July 31, 2007 ͉ vol. 104 ͉ no. 31 ͉ 12583–12950

Proceedings of the National Academy ofPNAS Sciences of the United States of America www.pnas.org Cover image: Single-molecule observation of catalytic turnover. The wide-field image was recorded during hydrolysis of fluorescein esters on a catalytic monolayer. Individual turnover events appear as isolated bright spots. Microscopic and spectroscopic studies of enzymes and inorganic agents provide evidence that catalysts, even of uniform composition, are ensembles possessing a range of activities. See the Perspective by Roeffaers et al. on pages 12603–12609. Image courtesy of Hiroshi Uji-i. From the Cover

12603 Fluorescence spectroscopy of catalysts 12709 DNA mismatch repair 12843 TNF-␣ suppresses clock genes 12942 Human impact on the biosphere

SINGLE-MOLECULE CHEMISTRY AND BIOLOGY Contents SPECIAL FEATURE

INTRODUCTORY PERSPECTIVE THIS WEEK IN PNAS 12595 Introduction to the Special Feature on Single-Molecule Chemistry and Biology 12583 In This Issue Robert J. Silbey

PERSPECTIVES COMMENTARY 12596 New directions in single-molecule imaging and analysis W. E. Moerner 12585 Our share of the planetary pie Jonathan A. Foley, Chad Monfreda, Navin Ramankutty, 12603 Single-molecule fluorescence spectroscopy in (bio)catalysis and David Zaks Maarten B. J. Roeffaers, Gert De Cremer, Hiroshi Uji-i, ➜ See companion article on page 12942 Benıˆot Muls, Bert F. Sels, Pierre A. Jacobs, Frans C. De Schryver, Dirk E. De Vos, and Johan Hofkens

RESEARCH ARTICLES INAUGURAL ARTICLE 12610 Single-molecule and ensemble fluorescence assays for a functionally important conformational change 12587 The role of skeletal muscle insulin resistance in the in T7 DNA polymerase pathogenesis of the metabolic syndrome Guobin Luo, Mina Wang, William H. Konigsberg, Kitt Falk Petersen, Sylvie Dufour, David B. Savage, and X. Sunney Xie Stefan Bilz, Gina Solomon, Shin Yonemitsu, Gary W. 12616 Strongly emissive individual DNA-encapsulated Ag Cline, Douglas Befroy, Laura Zemany, Barbara B. nanoclusters as single-molecule fluorophores Kahn, Xenophon Papademetris, Douglas L. Tom Vosch, Yasuko Antoku, Jung-Cheng Hsiang, Rothman, and Gerald I. Shulman Chris I. Richards, Jose I. Gonzalez, and Robert M. Dickson

12622 Principal-components analysis of shape fluctuations of single DNA molecules Freely available online through the PNAS open access option. Adam E. Cohen and W. E. Moerner

PNAS ͉ July 31, 2007 ͉ vol. 104 ͉ no. 31 ͉ iii–x Downloaded by guest on September 30, 2021 12628 Local viscosity of supercooled glycerol near Tg probed STATISTICS by rotational diffusion of ensembles and single 12663 Intracellular crowding defines the mode and sequence dye molecules of substrate uptake by Escherichia coli and constrains Rob Zondervan, Florian Kulzer, Gregorius C. G. Berkhout, its metabolic activity and Michel Orrit Q. K. Beg, A. Vazquez, J. Ernst, M. A. de Menezes, Z. Bar-Joseph, A.-L. Baraba´si, and Z. N. Oltvai 12634 Dissecting the multistep reaction pathway of an RNA enzyme by single-molecule kinetic ‘‘fingerprinting’’ Shixin Liu, Gregory Bokinsky, Nils G. Walter, SOCIAL SCIENCES and Xiaowei Zhuang

12640 Single-molecule FRET reveals sugar-induced PSYCHOLOGY conformational dynamics in LacY 12669 Visuomotor system uses target features unavailable Devdoot S. Majumdar, Irina Smirnova, Vladimir to conscious awareness Kasho, Eyal Nir, Xiangxu Kong, Shimon Weiss, Gordon Binsted, Kyle Brownell, Zofia Vorontsova, and H. Ronald Kaback Matthew Heath, and Deborah Saucier

12646 Fueling protein–DNA interactions inside BIOLOGICAL SCIENCES porous nanocontainers Ibrahim Cisse, Burak Okumus, Chirlmin Joo, and Taekjip Ha BIOCHEMISTRY

12651 Probing nucleation, reverse annealing, and chaperone 12610 Single-molecule and ensemble fluorescence assays function along the reaction path of HIV-1 for a functionally important conformational change single-strand transfer in T7 DNA polymerase Yining Zeng, Hsiao-Wei Liu, Christy F. Landes, Guobin Luo, Mina Wang, William H. Konigsberg, Yoen Joo Kim, Xiaojing Ma, Yongjin Zhu, and X. Sunney Xie Karin Musier-Forsyth, and Paul F. Barbara 12673 Single A326G mutation converts human CYP24A1 from 25-OH-D3-24-hydroxylase into -23-hydroxylase, generating 1␣,25-(OH)2D3-26,23-lactone PHYSICAL SCIENCES David E. Prosser, Martin Kaufmann, Brendan O’Leary, Valarie Byford, and Glenville Jones

APPLIED MATHEMATICS 12679 Increased prostate cell proliferation and loss of cell differentiation in mice lacking prostate epithelial 12657 Efficient Monte Carlo sampling by androgen receptor parallel marginalization Chun-Te Wu, Saleh Altuwaijri, William A. Ricke, Jonathan Weare Shu-Pin Huang, Shuyuan Yeh, Caixia Zhang, Yuanjie Niu, Meng-Ying Tsai, 12726 Combinatorial promoter design for engineering noisy and Chawnshang Chang gene expression Kevin F. Murphy, Ga´bor Bala´zsi, and James J. Collins 12685 Crystal structure of the GINS complex and functional insights into its role in DNA replication Y. Paul Chang, Ganggang Wang, Vladimir Bermudez, CHEMISTRY Jerard Hurwitz, and Xiaojiang S. Chen 12610 Single-molecule and ensemble fluorescence assays for a functionally important conformational change 12691 Epigenetic regulation of the Drosophila chromosome 4 in T7 DNA polymerase by the histone H3K9 methyltransferase dSETDB1 Guobin Luo, Mina Wang, William H. Konigsberg, Tsai-Yu Tzeng, Chi-Hua Lee, Li-Wei Chan, and X. Sunney Xie and C.-K. James Shen

12616 Strongly emissive individual DNA-encapsulated Ag 12697 Design of protein–membrane interaction inhibitors by nanoclusters as single-molecule fluorophores virtual ligand screening, proof of concept with the C2 Tom Vosch, Yasuko Antoku, Jung-Cheng Hsiang, domain of factor V Chris I. Richards, Jose I. Gonzalez, Kenneth Segers, Olivier Sperandio, Markus Sack, and Robert M. Dickson Rainer Fischer, Maria A. Miteva, Jan Rosing, Gerry A. F. Nicolaes, and Bruno O. Villoutreix

PHYSICS 12703 Phage escape libraries for checkmate analysis Tobin J. Dickerson, Kathleen M. McKenzie, Amanda S. 12622 Principal-components analysis of shape fluctuations Hoyt, Malcolm R. Wood, Kim D. Janda, Sydney B. of single DNA molecules Brenner, and Richard A. Lerner Adam E. Cohen and W. E. Moerner 12709 Protein roadblocks and helix discontinuities are barriers 12628 Local viscosity of supercooled glycerol near Tg probed to the initiation of mismatch repair by rotational diffusion of ensembles and single Anna Pluciennik and Paul Modrich dye molecules Rob Zondervan, Florian Kulzer, Gregorius C. G. Berkhout, 12714 A closer look at energy transduction in muscle and Michel Orrit Hirofumi Onishi and Manuel F. Morales

PNAS ͉ July 31, 2007 ͉ vol. 104 ͉ no. 31 ͉ v Downloaded by guest on September 30, 2021 12720 Reevaluating the relationship between EPR spectra 12767 15N photochemically induced dynamic nuclear and enzyme structure for the iron–sulfur clusters polarization magic-angle spinning NMR analysis in NADH:quinone oxidoreductase of the electron donor of photosystem II Gregory Yakovlev, Torsten Reda, and Judy Hirst Anna Diller, Esha Roy, Peter Gast, Hans J. van Gorkom, Huub J. M. de Groot, Clemens Glaubitz, Gunnar BIOPHYSICS Jeschke, Jo¨rg Matysik, and A. Alia 12622 Principal-components analysis of shape fluctuations of single DNA molecules 12772 Design of helical, oligomeric HIV-1 fusion inhibitor peptides with potent activity against Adam E. Cohen and W. E. Moerner enfuvirtide-resistant virus 12634 Dissecting the multistep reaction pathway of an RNA John J. Dwyer, Karen L. Wilson, Donna K. Davison, enzyme by single-molecule kinetic ‘‘fingerprinting’’ Stephanie A. Freel, Jennifer E. Seedorff, Stephen A. Shixin Liu, Gregory Bokinsky, Nils G. Walter, Wring, Nicolai A. Tvermoes, Thomas J. Matthews, and Xiaowei Zhuang Michael L. Greenberg, and Mary K. Delmedico 12640 Single-molecule FRET reveals sugar-induced conformational dynamics in LacY CELL BIOLOGY Devdoot S. Majumdar, Irina Smirnova, Vladimir Kasho, Eyal Nir, Xiangxu Kong, Shimon Weiss, 12778 RPA and ATR link transcriptional stress to p53 and H. Ronald Kaback Frederick A. Derheimer, Heather M. O’Hagan, Heather M. Krueger, Sheela Hanasoge, Michelle T. 12646 Fueling protein–DNA interactions inside Paulsen, and Mats Ljungman porous nanocontainers Ibrahim Cisse, Burak Okumus, Chirlmin Joo, and Taekjip Ha 12784 Protein 4.1B suppresses prostate cancer progression and metastasis 12651 Probing nucleation, reverse annealing, and chaperone Sunny Y. Wong, Herbert Haack, Joseph L. Kissil, Marc Barry, function along the reaction path of HIV-1 Roderick T. Bronson, Steven S. Shen, Charles A. Whittaker, single-strand transfer Denise Crowley, and Richard O. Hynes Yining Zeng, Hsiao-Wei Liu, Christy F. Landes, Yoen Joo Kim, Xiaojing Ma, Yongjin Zhu, Karin 12790 Elevated NF-␬B responses and FLIP levels in leukemic but Musier-Forsyth, and Paul F. Barbara not normal lymphocytes: Reduction by salicylate allows 12663 Intracellular crowding defines the mode and sequence TNF-induced apoptosis of substrate uptake by Escherichia coli and constrains Colin Rae, Susana Langa, Steven J. Tucker, its metabolic activity and David J. MacEwan Q. K. Beg, A. Vazquez, J. Ernst, M. A. de Menezes, Z. Bar-Joseph, A.-L. Baraba´si, and Z. N. Oltvai DEVELOPMENTAL BIOLOGY 12726 Combinatorial promoter design for engineering noisy gene expression 12796 Metabolic plasticity during mammalian development Kevin F. Murphy, Ga´bor Bala´zsi, and James J. Collins is directionally dependent on early nutritional status Peter D. Gluckman, Karen A. Lillycrop, Mark H. Vickers, 12732 Quantitative characterization of cell synchronization Anthony B. Pleasants, Emma S. Phillips, Alan S. Beedle, in yeast Graham C. Burdge, and Mark A. Hanson Sune Danø, Mads Find Madsen, and Preben Graae Sørensen 12737 An unusual cytokine:Ig-domain interaction revealed in the crystal structure of leukemia inhibitory factor (LIF) EVOLUTION in complex with the LIF receptor 12801 Coevolution of robustness, epistasis, and recombination Trevor Huyton, Jian-Guo Zhang, Cindy S. Luo, Mei-Zhen favors asexual reproduction Lou, Douglas J. Hilton, Nicos A. Nicola, Thomas MacCarthy and Aviv Bergman and Thomas P. J. Garrett 12743 Reversibility in nucleocytoplasmic transport 12807 Rapid asymmetric evolution of a dual-coding tumor Ronen Benjamine Kopito and Michael Elbaum suppressor INK4a/ARF locus contradicts its function Radek Szklarczyk, Jaap Heringa, Sergei Kosakovsky 12749 Energy transport in peptide helices Pond, and Anton Nekrutenko Virgiliu Botan, Ellen H. G. Backus, Rolf Pfister, Alessandro Moretto, Marco Crisma, Claudio Toniolo, Phuong H. Nguyen, Gerhard GENETICS Stock, and Peter Hamm 12813 Identification of a locus control region for 12755 Fast-scan atomic force microscopy reveals that the quadruplicated green-sensitive opsin type III restriction enzyme EcoP15I is capable genes in zebrafish of DNA translocation and looping Taro Tsujimura, Akito Chinen, and Shoji Kawamura Neal Crampton, Masatoshi Yokokawa, David T. F. Dryden, J. Michael Edwardson, Desirazu N. Rao, Kunio Takeyasu, 12819 High-resolution analysis of Drosophila heterochromatin Shige H. Yoshimura, and Robert M. Henderson organization using SuUR Su(var)3-9 double mutants 12761 Identification of a chloride ion binding site Eugenia N. Andreyeva, Tatyana D. Kolesnikova, Olga V. ,in Na؉/Cl؊-dependent transporters Demakova, Maria Mendez-Lago, Galina V. Pokholkova Lucy R. Forrest, Sotiria Tavoulari, Yuan-Wei Zhang, Elena S. Belyaeva, Fabrizio Rossi, Patrizio Dimitri, Gary Rudnick, and Barry Honig Alfredo Villasante, and Igor F. Zhimulev

PNAS ͉ July 31, 2007 ͉ vol. 104 ͉ no. 31 ͉ vii Downloaded by guest on September 30, 2021 12825 Genome sequencing and comparative analysis 12873 Epinephrine enhances lysosomal enzyme delivery across of Saccharomyces cerevisiae strain YJM789 the blood–brain barrier by up-regulation of the Wu Wei, John H. McCusker, Richard W. Hyman, Ted mannose 6-phosphate receptor Jones, Ye Ning, Zhiwei Cao, Zhenglong Gu, Dan Akihiko Urayama, Jeffrey H. Grubb, William A. Banks, Bruno, Molly Miranda, Michelle Nguyen, Julie and William S. Sly Wilhelmy, Caridad Komp, Raquel Tamse, Xiaojing Wang, Peilin Jia, Philippe Luedi, 12879 Attenuated Salmonella engineered to produce human Peter J. Oefner, Lior David, Fred S. cytokine LIGHT inhibit tumor growth Dietrich, Yixue Li, Ronald W. Markus Loeffler, Gaelle Le’Negrate, Maryla Krajewska, Davis, and Lars M. Steinmetz and John C. Reed 12831 A unified genetic theory for sporadic and inherited autism 12884 Cellular cofactors affecting hepatitis C virus infection and replication Xiaoyue Zhao, Anthony Leotta, Vlad Kustanovich, Clara Lajonchere, Daniel H. Geschwind, Kiely Law, Glenn Randall, Maryline Panis, Jacob D. Cooper, Paul Law, Shanping Qiu, Catherine Lord, Jonathan Timothy L. Tellinghuisen, Karen E. Sukhodolets, Sebat, Kenny Ye, and Michael Wigler Sebastien Pfeffer, Markus Landthaler, Pablo Landgraf, Sherry Kan, Brett D. Lindenbach, Minchen Chien, David B. Weir, James J. IMMUNOLOGY Russo, Jingyue Ju, Michael J. Brownstein, 12837 Vaccination with an NY-ESO-1 peptide of HLA class I/II Robert Sheridan, Chris Sander, Mihaela specificities induces integrated humoral and T cell Zavolan, Thomas Tuschl, and Charles M. Rice responses in ovarian cancer Kunle Odunsi, Feng Qian, Junko Matsuzaki, Paulette 12890 Transcriptional network governing the angiogenic Mhawech-Fauceglia, Christopher Andrews, Eric W. switch in human pancreatic cancer Hoffman, Linda Pan, Gerd Ritter, Jeannine Amir Abdollahi, Christian Schwager, Jo¨rg Kleeff, Villella, Bridget Thomas, Kerry Rodabaugh, Irene Esposito, Sophie Domhan, Peter Peschke, Shashikant Lele, Protul Shrikant, Kai Hauser, Philip Hahnfeldt, Lynn Hlatky, Lloyd J. Old, and Sacha Gnjatic Ju¨rgen Debus, Jeffrey M. Peters, Helmut Friess, Judah Folkman, and Peter E. Huber 12843 TNF-␣ suppresses the expression of clock genes by interfering with E-box-mediated transcription Gionata Cavadini, Saskia Petrzilka, Philipp Kohler, MICROBIOLOGY Corinne Jud, Irene Tobler, Thomas Birchler, 12896 ppGpp regulation of RpoS degradation via anti-adaptor and Adriano Fontana protein IraP Alexandre Bougdour and Susan Gottesman 12849 Innate immunity and transcription of MGAT-III and Toll-like receptors in Alzheimer’s disease patients are improved by bisdemethoxycurcumin 12902 Evidence that RNA silencing functions as an antiviral defense mechanism in fungi Milan Fiala, Philip T. Liu, Araceli Espinosa-Jeffrey, Mark J. Rosenthal, George Bernard, John M. Ringman, Gert C. Segers, Xuemin Zhang, Fuyou Deng, Qihong Sun, James Sayre, Laura Zhang, Justin Zaghi, Sheila and Donald L. Nuss Dejbakhsh, Ben Chiang, James Hui, Michelle Mahanian, Anita Baghaee, Pamela Hong, 12907 Clonal success of piliated penicillin and John Cashman nonsusceptible pneumococci K. Sjo¨stro¨m, C. Blomberg, J. Fernebro, J. Dagerhamn, MEDICAL SCIENCES E. Morfeldt, M. A. Barocchi, S. Browall, M. Moschioni, M. Andersson, F. Henriques, B. Albiger, Rino Rappuoli, 12587 The role of skeletal muscle insulin resistance in the S. Normark, and B. Henriques-Normark pathogenesis of the metabolic syndrome Kitt Falk Petersen, Sylvie Dufour, David B. Savage, Stefan Bilz, Gina Solomon, Shin Yonemitsu, Gary W. NEUROSCIENCE Cline, Douglas Befroy, Laura Zemany, Barbara B. 12669 Visuomotor system uses target features unavailable Kahn, Xenophon Papademetris, Douglas L. to conscious awareness Rothman, and Gerald I. Shulman Gordon Binsted, Kyle Brownell, Zofia Vorontsova, Matthew Heath, and Deborah Saucier 12855 Feedback activation of factor XI by thrombin does not occur in plasma 12913 Sumoylation in axons triggers retrograde transport Donna L. Pedicord, Dietmar Seiffert, and Yuval Blat of the RNA-binding protein La 12861 Fasting-dependent glucose and lipid metabolic Erna A. van Niekerk, Dianna E. Willis, Jay H. Chang, response through hepatic sirtuin 1 Kerstin Reumann, Tilman Heise, and Jeffery L. Twiss Joseph T. Rodgers and Pere Puigserver 12919 Smad-interacting protein-1 (Zfhx1b) acts upstream 12867 Quantitative analysis of EGFRvIII cellular signaling of Wnt signaling in the mouse hippocampus networks reveals a combinatorial therapeutic and controls its formation strategy for glioblastoma Amaya Miquelajauregui, Tom Van de Putte, Alexander Paul H. Huang, Akitake Mukasa, Rudy Bonavia, Polyakov, Anjana Nityanandam, Sridhar Boppana, Ryan A. Flynn, Zachary E. Brewer, Webster K. Eve Seuntjens, Anton Karabinos, Yujiro Higashi, Cavenee, Frank B. Furnari, and Forest M. White Danny Huylebroeck, and Victor Tarabykin

PNAS ͉ July 31, 2007 ͉ vol. 104 ͉ no. 31 ͉ ix Downloaded by guest on September 30, 2021 12925 Silencing of genes in cultured Drosophila neurons SUSTAINABILITY SCIENCE by RNA interference 12942 Quantifying and mapping the human appropriation of Shail K. Sharma and Marshall Nirenberg net primary production in earth’s terrestrial ecosystems Helmut Haberl, K. Heinz Erb, Fridolin Krausmann, 12931 General design principle for scalable neural circuits Veronika Gaube, Alberte Bondeau, Christoph in a vertebrate retina Plutzar, Simone Gingrich, Wolfgang Lucht, Sunhwa Lee and Charles F. Stevens and Marina Fischer-Kowalski ➜ See Commentary on page 12585 12948 Invasive range expansion by the Humboldt squid, PHARMACOLOGY Dosidicus gigas, in the eastern North Pacific 12936 Voluntary exercise together with oral caffeine markedly Louis D. Zeidberg and Bruce H. Robison stimulates UVB light-induced apoptosis and decreases tissue fat in SKH-1 mice xi–xii Author Index Yao-Ping Lu, Bonnie Nolan, You-Rong Lou, Qing-Yun Peng, George C. Wagner, and Allan H. Conney xiii Subscription Form

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