Table of Contents

March 1, 2005
Volume 44, Issue 8
Pages 2703-3122

About the Cover: Cover: Double ring-like supercomplexes with variable numbers of copies of the photosynthetic antenna protein IsiA are formed as a response to iron stress in cyanobacteria. These rings can enlarge the light-harvesting capacity of monomeric photosystem I, which can associate in the center of the rings. [Yeremenko, N., et al. (2004) Biochemistry 43, 10308-10313.]

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CURRENT TOPICS

Reward versus Risk:  DNA Cytidine Deaminases Triggering Immunity and Disease

Phuong Pham, Ronda Bransteitter, and Myron F. Goodman
pp 2703–2715
Publication Date (Web): February 03, 2005 (Current Topics/Perspectives)
DOI: 10.1021/bi047481+

ARTICLES

Interactions of the HIV-1 Tat and RAP74 Proteins with the RNA Polymerase II CTD Phosphatase FCP1

Karen L. Abbott, Jacques Archambault, Hua Xiao, Bao D. Nguyen, Robert G. Roeder, Jack Greenblatt, James G. Omichinski, and Pascale Legault
pp 2716–2731
Publication Date (Web): February 05, 2005 (Article)
DOI: 10.1021/bi047957p

Enhanced Binding of RNAP II CTD Phosphatase FCP1 to RAP74 Following CK2 Phosphorylation

Karen L. Abbott, Matthew B. Renfrow, Michael J. Chalmers, Bao D. Nguyen, Alan G. Marshall, Pascale Legault, and James G. Omichinski
pp 2732–2745
Publication Date (Web): February 05, 2005 (Article)
DOI: 10.1021/bi047958h

Crystal Structure of Lumazine Synthase from Mycobacterium tuberculosis as a Target for Rational Drug Design:  Binding Mode of a New Class of Purinetrione Inhibitors,

Ekaterina Morgunova, Winfried Meining, Boris Illarionov, Ilka Haase, Guangyi Jin, Adelbert Bacher, Mark Cushman, Markus Fischer, and Rudolf Ladenstein
pp 2746–2758
Publication Date (Web): February 02, 2005 (Article)
DOI: 10.1021/bi047848a

A Three-Dimensional Molecular Model of Lipid-Free Apolipoprotein A-I Determined by Cross-Linking/Mass Spectrometry and Sequence Threading

R. A. Gangani D. Silva, George M. Hilliard, Jianwen Fang, Stephen Macha, and W. Sean Davidson
pp 2759–2769
Publication Date (Web): February 01, 2005 (Article)
DOI: 10.1021/bi047717+

Characterization of the Formation of the Pyrrole Moiety during Clorobiocin and Coumermycin A1 Biosynthesis

Sylvie Garneau, Pieter C. Dorrestein, Neil L. Kelleher, and Christopher T. Walsh
pp 2770–2780
Publication Date (Web): February 01, 2005 (Article)
DOI: 10.1021/bi0476329

Probing the Cruzain S2 Recognition Subsite:  A Kinetic and Binding Energy Calculation Study

Fabio Polticelli, Germano Zaini, Alessandro Bolli, Giovanni Antonini, Luigi Gradoni, and Paolo Ascenzi
pp 2781–2789
Publication Date (Web): February 05, 2005 (Article)
DOI: 10.1021/bi048417v

Solution Structure of Human SUMO-3 C47S and Its Binding Surface for Ubc9,

Husheng Ding, Yingqi Xu, Quan Chen, Haiming Dai, Yajun Tang, Jihui Wu, and Yunyu Shi
pp 2790–2799
Publication Date (Web): February 04, 2005 (Article)
DOI: 10.1021/bi0477586

Association of Sindbis Virus Capsid Protein with Phospholipid Membranes and the E2 Glycoprotein:  Implications for Alphavirus Assembly

Thomas A. Wilkinson, Timothy L. Tellinghuisen, Richard J. Kuhn, and Carol Beth Post
pp 2800–2810
Publication Date (Web): February 04, 2005 (Article)
DOI: 10.1021/bi0479961

Phospholipase A2 Hydrolysis of Supported Phospholipid Bilayers:  A Neutron Reflectivity and Ellipsometry Study

Hanna P. Vacklin, Fredrik Tiberg, Giovanna Fragneto, and R. K. Thomas
pp 2811–2821
Publication Date (Web): February 02, 2005 (Article)
DOI: 10.1021/bi047727a

Solution Structure, Stability, and Flexibility of Sso10a:  A Hyperthermophile Coiled-Coil DNA-Binding Protein,

Mebrahtu A. Kahsai, Bernhard Vogler, Andrew T. Clark, Stephen P. Edmondson, and John W. Shriver
pp 2822–2832
Publication Date (Web): February 03, 2005 (Article)
DOI: 10.1021/bi047669t

The Conserved Core Domains of Annexins A1, A2, A5, and B12 Can Be Divided into Two Groups with Different Ca2+-Dependent Membrane-Binding Properties

Darshana R. Patel, J. Mario Isas, Alexey S. Ladokhin, Christine C. Jao, Yujin E. Kim, Thorsten Kirsch, Ralf Langen, and Harry T. Haigler
pp 2833–2844
Publication Date (Web): February 02, 2005 (Article)
DOI: 10.1021/bi047642+

Solution Structure of an RNA Internal Loop with Three Consecutive Sheared GA Pairs,

Gang Chen, Brent M. Znosko, Scott D. Kennedy, Thomas R. Krugh, and Douglas H. Turner
pp 2845–2856
Publication Date (Web): February 08, 2005 (Article)
DOI: 10.1021/bi048079y

Binding of Endostatin to Phosphatidylserine-Containing Membranes and Formation of Amyloid-like Fibers

Hongxia Zhao, Arimatti Jutila, Tuula Nurminen, Sara A. Wickström, Jorma Keski-Oja, and Paavo K. J. Kinnunen
pp 2857–2863
Publication Date (Web): February 04, 2005 (Article)
DOI: 10.1021/bi048510j

Structural Analysis of Sterol Distributions in the Plasma Membrane of Living Cells

Weimin Zhang, Avery L. McIntosh, Hai Xu, Di Wu, Todd Gruninger, Barbara Atshaves, J. C. Steve Liu, and Friedhelm Schroeder
pp 2864–2884
Publication Date (Web): February 05, 2005 (Article)
DOI: 10.1021/bi048172m

Toward Defining the Human Parotid Gland Salivary Proteome and Peptidome:  Identification and Characterization Using 2D SDS−PAGE, Ultrafiltration, HPLC, and Mass Spectrometry

Markus Hardt, Lindsay R. Thomas, Scott E. Dixon, George Newport, Nina Agabian, Akraporn Prakobphol, Steven C. Hall, H. Ewa Witkowska, and Susan J. Fisher
pp 2885–2899
Publication Date (Web): February 01, 2005 (Article)
DOI: 10.1021/bi048176r

Role of Hydrogen Bond Networks and Dynamics in Positive and Negative Cooperative Stabilization of a Protein

Jasmina S. Redzic and Bruce E. Bowler
pp 2900–2908
Publication Date (Web): February 01, 2005 (Article)
DOI: 10.1021/bi048218b

Structural Changes of the Complex between pharaonis Phoborhodopsin and Its Cognate Transducer upon Formation of the M Photointermediate

Yuji Furutani, Kentaro Kamada, Yuki Sudo, Kazumi Shimono, Naoki Kamo, and Hideki Kandori
pp 2909–2915
Publication Date (Web): February 05, 2005 (Article)
DOI: 10.1021/bi047893i

The Mcm467 Complex of Saccharomyces cerevisiae Is Preferentially Activated by Autonomously Replicating DNA Sequences

Esther E. Biswas-Fiss, Sujata M. Khopde, and Subhasis B. Biswas
pp 2916–2925
Publication Date (Web): February 02, 2005 (Article)
DOI: 10.1021/bi0491649

Hexitol Nucleic Acid-Containing Aptamers Are Efficient Ligands of HIV-1 TAR RNA

Gaëlle Kolb, Sandrine Reigadas, Claudine Boiziau, Arthur van Aerschot, Andrey Arzumanov, Michael J. Gait, Piet Herdewijn, and Jean-Jacques Toulmé
pp 2926–2933
Publication Date (Web): February 04, 2005 (Article)
DOI: 10.1021/bi048393s

Identification of a Disulfide Switch in BsSco, a Member of the Sco Family of Cytochrome c Oxidase Assembly Proteins,

Qilu Ye, Iveta Imriskova-Sosova, Bruce C. Hill, and Zongchao Jia
pp 2934–2942
Publication Date (Web): February 05, 2005 (Article)
DOI: 10.1021/bi0480537

Identification of Residues in Human Neuroglobin Crucial for Guanine Nucleotide Dissociation Inhibitor Activity

Keisuke Wakasugi and Isao Morishima
pp 2943–2948
Publication Date (Web): February 05, 2005 (Article)
DOI: 10.1021/bi0477539

Crystal Structures of 2-Methylisocitrate Lyase in Complex with Product and with Isocitrate Inhibitor Provide Insight into Lyase Substrate Specificity, Catalysis and Evolution,

Sijiu Liu, Zhibing Lu, Yin Han, Eugene Melamud, Debra Dunaway-Mariano, and Osnat Herzberg
pp 2949–2962
Publication Date (Web): February 01, 2005 (Article)
DOI: 10.1021/bi0479712

p-Cresol Methylhydroxylase:  Alteration of the Structure of the Flavoprotein Subunit upon Its Binding to the Cytochrome Subunit,

Louise M. Cunane, Zhi-wei Chen, William S. McIntire, and F. Scott Mathews
pp 2963–2973
Publication Date (Web): February 03, 2005 (Article)
DOI: 10.1021/bi048020r

Chemical Mechanism and Substrate Specificity of RhlI, an Acylhomoserine Lactone Synthase from Pseudomonas aeruginosa

Aniruddha Raychaudhuri, Agoston Jerga, and Peter A. Tipton
pp 2974–2981
Publication Date (Web): January 27, 2005 (Article)
DOI: 10.1021/bi048005m

Kinetic and Crystallographic Analysis of Active Site Mutants of Escherichia coli γ-Aminobutyrate Aminotransferase

Wenshe Liu, Peter E. Peterson, James A. Langston, Xueguang Jin, Xianzhi Zhou, Andrew J. Fisher, and Michael D. Toney
pp 2982–2992
Publication Date (Web): February 01, 2005 (Article)
DOI: 10.1021/bi048657a

Local Conformational Changes Induced in B-DNA by Ethidium Intercalation

James M. Benevides and George J. Thomas, Jr.
pp 2993–2999
Publication Date (Web): February 04, 2005 (Article)
DOI: 10.1021/bi048651l

Initiation of Repair of DNA−Polypeptide Cross-Links by the UvrABC Nuclease

Irina G. Minko, Andrew J. Kurtz, Deborah L. Croteau, Bennett Van Houten, Thomas M. Harris, and R. Stephen Lloyd
pp 3000–3009
Publication Date (Web): February 01, 2005 (Article)
DOI: 10.1021/bi0478805

An Aminoacyl-tRNA Synthetase with a Defunct Editing Site

Stanley W. Lue and Shana O. Kelley
pp 3010–3016
Publication Date (Web): February 05, 2005 (Article)
DOI: 10.1021/bi047901v

Directing the Outcome of Deoxyribozyme Selections To Favor Native 3‘−5‘ RNA Ligation

Yangming Wang and Scott K. Silverman
pp 3017–3023
Publication Date (Web): February 03, 2005 (Article)
DOI: 10.1021/bi0478291

Two-State Folding of Horse Ferrocytochrome c:  Analyses of Linear Free Energy Relationship, Chevron Curvature, and Stopped-Flow Burst Relaxation Kinetics

Rajesh Kumar and Abani K. Bhuyan
pp 3024–3033
Publication Date (Web): February 01, 2005 (Article)
DOI: 10.1021/bi0478998

Protein Folding in Classical Perspective:  Folding of Horse Cytochrome c

Abani K. Bhuyan, D. Krishna Rao, and N. Prakash Prabhu
pp 3034–3040
Publication Date (Web): February 01, 2005 (Article)
DOI: 10.1021/bi047897n

Oleate-Mediated Stimulation of Microsomal Triglyceride Transfer Protein (MTP) Gene Promoter:  Implications for Hepatic MTP Overexpression in Insulin Resistance

Wei Qiu, Changiz Taghibiglou, Rita Kohen Avramoglu, Stephen C. Van Iderstine, Mark Naples, Homa Ashrafpour, Shailen Mhapsekar, Ryuichiro Sato, and Khosrow Adeli
pp 3041–3049
Publication Date (Web): February 02, 2005 (Article)
DOI: 10.1021/bi047803+

Chromophore Exchange in the LOV2 Domain of the Plant Photoreceptor Phototropin1 from Oat

Harald Dürr, Michael Salomon, and Wolfhart Rüdiger
pp 3050–3055
Publication Date (Web): February 04, 2005 (Article)
DOI: 10.1021/bi0478897

Investigating the Cause of the Alkaline Transition of Phytocyanins

Mark D. Harrison, Sachiko Yanagisawa, and Christopher Dennison
pp 3056–3064
Publication Date (Web): February 03, 2005 (Article)
DOI: 10.1021/bi048256v

Structure of the Higher Plant Light Harvesting Complex I:  In Vivo Characterization and Structural Interdependence of the Lhca Proteins

Frank Klimmek, Ulrika Ganeteg, Janne A. Ihalainen, Henny van Roon, Poul E. Jensen, Henrik V. Scheller, Jan P. Dekker, and Stefan Jansson
pp 3065–3073
Publication Date (Web): February 04, 2005 (Article)
DOI: 10.1021/bi047873g

pH and Kinetic Isotope Effects on Sarcosine Oxidation by N-Methyltryptophan Oxidase

Erik C. Ralph and Paul F. Fitzpatrick
pp 3074–3081
Publication Date (Web): February 04, 2005 (Article)
DOI: 10.1021/bi047716h

Swapping Core Residues in Homologous Proteins Swaps Folding Mechanism

Paula M. Dalessio, Joshua A. Boyer, Jessica L. McGettigan, and Ira J. Ropson
pp 3082–3090
Publication Date (Web): February 03, 2005 (Article)
DOI: 10.1021/bi048125u

Structural Characterization of the Filamentous Bacteriophage PH75 from Thermus thermophilus by Raman and UV-Resonance Raman Spectroscopy

Stacy A. Overman, Priya Bondre, Nakul C. Maiti, and George J. Thomas, Jr.
pp 3091–3100
Publication Date (Web): February 04, 2005 (Article)
DOI: 10.1021/bi048163d

Structural Investigation into the Differential Target Enzyme Regulation Displayed by Plant Calmodulin Isoforms

Aaron P. Yamniuk and Hans J. Vogel
pp 3101–3111
Publication Date (Web): February 02, 2005 (Article)
DOI: 10.1021/bi047770y

Use of Binding Enthalpy To Drive an Allosteric Transition

Patrick H. Brown and Dorothy Beckett
pp 3112–3121
Publication Date (Web): February 02, 2005 (Article)
DOI: 10.1021/bi047792k

CORRECTIONS

Specific Triazine Resistance in Bacterial Reaction Centers Induced by a Single Mutation in the QA Protein Pocket

Jean-Alexis Spitz, Valérie Derrien, Laura Baciou, and Pierre Sebban,
p 3122
Publication Date (Web): February 04, 2005 (Addition/Correction)
DOI: 10.1021/bi0580005
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