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Items: 1 to 50 of 366

1.

Structures of the intermediates of Kok's photosynthetic water oxidation clock.

Kern J, Chatterjee R, Young ID, Fuller FD, Lassalle L, Ibrahim M, Gul S, Fransson T, Brewster AS, Alonso-Mori R, Hussein R, Zhang M, Douthit L, de Lichtenberg C, Cheah MH, Shevela D, Wersig J, Seuffert I, Sokaras D, Pastor E, Weninger C, Kroll T, Sierra RG, Aller P, Butryn A, Orville AM, Liang M, Batyuk A, Koglin JE, Carbajo S, Boutet S, Moriarty NW, Holton JM, Dobbek H, Adams PD, Bergmann U, Sauter NK, Zouni A, Messinger J, Yano J, Yachandra VK.

Nature. 2018 Nov 7. doi: 10.1038/s41586-018-0681-2. [Epub ahead of print]

PMID:
30405241
2.

Renewable production of high density jet fuel precursor sesquiterpenes from Escherichia coli.

Liu CL, Tian T, Alonso-Gutierrez J, Garabedian B, Wang S, Baidoo EEK, Benites V, Chen Y, Petzold CJ, Adams PD, Keasling JD, Tan T, Lee TS.

Biotechnol Biofuels. 2018 Oct 20;11:285. doi: 10.1186/s13068-018-1272-z. eCollection 2018.

3.

A fully automatic method yielding initial models from high-resolution cryo-electron microscopy maps.

Terwilliger TC, Adams PD, Afonine PV, Sobolev OV.

Nat Methods. 2018 Nov;15(11):905-908. doi: 10.1038/s41592-018-0173-1. Epub 2018 Oct 30.

PMID:
30377346
4.

Author Correction: Jungle Express is a versatile repressor system for tight transcriptional control.

Ruegg TL, Pereira JH, Chen JC, DeGiovanni A, Novichkov P, Mutalik VK, Tomaleri GP, Singer SW, Hillson NJ, Simmons BA, Adams PD, Thelen MP.

Nat Commun. 2018 Oct 30;9(1):4596. doi: 10.1038/s41467-018-07111-2.

5.

Iron- and Aluminum-Induced Depletion of Molybdenum in Acidic Environments Impedes the Nitrogen Cycle.

Ge X, Vaccaro BJ, Thorgersen MP, Poole FL 2nd, Majumder EL, Zane GM, De León KB, Lancaster WA, Moon JW, Paradis CJ, von Netzer F, Stahl DA, Adams PD, Arkin AP, Wall JD, Hazen TC, Adams MWW.

Environ Microbiol. 2018 Oct 5. doi: 10.1111/1462-2920.14435. [Epub ahead of print]

PMID:
30289197
6.

Rapid characterization of the activities of lignin-modifying enzymes based on nanostructure-initiator mass spectrometry (NIMS).

Deng K, Zeng J, Cheng G, Gao J, Sale KL, Simmons BA, Singh AK, Adams PD, Northen TR.

Biotechnol Biofuels. 2018 Sep 27;11:266. doi: 10.1186/s13068-018-1261-2. eCollection 2018.

7.

Distribution of evaluation scores for the models submitted to the second cryo-EM model challenge.

Kryshtafovych A, Monastyrskyy B, Adams PD, Lawson CL, Chiu W.

Data Brief. 2018 Sep 8;20:1629-1638. doi: 10.1016/j.dib.2018.08.214. eCollection 2018 Oct.

8.

DNA Methylation Clocks in Aging: Categories, Causes, and Consequences.

Field AE, Robertson NA, Wang T, Havas A, Ideker T, Adams PD.

Mol Cell. 2018 Sep 20;71(6):882-895. doi: 10.1016/j.molcel.2018.08.008. Review.

PMID:
30241605
9.

New tools for the analysis and validation of cryo-EM maps and atomic models.

Afonine PV, Klaholz BP, Moriarty NW, Poon BK, Sobolev OV, Terwilliger TC, Adams PD, Urzhumtsev A.

Acta Crystallogr D Struct Biol. 2018 Sep 1;74(Pt 9):814-840. doi: 10.1107/S2059798318009324. Epub 2018 Sep 3.

10.

Jungle Express is a versatile repressor system for tight transcriptional control.

Ruegg TL, Pereira JH, Chen JC, DeGiovanni A, Novichkov P, Mutalik VK, Tomaleri GP, Singer SW, Hillson NJ, Simmons BA, Adams PD, Thelen MP.

Nat Commun. 2018 Sep 6;9(1):3617. doi: 10.1038/s41467-018-05857-3. Erratum in: Nat Commun. 2018 Oct 30;9(1):4596.

11.

A Role for p53 in the Adaptation to Glutamine Starvation through the Expression of SLC1A3.

Tajan M, Hock AK, Blagih J, Robertson NA, Labuschagne CF, Kruiswijk F, Humpton TJ, Adams PD, Vousden KH.

Cell Metab. 2018 Nov 6;28(5):721-736.e6. doi: 10.1016/j.cmet.2018.07.005. Epub 2018 Aug 16.

12.

Evaluation of models determined by neutron diffraction and proposed improvements to their validation and deposition.

Liebschner D, Afonine PV, Moriarty NW, Langan P, Adams PD.

Acta Crystallogr D Struct Biol. 2018 Aug 1;74(Pt 8):800-813. doi: 10.1107/S2059798318004588. Epub 2018 Jul 24.

13.

Map segmentation, automated model-building and their application to the Cryo-EM Model Challenge.

Terwilliger TC, Adams PD, Afonine PV, Sobolev OV.

J Struct Biol. 2018 Nov;204(2):338-343. doi: 10.1016/j.jsb.2018.07.016. Epub 2018 Jul 29.

14.

Evaluation system and web infrastructure for the second cryo-EM model challenge.

Kryshtafovych A, Adams PD, Lawson CL, Chiu W.

J Struct Biol. 2018 Oct;204(1):96-108. doi: 10.1016/j.jsb.2018.07.006. Epub 2018 Jul 12.

15.

Engineering glycoside hydrolase stability by the introduction of zinc binding.

Ellinghaus TL, Pereira JH, McAndrew RP, Welner DH, DeGiovanni AM, Guenther JM, Tran HM, Feldman T, Simmons BA, Sale KL, Adams PD.

Acta Crystallogr D Struct Biol. 2018 Jul 1;74(Pt 7):702-710. doi: 10.1107/S2059798318006678. Epub 2018 Jun 27.

16.

From deep TLS validation to ensembles of atomic models built from elemental motions. II. Analysis of TLS refinement results by explicit interpretation.

Afonine PV, Adams PD, Urzhumtsev A.

Acta Crystallogr D Struct Biol. 2018 Jul 1;74(Pt 7):621-631. doi: 10.1107/S2059798318005764. Epub 2018 Jun 8.

17.

Automated map sharpening by maximization of detail and connectivity.

Terwilliger TC, Sobolev OV, Afonine PV, Adams PD.

Acta Crystallogr D Struct Biol. 2018 Jun 1;74(Pt 6):545-559. doi: 10.1107/S2059798318004655. Epub 2018 May 18.

18.

Real-space refinement in PHENIX for cryo-EM and crystallography.

Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD.

Acta Crystallogr D Struct Biol. 2018 Jun 1;74(Pt 6):531-544. doi: 10.1107/S2059798318006551. Epub 2018 May 30.

19.

Discovery of enzymes for toluene synthesis from anoxic microbial communities.

Beller HR, Rodrigues AV, Zargar K, Wu YW, Saini AK, Saville RM, Pereira JH, Adams PD, Tringe SG, Petzold CJ, Keasling JD.

Nat Chem Biol. 2018 May;14(5):451-457. doi: 10.1038/s41589-018-0017-4. Epub 2018 Mar 19.

20.

Integrated analysis of isopentenyl pyrophosphate (IPP) toxicity in isoprenoid-producing Escherichia coli.

George KW, Thompson MG, Kim J, Baidoo EEK, Wang G, Benites VT, Petzold CJ, Chan LJG, Yilmaz S, Turhanen P, Adams PD, Keasling JD, Lee TS.

Metab Eng. 2018 May;47:60-72. doi: 10.1016/j.ymben.2018.03.004. Epub 2018 Mar 9.

PMID:
29530749
21.

DiSCaMB: a software library for aspherical atom model X-ray scattering factor calculations with CPUs and GPUs.

Chodkiewicz ML, Migacz S, Rudnicki W, Makal A, Kalinowski JA, Moriarty NW, Grosse-Kunstleve RW, Afonine PV, Adams PD, Dominiak PM.

J Appl Crystallogr. 2018 Feb 1;51(Pt 1):193-199. doi: 10.1107/S1600576717015825. eCollection 2018 Feb 1.

PMID:
29507550
22.

Microbial Functional Gene Diversity Predicts Groundwater Contamination and Ecosystem Functioning.

He Z, Zhang P, Wu L, Rocha AM, Tu Q, Shi Z, Wu B, Qin Y, Wang J, Yan Q, Curtis D, Ning D, Van Nostrand JD, Wu L, Yang Y, Elias DA, Watson DB, Adams MWW, Fields MW, Alm EJ, Hazen TC, Adams PD, Arkin AP, Zhou J.

MBio. 2018 Feb 20;9(1). pii: e02435-17. doi: 10.1128/mBio.02435-17.

23.

Employing a biochemical protecting group for a sustainable indigo dyeing strategy.

Hsu TM, Welner DH, Russ ZN, Cervantes B, Prathuri RL, Adams PD, Dueber JE.

Nat Chem Biol. 2018 Mar;14(3):256-261. doi: 10.1038/nchembio.2552. Epub 2018 Jan 8.

24.

Expression of naturally ionic liquid-tolerant thermophilic cellulases in Aspergillus niger.

Amaike Campen S, Lynn J, Sibert SJ, Srikrishnan S, Phatale P, Feldman T, Guenther JM, Hiras J, Tran YTA, Singer SW, Adams PD, Sale KL, Simmons BA, Baker SE, Magnuson JK, Gladden JM.

PLoS One. 2017 Dec 27;12(12):e0189604. doi: 10.1371/journal.pone.0189604. eCollection 2017.

25.

Toward industrial production of isoprenoids in Escherichia coli: Lessons learned from CRISPR-Cas9 based optimization of a chromosomally integrated mevalonate pathway.

Alonso-Gutierrez J, Koma D, Hu Q, Yang Y, Chan LJG, Petzold CJ, Adams PD, Vickers CE, Nielsen LK, Keasling JD, Lee TS.

Biotechnol Bioeng. 2018 Apr;115(4):1000-1013. doi: 10.1002/bit.26530. Epub 2018 Feb 7.

26.

A bacterial pioneer produces cellulase complexes that persist through community succession.

Kolinko S, Wu YW, Tachea F, Denzel E, Hiras J, Gabriel R, Bäcker N, Chan LJG, Eichorst SA, Frey D, Chen Q, Azadi P, Adams PD, Pray TR, Tanjore D, Petzold CJ, Gladden JM, Simmons BA, Singer SW.

Nat Microbiol. 2018 Jan;3(1):99-107. doi: 10.1038/s41564-017-0052-z. Epub 2017 Nov 6.

27.

MolProbity: More and better reference data for improved all-atom structure validation.

Williams CJ, Headd JJ, Moriarty NW, Prisant MG, Videau LL, Deis LN, Verma V, Keedy DA, Hintze BJ, Chen VB, Jain S, Lewis SM, Arendall WB 3rd, Snoeyink J, Adams PD, Lovell SC, Richardson JS, Richardson DC.

Protein Sci. 2018 Jan;27(1):293-315. doi: 10.1002/pro.3330. Epub 2017 Nov 27.

28.

Berkeley Screen: a set of 96 solutions for general macromolecular crystallization.

Pereira JH, McAndrew RP, Tomaleri GP, Adams PD.

J Appl Crystallogr. 2017 Sep 5;50(Pt 5):1352-1358. doi: 10.1107/S1600576717011347. eCollection 2017 Oct 1.

29.

Histone chaperone HIRA deposits histone H3.3 onto foreign viral DNA and contributes to anti-viral intrinsic immunity.

Rai TS, Glass M, Cole JJ, Rather MI, Marsden M, Neilson M, Brock C, Humphreys IR, Everett RD, Adams PD.

Nucleic Acids Res. 2017 Nov 16;45(20):11673-11683. doi: 10.1093/nar/gkx771.

30.

Cytoplasmic chromatin triggers inflammation in senescence and cancer.

Dou Z, Ghosh K, Vizioli MG, Zhu J, Sen P, Wangensteen KJ, Simithy J, Lan Y, Lin Y, Zhou Z, Capell BC, Xu C, Xu M, Kieckhaefer JE, Jiang T, Shoshkes-Carmel M, Tanim KMAA, Barber GN, Seykora JT, Millar SE, Kaestner KH, Garcia BA, Adams PD, Berger SL.

Nature. 2017 Oct 19;550(7676):402-406. doi: 10.1038/nature24050. Epub 2017 Oct 4.

31.

AKT overactivation can suppress DNA repair via p70S6 kinase-dependent downregulation of MRE11.

Piscitello D, Varshney D, Lilla S, Vizioli MG, Reid C, Gorbunova V, Seluanov A, Gillespie DA, Adams PD.

Oncogene. 2018 Jan 25;37(4):427-438. doi: 10.1038/onc.2017.340. Epub 2017 Oct 2.

32.

The cryo-electron microscopy structure of human transcription factor IIH.

Greber BJ, Nguyen THD, Fang J, Afonine PV, Adams PD, Nogales E.

Nature. 2017 Sep 21;549(7672):414-417. doi: 10.1038/nature23903. Epub 2017 Sep 13.

33.

Interactive comparison and remediation of collections of macromolecular structures.

Moriarty NW, Liebschner D, Klei HE, Echols N, Afonine PV, Headd JJ, Poon BK, Adams PD.

Protein Sci. 2018 Jan;27(1):182-194. doi: 10.1002/pro.3296. Epub 2017 Nov 11.

PMID:
28901593
34.

The Experiment Data Depot: A Web-Based Software Tool for Biological Experimental Data Storage, Sharing, and Visualization.

Morrell WC, Birkel GW, Forrer M, Lopez T, Backman TWH, Dussault M, Petzold CJ, Baidoo EEK, Costello Z, Ando D, Alonso-Gutierrez J, George KW, Mukhopadhyay A, Vaino I, Keasling JD, Adams PD, Hillson NJ, Garcia Martin H.

ACS Synth Biol. 2017 Dec 15;6(12):2248-2259. doi: 10.1021/acssynbio.7b00204. Epub 2017 Sep 8.

35.

Reply to Kiser: Dioxygen binding in NOV1 crystal structures.

McAndrew RP, Sathitsuksanoh N, Mbughuni MM, Heins RA, Pereira JH, George A, Sale KL, Fox BG, Simmons BA, Adams PD.

Proc Natl Acad Sci U S A. 2017 Jul 25;114(30):E6029-E6030. doi: 10.1073/pnas.1708124114. Epub 2017 Jul 5. No abstract available.

36.

Oncogene-Expressing Senescent Melanocytes Up-Regulate MHC Class II, a Candidate Melanoma Suppressor Function.

van Tuyn J, Jaber-Hijazi F, MacKenzie D, Cole JJ, Mann E, Pawlikowski JS, Rai TS, Nelson DM, McBryan T, Ivanov A, Blyth K, Wu H, Milling S, Adams PD.

J Invest Dermatol. 2017 Oct;137(10):2197-2207. doi: 10.1016/j.jid.2017.05.030. Epub 2017 Jun 22.

37.

Structure of the human TRiC/CCT Subunit 5 associated with hereditary sensory neuropathy.

Pereira JH, McAndrew RP, Sergeeva OA, Ralston CY, King JA, Adams PD.

Sci Rep. 2017 Jun 16;7(1):3673. doi: 10.1038/s41598-017-03825-3.

38.

Epigenetics meets metabolism through PHB-mediated histone H3.3 deposition by HIRA.

Marmorstein R, Adams PD.

Stem Cell Investig. 2017 May 26;4:46. doi: 10.21037/sci.2017.05.08. eCollection 2017. No abstract available.

39.

Plant cell wall glycosyltransferases: High-throughput recombinant expression screening and general requirements for these challenging enzymes.

Welner DH, Shin D, Tomaleri GP, DeGiovanni AM, Tsai AY, Tran HM, Hansen SF, Green DT, Scheller HV, Adams PD.

PLoS One. 2017 Jun 9;12(6):e0177591. doi: 10.1371/journal.pone.0177591. eCollection 2017.

40.

DNA damage marker phosphorylated histone H2AX is a potential predictive marker for progression of epithelial dysplasia of the oral cavity.

Leung EY, McMahon JD, McLellan DR, Syyed N, McCarthy CE, Nixon C, Orange C, Brock C, Hunter KD, Adams PD.

Histopathology. 2017 Oct;71(4):522-528. doi: 10.1111/his.13260. Epub 2017 Jul 21.

41.

Structure of aryl O-demethylase offers molecular insight into a catalytic tyrosine-dependent mechanism.

Kohler AC, Mills MJL, Adams PD, Simmons BA, Sale KL.

Proc Natl Acad Sci U S A. 2017 Apr 18;114(16):E3205-E3214. doi: 10.1073/pnas.1619263114. Epub 2017 Apr 3.

42.

Production of jet fuel precursor monoterpenoids from engineered Escherichia coli.

Mendez-Perez D, Alonso-Gutierrez J, Hu Q, Molinas M, Baidoo EEK, Wang G, Chan LJG, Adams PD, Petzold CJ, Keasling JD, Lee TS.

Biotechnol Bioeng. 2017 Aug;114(8):1703-1712. doi: 10.1002/bit.26296. Epub 2017 May 18.

43.

X-ray diffraction analysis and in vitro characterization of the UAM2 protein from Oryza sativa.

Welner DH, Tsai AY, DeGiovanni AM, Scheller HV, Adams PD.

Acta Crystallogr F Struct Biol Commun. 2017 Apr 1;73(Pt 4):241-245. doi: 10.1107/S2053230X17004587. Epub 2017 Mar 29.

44.

Epigenetic aging signatures in mice livers are slowed by dwarfism, calorie restriction and rapamycin treatment.

Wang T, Tsui B, Kreisberg JF, Robertson NA, Gross AM, Yu MK, Carter H, Brown-Borg HM, Adams PD, Ideker T.

Genome Biol. 2017 Mar 28;18(1):57. doi: 10.1186/s13059-017-1186-2.

45.

Diverse interventions that extend mouse lifespan suppress shared age-associated epigenetic changes at critical gene regulatory regions.

Cole JJ, Robertson NA, Rather MI, Thomson JP, McBryan T, Sproul D, Wang T, Brock C, Clark W, Ideker T, Meehan RR, Miller RA, Brown-Borg HM, Adams PD.

Genome Biol. 2017 Mar 28;18(1):58. doi: 10.1186/s13059-017-1185-3.

46.

Accurate model annotation of a near-atomic resolution cryo-EM map.

Hryc CF, Chen DH, Afonine PV, Jakana J, Wang Z, Haase-Pettingell C, Jiang W, Adams PD, King JA, Schmid MF, Chiu W.

Proc Natl Acad Sci U S A. 2017 Mar 21;114(12):3103-3108. doi: 10.1073/pnas.1621152114. Epub 2017 Mar 7.

47.

Polder maps: improving OMIT maps by excluding bulk solvent.

Liebschner D, Afonine PV, Moriarty NW, Poon BK, Sobolev OV, Terwilliger TC, Adams PD.

Acta Crystallogr D Struct Biol. 2017 Feb 1;73(Pt 2):148-157. doi: 10.1107/S2059798316018210. Epub 2017 Feb 1.

48.

An editor for the generation and customization of geometry restraints.

Moriarty NW, Draizen EJ, Adams PD.

Acta Crystallogr D Struct Biol. 2017 Feb 1;73(Pt 2):123-130. doi: 10.1107/S2059798316016570. Epub 2017 Feb 1.

49.

Targeting chromatin aging - The epigenetic impact of longevity-associated interventions.

Field AE, Adams PD.

Exp Gerontol. 2017 Aug;94:29-33. doi: 10.1016/j.exger.2016.12.010. Epub 2016 Dec 13.

PMID:
27986499
50.

On-chip integration of droplet microfluidics and nanostructure-initiator mass spectrometry for enzyme screening.

Heinemann J, Deng K, Shih SC, Gao J, Adams PD, Singh AK, Northen TR.

Lab Chip. 2017 Jan 17;17(2):323-331. doi: 10.1039/c6lc01182a.

PMID:
27957569

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