| | This journal provides immediate access to some articles. In This Issue Proc Natl Acad Sci U S A. 2005 May 10; 102(19): 6637–6638. doi: 10.1073/iti1905102.PMCID: PMC1100804 Introduction Chemical Theory and Computation Special Feature: Chemical theory and computation Bruce J. Berne PMCID: PMC1100803 Commentary Remarkable diversity of mammalian pheromone receptor repertoires Ivan Rodriguez PMCID: PMC1100792 Perspective Proof of physical exchange of genes on the chromosomes Edward Coe and Lee B. Kass PMCID: PMC1100733 Chemical Theory and Computation Special Feature Perspective Ab initio quantum chemistry: Methodology and applications Richard A. Friesner PMCID: PMC1100737 Ab initio molecular dynamics: Concepts, recent developments, and future trends Radu Iftimie, Peter Minary, and Mark E. Tuckerman PMCID: PMC1100773 Quantum dynamics of complex molecular systems William H. Miller PMCID: PMC1100740 Potential energy functions for atomic-level simulations of water and organic and biomolecular systems William L. Jorgensen and Julian Tirado-Rives PMCID: PMC1100738 Materials by numbers: Computations as tools of discovery Uzi Landman PMCID: PMC1100739 Molecular dynamics and protein function M. Karplus and J. Kuriyan PMCID: PMC1100762 Molecular dynamics studies of heterogeneous dynamics and dynamic crossover in supercooled atomic liquids Hans C. Andersen PMCID: PMC1100779 Chemical Theory and Computation Special Feature: Auxiliary basis expansions for large-scale electronic structure calculations Yousung Jung, Alex Sodt, Peter M. W. Gill, and Martin Head-Gordon PMCID: PMC1100752 Chemical Theory and Computation Special Feature: (G–H)•–C and G–(C–H)• radicals derived from the guanine·cytosine base pair cause DNA subunit lesions Partha Pratim Bera and Henry F. Schaefer, III PMCID: PMC1100756 Chemical Theory and Computation Special Feature: Ab initio molecular dynamics and quasichemical study of H+(aq) D. Asthagiri, L. R. Pratt, and J. D. Kress PMCID: PMC1100742 Chemical Theory and Computation Special Feature: Static and dynamic quantum effects in molecular liquids: A linearized path integral description of water Jens Aage Poulsen, Gunnar Nyman, and Peter J. Rossky PMCID: PMC1100757 Chemical Theory and Computation Special Feature: Linearized path integral approach for calculating nonadiabatic time correlation functions Sara Bonella, Daniel Montemayor, and David F. Coker PMCID: PMC1100750 Chemical Theory and Computation Special Feature: Quantum corrections in vibrational and electronic condensed phase spectroscopy: Line shapes and echoes C. P. Lawrence and J. L. Skinner PMCID: PMC1100759 Chemical Theory and Computation Special Feature: Vibrational energy relaxation in proteins Hiroshi Fujisaki and John E. Straub PMCID: PMC1100765 Chemical Theory and Computation Special Feature: Reaction coordinates and rates from transition paths Robert B. Best and Gerhard Hummer PMCID: PMC1100744 Chemical Theory and Computation Special Feature: Finding transition states for crystalline solid–solid phase transformations Kyle J. Caspersen and Emily A. Carter PMCID: PMC1100746 Chemical Theory and Computation Special Feature: Quantum mechanical reaction rate constants by vibrational configuration interaction: The OH + H2→H2O + H reaction as a function of temperature Arindam Chakraborty and Donald G. Truhlar PMCID: PMC1100741 Chemical Theory and Computation Special Feature: Free energies of ligand binding for structurally diverse compounds Chris Oostenbrink and Wilfred F. van Gunsteren PMCID: PMC1100734 Chemical Theory and Computation Special Feature: Perspective on the reactions between F– and CH3CH2F: The free energy landscape of the E2 and SN2 reaction channels Bernd Ensing and Michael L. Klein PMCID: PMC1100743 Chemical Theory and Computation Special Feature: Comparative study of generalized Born models: Protein dynamics Hao Fan, Alan E. Mark, Jiang Zhu, and Barry Honig PMCID: PMC1100760 Chemical Theory and Computation Special Feature: Simulations of the pressure and temperature unfolding of an α-helical peptide Dietmar Paschek, S. Gnanakaran, and Angel E. Garcia PMCID: PMC1100754 Chemical Theory and Computation Special Feature: Interfacial folding and membrane insertion of designed peptides studied by molecular dynamics simulations Wonpil Im and Charles L. Brooks, III PMCID: PMC1100747 Chemical Theory and Computation Special Feature: Nonpolar solutes enhance water structure within hydration shells while reducing interactions between them Tanya M. Raschke and Michael Levitt PMCID: PMC1100774 Chemical Theory and Computation Special Feature: Structural dynamics of the lac repressor–DNA complex revealed by a multiscale simulation Elizabeth Villa, Alexander Balaeff, and Klaus Schulten PMCID: PMC1100768 Chemical Theory and Computation Special Feature: Mechanical unfolding of RNA hairpins Changbong Hyeon and D. Thirumalai PMCID: PMC1100749 Chemical Theory and Computation Special Feature: Computer simulation of explicit proton translocation in cytochrome c oxidase: The D-pathway Jiancong Xu and Gregory A. Voth PMCID: PMC1100745 Chemical Theory and Computation Special Feature: Protein folding pathways from replica exchange simulations and a kinetic network model Michael Andrec, Anthony K. Felts, Emilio Gallicchio, and Ronald M. Levy PMCID: PMC1100763 Chemical Theory and Computation Special Feature: Impact of distal mutations on the network of coupled motions correlated to hydride transfer in dihydrofolate reductase Kim F. Wong, Tzvia Selzer, Stephen J. Benkovic, and Sharon Hammes-Schiffer PMCID: PMC1100751 Chemical Theory and Computation Special Feature: A gating mechanism proposed from a simulation of a human α7 nicotinic acetylcholine receptor Richard J. Law, Richard H. Henchman, and J. Andrew McCammon PMCID: PMC1100735 Chemical Theory and Computation Special Feature: Computer simulations of protein functions: Searching for the molecular origin of the replication fidelity of DNA polymerases Jan Florián, Myron F. Goodman, and Arieh Warshel PMCID: PMC1100748 Chemical Theory and Computation Special Feature: Calculation of absolute protein–ligand binding free energy from computer simulations Hyung-June Woo and Benoît Roux PMCID: PMC1100764 Physical Sciences Chemistry Chemical Theory and Computation Special Feature: Auxiliary basis expansions for large-scale electronic structure calculations Yousung Jung, Alex Sodt, Peter M. W. Gill, and Martin Head-Gordon PMCID: PMC1100752 Chemical Theory and Computation Special Feature: (G–H)•–C and G–(C–H)• radicals derived from the guanine·cytosine base pair cause DNA subunit lesions Partha Pratim Bera and Henry F. Schaefer, III PMCID: PMC1100756 Chemical Theory and Computation Special Feature: Ab initio molecular dynamics and quasichemical study of H+(aq) D. Asthagiri, L. R. Pratt, and J. D. Kress PMCID: PMC1100742 Chemical Theory and Computation Special Feature: Static and dynamic quantum effects in molecular liquids: A linearized path integral description of water Jens Aage Poulsen, Gunnar Nyman, and Peter J. Rossky PMCID: PMC1100757 Chemical Theory and Computation Special Feature: Linearized path integral approach for calculating nonadiabatic time correlation functions Sara Bonella, Daniel Montemayor, and David F. Coker PMCID: PMC1100750 Chemical Theory and Computation Special Feature: Quantum corrections in vibrational and electronic condensed phase spectroscopy: Line shapes and echoes C. P. Lawrence and J. L. Skinner PMCID: PMC1100759 Chemical Theory and Computation Special Feature: Reaction coordinates and rates from transition paths Robert B. Best and Gerhard Hummer PMCID: PMC1100744 Chemical Theory and Computation Special Feature: Finding transition states for crystalline solid–solid phase transformations Kyle J. Caspersen and Emily A. Carter PMCID: PMC1100746 Chemical Theory and Computation Special Feature: Quantum mechanical reaction rate constants by vibrational configuration interaction: The OH + H2→H2O + H reaction as a function of temperature Arindam Chakraborty and Donald G. Truhlar PMCID: PMC1100741 Chemical Theory and Computation Special Feature: Free energies of ligand binding for structurally diverse compounds Chris Oostenbrink and Wilfred F. van Gunsteren PMCID: PMC1100734 Chemical Theory and Computation Special Feature: Perspective on the reactions between F– and CH3CH2F: The free energy landscape of the E2 and SN2 reaction channels Bernd Ensing and Michael L. Klein PMCID: PMC1100743 Chemical Theory and Computation Special Feature: Comparative study of generalized Born models: Protein dynamics Hao Fan, Alan E. Mark, Jiang Zhu, and Barry Honig PMCID: PMC1100760 Chemical Theory and Computation Special Feature: Simulations of the pressure and temperature unfolding of an α-helical peptide Dietmar Paschek, S. Gnanakaran, and Angel E. Garcia PMCID: PMC1100754 Chemical Theory and Computation Special Feature: Interfacial folding and membrane insertion of designed peptides studied by molecular dynamics simulations Wonpil Im and Charles L. Brooks, III PMCID: PMC1100747 Chemical Theory and Computation Special Feature: Nonpolar solutes enhance water structure within hydration shells while reducing interactions between them Tanya M. Raschke and Michael Levitt PMCID: PMC1100774 Chemical Theory and Computation Special Feature: Structural dynamics of the lac repressor–DNA complex revealed by a multiscale simulation Elizabeth Villa, Alexander Balaeff, and Klaus Schulten PMCID: PMC1100768 Chemical Theory and Computation Special Feature: Mechanical unfolding of RNA hairpins Changbong Hyeon and D. Thirumalai PMCID: PMC1100749 Chemical Theory and Computation Special Feature: Computer simulation of explicit proton translocation in cytochrome c oxidase: The D-pathway Jiancong Xu and Gregory A. Voth PMCID: PMC1100745 Chemical Theory and Computation Special Feature: Protein folding pathways from replica exchange simulations and a kinetic network model Michael Andrec, Anthony K. Felts, Emilio Gallicchio, and Ronald M. Levy PMCID: PMC1100763 Chemical Theory and Computation Special Feature: Impact of distal mutations on the network of coupled motions correlated to hydride transfer in dihydrofolate reductase Kim F. Wong, Tzvia Selzer, Stephen J. Benkovic, and Sharon Hammes-Schiffer PMCID: PMC1100751 Chemical Theory and Computation Special Feature: A gating mechanism proposed from a simulation of a human α7 nicotinic acetylcholine receptor Richard J. Law, Richard H. Henchman, and J. Andrew McCammon PMCID: PMC1100735 Chemical Theory and Computation Special Feature: Computer simulations of protein functions: Searching for the molecular origin of the replication fidelity of DNA polymerases Jan Florián, Myron F. Goodman, and Arieh Warshel PMCID: PMC1100748 Chemical Theory and Computation Special Feature: Calculation of absolute protein–ligand binding free energy from computer simulations Hyung-June Woo and Benoît Roux PMCID: PMC1100764 Calix[6]tren and copper(II): A third generation of funnel complexes on the way to redox calix-zymes Guillaume Izzet, Bénédicte Douziech, Thierry Prangé, Alain Tomas, Ivan Jabin, Yves Le Mest, and Olivia Reinaud PMCID: PMC1100775 Computer Sciences Spatiotemporal maturation patterns of murine brain quantified by diffusion tensor MRI and deformation-based morphometry Ragini Verma, Susumu Mori, Dinggang Shen, Paul Yarowsky, Jiangyang Zhang, and Christos Davatzikos PMCID: PMC1100736 Mathematics Lower bounds for moments of L-functions Z. Rudnick and K. Soundararajan PMCID: PMC1100781 Physics Origin of the long-range attraction between surfactant-coated surfaces Emily E. Meyer, Qi Lin, Tue Hassenkam, Emin Oroudjev, and Jacob N. Israelachvili PMCID: PMC1100788 Biological Sciences Chemical Theory and Computation Special Feature: Comparative study of generalized Born models: Protein dynamics Hao Fan, Alan E. Mark, Jiang Zhu, and Barry Honig PMCID: PMC1100760 Chemical Theory and Computation Special Feature: Simulations of the pressure and temperature unfolding of an α-helical peptide Dietmar Paschek, S. Gnanakaran, and Angel E. Garcia PMCID: PMC1100754 Chemical Theory and Computation Special Feature: Structural dynamics of the lac repressor–DNA complex revealed by a multiscale simulation Elizabeth Villa, Alexander Balaeff, and Klaus Schulten PMCID: PMC1100768 Chemical Theory and Computation Special Feature: Protein folding pathways from replica exchange simulations and a kinetic network model Michael Andrec, Anthony K. Felts, Emilio Gallicchio, and Ronald M. Levy PMCID: PMC1100763 Chemical Theory and Computation Special Feature: A gating mechanism proposed from a simulation of a human α7 nicotinic acetylcholine receptor Richard J. Law, Richard H. Henchman, and J. Andrew McCammon PMCID: PMC1100735 Applied Biological Sciences Interleukin-6 regulates the zinc transporter Zip14 in liver and contributes to the hypozincemia of the acute-phase response Juan P. Liuzzi, Louis A. Lichten, Seth Rivera, Raymond K. Blanchard, Tolunay Beker Aydemir, Mitchell D. Knutson, Tomas Ganz, and Robert J. Cousins PMCID: PMC1100791 Biochemistry A single intermolecular contact mediates intramolecular stabilization of both RNA and protein Valerie Calabro, Matthew D. Daugherty, and Alan D. Frankel PMCID: PMC1100766 Engineering of protease variants exhibiting high catalytic activity and exquisite substrate selectivity Navin Varadarajan, Jongsik Gam, Mark J. Olsen, George Georgiou, and Brent L. Iverson PMCID: PMC1100772 A unified assembly mode revealed by the structures of tetrameric L27 domain complexes formed by mLin-2/mLin-7 and Patj/Pals1 scaffold proteins Wei Feng, Jia-fu Long, and Mingjie Zhang PMCID: PMC1100767 Holliday junction-binding peptides inhibit distinct junction-processing enzymes Kevin V. Kepple, Jeffrey L. Boldt, and Anca M. Segall PMCID: PMC1100769 Biophysics Chemical Theory and Computation Special Feature: Vibrational energy relaxation in proteins Hiroshi Fujisaki and John E. Straub PMCID: PMC1100765 From the Cover:
Structural mechanism of the recovery stroke in the Myosin molecular motor Stefan Fischer, Björn Windshügel, Daniel Horak, Kenneth C. Holmes, and Jeremy C. Smith PMCID: PMC1100758 From the Cover:
Leptosphaeria rhodopsin: Bacteriorhodopsin-like proton pump from a eukaryote Stephen A. Waschuk, Arandi G. Bezerra, Jr., Lichi Shi, and Leonid S. Brown PMCID: PMC1100770 Cell Biology Neutrophil microtubules suppress polarity and enhance directional migration Jingsong Xu, Fei Wang, Alexandra Van Keymeulen, Maike Rentel, and Henry R. Bourne PMCID: PMC1087512 Developmental Biology p130Rb2 and p27kip1 cooperate to control mobilization of angiogenic progenitors from the bone marrow Anxo Vidal, Stergios Zacharoulis, Wenjun Guo, David Shaffer, Filippo Giancotti, Anna H. Bramley, Carmen de la Hoz, Kristian K. Jensen, Daniel Kato, Daniel D. MacDonald, Joseph Knowles, Nancy Yeh, Lawrence A. Frohman, Shahin Rafii, David Lyden, and Andrew Koff PMCID: PMC1088064 Genetics Fine-mapping milk production quantitative trait loci on BTA6: Analysis of the bovine osteopontin gene Robert D. Schnabel, Jong-Joo Kim, Melissa S. Ashwell, Tad S. Sonstegard, Curtis P. Van Tassell, Erin E. Connor, and Jeremy F. Taylor PMCID: PMC1100795 Targeting c-Myc-activated genes with a correlation method: Detection of global changes in large gene expression network dynamics D. Remondini, B. O'Connell, N. Intrator, J. M. Sedivy, N. Neretti, G. C. Castellani, and L. N. Cooper PMCID: PMC1100785 The THAP domain of THAP1 is a large C2CH module with zinc-dependent sequence-specific DNA-binding activity Thomas Clouaire, Myriam Roussigne, Vincent Ecochard, Catherine Mathe, François Amalric, and Jean-Philippe Girard PMCID: PMC1100732 Evidence in vivo that the DEAD-box RNA helicase RhlB facilitates the degradation of ribosome-free mRNA by RNase E Vanessa Khemici, Leonora Poljak, Isabelle Toesca, and Agamemnon J. Carpousis PMCID: PMC1100780 Immunology Discovery of a unique Ig heavy-chain isotype (IgT) in rainbow trout: Implications for a distinctive B cell developmental pathway in teleost fish John D. Hansen, Eric D. Landis, and Ruth B. Phillips PMCID: PMC1100771 Immunomodulatory oligonucleotides containing a cytosine-phosphate-2′-deoxy-7-deazaguanosine motif as potent Toll-like receptor 9 agonists Ekambar R. Kandimalla, Lakshmi Bhagat, Yukui Li, Dong Yu, Daqing Wang, Yan-Ping Cong, Sam S. Song, Jimmy X. Tang, Tim Sullivan, and Sudhir Agrawal PMCID: PMC1100782 Disruption of the Jnk2 (Mapk9) gene reduces destructive insulitis and diabetes in a mouse model of type I diabetes Anja Jaeschke, Mercedes Rincón, Beth Doran, Judith Reilly, Donna Neuberg, Dale L. Greiner, Leonard D. Shultz, Aldo A. Rossini, Richard A. Flavell, and Roger J. Davis PMCID: PMC1100789 Medical Sciences A genetically defined mouse ovarian carcinoma model for the molecular characterization of pathway-targeted therapy and tumor resistance Deyin Xing and Sandra Orsulic PMCID: PMC1087513 The Sca-1 cell surface marker enriches for a prostate-regenerating cell subpopulation that can initiate prostate tumorigenesis Li Xin, Devon A. Lawson, and Owen N. Witte PMCID: PMC1087514 STAT3- and DNA methyltransferase 1-mediated epigenetic silencing of SHP-1 tyrosine phosphatase tumor suppressor gene in malignant T lymphocytes Qian Zhang, Hong Y. Wang, Michal Marzec, Puthiyaveettil N. Raghunath, Tomohiko Nagasawa, and Mariusz A. Wasik PMCID: PMC1100783 Caspase inhibition reduces tubular apoptosis and proliferation and slows disease progression in polycystic kidney disease Yunxia Tao, Jun Kim, Sarah Faubel, Joe C. Wu, Sandor A. Falk, Robert W. Schrier, and Charles L. Edelstein PMCID: PMC1100753 From the Cover:
Polyclonality of familial murine adenomas: Analyses of mouse chimeras with low tumor multiplicity suggest short-range interactions Andrew T. Thliveris, Richard B. Halberg, Linda Clipson, William F. Dove, Ruth Sullivan, Mary Kay Washington, Stephen Stanhope, and Michael A. Newton PMCID: PMC1100801 Exogenous nitric oxide reduces glucose transporters translocation and lactate production in ischemic myocardium in vivo Biao Lei, Ken Matsuo, Volodymyr Labinskyy, Naveen Sharma, Margaret P. Chandler, Anna Ahn, Thomas H. Hintze, William C. Stanley, and Fabio A. Recchia PMCID: PMC1100777 Microbiology bptA (bbe16) is essential for the persistence of the Lyme disease spirochete, Borrelia burgdorferi, in its natural tick vector Andrew T. Revel, Jon S. Blevins, Consuelo Almazán, Lori Neil, Katherine M. Kocan, José de la Fuente, Kayla E. Hagman, and Michael V. Norgard PMCID: PMC1100799 Neuroscience Spatiotemporal maturation patterns of murine brain quantified by diffusion tensor MRI and deformation-based morphometry Ragini Verma, Susumu Mori, Dinggang Shen, Paul Yarowsky, Jiangyang Zhang, and Christos Davatzikos PMCID: PMC1100736 Bone morphogenetic protein 9 induces the transcriptome of basal forebrain cholinergic neurons Ignacio Lopez-Coviella, Maximillian T. Follettie, Tiffany J. Mellott, Vesela P. Kovacheva, Barbara E. Slack, Veronica Diesl, Brygida Berse, R. Scott Thies, and Jan Krzysztof Blusztajn PMCID: PMC1088172 Inhibition of glycogen synthase kinase-3 by lithium correlates with reduced tauopathy and degeneration in vivo Wendy Noble, Emmanuel Planel, Cindy Zehr, Vicki Olm, Jordana Meyerson, Farhana Suleman, Kate Gaynor, Lili Wang, John LaFrancois, Boris Feinstein, Mark Burns, Pavan Krishnamurthy, Yi Wen, Ratan Bhat, Jada Lewis, Dennis Dickson, and Karen Duff PMCID: PMC1088065 Representations of faces and body parts in macaque temporal cortex: A functional MRI study Mark A. Pinsk, Kevin DeSimone, Tirin Moore, Charles G. Gross, and Sabine Kastner PMCID: PMC1100800 Background gamma rhythmicity and attention in cortical local circuits: A computational study Christoph Börgers, Steven Epstein, and Nancy J. Kopell PMCID: PMC1100794 Pharmacology 5-Methyltetrahydrofolate and tetrahydrobiopterin can modulate electrotonically mediated endothelium-dependent vascular relaxation Tudor M. Griffith, Andrew T. Chaytor, Linda M. Bakker, and David H. Edwards PMCID: PMC1100761 Physiology Estrogenic chemicals in plastic and oral contraceptives disrupt development of the fetal mouse prostate and urethra Barry G. Timms, Kembra L. Howdeshell, Lesley Barton, Sarahann Bradley, Catherine A. Richter, and Frederick S. vom Saal PMCID: PMC1088066 Plant Biology Enhanced dihydroflavonol-4-reductase activity and NAD homeostasis leading to cell death tolerance in transgenic rice Mitsunori Hayashi, Hideyuki Takahashi, Katsunori Tamura, Jirong Huang, Li-Hua Yu, Maki Kawai-Yamada, Takafumi Tezuka, and Hirofumi Uchimiya PMCID: PMC1100798 Inhibition of tumor growth by plant-derived mAb Kisung Ko, Zenon Steplewski, Magdalena Glogowska, and Hilary Koprowski PMCID: PMC1100796 Release of oxidized plastocyanin from photosystem I limits electron transfer between photosystem I and cytochrome b6f complex in vivo Giovanni Finazzi, Frederik Sommer, and Michael Hippler PMCID: PMC1100731 From the Cover:
Winter disruption of the circadian clock in chestnut Alberto Ramos, Estefanía Pérez-Solís, Cristian Ibáñez, Rosa Casado, Carmen Collada, Luis Gómez, Cipriano Aragoncillo, and Isabel Allona PMCID: PMC1100755 Social Sciences Anthropology Chayanov revisited: A model for the economics of complex kin units E. A. Hammel PMCID: PMC1100784 Social Sciences Altruistic punishment and the origin of cooperation James H. Fowler PMCID: PMC1100778 Correction Proc Natl Acad Sci U S A. 2005 May 10; 102(19): 7050. doi: 10.1073/pnas.0502971102.PMCID: PMC1100802 Corrects: Ning Zhang, et al. A proinflammatory chemokine, CCL3, sensitizes the heat- and capsaicin-gated ion channel TRPV1. Proc Natl Acad Sci U S A. 2005 March 22; 102(12): 4536–4541. |
