• Issue

    Proteins: Structure, Function, and Bioinformatics: Volume 55, Issue 3

    483-783
    15 May 2004
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Short Communications

DRESS: a database of REfined solution NMR structures

Sander B. Nabuurs,  Aart J. Nederveen,  Wim Vranken,  Jurgen F. Doreleijers,  Alexandre M.J.J. Bonvin,  Geerten W. Vuister,  Gert Vriend,  Christian A.E.M. Spronk, 
  • Pages: 483-486
  • First Published: 01 April 2004

Crystal structure of a putative aspartate aminotransferase belonging to subgroup IV†

Yasuhiro Katsura,  Mikako Shirouzu,  Hiroto Yamaguchi,  Ryuichiro Ishitani,  Osamu Nureki,  Seiki Kuramitsu,  Hideyuki Hayashi,  Shigeyuki Yokoyama, 
  • Pages: 487-492
  • First Published: 01 April 2004

Short Communication

Unfolded state of polyalanine is a segmented polyproline II helix

Alex Kentsis,  Mihaly Mezei,  Tatyana Gindin,  Roman Osman, 
  • Pages: 493-501
  • First Published: 01 April 2004

Research Articles

Polyproline II helix is the preferred conformation for unfolded polyalanine in water

Mihaly Mezei,  Patrick J. Fleming,  Rajgopal Srinivasan,  George D. Rose, 
  • Pages: 502-507
  • First Published: 05 March 2004

Evaluation of local structure alphabets based on residue burial

Rachel Karchin,  Melissa Cline,  Kevin Karplus, 
  • Pages: 508-518
  • First Published: 05 March 2004

Protein secondary structure assignment through Voronoï tessellation

Franck Dupuis,  Jean-François Sadoc,  Jean-Paul Mornon, 
  • Pages: 519-528
  • First Published: 01 April 2004

Topological thermal instability and length of proteins

Raffaella Burioni,  Davide Cassi,  Fabio Cecconi,  Angelo Vulpiani, 
  • Pages: 529-535
  • First Published: 14 April 2004

Recognition of coarse-grained protein tertiary structure

Timothy Lezon,  Jayanth R. Banavar,  Amos Maritan, 
  • Pages: 536-547
  • First Published: 05 March 2004

Folding of β/α-unit scrambled forms of S. cerevisiae triosephosphate isomerase: Evidence for autonomy of substructure formation and plasticity of hydrophobic and hydrogen bonding interactions in core of (β/α)8-barrel

Anshuman Shukla,  Purnananda Guptasarma, 
  • Pages: 548-557
  • First Published: 01 April 2004

A set of homology models of pore loop domain of six eukaryotic voltage-gated potassium channels Kv1.1-Kv1.6

Hsuan-Liang Liu,  Jin-Chung Lin, 
  • Pages: 558-567
  • First Published: 27 February 2004

Investigation of glucose binding sites on insulin

Vincent Zoete,  Markus Meuwly,  Martin Karplus, 
  • Pages: 568-581
  • First Published: 01 April 2004

Atomic insight into the CD4 binding-induced conformational changes in HIV-1 gp120

Shang-Te D. Hsu,  Alexandre M.J.J. Bonvin, 
  • Pages: 582-593
  • First Published: 14 April 2004

A structural and thermodynamic escape mechanism from a drug resistant mutation of the HIV-1 protease

Sonia Vega,  Lin-Woo Kang,  Adrian Velazquez-Campoy,  Yoshiaki Kiso,  L. Mario Amzel,  Ernesto Freire, 
  • Pages: 594-602
  • First Published: 01 April 2004

The architecture of the binding site in redox protein complexes: Implications for fast dissociation

Peter B. Crowley,  Maria Arménia Carrondo, 
  • Pages: 603-612
  • First Published: 05 March 2004

NrdH-redoxin of Corynebacterium ammoniagenes forms a domain-swapped dimer

Matthias Stehr,  Ylva Lindqvist, 
  • Pages: 613-619
  • First Published: 01 April 2004

Distinguish protein decoys by Using a scoring function based on a new AMBER force field, short molecular dynamics simulations, and the generalized born solvent model

Mathew C. Lee,  Yong Duan, 
  • Pages: 620-634
  • First Published: 01 April 2004

Accurate and efficient description of protein vibrational dynamics: Comparing molecular dynamics and Gaussian models

Cristian Micheletti,  Paolo Carloni,  Amos Maritan, 
  • Pages: 635-645
  • First Published: 05 March 2004

On the functional significance of electron density protein structure alignments

Pere Constans, 
  • Pages: 646-655
  • First Published: 05 March 2004

Modeling structurally variable regions in homologous proteins with rosetta

Carol A. Rohl,  Charlie E.M. Strauss,  Dylan Chivian,  David Baker, 
  • Pages: 656-677
  • First Published: 01 April 2004

CHOP proteins into structural domain-like fragments

Jinfeng Liu,  Burkhard Rost, 
  • Pages: 678-688
  • First Published: 01 April 2004

The determinants of carboxyl pKa values in turkey ovomucoid third domain

Hui Li,  Andrew D. Robertson,  Jan H. Jensen, 
  • Pages: 689-704
  • First Published: 05 March 2004

Is histoaspartic protease a serine protease with a pepsin-like fold?

N. Andreeva,  P. Bogdanovich,  I. Kashparov,  M. Popov,  M. Stengach, 
  • Pages: 705-710
  • First Published: 01 April 2004

The low barrier hydrogen bond (LBHB) proposal revisited: The case of the Asp ··· His pair in serine proteases

Claudia N. Schutz,  Arieh Warshel, 
  • Pages: 711-723
  • First Published: 01 April 2004

Crystal structure of human L-xylulose reductase holoenzyme: Probing the role of Asn107 with site-directed mutagenesis

Ossama El-Kabbani,  Shuhei Ishikura,  Connie Darmanin,  Vincenzo Carbone,  Roland P.-T. Chung,  Noriyuki Usami,  Akira Hara, 
  • Pages: 724-732
  • First Published: 14 April 2004

X-ray structural and simulation analysis of a protein mutant: The value of a combined approach

Carla Mattos,  Justin D. Cohen,  David F. Green,  Bruce Tidor,  Martin Karplus, 
  • Pages: 733-742
  • First Published: 05 March 2004

Discrimination of single amino acid mutations of the p53 protein by means of deterministic singularities of recurrence quantification analysis

Alessandro Porrello,  Silvia Soddu,  Joseph P. Zbilut,  Marco Crescenzi,  Alessandro Giuliani, 
  • Pages: 743-755
  • First Published: 05 March 2004

Structure Notes

Free Access

NMR structure of the hypothetical protein NMA1147 from Neisseria meningitidis Reveals a distinct 5-helix bundle

Gaohua Liu,  Dinesh K. Sukumaran,  Duanxiang Xu,  Yiwen Chiang,  Thomas Acton,  Sharon Goldsmith-Fischman,  Barry Honig,  Gaetano T. Montelione,  Thomas Szyperski, 
  • Pages: 756-758
  • First Published: 14 April 2004
Free Access

Crystal structure of an aspartate aminotransferase (TM1255) from Thermotoga maritima at 1.90 Å resolution

Robert Schwarzenbacher,  Lukasz Jaroszewski,  Frank von Delft,  Polat Abdubek,  Eileen Ambing,  Tanja Biorac,  Linda S. Brinen,  Jaume M. Canaves,  Jamison Cambell,  Hsui-Ju Chiu,  Xiaoping Dai,  Ashley M. Deacon,  Mike DiDonato,  Marc-André Elsliger,  Said Eshagi,  Ross Floyd,  Adam Godzik,  Carina Grittini,  Slawomir K. Grzechnik,  Eric Hampton,  Cathy Karlak,  Heath E. Klock,  Eric Koesema,  John S. Kovarik,  Andreas Kreusch,  Peter Kuhn,  Scott A. Lesley,  Inna Levin,  Daniel McMullan,  Timothy M. McPhillips,  Mitchell D. Miller,  Andrew Morse,  Kin Moy,  Jie Ouyang,  Rebecca Page,  Kevin Quijano,  Alyssa Robb,  Glen Spraggon,  Raymond C. Stevens,  Henry van den Bedem,  Jeff Velasquez,  Juli Vincent,  Xianhong Wang,  Bill West,  Guenter Wolf,  Qingping Xu,  Keith O. Hodgson,  John Wooley,  Ian A. Wilson, 
  • Pages: 759-763
  • First Published: 01 April 2004
Free Access

Crystal structure of E. coli yddE protein reveals a striking homology with diaminopimelate epimerase

Alice Grassick,  Gerlind Sulzenbacher,  Véronique Roig-Zamboni,  Valérie Campanacci,  Christian Cambillau,  Yves Bourne, 
  • Pages: 764-767
  • First Published: 01 April 2004
Free Access

Crystal structure of a type II quinolic acid phosphoribosyltransferase (TM1645) from Thermotoga maritima at 2.50 Å resolution

Robert Schwarzenbacher,  Lukasz Jaroszewski,  Frank von Delft,  Polat Abdubek,  Eileen Ambing,  Tanja Biorac,  Linda S. Brinen,  Jaume M. Canaves,  Jamison Cambell,  Hsiu-Ju Chiu,  Xiaoping Dai,  Ashley M. Deacon,  Mike DiDonato,  Marc-André Elsliger,  Said Eshagi,  Ross Floyd,  Adam Godzik,  Carina Grittini,  Slawomir K. Grzechnik,  Eric Hampton,  Cathy Karlak,  Heath E. Klock,  Eric Koesema,  John S. Kovarik,  Andreas Kreusch,  Peter Kuhn,  Scott A. Lesley,  Inna Levin,  Daniel McMullan,  Timothy M. McPhillips,  Mitchell D. Miller,  Andrew Morse,  Kin Moy,  Jie Ouyang,  Rebecca Page,  Kevin Quijano,  Alyssa Robb,  Glen Spraggon,  Raymond C. Stevens,  Henry van den Bedem,  Jeff Velasquez,  Juli Vincent,  Xianhong Wang,  Bill West,  Guenter Wolf,  Qingping Xu,  Keith O. Hodgson,  John Wooley,  Ian A. Wilson, 
  • Pages: 768-771
  • First Published: 05 March 2004
Free Access

The 1.59 Å resolution crystal structure of TM0096, a flavin mononucleotide binding protein from Thermotoga maritima

Frances Park,  Ketan Gajiwala,  Brian Noland,  Lydia Wu,  Dongmei He,  Janessa Molinari,  Kim Loomis,  Barbra Pagarigan,  Peggy Kearins,  Jon Christopher,  Tom Peat,  John Badger,  Jorg Hendle,  Johann Lin,  Sean Buchanan, 
  • Pages: 772-774
  • First Published: 05 March 2004
Free Access

Crystal structure of YIGZ, a conserved hypothetical protein from Escherichia coli k12 with a novel fold

Frances Park,  Ketan Gajiwala,  Galina Eroshkina,  Eva Furlong,  Dongmei He,  Yelena Batiyenko,  Rich Romero,  Jon Christopher,  John Badger,  Jorg Hendle,  Johann Lin,  Tom Peat,  Sean Buchanan, 
  • Pages: 775-777
  • First Published: 14 April 2004
Free Access

Crystal structure of the conserved hypothetical protein TT1380 from Thermus thermophilus HB8

Takashi Wada,  Mikako Shirouzu,  Takaho Terada,  Yuki Kamewari,  Sam-Yong Park,  Jeremy R.H. Tame,  Seiki Kuramitsu,  Shigeyuki Yokoyama, 
  • Pages: 778-780
  • First Published: 01 April 2004

Erratum

Free Access

Predicting protein quaternary structure by pseudo amino acid composition

Kuo-Chen Chou,  Yu-Dong Cai, 
  • Page: 781
  • First Published: 14 April 2004
Free Access

Assessment of homology-based predictions in CASP5

Anna Tramontano,  Veronica Morea, 
  • Page: 782
  • First Published: 14 April 2004
Free Access

Crystal structure of Homo sapiens protein hp14.5

Babu A. Manjasetty,  Heinrich Delbrück,  Dinh-Trung Pham,  Uwe Mueller,  Martin Fieber-Erdmann,  Christoph Scheich,  Volker Sievert,  Konrad Büssow,  Frank H. Niesen,  Wilhelm Weihofen,  Bernhard Loll,  Wolfram Saenger,  Udo Heinemann, 
  • Page: 783
  • First Published: 14 April 2004