Volume 71; Issue 4

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Proteins: Structure, Function, and Bioinformatics
Volume 71; Issue 4

Proteins: Structure, Function, and Bioinformatics

Volume 71; Issue 4

1

Analyzing and modeling the inhibitory effect of phosphatidic acid on the GTP-γ-S binding activity of Goα

Liang Qu, Jia Wan, Yu Cao, Yinghao Zhang, Runsheng Chen, Youguo Huang

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2008

Language:

english

File:

PDF, 537 KB

english, 2008

2

Statistical geometry based prediction of nonsynonymous SNP functional effects using random forest and neuro-fuzzy classifiers

Maxim Barenboim, Majid Masso, Iosif I. Vaisman, D. Curtis Jamison

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2008

Language:

english

File:

PDF, 197 KB

english, 2008

3

Complex assembly mechanism and an RNA-binding mode of the human p14-SF3b155 spliceosomal protein complex identified by NMR solution structure and functional analyses

Kanako Kuwasako, Naoshi Dohmae, Mio Inoue, Mikako Shirouzu, Seiichi Taguchi, Peter Güntert, Bertrand Séraphin, Yutaka Muto, Shigeyuki Yokoyama

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2008

Language:

english

File:

PDF, 2.37 MB

english, 2008

4

Using quantum mechanics to improve estimates of amino acid side chain rotamer energies

P. Douglas Renfrew, Glenn L. Butterfoss, Brian Kuhlman

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2008

Language:

english

File:

PDF, 335 KB

english, 2008

5

Exploring the protein G helix free-energy surface by solute tempering metadynamics

Carlo Camilloni, Davide Provasi, Guido Tiana, Ricardo A. Broglia

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2008

Language:

english

File:

PDF, 573 KB

english, 2008

6

Computational prediction of the binding site of proteinase 3 to the plasma membrane

Eric Hajjar, Maja Mihajlovic, Véronique Witko-Sarsat, Themis Lazaridis, Nathalie Reuter

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.08 MB

english, 2008

7

Solvent-exposed residues located in the β-sheet modulate the stability of the tetramerization domain of p53—A structural and combinatorial approach

Puig Mora, Rodrigo J. Carbajo, Antonio Pineda-Lucena, Manuel M. Sánchez del Pino, Enrique Pérez-Payá

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2008

Language:

english

File:

PDF, 462 KB

english, 2008

8

Huntingtin interacting protein HYPK is intrinsically unstructured

Swasti Raychaudhuri, Pritha Majumder, Somosree Sarkar, Kalyan Giri, Debashis Mukhopadhyay, Nitai P. Bhattacharyya

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2008

Language:

english

File:

PDF, 535 KB

english, 2008

9

The protein fluorescence and structural toolkit: Database and programs for the analysis of protein fluorescence and structural data

Chi Shen, Rajiv Menon, Dipanwita Das, Nidhi Bansal, Neha Nahar, Neelima Guduru, Stephen Jaegle, Joan Peckham, Yana K. Reshetnyak

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2008

Language:

english

File:

PDF, 406 KB

english, 2008

10

A simple and fuzzy method to align and compare druggable ligand-binding sites

Claire Schalon, Jean-Sébastien Surgand, Esther Kellenberger, Didier Rognan

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.43 MB

english, 2008

11

Functional and computational studies of the ligand-associated metal binding site of β3 integrins

Marta Murcia, Marketa Jirouskova, Jihong Li, Barry S. Coller, Marta Filizola

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.28 MB

english, 2008

12

Interdomain cooperativity of calmodulin bound to melittin preferentially increases calcium affinity of sites I and II

Rhonda A. Newman, Wendy S. Van Scyoc, Brenda R. Sorensen, Olav R. Jaren, Madeline A. Shea

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.32 MB

english, 2008

13

The conformational plasticity of calmodulin upon calcium complexation gives a model of its interaction with the oedema factor of Bacillus anthracis

Elodie Laine, Julliane D. Yoneda, Arnaud Blondel, Thérèse E. Malliavin

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2008

Language:

english

File:

PDF, 898 KB

english, 2008

14

Overexpression, physicochemical characterization, and modeling of a hyperthermophilic pyrococcus furiosus type 2 IPP isomerase

Raphaël Dutoit, Jérôme de Ruyck, Virginie Durisotti, Christianne Legrain, Eric Jacobs, Johan Wouters

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2008

Language:

english

File:

PDF, 514 KB

english, 2008

15

pH sensitivity of type III secretion system tip proteins

Aaron P. Markham, Susan E. Birket, William D. Picking, Wendy L. Picking, C. Russell Middaugh

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2008

Language:

english

File:

PDF, 561 KB

english, 2008

16

An insight into the general relationship between the three dimensional structures of enzymes and their electronic wave functions: Implication for the prediction of functional sites of enzymes

K. Fukushima, M. Wada, M. Sakurai

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1019 KB

english, 2008

17

Tandem use of X-ray crystallography and mass spectrometry to obtain ab initio the complete and exact amino acids sequence of HPBP, a human 38-kDa apolipoprotein

Hélène Diemer, Mikael Elias, Frédérique Renault, Daniel Rochu, Carlos Contreras-Martel, Christine Schaeffer, Alain Van Dorsselaer, Eric Chabriere

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2008

Language:

english

File:

PDF, 899 KB

english, 2008

18

Protein–protein docking by simulating the process of association subject to biochemical constraints

Domantas Motiejunas, Razif Gabdoulline, Ting Wang, Anna Feldman-Salit, Tim Johann, Peter J. Winn, Rebecca C. Wade

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2008

Language:

english

File:

PDF, 355 KB

english, 2008

19

A combined approach of mass spectrometry, molecular modeling, and site-directed mutagenesis highlights key structural features responsible for the thermostability of Sulfolobus solfataricus carboxypeptidase

Silvia Sommaruga, Antonella De Palma, Pier Luigi Mauri, Manuela Trisciani, Fabrizio Basilico, Pier Luigi Martelli, Rita Casadio, Paolo Tortora, Emanuela Occhipinti

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2008

Language:

english

File:

PDF, 521 KB

english, 2008

20

Structure–function relationship of inhibitory Smads: Structural flexibility contributes to functional divergence

Ramkumar Hariharan, M. Radhakrishna Pillai

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2008

Language:

english

File:

PDF, 494 KB

english, 2008

21

Comparison of the efficiency of evolutionary change-based and side chain orientation-based fold recognition potentials

Boris Vishnepolsky, Grigol Managadze, Malak Pirtskhalava

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2008

Language:

english

File:

PDF, 264 KB

english, 2008

22

Toxoplasma gondii ferredoxin-NADP+ reductase: Role of ionic interactions in stabilization of native conformation and structural cooperativity

Kulwant Singh, Vinod Bhakuni

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2008

Language:

english

File:

PDF, 513 KB

english, 2008

23

Water-mediated interactions between DNA and PhoB DNA-binding/transactivation domain: NMR-restrained molecular dynamics in explicit water environment

Tsutomu Yamane, Hideyasu Okamura, Mitsunori Ikeguchi, Yoshifumi Nishimura, Akinori Kidera

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.24 MB

english, 2008

24

Conformational and dynamics changes induced by bile acids binding to chicken liver bile acid binding protein

Ivano Eberini, Alessandro Guerini Rocco, Anna Rita Ientile, António M. Baptista, Elisabetta Gianazza, Simona Tomaselli, Henriette Molinari, Laura Ragona

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.16 MB

english, 2008

25

The type IA topoisomerase catalytic cycle: A normal mode analysis and molecular dynamics simulation

Bing Xiong, David L. Burk, Jianhua Shen, Xiaomin Luo, Hong Liu, Jingkang Shen, Albert M. Berghuis

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2008

Language:

english

File:

PDF, 525 KB

english, 2008

26

Functional and structural features of the oxyanion hole in a thermophilic esterase from Alicyclobacillus acidocaldarius

Luigi Mandrich, Valeria Menchise, Vincenzo Alterio, Giuseppina De Simone, Carlo Pedone, Mosè Rossi, Giuseppe Manco

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2008

Language:

english

File:

PDF, 597 KB

english, 2008

27

Insights into activation and RNA binding of trp RNA-binding attenuation protein (TRAP) through all-atom simulations

Teemu Murtola, Ilpo Vattulainen, Emma Falck

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2008

Language:

english

File:

PDF, 987 KB

english, 2008

28

Hydrophobic clusters in protein structures

J. Arunachalam, N. Gautham

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.95 MB

english, 2008

29

Stacking efficiency and flexibility analysis of aromatic amino acids in cap-binding proteins

Remigiusz Worch, Ryszard Stolarski

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2008

Language:

english

File:

PDF, 390 KB

english, 2008

30

A phospho-sugar binding domain homologous to NagB enzymes regulates the activity of the central glycolytic genes repressor

Thierry Doan, Laetitia Martin, Silvia Zorrilla, Denis Chaix, Stéphane Aymerich, Gilles Labesse, Nathalie Declerck

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2008

Language:

english

File:

PDF, 905 KB

english, 2008

31

The solution structure of the outer membrane lipoprotein OmlA from Xanthomonas axonopodis pv. citri reveals a protein fold implicated in protein–protein interaction

Marina Marques Teixeira Vanini, Alberto Spisni, Maurício Luis Sforça, Thelma Aguiar Pertinhez, Celso Eduardo Benedetti

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.01 MB

english, 2008

32

Identifying folding nucleus based on residue contact networks of proteins

Jie Li, Jun Wang, Wei Wang

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2008

Language:

english

File:

PDF, 466 KB

english, 2008

33

Understanding of known drug-target interactions in the catalytic pocket of neuraminidase subtype N1

Maturos Malaisree, Thanyada Rungrotmongkol, Panita Decha, Pathumwadee Intharathep, Ornjira Aruksakunwong, Supot Hannongbua

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2008

Language:

english

File:

PDF, 487 KB

english, 2008

34

The X-ray structure of N-methyltryptophan oxidase reveals the structural determinants of substrate specificity

Andrea Ilari, Alessandra Bonamore, Stefano Franceschini, Annarita Fiorillo, Alberto Boffi, Gianni Colotti

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2008

Language:

english

File:

PDF, 997 KB

english, 2008

35

Expanding GPCR homology model binding sites via a balloon potential: A molecular dynamics refinement approach

S. Roy Kimura, Andrew J. Tebben, David R. Langley

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2008

Language:

english

File:

PDF, 706 KB

english, 2008

36

Sequence–structure–function analysis of the bifunctional enzyme MnmC that catalyses the last two steps in the biosynthesis of hypermodified nucleoside mnm5s2U in tRNA

Martine Roovers, Yamina Oudjama, Katarzyna H. Kaminska, Elzbieta Purta, Joël Caillet, Louis Droogmans, Janusz M. Bujnicki

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.02 MB

english, 2008

37

A mathematically related singularity and the maximum size of protein domains

András Szilágyi

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2008

Language:

english

File:

PDF, 98 KB

english, 2008

38

Calcineurin B-like domains in the large regulatory α/β subunits of phosphorylase kinase

Cathelène Carrière, Jean-Paul Mornon, Catherine Venien-Bryan, Nicolas Boisset, Isabelle Callebaut

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2008

Language:

english

File:

PDF, 717 KB

english, 2008

39

Crystal structure of single-domain VL of an anti-DNA binding antibody 3D8 scFv and its active site revealed by complex structures of a small molecule and metals

Suk-Youl Park, Woo-Ram Lee, Suk-Chan Lee, Myung-Hee Kwon, Yong-Sung Kim, Jeong-Sun Kim

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2008

Language:

english

File:

PDF, 281 KB

english, 2008

40

Refinement of noncalorimetric determination of the change in heat capacity, ΔCp, of protein unfolding and validation across a wide temperature range

Deepika Talla-Singh, Wesley E. Stites

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2008

Language:

english

File:

PDF, 333 KB

english, 2008

41

Crystal structure of uncharacterized protein TTHA1756 from Thermus thermophilus HB8: Structural variety in UPF0150 family proteins

Akio Ebihara, Miho Manzoku, Hitoshi Iino, Mayumi Kanagawa, Akeo Shinkai, Shigeyuki Yokoyama, Seiki Kuramitsu

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2008

Language:

english

File:

PDF, 451 KB

english, 2008

42

Crystal structure of YagE, a putative DHDPS-like protein from Escherichia coli K12

Sankar Manicka, Yoav Peleg, Tamar Unger, Shira Albeck, Orly Dym, Harry M. Greenblatt, Gleb Bourenkov, Victor Lamzin, Sankaran Krishnaswamy, Joel L. Sussman

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2008

Language:

english

File:

PDF, 771 KB

english, 2008

43

Crystal structure of a novel non-Pfam protein AF1514 from Archeoglobus fulgidus DSM 4304 solved by S-SAD using a Cr X-ray source

Yang Li, Pazilat Bahti, Neil Shaw, Gaojie Song, Shunmei Chen, Xuejun Zhang, Min Zhang, Chongyun Cheng, Jie Yin, Jin-Yi Zhu, Hua Zhang, Dongsheng Che, Hao Xu, Abdulla Abbas, Bi-Cheng Wang, Zhi-Jie Liu

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2008

Language:

english

File:

PDF, 256 KB

english, 2008

44

Response to András Szilágyi's Commentary

Joseph P. Zbilut, Alessandro Giuliani, Charles L. Webber Jr

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2008

Language:

english

File:

PDF, 56 KB

english, 2008

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