shark antibodies.

    abstract::The 10th human fibronectin type III domain ((10)Fn3) is one of several protein scaffolds used to design and select families of proteins that bind with high affinity and specificity to macromolecular targets. To date, the highest affinity (10)Fn3 variants have been selected by mRNA display of libraries generated by ran...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2007.02.029

    authors: Lipovsek D,Lippow SM,Hackel BJ,Gregson MW,Cheng P,Kapila A,Wittrup KD

    更新日期:2007-05-11 00:00:00

  • The three-dimensional solution structure of NaD1, a new floral defensin from Nicotiana alata and its application to a homology model of the crop defense protein alfAFP.

    abstract::NMR spectroscopy and simulated annealing calculations have been used to determine the three-dimensional structure of NaD1, a novel antifungal and insecticidal protein isolated from the flowers of Nicotiana alata. NaD1 is a basic, cysteine-rich protein of 47 residues and is the first example of a plant defensin from fl...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(02)01103-8

    authors: Lay FT,Schirra HJ,Scanlon MJ,Anderson MA,Craik DJ

    更新日期:2003-01-03 00:00:00

  • Purification, characterization and crystallization of human platelet profilin expressed in Escherichia coli.

    abstract::Human platelet profilin was expressed in Escherichia coli using a T7 based expression vector. The recombinant material is similar to authentic human platelet profilin based on the measured Kd for rabbit skeletal muscle actin. Crystals of the recombinant material were obtained from both PEG 8000 and (NH4)2SO4. These cr...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1994.1522

    authors: Fedorov AA,Pollard TD,Almo SC

    更新日期:1994-08-19 00:00:00

  • The C-Box Region of MAF1 Regulates Transcriptional Activity and Protein Stability.

    abstract::MAF1 is a conserved negative regulator of RNA polymerase (pol) III and intracellular lipid homeostasis across species. Here, we show that the MAF1 C-box region negatively regulates its activity. Mutations in Caenorhabditis elegans mafr-1 that truncate the C-box retain the ability to inhibit the transcription of RNA po...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2016.12.012

    authors: Pradhan A,Hammerquist AM,Khanna A,Curran SP

    更新日期:2017-01-20 00:00:00

  • Assessing the flexibility of intermediate filaments by atomic force microscopy.

    abstract::Eukaryotic cells contain three cytoskeletal filament systems that exhibit very distinct assembly properties, supramolecular architectures, dynamic behaviour and mechanical properties. Microtubules and microfilaments are relatively stiff polar structures whose assembly is modulated by the state of hydrolysis of the bou...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2003.11.038

    authors: Mücke N,Kreplak L,Kirmse R,Wedig T,Herrmann H,Aebi U,Langowski J

    更新日期:2004-01-30 00:00:00

  • Ensemble Modeling and Intracellular Aggregation of an Engineered Immunoglobulin-Like Domain.

    abstract::The production of recombinant proteins in Escherichia coli frequently results in the formation of insoluble protein aggregates called inclusion bodies (IBs). The determinants of IB formation remain poorly understood and are of much interest for biotechnological and research applications, as well as offering insight in...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2016.02.016

    authors: Trainor K,Gingras Z,Shillingford C,Malakian H,Gosselin M,Lipovšek D,Meiering EM

    更新日期:2016-03-27 00:00:00

  • Internalizing cancer antibodies from phage libraries selected on tumor cells and yeast-displayed tumor antigens.

    abstract::A number of approaches have been utilized to generate antibodies to cancer cell surface receptors that can be used as potential therapeutics. A number of these therapeutic approaches, including antibody-drug conjugates, immunotoxins, and targeted nucleic acid delivery, require antibodies that not only bind receptor bu...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2010.09.006

    authors: Zhou Y,Zou H,Zhang S,Marks JD

    更新日期:2010-11-19 00:00:00

  • Asp-to-Asn substitution at the first position of the DxD TOPRIM motif of recombinant bacterial topoisomerase I is extremely lethal to E. coli.

    abstract::The TOPRIM domain found in many nucleotidyl transferases contains a DxD motif involved in magnesium ion coordination for catalysis. Medium- to high-copy-number plasmid clones of Yersinia pestis topoisomerase I (YpTOP) with Asp-to-Asn substitution at the first aspartate residue (D117N) of this motif could not be genera...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2008.10.073

    authors: Cheng B,Annamalai T,Sorokin E,Abrenica M,Aedo S,Tse-Dinh YC

    更新日期:2009-01-16 00:00:00

  • Structure of Mutant Hepatitis B Core Protein Capsids with Premature Secretion Phenotype.

    abstract::Hepatitis B virus is a major human pathogen that consists of a viral genome surrounded by an icosahedrally ordered core protein and a polymorphic, lipidic envelope that is densely packed with surface proteins. A point mutation in the core protein in which a phenylalanine at position 97 is exchanged for a smaller leuci...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2018.10.018

    authors: Böttcher B,Nassal M

    更新日期:2018-12-07 00:00:00

  • Dominant mutations affecting muscle structure in Caenorhabditis elegans that map near the actin gene cluster.

    abstract::By examining F1 progeny of mutagenized Caenorhabditis elegans larvae, we recovered several dominant mutations which affect muscle structure. Five of these new mutations resulted in phenotypes unlike the previously recognized unc-54 and unc-15 dominant alleles. Mapping studies placed all five mutations in the same smal...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(84)90023-8

    authors: Waterston RH,Hirsh D,Lane TR

    更新日期:1984-12-15 00:00:00

  • Beyond plasma membrane targeting: role of the MA domain of Gag in retroviral genome encapsidation.

    abstract::The MA (matrix) domain of the retroviral Gag polyprotein plays several critical roles during virus assembly. Although best known for targeting the Gag polyprotein to the inner leaflet of the plasma membrane for virus budding, recent studies have revealed that MA also contributes to selective packaging of the genomic R...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.jmb.2011.04.072

    authors: Parent LJ,Gudleski N

    更新日期:2011-07-22 00:00:00

  • The conserved asparagine in the HNH motif serves an important structural role in metal finger endonucleases.

    abstract::The HNH motif is a small nucleic acid binding and cleavage module, widespread in metal finger endonucleases in all life kingdoms. Here we studied a non-specific endonuclease, the nuclease domain of ColE7 (N-ColE7), to decipher the role of the conserved asparagine and histidine residues in the HNH motif. We found, usin...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2007.02.044

    authors: Huang H,Yuan HS

    更新日期:2007-05-04 00:00:00

  • Structure of cobra cardiotoxin CTX I as derived from nuclear magnetic resonance spectroscopy and distance geometry calculations.

    abstract::The structure of cardiotoxin CTX I from Naja naja atra has been investigated by NMR spectroscopy. Sequence specific resonance assignments have been obtained for all backbone protons as well as for most side-chain protons. Distance geometry calculations were carried out using a metric matrix DG program. A total of 715 ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1994.1460

    authors: Jahnke W,Mierke DF,Béress L,Kessler H

    更新日期:1994-07-29 00:00:00

  • Structural characterisation and comparison of the native and A-states of equine lysozyme.

    abstract::Native state 1H NMR resonance assignments for 125 of the 129 residues of equine lysozyme have enabled measurement of the hydrogen exchange kinetics for over 60 backbone amide and three tryptophan indole hydrogen atoms in the native state. Native holo equine lysozyme hydrogen exchange protection factors are as large as...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1997.0996

    authors: Morozova-Roche LA,Arico-Muendel CC,Haynie DT,Emelyanenko VI,Van Dael H,Dobson CM

    更新日期:1997-05-23 00:00:00

  • Oxygen transport by fetal bovine hemoglobin.

    abstract::The functional properties of fetal bovine hemoglobin have been studied as a function of temperature, chloride and 2,3-diphosphoglycerate (DPG) concentration. The fetal bovine erythrocyte has six times the concentration of the allosteric modulator DPG compared with the adult cell, and yet the oxygen affinity of the fet...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1996.0019

    authors: Clementi ME,Scatena R,Mordente A,Condò SG,Castagnola M,Giardina B

    更新日期:1996-01-12 00:00:00

  • Innate immune response to arenaviral infection: a focus on the highly pathogenic New World hemorrhagic arenaviruses.

    abstract::Arenaviruses are enveloped, negative-stranded RNA viruses that belong to the family Arenaviridae. This diverse family can be further classified into OW (Old World) and NW (New World) arenaviruses based on their antigenicity, phylogeny, and geographical distribution. Many of the NW arenaviruses are highly pathogenic vi...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.jmb.2013.09.028

    authors: Koma T,Huang C,Kolokoltsova OA,Brasier AR,Paessler S

    更新日期:2013-12-13 00:00:00

  • Mutational studies uncover non-native structure in the dimeric kinetic intermediate of the H2A-H2B heterodimer.

    abstract::The folding pathway of the histone H2A-H2B heterodimer minimally includes an on-pathway, dimeric, burst-phase intermediate, I(2). The partially folded H2A and H2B monomers populated at equilibrium were characterized as potential monomeric kinetic intermediates. Folding kinetics were compared for initiation from isolat...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2010.06.034

    authors: Stump MR,Gloss LM

    更新日期:2010-08-20 00:00:00

  • Cold-adaptation in sea-water-borne signal proteins: sequence and NMR structure of the pheromone En-6 from the Antarctic ciliate Euplotes nobilii.

    abstract::Ciliates of Euplotes species constitutively secrete pleiotropic protein pheromones, which are capable to function as prototypic autocrine growth factors as well as paracrine inducers of mating processes. This paper reports the amino acid sequence and the NMR structure of the pheromone En-6 isolated from the antarctic ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2007.06.046

    authors: Pedrini B,Placzek WJ,Koculi E,Alimenti C,LaTerza A,Luporini P,Wüthrich K

    更新日期:2007-09-14 00:00:00

  • Structural Principles Governing Disease-Causing Germline Mutations.

    abstract::Advancements in sequencing in the past decades enabled not only the determination of the human proteome but also the identification of a large number of genetic variations in the human population. The phenotypic effects of these mutations range from neutral for polymorphisms to severe for some somatic mutations. Disea...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2018.10.005

    authors: Dobson L,Mészáros B,Tusnády GE

    更新日期:2018-12-07 00:00:00

  • Novel Insights into Cell Entry of Emerging Human Pathogenic Arenaviruses.

    abstract::Viral hemorrhagic fevers caused by emerging RNA viruses of the Arenavirus family are among the most devastating human diseases. Climate change, global trade, and increasing urbanization promote the emergence and re-emergence of these human pathogenic viruses. Emerging pathogenic arenaviruses are of zoonotic origin and...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.jmb.2018.04.026

    authors: Fedeli C,Moreno H,Kunz S

    更新日期:2018-06-22 00:00:00

  • DNA polymerase X from African swine fever virus: quantitative analysis of the enzyme-ssDNA interactions and the functional structure of the complex.

    abstract::Interactions of polymerase X from African swine fever virus with single-stranded DNA (ssDNA) have been studied, using quantitative fluorescence titration and analytical ultracentrifugation techniques. Experiments were performed with a fluorescent etheno-derivative of ssDNA oligomers. Studies of unmodified ssDNA oligom...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2005.10.061

    authors: Jezewska MJ,Marcinowicz A,Lucius AL,Bujalowski W

    更新日期:2006-02-10 00:00:00

  • Biochemical and structural characterization of a novel family of cystathionine beta-synthase domain proteins fused to a Zn ribbon-like domain.

    abstract::We have identified a novel family of proteins, in which the N-terminal cystathionine beta-synthase (CBS) domain is fused to the C-terminal Zn ribbon domain. Four proteins were overexpressed in Escherichia coli and purified: TA0289 from Thermoplasma acidophilum, TV1335 from Thermoplasma volcanium, PF1953 from Pyrococcu...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2007.10.060

    authors: Proudfoot M,Sanders SA,Singer A,Zhang R,Brown G,Binkowski A,Xu L,Lukin JA,Murzin AG,Joachimiak A,Arrowsmith CH,Edwards AM,Savchenko AV,Yakunin AF

    更新日期:2008-01-04 00:00:00

  • The human homologue of the yeast splicing factor prp6p contains multiple TPR elements and is stably associated with the U5 snRNP via protein-protein interactions.

    abstract::An essential step of pre-mRNA spliceosome assembly is the interaction between the snRNPs U4/U6 and U5, to form the [U4/U6.U5] tri-snRNP. While the tri-snRNP protein Prp6p appears to play an important role for tri-snRNP formation in yeast, little is known about the interactions that connect the two snRNP particles in h...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2000.3685

    authors: Makarov EM,Makarova OV,Achsel T,Lührmann R

    更新日期:2000-05-12 00:00:00

  • A large region controls tRNA gene transcription.

    abstract::We find that tRNA gene transcription is controlled by a region much larger than the previously described internal segments known as A and B boxes. In a Bombyx mori silkworm tRNA2Ala gene, transcriptionally important sequences extend at least from -13 to +146, and thus include sequences both upstream and downstream fro...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(85)90209-8

    authors: Wilson ET,Larson D,Young LS,Sprague KU

    更新日期:1985-05-25 00:00:00

  • A deoxyribozyme with a novel guanine quartet-helix pseudoknot structure.

    abstract::Here we report a deoxyribozyme with a unique structure that contains a two-tiered guanine quadruplex interlinked to a Watson-Crick duplex. Through in vitro selection, sequence mutation, and methylation interference, we show the presence of both the two-tiered guanine-quadruplex and two helical regions contained in the...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2007.10.080

    authors: McManus SA,Li Y

    更新日期:2008-01-25 00:00:00

  • An oligomeric form of E. coli UvrD is required for optimal helicase activity.

    abstract::Pre-steady-state chemical quenched-flow techniques were used to study DNA unwinding catalyzed by Escherichia coli UvrD helicase (helicase II), a member of the SF1 helicase superfamily. Single turnover experiments, with respect to unwinding of a DNA oligonucleotide, were used to examine the DNA substrate and UvrD conce...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1999.3185

    authors: Ali JA,Maluf NK,Lohman TM

    更新日期:1999-11-05 00:00:00

  • Stalling of human DNA (cytosine-5) methyltransferase at single-strand conformers from a site of dynamic mutation.

    abstract::Single-strand conformers (SSCs) from the C-rich strand of the triplet repeat at the FMR-1 locus are rapidly and selectively methylated by the human DNA (cytosine-5) methyltransferase. The apparent affinity of the enzyme for the FMR-1 SSC is about tenfold higher than it is for a control Watson-Crick paired duplex. The ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1997.1430

    authors: Kho MR,Baker DJ,Laayoun A,Smith SS

    更新日期:1998-01-09 00:00:00

  • Modular structure, local flexibility and cold-activity of a novel chitobiase from a psychrophilic Antarctic bacterium.

    abstract::The gene archb encoding for the cell-bound chitobiase from the Antarctic Gram-positive bacterium Arthrobacter sp. TAD20 was cloned and expressed in Escherichia coli in a soluble form. The mature chitobiase ArChb possesses four functionally independent domains: a catalytic domain stabilized by Ca(2+), a galactose-bindi...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2001.4774

    authors: Lonhienne T,Zoidakis J,Vorgias CE,Feller G,Gerday C,Bouriotis V

    更新日期:2001-07-06 00:00:00