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  1. Several methods are currently available for the comparison of protein structures. These methods have been analysed regarding the performance in the identification of structurally/evolutionary related proteins,...

    Authors: Gabriele Mayr, Francisco S Domingues and Peter Lackner

    Citation: BMC Structural Biology 2007 7:50

    Content type: Research article

    Published on:

  2. Allosteric disulfide bonds regulate protein function when they break and/or form. They typically have a -RHStaple configuration, which is defined by the sign of the five chi angles that make up the disulfide b...

    Authors: Bryan Schmidt and Philip J Hogg

    Citation: BMC Structural Biology 2007 7:49

    Content type: Research article

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  3. The majority of experimentally determined crystal structures of Type II restriction endonucleases (REases) exhibit a common PD-(D/E)XK fold. Crystal structures have been also determined for single representati...

    Authors: Elena M Ibryashkina, Marina V Zakharova, Vladimir B Baskunov, Ekaterina S Bogdanova, Maxim O Nagornykh, Marat M Den'mukhamedov, Bogdan S Melnik, Andrzej Kolinski, Dominik Gront, Marcin Feder, Alexander S Solonin and Janusz M Bujnicki

    Citation: BMC Structural Biology 2007 7:48

    Content type: Research article

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  4. EstE1 is a hyperthermophilic esterase belonging to the hormone-sensitive lipase family and was originally isolated by functional screening of a metagenomic library constructed from a thermal environmental samp...

    Authors: Jung-Sue Byun, Jin-Kyu Rhee, Nam Doo Kim, JeongHyeok Yoon, Dong-Uk Kim, Eunhee Koh, Jong-Won Oh and Hyun-Soo Cho

    Citation: BMC Structural Biology 2007 7:47

    Content type: Research article

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  5. The major bottleneck for determination of 3 D structures of proteins using X-rays is the production of diffraction quality crystals. Often proteins are subjected to chemical modification to improve the chances...

    Authors: Neil Shaw, Chongyun Cheng, Wolfram Tempel, Jessie Chang, Joseph Ng, Xin-Yu Wang, Sarah Perrett, John Rose, Zihe Rao, Bi-Cheng Wang and Zhi-Jie Liu

    Citation: BMC Structural Biology 2007 7:46

    Content type: Methodology article

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  6. Uracil-DNA glycosylases (UDGs) catalyze excision of uracil from DNA. Vaccinia virus, which is the prototype of poxviruses, encodes a UDG (vvUDG) that is significantly different from the UDGs of other organisms...

    Authors: Norbert Schormann, Alexei Grigorian, Alexandra Samal, Raman Krishnan, Lawrence DeLucas and Debasish Chattopadhyay

    Citation: BMC Structural Biology 2007 7:45

    Content type: Research article

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  7. Three-dimensional (3D) structures of numerous peripheral membrane proteins have been determined. Biological activity, stability, and conformations of these proteins depend on their spatial positions with respe...

    Authors: Andrei L Lomize, Irina D Pogozheva, Mikhail A Lomize and Henry I Mosberg

    Citation: BMC Structural Biology 2007 7:44

    Content type: Research article

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  8. Although experimental methods for determining protein structure are providing high resolution structures, they cannot keep the pace at which amino acid sequences are resolved on the scale of entire genomes. Fo...

    Authors: Sebastian Kmiecik, Dominik Gront and Andrzej Kolinski

    Citation: BMC Structural Biology 2007 7:43

    Content type: Research article

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  9. Human hookworm infection is a major cause of anemia and malnutrition of adults and children in the developing world. As part of on-going efforts to control hookworm infection, The Human Hookworm Vaccine Initia...

    Authors: Oluwatoyin A Asojo, Kohei Homma, Meghan Sedlacek, Michelle Ngamelue, Gaddam N Goud, Bin Zhan, Vehid Deumic, Oluyomi Asojo and Peter J Hotez

    Citation: BMC Structural Biology 2007 7:42

    Content type: Research article

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  10. Thermal denaturation experiments were extended to study the thermal behaviour of the main motor proteins (actin and myosin) in their native environment in striated muscle fibres. The interaction of actin with ...

    Authors: Timea Dergez, Dénes Lőrinczy, Franciska Könczöl, Nelli Farkas and Joseph Belagyi

    Citation: BMC Structural Biology 2007 7:41

    Content type: Research article

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  11. PD-(D/E)XK nucleases constitute a large and highly diverse superfamily of enzymes that display little sequence similarity despite retaining a common core fold and a few critical active site residues. This make...

    Authors: Lukasz Knizewski, Lisa N Kinch, Nick V Grishin, Leszek Rychlewski and Krzysztof Ginalski

    Citation: BMC Structural Biology 2007 7:40

    Content type: Research article

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  12. α-isopropylmalate synthase (MtαIPMS), an enzyme that catalyzes the first committed step of the leucine biosynthetic pathway of Mycobacterium tuberculosis is a potential drug target for the anti-tuberculosis drugs...

    Authors: Kulwant Singh and Vinod Bhakuni

    Citation: BMC Structural Biology 2007 7:39

    Content type: Research article

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  14. Molecular recognition between enzymes and proteic inhibitors is crucial for normal functioning of many biological pathways. Mutations in either the enzyme or the inhibitor protein often lead to a modulation of...

    Authors: Daniele Dell'Orco, Pier Giuseppe De Benedetti and Francesca Fanelli

    Citation: BMC Structural Biology 2007 7:37

    Content type: Research article

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  15. Lectins are proteins of non-immune origin capable of binding saccharide structures with high specificity and affinity. Considering the high encoding capacity of oligosaccharides, this makes lectins important f...

    Authors: Jan Adam, Martina Pokorná, Charles Sabin, Edward P Mitchell, Anne Imberty and Michaela Wimmerová

    Citation: BMC Structural Biology 2007 7:36

    Content type: Research article

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  16. Pediocin-like bacteriocins, ribosomally-synthesized antimicrobial peptides, are generally coexpressed with cognate immunity proteins in order to protect the bacteriocin-producer from its own bacteriocin. As a ...

    Authors: In-Kwon Kim, Min-Kyu Kim, Ji-Hye Kim, Hyung-Soon Yim, Sun-Shin Cha and Sa-Ouk Kang

    Citation: BMC Structural Biology 2007 7:35

    Content type: Research article

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  18. Serine proteases secreted by nematode and insect pathogenic fungi are bio-control agents which have commercial potential for developing into effective bio-pesticides. A thorough understanding of the structural...

    Authors: Shu-Qun Liu, Zhao-Hui Meng, Jin-Kui Yang, Yun-Xin Fu and Ke-Qin Zhang

    Citation: BMC Structural Biology 2007 7:33

    Content type: Research article

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  19. Fungal β-N-acetylhexosaminidases catalyze the hydrolysis of chitobiose into its constituent monosaccharides. These enzymes are physiologically important during the life cycle of the fungus for the formation of se...

    Authors: Rüdiger Ettrich, Vladimír Kopecký Jr, Kateřina Hofbauerová, Vladimír Baumruk, Petr Novák, Petr Pompach, Petr Man, Ondřej Plíhal, Michal Kutý, Natallia Kulik, Jan Sklenář, Helena Ryšlavá, Vladimír Křen and Karel Bezouška

    Citation: BMC Structural Biology 2007 7:32

    Content type: Research article

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  21. The YjgF/YER057c/UK114 family of proteins is widespread in nature, but has as yet no clearly defined biological role. Members of the family exist as homotrimers and are characterised by intersubunit clefts tha...

    Authors: Julia D Burman, Clare EM Stevenson, R Gary Sawers and David M Lawson

    Citation: BMC Structural Biology 2007 7:30

    Content type: Research article

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  22. Protein sequence can be obtained through Edman degradation, mass spectrometry, or cDNA sequencing. High resolution X-ray crystallography can also be used to derive protein sequence information, but faces the d...

    Authors: Xiaomin Hou, Minghuang Chen, Liqing Chen, Edward J Meehan, Jieming Xie and Mingdong Huang

    Citation: BMC Structural Biology 2007 7:29

    Content type: Research article

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  23. α-Conotoxins have exciting therapeutic potential based on their high selectivity and affinity for nicotinic acetylcholine receptors. The spacing between the cysteine residues in α-conotoxins is variable, leadi...

    Authors: Ai-Hua Jin, Hemma Brandstaetter, Simon T Nevin, Chia Chia Tan, Richard J Clark, David J Adams, Paul F Alewood, David J Craik and Norelle L Daly

    Citation: BMC Structural Biology 2007 7:28

    Content type: Research article

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  24. The major intrinsic proteins (MIPs) facilitate the transport of water and neutral solutes across the lipid bilayers. Plant MIPs are believed to be important in cell division and expansion and in water transpor...

    Authors: Anjali Bansal and Ramasubbu Sankararamakrishnan

    Citation: BMC Structural Biology 2007 7:27

    Content type: Research article

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  25. The brine shrimp Artemia expresses four different types of haemoglobin subunits namely C1, C2, T1 and T2. Two of these four subunits dimerize in different combinations to produce the three isoforms of the heterod...

    Authors: David T Chyou, Vincent L Rawle and Clive NA Trotman

    Citation: BMC Structural Biology 2007 7:26

    Content type: Research article

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  27. The C-terminal tetratricopeptide (TPR) repeat domain of Pex5p recognises proteins carrying a peroxisomal targeting signal type 1 (PTS1) tripeptide in their C-terminus. Previously, structural data have been obt...

    Authors: Will A Stanley, Niko V Pursiainen, Elspeth F Garman, André H Juffer, Matthias Wilmanns and Petri Kursula

    Citation: BMC Structural Biology 2007 7:24

    Content type: Research article

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  28. To discover remote evolutionary relationships and functional similarities between proteins, biologists rely on comparative sequence analysis, and when structures are available, on structural alignments and var...

    Authors: Thomas Madej, Anna R Panchenko, Jie Chen and Stephen H Bryant

    Citation: BMC Structural Biology 2007 7:23

    Content type: Research article

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  29. SH3 domains are small protein modules of 60–85 amino acids that bind to short proline-rich sequences with moderate-to-low affinity and specificity. Interactions with SH3 domains play a crucial role in regulation ...

    Authors: Salvador Casares, Eiso AB, Henk Eshuis, Obdulio Lopez-Mayorga, Nico AJ van Nuland and Francisco Conejero-Lara

    Citation: BMC Structural Biology 2007 7:22

    Content type: Research article

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  34. Histones organize the genomic DNA of eukaryotes into chromatin. The four core histone subunits consist of two consecutive helix-strand-helix motifs and are interleaved into heterodimers with a unique fold. We ...

    Authors: Vikram Alva, Moritz Ammelburg, Johannes Söding and Andrei N Lupas

    Citation: BMC Structural Biology 2007 7:17

    Content type: Research article

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  35. Sudan red compounds are hydrophobic azo dyes, still used as food additives in some countries. However, they have been shown to be unsafe, causing tumors in the liver and urinary bladder in rats. They have been...

    Authors: Lu Li, Hong-Wen Gao, Jiao-Rong Ren, Ling Chen, Yu-Cheng Li, Jian-Fu Zhao, He-Ping Zhao and Yuan Yuan

    Citation: BMC Structural Biology 2007 7:16

    Content type: Research article

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  36. Reduced representations of proteins have been playing a keyrole in the study of protein folding. Many such models are available, with different representation detail. Although the usefulness of many such model...

    Authors: Federico Fogolari, Lidia Pieri, Agostino Dovier, Luca Bortolussi, Gilberto Giugliarelli, Alessandra Corazza, Gennaro Esposito and Paolo Viglino

    Citation: BMC Structural Biology 2007 7:15

    Content type: Research article

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  37. The N-terminal SH2 domain (N-SH2) of the non-receptor tyrosine phosphatase SHP-2 is involved both in localization of SHP-2 by recognition of phosphotyrosine (pY) peptides and self-inhibition of SHP-2 phosphata...

    Authors: Olgun Guvench, Cheng-Kui Qu and Alexander D MacKerell Jr

    Citation: BMC Structural Biology 2007 7:14

    Content type: Research article

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  39. The reliable prediction of protein tertiary structure from the amino acid sequence remains challenging even for small proteins. We have developed an all-atom free-energy protein forcefield (PFF01) that we coul...

    Authors: Abhinav Verma and Wolfgang Wenzel

    Citation: BMC Structural Biology 2007 7:12

    Content type: Research article

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  40. The import of solutes into the bacterial cytoplasm involves several types of membrane transporters, which may be driven by ATP hydrolysis (ABC transporters) or by an ion or H+ electrochemical membrane potential, ...

    Authors: Sophie Gonin, Pascal Arnoux, Bénédicte Pierru, Jérôme Lavergne, Béatrice Alonso, Monique Sabaty and David Pignol

    Citation: BMC Structural Biology 2007 7:11

    Content type: Research article

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  41. The initial step involved in oxidative hydroxylation of monoaromatic and polyaromatic compounds by the microorganism Sphingobium yanoikuyae strain B1 (B1), previously known as Sphingomonas yanoikuyae strain B1 an...

    Authors: Daniel J Ferraro, Eric N Brown, Chi-Li Yu, Rebecca E Parales, David T Gibson and S Ramaswamy

    Citation: BMC Structural Biology 2007 7:10

    Content type: Research article

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  43. The chicken genome contains a BBP-A gene showing similar characteristics to avidin family genes. In a previous study we reported that the BBP-A gene may encode a biotin-binding protein due to the high sequence si...

    Authors: Vesa P Hytönen, Juha AE Määttä, Einari A Niskanen, Juhani Huuskonen, Kaisa J Helttunen, Katrin K Halling, Henri R Nordlund, Kari Rissanen, Mark S Johnson, Tiina A Salminen, Markku S Kulomaa, Olli H Laitinen and Tomi T Airenne

    Citation: BMC Structural Biology 2007 7:8

    Content type: Research article

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  44. 8-Oxoguanine (8-oxoG) is a common oxidative lesion frequently encountered by DNA polymerases such as the repair enzyme DNA polymerase β (pol β). To interpret in atomic and energetic detail how pol β processes 8-o...

    Authors: Yanli Wang and Tamar Schlick

    Citation: BMC Structural Biology 2007 7:7

    Content type: Research article

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  45. Bone morphogenetic proteins (BMPs) are key regulators in the embryonic development and postnatal tissue homeostasis in all animals. Loss of function or dysregulation of BMPs results in severe diseases or even ...

    Authors: Dionys Weber, Alexander Kotzsch, Joachim Nickel, Stefan Harth, Axel Seher, Uwe Mueller, Walter Sebald and Thomas D Mueller

    Citation: BMC Structural Biology 2007 7:6

    Content type: Research article

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  46. Correolide, a nortriterpene isolated from the Costa Rican tree Spachea correa, is a novel immunosuppressant, which blocks Kv1.3 channels in human T lymphocytes. Earlier mutational studies suggest that correolide ...

    Authors: Iva Bruhova and Boris S Zhorov

    Citation: BMC Structural Biology 2007 7:5

    Content type: Research article

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  47. To understand the energetics of the interaction between protein and DNA we analyzed 39 crystallographically characterized complexes with the HINT (Hydropathic INTeractions) computational model. HINT is an empi...

    Authors: Francesca Spyrakis, Pietro Cozzini, Chiara Bertoli, Anna Marabotti, Glen E Kellogg and Andrea Mozzarelli

    Citation: BMC Structural Biology 2007 7:4

    Content type: Research article

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  49. Hydrophobic Cluster Analysis (HCA) is an efficient way to compare highly divergent sequences through the implicit secondary structure information directly derived from hydrophobic clusters. However, its effici...

    Authors: Richard Eudes, Khanh Le Tuan, Jean Delettré, Jean-Paul Mornon and Isabelle Callebaut

    Citation: BMC Structural Biology 2007 7:2

    Content type: Methodology article

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  50. Protein-Carbohydrate interactions are crucial in many biological processes with implications to drug targeting and gene expression. Nature of protein-carbohydrate interactions may be studied at individual resi...

    Authors: Adeel Malik and Shandar Ahmad

    Citation: BMC Structural Biology 2007 7:1

    Content type: Research article

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