Coupled protein domain motion in Taq polymerase revealed by neutron spin-echo spectroscopy.

Abstract:

:Long-range conformational changes in proteins are ubiquitous in biology for the transmission and amplification of signals; such conformational changes can be triggered by small-amplitude, nanosecond protein domain motion. Understanding how conformational changes are initiated requires the characterization of protein domain motion on these timescales and on length scales comparable to protein dimensions. Using neutron spin-echo spectroscopy (NSE), normal mode analysis, and a statistical-mechanical framework, we reveal overdamped, coupled domain motion within DNA polymerase I from Thermus aquaticus (Taq polymerase). This protein utilizes correlated domain dynamics over 70 angstroms to coordinate nucleotide synthesis and cleavage during DNA synthesis and repair. We show that NSE spectroscopy can determine the domain mobility tensor, which determines the degree of dynamical coupling between domains. The mobility tensor defines the domain velocity response to a force applied to it or to another domain, just as the sails of a sailboat determine its velocity given the applied wind force. The NSE results provide insights into the nature of protein domain motion that are not appreciated by conventional biophysical techniques.

authors

Bu Z,Biehl R,Monkenbusch M,Richter D,Callaway DJ

doi

10.1073/pnas.0503388102

keywords:

subject

Has Abstract

pub_date

2005-12-06 00:00:00

pages

17646-51

issue

49

eissn

0027-8424

issn

1091-6490

pii

0503388102

journal_volume

102

pub_type

杂志文章
  • Neuroethology of primate social behavior.

    abstract::A neuroethological approach to human and nonhuman primate behavior and cognition predicts biological specializations for social life. Evidence reviewed here indicates that ancestral mechanisms are often duplicated, repurposed, and differentially regulated to support social behavior. Focusing on recent research from no...

    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.1301213110

    authors: Chang SW,Brent LJ,Adams GK,Klein JT,Pearson JM,Watson KK,Platt ML

    更新日期:2013-06-18 00:00:00

  • An acquired and a native penicillin-binding protein cooperate in building the cell wall of drug-resistant staphylococci.

    abstract::The blanket resistance of methicillin-resistant Staphylococcus aureus to all beta-lactam antibiotics--which had such a devastating impact on chemotherapy of staphylococcal infections--is related to the properties of the key component of this resistance mechanism: the "acquired" penicillin-binding protein (PBP)-2A, whi...

    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.191260798

    authors: Pinho MG,de Lencastre H,Tomasz A

    更新日期:2001-09-11 00:00:00

  • Analysis of oscillatory rocking curve by dynamical diffraction in protein crystals.

    abstract::High-quality protein crystals meant for structural analysis by X-ray diffraction have been grown by various methods. The observation of dynamical diffraction in protein crystals is an interesting topic because dynamical diffraction generally occurs in perfect crystals such as Si crystals. However, to our knowledge, 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.1720098115

    authors: Suzuki R,Koizumi H,Hirano K,Kumasaka T,Kojima K,Tachibana M

    更新日期:2018-04-03 00:00:00

  • Biosynthesis of a major lipofuscin fluorophore in mice and humans with ABCR-mediated retinal and macular degeneration.

    abstract::Increased accumulation of lipofuscin in cells of the retinal pigment epithelium (RPE) is seen in several forms of macular degeneration, a common cause of blindness in humans. A major fluorophore of lipofuscin is the toxic bis-retinoid, N-retinylidene-N-retinylethanolamine (A2E). Previously, we generated mice with a kn...

    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.130110497

    authors: Mata NL,Weng J,Travis GH

    更新日期:2000-06-20 00:00:00

  • Ethological observations of social behavior in the operating room.

    abstract::Operating rooms (ORs) are inhabited by hierarchical, mixed-gender clinical teams that are often prone to conflict. In evolutionary terms, one expects more within- than between-gender rivalries, especially since the OR is a place where all sorts of social interactions occur, not merely technical communications. To docu...

    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.1716883115

    authors: Jones LK,Jennings BM,Higgins MK,de Waal FBM

    更新日期:2018-07-17 00:00:00

  • Galphai generates multiple Pins activation states to link cortical polarity and spindle orientation in Drosophila neuroblasts.

    abstract::Drosophila neuroblasts divide asymmetrically by aligning their mitotic spindle with cortical cell polarity to generate distinct sibling cell types. Neuroblasts asymmetrically localize Galphai, Pins, and Mud proteins; Pins/Galphai direct cortical polarity, whereas Mud is required for spindle orientation. It is currentl...

    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.0701812104

    authors: Nipper RW,Siller KH,Smith NR,Doe CQ,Prehoda KE

    更新日期:2007-09-04 00:00:00

  • Encoding biological recognition in a bicomponent cell-membrane mimic.

    abstract::Self-assembling dendrimers have facilitated the discovery of periodic and quasiperiodic arrays of supramolecular architectures and the diverse functions derived from them. Examples are liquid quasicrystals and their approximants plus helical columns and spheres, including some that disregard chirality. The same period...

    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.1821924116

    authors: Rodriguez-Emmenegger C,Xiao Q,Kostina NY,Sherman SE,Rahimi K,Partridge BE,Li S,Sahoo D,Reveron Perez AM,Buzzacchera I,Han H,Kerzner M,Malhotra I,Möller M,Wilson CJ,Good MC,Goulian M,Baumgart T,Klein ML,Percec V

    更新日期:2019-03-19 00:00:00

  • Dermorphin-related peptides from the skin of Phyllomedusa bicolor and their amidated analogs activate two mu opioid receptor subtypes that modulate antinociception and catalepsy in the rat.

    abstract::Three naturally occurring dermorphin-like peptides from the skin of the frog Phyllomedusa bicolor, the related carboxyl-terminal amides, and some substituted analogs were synthesized, their binding profiles to opioid receptors were determined, and their biological activities were studied in isolated organ preparations...

    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.89.15.7203

    authors: Negri L,Erspamer GF,Severini C,Potenza RL,Melchiorri P,Erspamer V

    更新日期:1992-08-01 00:00:00

  • p53 as a target for cancer vaccines: recombinant canarypox virus vectors expressing p53 protect mice against lethal tumor cell challenge.

    abstract::The p53 protein is an attractive target for immunotherapy, because mutations in the p53 gene are the most common genetic alterations found in human tumors. These mutations result in high levels of p53 protein in the tumor cell, whereas the expression level of wild-type p53 in nonmalignant tissue is usually much lower....

    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.93.10.4781

    authors: Roth J,Dittmer D,Rea D,Tartaglia J,Paoletti E,Levine AJ

    更新日期:1996-05-14 00:00:00

  • Expression of a swine class II gene in murine bone marrow hematopoietic cells by retroviral-mediated gene transfer.

    abstract::As a first step in assessing the efficacy of a gene transfer approach to the induction of transplantation tolerance in our miniature swine model, double-copy retroviral vectors engineered to express a drug-resistance marker (neomycin) and a swine class II DRB cDNA were constructed. Infectious particles containing thes...

    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.88.21.9760

    authors: Shafer GE,Emery DW,Gustafsson K,Germana S,Anderson WF,Sachs DH,LeGuern C

    更新日期:1991-11-01 00:00:00

  • Dual origin of mesenchymal stem cells contributing to organ growth and repair.

    abstract::In many adult tissues, mesenchymal stem cells (MSCs) are closely associated with perivascular niches and coexpress many markers in common with pericytes. The ability of pericytes to act as MSCs, however, remains controversial. By using genetic lineage tracing, we show that some pericytes differentiate into specialized...

    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.1015449108

    authors: Feng J,Mantesso A,De Bari C,Nishiyama A,Sharpe PT

    更新日期:2011-04-19 00:00:00

  • 3-Hydroxyanthranilic acid inhibits PDK1 activation and suppresses experimental asthma by inducing T cell apoptosis.

    abstract::3-Hydroxyanthranilic acid (HAA), a compound generated during tryptophan metabolism initiated by indoleamine 2,3-dioxygenase, is known to induce T cell death, but its molecular target is not known. Here we report that HAA inhibits NF-kappaB activation upon T cell antigen receptor engagement by specifically targeting PD...

    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.0709261104

    authors: Hayashi T,Mo JH,Gong X,Rossetto C,Jang A,Beck L,Elliott GI,Kufareva I,Abagyan R,Broide DH,Lee J,Raz E

    更新日期:2007-11-20 00:00:00

  • Sequence requirements for cleavage activation of influenza virus hemagglutinin expressed in mammalian cells.

    abstract::Cleavage of the hemagglutinin (HA) in tissue culture systems has been correlated with virulence of avian influenza viruses. To examine the structural requirements for cleavage of the HA, the HA gene from a virulent H5 influenza virus was expressed in mammalian cells (CV-1), and the cleavage site of the HA was explored...

    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.85.2.324

    authors: Kawaoka Y,Webster RG

    更新日期:1988-01-01 00:00:00

  • Location and nucleotide sequence of the gene for the proton-translocating subunit of wheat chloroplast ATP synthase.

    abstract::The proton-translocating subunit of wheat chloroplast ATP synthase is encoded by a chloroplast gene that has been accurately mapped and whose nucleotide sequence has been determined. The predicted sequence of 81 amino acids has been confirmed in part by determination of the sequence of the first 40 amino acids from 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.79.22.6903

    authors: Howe CJ,Auffret AD,Doherty A,Bowman CM,Dyer TA,Gray JC

    更新日期:1982-11-01 00:00:00

  • Primary photochemistry of iron-depleted and zinc-reconstituted reaction centers from Rhodopseudomonas sphaeroides.

    abstract::The primary photochemistry of Fe-depleted and Zn-reconstituted reaction centers from Rhodopseudomonas sphaeroides R-26.1 was studied by transient absorption spectroscopy and compared with native, Fe(2+)-containing reaction centers. Excitation of metal-free reaction centers with 30-ps flashes produced the initial charg...

    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.83.17.6407

    authors: Kirmaier C,Holten D,Debus RJ,Feher G,Okamura MY

    更新日期:1986-09-01 00:00:00

  • Distinct calcium-independent and calcium-dependent adhesion systems of chicken embryo cells.

    abstract::Three criteria have been used to distinguish among different systems of embryonic cell adhesion: dependence on Ca2+, involvement of particular cell-surface molecules, and binding specificity. The characterization of the adhesion with respect to cell-surface molecules was carried out by using specific antibodies agains...

    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.78.1.387

    authors: Brackenbury R,Rutishauser U,Edelman GM

    更新日期:1981-01-01 00:00:00

  • Structural insight on the recognition of surface-bound opsonins by the integrin I domain of complement receptor 3.

    abstract::Complement receptors (CRs), expressed notably on myeloid and lymphoid cells, play an essential function in the elimination of complement-opsonized pathogens and apoptotic/necrotic cells. In addition, these receptors are crucial for the cross-talk between the innate and adaptive branches of the immune system. CR3 (also...

    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.1311261110

    authors: Bajic G,Yatime L,Sim RB,Vorup-Jensen T,Andersen GR

    更新日期:2013-10-08 00:00:00

  • Determination of the minimum polypeptide lengths of the functionally active sites of human interleukins 1 alpha and 1 beta.

    abstract::Interleukin 1 (IL-1) is a two-member family of proteins (IL-1 alpha and IL-1 beta) that mediates a diverse series of immune and inflammatory responses. These two proteins have only 26% amino acid homology yet bind to the same receptor. It is of importance to define the active sites of these molecules in order to under...

    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.84.13.4572

    authors: Mosley B,Dower SK,Gillis S,Cosman D

    更新日期:1987-07-01 00:00:00

  • Structural and mechanistic insights into VEGF receptor 3 ligand binding and activation.

    abstract::Vascular endothelial growth factors (VEGFs) and their receptors (VEGFRs) are key drivers of blood and lymph vessel formation in development, but also in several pathological processes. VEGF-C signaling through VEGFR-3 promotes lymphangiogenesis, which is a clinically relevant target for treating lymphatic insufficienc...

    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.1301415110

    authors: Leppänen VM,Tvorogov D,Kisko K,Prota AE,Jeltsch M,Anisimov A,Markovic-Mueller S,Stuttfeld E,Goldie KN,Ballmer-Hofer K,Alitalo K

    更新日期:2013-08-06 00:00:00

  • C factor, a cell-surface-associated intercellular signaling protein, stimulates the cytoplasmic Frz signal transduction system in Myxococcus xanthus.

    abstract::C factor, an intercellular signaling protein, is required for aggregation and sporulation of the social bacterium, Myxococcus xanthus. We report that C factor, which normally is associated with the cell surface, provides input to the Frz signal transduction cascade. Elements of this cascade have sequence homology to 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.93.7.2675

    authors: Søgaard-Andersen L,Kaiser D

    更新日期:1996-04-02 00:00:00

  • Transmembrane E3 ligase RNF183 mediates ER stress-induced apoptosis by degrading Bcl-xL.

    abstract::The accumulation of misfolded proteins in the endoplasmic reticulum (ER) causes ER stress and triggers the unfolded protein response (UPR). Failure to resolve ER stress leads to apoptotic cell death via a yet unclear mechanism. Here, we show that RNF183, a membrane-spanning RING finger protein, localizes to the ER and...

    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.1716439115

    authors: Wu Y,Li X,Jia J,Zhang Y,Li J,Zhu Z,Wang H,Tang J,Hu J

    更新日期:2018-03-20 00:00:00

  • Ensemble quantum computing by NMR spectroscopy.

    abstract::A quantum computer (QC) can operate in parallel on all its possible inputs at once, but the amount of information that can be extracted from the result is limited by the phenomenon of wave function collapse. We present a new computational model, which differs from a QC only in that the result of a measurement is the e...

    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.94.5.1634

    authors: Cory DG,Fahmy AF,Havel TF

    更新日期:1997-03-04 00:00:00

  • A new high molecular weight immunoglobulin class from the carcharhine shark: implications for the properties of the primordial immunoglobulin.

    abstract::All immunoglobulins and T-cell receptors throughout phylogeny share regions of highly conserved amino acid sequence. To identify possible primitive immunoglobulins and immunoglobulin-like molecules, we utilized 3' RACE (rapid amplification of cDNA ends) and a highly conserved constant region consensus amino acid seque...

    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.93.8.3289

    authors: Berstein RM,Schluter SF,Shen S,Marchalonis JJ

    更新日期:1996-04-16 00:00:00

  • Forkhead box transcription factor FoxC1 preserves corneal transparency by regulating vascular growth.

    abstract::Normal vision requires the precise control of vascular growth to maintain corneal transparency. Here we provide evidence for a unique mechanism by which the Forkhead box transcription factor FoxC1 regulates corneal vascular development. Murine Foxc1 is essential for development of the ocular anterior segment, and in h...

    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.1109540109

    authors: Seo S,Singh HP,Lacal PM,Sasman A,Fatima A,Liu T,Schultz KM,Losordo DW,Lehmann OJ,Kume T

    更新日期:2012-02-07 00:00:00

  • Construction of an extended three-dimensional idiotope map by electron microscopic analysis of idiotope-anti-idiotope complexes.

    abstract::A three-dimensional map of the positions of four idiotypic determinants (idiotopes or Ids) and an isotypic determinant was derived by transmission electron microscopy of negatively stained immune complexes. Each complex was composed of a monoclonal Id-expressing IgG and one or two varieties of monoclonal anti-Id (or a...

    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.84.14.4984

    authors: Roux KH,Monafo WJ,Davie JM,Greenspan NS

    更新日期:1987-07-01 00:00:00

  • Spinal motor neuron protein supersaturation patterns are associated with inclusion body formation in ALS.

    abstract::Amyotrophic lateral sclerosis (ALS) is a heterogeneous degenerative motor neuron disease linked to numerous genetic mutations in apparently unrelated proteins. These proteins, including SOD1, TDP-43, and FUS, are highly aggregation-prone and form a variety of intracellular inclusion bodies that are characteristic of d...

    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.1613854114

    authors: Ciryam P,Lambert-Smith IA,Bean DM,Freer R,Cid F,Tartaglia GG,Saunders DN,Wilson MR,Oliver SG,Morimoto RI,Dobson CM,Vendruscolo M,Favrin G,Yerbury JJ

    更新日期:2017-05-16 00:00:00

  • Snapshots of a protein folding intermediate.

    abstract::We have investigated the folding dynamics of Thermus thermophilus cytochrome c(552) by time-resolved fluorescence energy transfer between the heme and each of seven site-specific fluorescent probes. We have found both an equilibrium unfolding intermediate and a distinct refolding intermediate from kinetics studies. De...

    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.1221832110

    authors: Yamada S,Bouley Ford ND,Keller GE,Ford WC,Gray HB,Winkler JR

    更新日期:2013-01-29 00:00:00

  • beta-endorphin is a potent analgesic agent.

    abstract::beta-Endorphin, an opiate-like peptide, has potent antinociceptive properties when it is administered directly into the brain and assayed in the the tail-flick, hot-plate, and writhing tests in mice and in the wet shake test in rats. On a molar basis, beta-endorphin is 18 to 33 times more potent than morphine and its ...

    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.73.8.2895

    authors: Loh HH,Tseng LF,Wei E,Li CH

    更新日期:1976-08-01 00:00:00

  • Reconstruction of bacteriophage T4 DNA replication apparatus from purified components: rolling circle replication following de novo chain initiation on a single-stranded circular DNA template.

    abstract::The protein products of T4 bacteriophage genes 41, 43, 45, 44, and 62 have been purified to near homogeneity using an assay which measures their stimulation of DNA synthesis in a crude lysate of Escherichia coli cells in fected by an appropriate mutant phage. When all of these proteins and T4 gene 32 protein are incub...

    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.72.12.4800

    authors: Morris CF,Sinha NK,Alberts BM

    更新日期:1975-12-01 00:00:00

  • Protein kinase D1 is essential for Ras-induced senescence and tumor suppression by regulating senescence-associated inflammation.

    abstract::Oncogene-induced senescence (OIS) is an initial barrier to tumor development. Reactive oxygen species (ROS) is critical for oncogenic Ras OIS, but the downstream effectors to mediate ROS signaling are still relatively elusive. Senescent cells develop a senescence-associated secretory phenotype (SASP). However, the mec...

    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.1310972111

    authors: Wang P,Han L,Shen H,Wang P,Lv C,Zhao G,Niu J,Xue L,Wang QJ,Tong T,Chen J

    更新日期:2014-05-27 00:00:00