• Issue

    Proteins: Structure, Function, and Bioinformatics: Volume 70, Issue 1

    1-309
    January 2008
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Prediction Reports

Structural bioinformatics analysis of enzymes involved in the biosynthesis pathway of the hypermodified nucleoside ms2io6A37 in tRNA

Katarzyna H. Kaminska,  Urszula Baraniak,  Michal Boniecki,  Katarzyna Nowaczyk,  Anna Czerwoniec,  Janusz M. Bujnicki, 
  • Pages: 1-18
  • First Published: 01 October 2007

Short Communications

Beyond Lumry–Eyring: An unexpected pattern of operational reversibility/irreversibility in protein denaturation

David Rodriguez-Larrea,  Beatriz Ibarra-Molero,  Leonardo de Maria,  Torben V. Borchert,  Jose M. Sanchez-Ruiz, 
  • Pages: 19-24
  • First Published: 19 July 2007

A potential molecular switch in an α-helical coiled coil

Charles A. Laughton,  Ben F. Luisi,  J. Venkatesh Pratap,  Chris R. Calladine, 
  • Pages: 25-30
  • First Published: 24 July 2007

Research Articles

Functional and structural characterization of the catalytic domain of the starch synthase III from Arabidopsis thaliana

Maria V. Busi,  Nicolas Palopoli,  Hugo A. Valdez,  Maria S. Fornasari,  Nahuel Z. Wayllace,  Diego F. Gomez-Casati,  Gustavo Parisi,  Rodolfo A. Ugalde, 
  • Pages: 31-40
  • First Published: 10 July 2007

Protein-inhibitor flexible docking by a multicanonical sampling: Native complex structure with the lowest free energy and a free-energy barrier distinguishing the native complex from the others†

Narutoshi Kamiya,  Yasushige Yonezawa,  Haruki Nakamura,  Junichi Higo, 
  • Pages: 41-53
  • First Published: 16 July 2007

A comparison of SCOP and CATH with respect to domain–domain interactions

Emily R. Jefferson,  Thomas P. Walsh,  Geoffrey J. Barton, 
  • Pages: 54-62
  • First Published: 16 July 2007

Structure and quantum chemical analysis of NAD+-dependent isocitrate dehydrogenase: Hydride transfer and co-factor specificity†

Katsumi Imada,  Takashi Tamura,  Ryo Takenaka,  Issei Kobayashi,  Keiichi Namba,  Kenji Inagaki, 
  • Pages: 63-71
  • First Published: 16 July 2007

Investigating the structural stability of the Tup1-interaction domain of Ssn6: Evidence for a conformational change on the complex

Maria Palaiomylitou,  Athanassios Tartas,  Dimitrios Vlachakis,  Dimitris Tzamarias,  Metaxia Vlassi, 
  • Pages: 72-82
  • First Published: 16 July 2007

High resolution X-ray crystallographic structure of bovine heart cytochrome c and its application to the design of an electron transfer biosensor

Nurit Mirkin,  Jean Jaconcic,  Vivian Stojanoff,  Abel Moreno, 
  • Pages: 83-92
  • First Published: 16 July 2007

Structure and dynamics of γ-SNAP: Insight into flexibility of proteins from the SNAP family

Eduard Bitto,  Craig A. Bingman,  Dmitry A. Kondrashov,  Jason G. McCoy,  Ryan M. Bannen,  Gary E. Wesenberg,  George N. Phillips Jr., 
  • Pages: 93-104
  • First Published: 16 July 2007

Assessing model accuracy using the homology modeling automatically software

Aneerban Bhattacharya,  Zeba Wunderlich,  Daniel Monleon,  Roberto Tejero,  Gaetano T. Montelione, 
  • Pages: 105-118
  • First Published: 19 July 2007

Dissecting contact potentials for proteins: Relative contributions of individual amino acids

N.-V. Buchete,  J. E. Straub,  D. Thirumalai, 
  • Pages: 119-130
  • First Published: 19 July 2007

An NMA-guided path planning approach for computing large-amplitude conformational changes in proteins

Svetlana Kirillova,  Juan Cortés,  Alin Stefaniu,  Thierry Siméon, 
  • Pages: 131-143
  • First Published: 19 July 2007

Modulation of human cytidine deaminase by specific aminoacids involved in the intersubunit interactions

S. Vincenzetti,  B. Quadrini,  P. Mariani,  G. De Sanctis,  N. Cammertoni,  V. Polzonetti,  S. Pucciarelli,  P. Natalini,  A. Vita, 
  • Pages: 144-156
  • First Published: 19 July 2007

Identification of fungal oxaloacetate hydrolyase within the isocitrate lyase/PEP mutase enzyme superfamily using a sequence marker-based method

Henk-Jan Joosten,  Ying Han,  Weiling Niu,  Jacques Vervoort,  Debra Dunaway-Mariano,  Peter J. Schaap, 
  • Pages: 157-166
  • First Published: 24 July 2007

Classification of conformational stability of protein mutants from 3D pseudo-folding graph representation of protein sequences using support vector machines

Michael Fernández,  Julio Caballero,  Leyden Fernández,  Jose Ignacio Abreu,  Gianco Acosta, 
  • Pages: 167-175
  • First Published: 24 July 2007

Structures of dimeric dihydrodiol dehydrogenase apoenzyme and inhibitor complex: Probing the subunit interface with site-directed mutagenesis

Vincenzo Carbone,  Satoshi Endo,  Rie Sumii,  Roland P.-T. Chung,  Toshiyuki Matsunaga,  Akira Hara,  Ossama El-Kabbani, 
  • Pages: 176-187
  • First Published: 24 July 2007

Amino acid pairing at the N- and C-termini of helical segments in proteins

Nuno A. Fonseca,  Rui Camacho,  A. L. Magalhães, 
  • Pages: 188-196
  • First Published: 24 July 2007

The X-ray crystallographic structure and activity analysis of a Pseudomonas-specific subfamily of the HAD enzyme superfamily evidences a novel biochemical function†

Ezra Peisach,  Liangbing Wang,  A. Maxwell Burroughs,  L. Aravind,  Debra Dunaway-Mariano,  Karen N. Allen, 
  • Pages: 197-207
  • First Published: 24 July 2007

Prediction of transition metal-binding sites from apo protein structures

Mariana Babor,  Sergey Gerzon,  Barak Raveh,  Vladimir Sobolev,  Marvin Edelman, 
  • Pages: 208-217
  • First Published: 26 July 2007

Modeling the structure of mAb 14B7 bound to the anthrax protective antigen

Arvind Sivasubramanian,  Jennifer A. Maynard,  Jeffrey J. Gray, 
  • Pages: 218-230
  • First Published: 01 August 2007

Exploring the role of large conformational changes in the fidelity of DNA polymerase β

Yun Xiang,  Myron F. Goodman,  William A. Beard,  Samuel H. Wilson,  Arieh Warshel, 
  • Pages: 231-247
  • First Published: 01 August 2007

Protein homology detection and fold inference through multiple alignment entropy profiles

Alejandro Sánchez-Flores,  Ernesto Pérez-Rueda,  Lorenzo Segovia, 
  • Pages: 248-256
  • First Published: 01 August 2007

Structure Notes

Free Access

Structural insight of the role of the Hahella chejuensis HapK protein in prodigiosin biosynthesis

Hyo Je Cho,  Kyung-Jin Kim,  Myung Hee Kim,  Beom Sik Kang, 
  • Pages: 257-262
  • First Published: 29 August 2007
Free Access

Crystal structure solution of a ParB-like nuclease at atomic resolution

Neil Shaw,  Wolfram Tempel,  Jessie Chang,  Hua Yang,  Chongyun Cheng,  Joseph Ng,  John Rose,  Zihe Rao,  Bi-Cheng Wang,  Zhi-Jie Liu, 
  • Pages: 263-267
  • First Published: 29 August 2007
Free Access

Crystal structure of the biotin carboxylase domain of human acetyl-CoA carboxylase 2

Yong Soon Cho,  Jae Il Lee,  Dongkyu Shin,  Hyun Tae Kim,  Young Hoon Cheon,  Chang Il Seo,  Yong Eun Kim,  Young-Lan Hyun,  Yoon Sup Lee,  Kanako Sugiyama,  Sam-Yong Park,  Seonggu Ro,  Joong Myung Cho,  Tae Gyu Lee,  Yong-Seok Heo, 
  • Pages: 268-272
  • First Published: 17 September 2007
Free Access

Crystal structure of aminopeptidase N from human pathogen Neisseria meningitidis†

B. Nocek,  R. Mulligan,  M. Bargassa,  F. Collart,  A. Joachimiak, 
  • Pages: 273-279
  • First Published: 17 September 2007
Free Access

Crystal structure of the mouse p53 core domain in zinc-free state

Eunju Kwon,  Dong Young Kim,  Se Won Suh,  Kyeong Kyu Kim, 
  • Pages: 280-283
  • First Published: 17 September 2007
Free Access

Crystal structure of a monoclonal antibody directed against an antigenic determinant common to Ogawa and Inaba serotypes of Vibrio cholerae O1

Firoz Ahmed,  Gwénaëlle André-Leroux,  Ahmed Haouz,  Alain Boutonnier,  Muriel Delepierre,  Firdausi Qadri,  Farida Nato,  Jean-Michel Fournier,  Pedro M. Alzari, 
  • Pages: 284-288
  • First Published: 17 September 2007
Free Access

The structure of flavin-dependent tryptophan 7-halogenase RebH

Eduard Bitto,  Yu Huang,  Craig A. Bingman,  Shanteri Singh,  Jon S. Thorson,  George N. Phillips Jr., 
  • Pages: 289-293
  • First Published: 17 September 2007
Free Access

Crystal structure of the endopolygalacturonase from the phytopathogenic fungus Colletotrichum lupini and its interaction with polygalacturonase-inhibiting proteins

Daniele Bonivento,  Daniela Pontiggia,  Adele Di Matteo,  Juan Fernandez-Recio,  Gianni Salvi,  Demetrius Tsernoglou,  Felice Cervone,  Giulia De Lorenzo,  Luca Federici, 
  • Pages: 294-299
  • First Published: 17 September 2007
Free Access

Solution structure of FK506 binding domain (FKBD) of Plasmodium falciparum FK506 binding protein 35 (PfFKBP35)

Cong Bao Kang,  Hong Ye,  Hye Rim Yoon,  Ho Sup Yoon, 
  • Pages: 300-302
  • First Published: 17 September 2007
Free Access

Crystal structure of Arabidopsis thaliana cytokinin dehydrogenase

Euiyoung Bae,  Craig A. Bingman,  Eduard Bitto,  David J. Aceti,  George N. Phillips Jr., 
  • Pages: 303-306
  • First Published: 20 September 2007

Errata

Free Access

Correction of “Dynamical behavior of the vascular endothelial growth factor: Biological implications”

Bruno A. C. Horta,  José J. V. Cirino,  Ricardo B. de Alencastro, 
  • Pages: 307-308
  • First Published: 25 September 2007
Free Access

Correction to the article “Study of the Villin Headpiece folding dynamics by combining coarse-grained Monte Carlo evolution and all-atom molecular dynamics”

Cristian Micheletti,  Giorgio Colombo, 
  • Page: 309
  • First Published: 05 October 2007