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Contents list
Volume 337, Number 1 Contents Articles Excision of Incorporated Nucleotide Analogue Chainterminators can Diminish their Inhibitory Effects on Viral RNA-dependent RNA Polymerases
C. M. D’Abramo, L. Cellai and M. Go¨tte
1-14
Interactions of Translation Factor EF-G with the Bacterial Ribosome Before and After mRNA Translocation
K. S. Wilson and R. Nechifor
15-30
Exploring the Regulation of tRNA Distribution on the Genomic Scale
K. A. Dittmar, E. M. Mobley, A. J. Radek and T. Pan
31-47
A Novel Zinc-binding Motif Revealed by Solution Structures of DNA-binding Domains of Arabidopsis SBP-family Transcription Factors
K. Yamasaki, T. Kigawa, M. Inoue, M. Tateno, T. Yamasaki, T. Yabuki, M. Aoki, E. Seki, T. Matsuda, E. Nunokawa, Y. Ishizuka, T. Terada, M. Shirouzu, T. Osanai, A. Tanaka, M. Seki, K. Shinozaki and S. Yokoyama
49-63
Protein –DNA Hydrophobic Recognition in the Minor Groove is Facilitated by Sugar Switching
M. Y. Tolstorukov, R. L. Jernigan and V. B. Zhurkin
65-76
Protelomerase Uses a Topoisomerase IB/ Y-Recombinase Type Mechanism to Generate DNA Hairpin Ends
W. M. Huang, L. Joss, T. T. Hsieh and S. Casjens
77-92
Cofilin (ADF) Affects Lateral Contacts in F-actin
A. A. Bobkov, A. Muhlrad, A. Shvetsov, S. Benchaar, D. Scoville, S. C. Almo and E. Reisler
Structure of the Rotor of the Bacterial Flagellar Motor Revealed by Electron Cryomicroscopy and Single-particle Image Analysis
H. Suzuki, K. Yonekura and K. Namba
105-113
Phage-peptide Display Identifies the Interferonresponsive, Death-activated Protein Kinase Family as a Novel Modifier of MDM2 and p21WAF1
L. R. Burch, M. Scott, E. Pohler, D. Meek and T. Hupp
115-128
Expansion of Protein Interaction Maps by Phage Peptide Display Using MDM2 as a Prototypical Conformationally Flexible Target Protein
L. Burch, H. Shimizu, A. Smith, C. Patterson and T. R. Hupp
129-145
The Mechanism of Nucleic Acid Melting by a CspA Family Protein
S. Phadtare, M. Inouye and K. Severinov
147-155
The Solution NMR Structure of Antheraea polyphemus PBP Provides New Insight into Pheromone Recognition by Pheromone-binding Proteins
S. Mohanty, S. Zubkov and A. M. Gronenborn
157-165
NMR Solution Structure of Mob1, a Mitotic Exit Network Protein and its Interaction with an NDR Kinase Peptide
L. Ponchon, C. Dumas, A. V. Kajava, D. Fesquet and A. Padilla
167-182
Equilibrium Hydrogen Exchange Reveals Extensive Hydrogen Bonded Secondary Structure in the On-pathway Intermediate of Im7
S. A. Gorski, C. S. Le Duff, A. P. Capaldi, A. P. Kalverda, G. S. Beddard, G. R. Moore and S. E. Radford
183-193
93-104
Folding Barrier in Horse Cytochrome c: Support for a Classical Folding Pathway
N. P. Prabhu, R. Kumar and A. K. Bhuyan
195-208
Protein Flexibility in Ligand Docking and Virtual Screening to Protein Kinases
C. N. Cavasotto and R. A. Abagyan
209-225
Computational Modeling of the Catalytic Reaction in Triosephosphate Isomerase
V. Guallar, M. Jacobson, A. McDermott and R. A. Friesner
227-239 241
Author Index
Full text of this journal is available, on-line from ScienceDirect. Visit www.sciencedirect.com for more information. q 2004 Elsevier Ltd All rights reserved. This journal and the individual contributions contained in it are protected under copyright by Elsevier, and the following terms and conditions apply to their use: Photocopying. Single photocopies of single articles may be made for personal use as allowed by national copyright laws. Permission of the Publisher and payment of a fee is required for all other photocopying, including multiple or systematic copying, copying for advertising or promotional purposes, resale, and all forms of document delivery. Special rates are available for educational institutions that wish to make photocopies for non-profit educational classroom use. Permissions may be sought directly from Elsevier’s Global Rights Department in Oxford, by phone, fax, e-mail or via Elsevier’s homepage. In the USA, users may clear permissions and make payments through the Copyright Clearance Centre (CCC), and in the UK through the Copyright Licensing Agency Rapid Clearance Service (CLARCS). Other countries may have a local reprographic rights agency for payments. Derivative Works. Subscribers may reproduce tables of contents or prepare lists of articles including abstracts for internal circulation within their institutions. Permission of the Publisher is required for resale or distribution outside the institution. Permission of the Publisher is required for all other derivative works, including compilations and translations. Electronic Storage or Usage. Permission of the Publisher is required to store or use electronically any material contained in this journal, including any article or part of an article. Except as outlined above, no part of this publication may be reproduced, stored in a retrieval system or transmitted in any form or by any means, electronic, mechanical, photocopying, recording or otherwise, without prior written permission of the Publisher. Volume 337, Number 1, 12 March 2004
Notice. No responsibility is assumed by the Publisher for any injury and/or damage to persons or property as a matter of products liability, negligence or otherwise, or from any use or operation of any methods, products, instructions or ideas contained in the material herein. Because of rapid advances in the medical sciences, in particular, independent verification of diagnoses and drug dosages should be made. Although all advertising material is expected to conform to ethical (medical) standards, inclusion in this publication does not constitute a guarantee or endorsement of the quality or value of such product or of the claims made of it by its manufacturer. Cover Illustration: Interactions of elongation factor EF-G with the bacterial ribosome as deduced from hydroxyl radical probing. See article by Wilson and Nechifor. J. Mol. Biol. 337, 15 – 30. Typeset and printed in Europe by the Alden Group, Oxford
ISSN 0022-2836
C. M. D’Abramo, L. Cellai and M. Go¨tte
1-14
Interactions of Translation Factor EF-G with the Bacterial Ribosome Before and After mRNA Translocation
K. S. Wilson and R. Nechifor
15-30
Exploring the Regulation of tRNA Distribution on the Genomic Scale
K. A. Dittmar, E. M. Mobley, A. J. Radek and T. Pan
31-47
A Novel Zinc-binding Motif Revealed by Solution Structures of DNA-binding Domains of Arabidopsis SBP-family Transcription Factors
K. Yamasaki, T. Kigawa, M. Inoue, M. Tateno, T. Yamasaki, T. Yabuki, M. Aoki, E. Seki, T. Matsuda, E. Nunokawa, Y. Ishizuka, T. Terada, M. Shirouzu, T. Osanai, A. Tanaka, M. Seki, K. Shinozaki and S. Yokoyama
49-63
Protein –DNA Hydrophobic Recognition in the Minor Groove is Facilitated by Sugar Switching
M. Y. Tolstorukov, R. L. Jernigan and V. B. Zhurkin
65-76
Protelomerase Uses a Topoisomerase IB/ Y-Recombinase Type Mechanism to Generate DNA Hairpin Ends
W. M. Huang, L. Joss, T. T. Hsieh and S. Casjens
77-92
Cofilin (ADF) Affects Lateral Contacts in F-actin
A. A. Bobkov, A. Muhlrad, A. Shvetsov, S. Benchaar, D. Scoville, S. C. Almo and E. Reisler
Structure of the Rotor of the Bacterial Flagellar Motor Revealed by Electron Cryomicroscopy and Single-particle Image Analysis
H. Suzuki, K. Yonekura and K. Namba
105-113
Phage-peptide Display Identifies the Interferonresponsive, Death-activated Protein Kinase Family as a Novel Modifier of MDM2 and p21WAF1
L. R. Burch, M. Scott, E. Pohler, D. Meek and T. Hupp
115-128
Expansion of Protein Interaction Maps by Phage Peptide Display Using MDM2 as a Prototypical Conformationally Flexible Target Protein
L. Burch, H. Shimizu, A. Smith, C. Patterson and T. R. Hupp
129-145
The Mechanism of Nucleic Acid Melting by a CspA Family Protein
S. Phadtare, M. Inouye and K. Severinov
147-155
The Solution NMR Structure of Antheraea polyphemus PBP Provides New Insight into Pheromone Recognition by Pheromone-binding Proteins
S. Mohanty, S. Zubkov and A. M. Gronenborn
157-165
NMR Solution Structure of Mob1, a Mitotic Exit Network Protein and its Interaction with an NDR Kinase Peptide
L. Ponchon, C. Dumas, A. V. Kajava, D. Fesquet and A. Padilla
167-182
Equilibrium Hydrogen Exchange Reveals Extensive Hydrogen Bonded Secondary Structure in the On-pathway Intermediate of Im7
S. A. Gorski, C. S. Le Duff, A. P. Capaldi, A. P. Kalverda, G. S. Beddard, G. R. Moore and S. E. Radford
183-193
93-104
Folding Barrier in Horse Cytochrome c: Support for a Classical Folding Pathway
N. P. Prabhu, R. Kumar and A. K. Bhuyan
195-208
Protein Flexibility in Ligand Docking and Virtual Screening to Protein Kinases
C. N. Cavasotto and R. A. Abagyan
209-225
Computational Modeling of the Catalytic Reaction in Triosephosphate Isomerase
V. Guallar, M. Jacobson, A. McDermott and R. A. Friesner
227-239 241
Author Index
Full text of this journal is available, on-line from ScienceDirect. Visit www.sciencedirect.com for more information. q 2004 Elsevier Ltd All rights reserved. This journal and the individual contributions contained in it are protected under copyright by Elsevier, and the following terms and conditions apply to their use: Photocopying. Single photocopies of single articles may be made for personal use as allowed by national copyright laws. Permission of the Publisher and payment of a fee is required for all other photocopying, including multiple or systematic copying, copying for advertising or promotional purposes, resale, and all forms of document delivery. Special rates are available for educational institutions that wish to make photocopies for non-profit educational classroom use. Permissions may be sought directly from Elsevier’s Global Rights Department in Oxford, by phone, fax, e-mail or via Elsevier’s homepage. In the USA, users may clear permissions and make payments through the Copyright Clearance Centre (CCC), and in the UK through the Copyright Licensing Agency Rapid Clearance Service (CLARCS). Other countries may have a local reprographic rights agency for payments. Derivative Works. Subscribers may reproduce tables of contents or prepare lists of articles including abstracts for internal circulation within their institutions. Permission of the Publisher is required for resale or distribution outside the institution. Permission of the Publisher is required for all other derivative works, including compilations and translations. Electronic Storage or Usage. Permission of the Publisher is required to store or use electronically any material contained in this journal, including any article or part of an article. Except as outlined above, no part of this publication may be reproduced, stored in a retrieval system or transmitted in any form or by any means, electronic, mechanical, photocopying, recording or otherwise, without prior written permission of the Publisher. Volume 337, Number 1, 12 March 2004
Notice. No responsibility is assumed by the Publisher for any injury and/or damage to persons or property as a matter of products liability, negligence or otherwise, or from any use or operation of any methods, products, instructions or ideas contained in the material herein. Because of rapid advances in the medical sciences, in particular, independent verification of diagnoses and drug dosages should be made. Although all advertising material is expected to conform to ethical (medical) standards, inclusion in this publication does not constitute a guarantee or endorsement of the quality or value of such product or of the claims made of it by its manufacturer. Cover Illustration: Interactions of elongation factor EF-G with the bacterial ribosome as deduced from hydroxyl radical probing. See article by Wilson and Nechifor. J. Mol. Biol. 337, 15 – 30. Typeset and printed in Europe by the Alden Group, Oxford
ISSN 0022-2836