MOLCAD — Computer Aided Visualization and Manipulation of Models in Molecular Science

Waldherr-Teschner, Michael; Goetze, T.; Heiden, Wolfgang; Knoblauch, Martin; Vollhardt, H.; Brickmann, Jürgen

doi:10.1007/978-3-642-77334-1_5

Cited by 49 publications

(35 citation statements)

References 13 publications

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“…The oligosaccharides were built using the graphics program Sybyl (Tripos Associates, St. Louis, MO). Solvent-accessible surfaces were calculated with the Molcad program (33), and electrostatic potentials were calculated using atomic charges corresponding to parameters developed for carbohydrates (34). Table 1 Although the H-1 signals of GlcA-2, GalNAc-3, GalNAc-5, and GalNAc-7 are overlapping at δ 4.54, the NOESY spectrum could be assigned without any ambiguity, showing the interresidual cross-peaks expected.…”

Section: Methodsmentioning

confidence: 99%

Conformational Studies on Five Octasaccharides Isolated from Chondroitin Sulfate Using NMR Spectroscopy and Molecular Modeling

et al. 2007

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Chondroitin sulfate proteoglycans (CS-PG) are involved in the regulation of the central nervous system in vertebrates due to their presence on cell surfaces and in the extracellular matrix of tissues. The CS moieties are built up from repeating -4)GlcA( 1-3)GalNAc( 1-disaccharide units, partly O-sulfated at different positions. The presence of the disulfated disaccharide D-unit, GlcA2S( 1-3)GalNAc6S, in the CS moiety of the proteoglycan DSD-1-PG/phosphacan, correlates with neurite outgrowth promotion. The binding of monoclonal antibody (mAb) 473HD to DSD-1-PG, reducing neuronal stimulation, is inhibited by shark cartilage CS-D. CS-D is also recognized by two other mAbs, MO-225 and CS-56. Conformational studies were performed using NMR spectroscopy and molecular modeling on five octasaccharides isolated from shark cartilage CS-D. These octasaccharides present different binding properties toward the three mAbs. The combination of the experimental and theoretical approaches revealed that the sulfate group at position 2 of GlcA in disaccharide D and the presence of an exocyclic negative tail in disaccharides C [GlcA( 1-3)GalNAc6S] and ∆C [∆ 4,5 HexA(R1-3)GalNAc6S] are important for antibody recognition.

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Section: Methodsmentioning

confidence: 99%

Conformational Studies on Five Octasaccharides Isolated from Chondroitin Sulfate Using NMR Spectroscopy and Molecular Modeling

et al. 2007

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“…All energy calculations were performed with the Tripos force-field (Clark et al, 1989) using energy parameters previously derived for carbohydrates . Connolly surface of the protein was calculated using the MOLCAD program (Waldherr-Teschner et al, 1992).…”

Section: Molecular Modelingmentioning

confidence: 99%

Characterization of Four Lectin-Like Receptor Kinases Expressed in Roots of Medicago truncatula. Structure, Location, Regulation of Expression, and Potential Role in the Symbiosis with Sinorhizobium meliloti

et al. 2003

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To study the role of LecRK (lectin-like receptor kinase) genes in the legume-rhizobia symbiosis, we have characterized the four Medicago truncatula Gaernt. LecRK genes that are most highly expressed in roots. Three of these genes, MtLecRK7;1, MtLecRK7;2, and MtLecRK7;3, encode proteins most closely related to the Class A LecRKs of Arabidopsis, whereas the protein encoded by the fourth gene, MtLecRK1;1, is most similar to a Class B Arabidopsis LecRK. All four genes show a strongly enhanced root expression, and detailed studies on MtLecRK1;1 and MtLecRK7;2 revealed that the levels of their mRNAs are increased by nitrogen starvation and transiently repressed after either rhizobial inoculation or addition of lipochitooligosaccharidic Nod factors. Studies of the MtLecRK1;1 and MtLecRK7;2 proteins, using green fluorescent protein fusions in transgenic M. truncatula roots, revealed that they are located in the plasma membrane and that their central transmembrane-spanning helix is required for correct sorting. Moreover, their lectin-like domains appear to be highly glycosylated. Of the four proteins, only MtLecRK1;1 shows a high conservation of key residues implicated in monosaccharide binding, and molecular modeling revealed that this protein may be capable of interacting with Nod factors. However, no increase in Nod factor binding was found in roots overexpressing a fusion in which the kinase domain of this protein had been replaced with green fluorescent protein. Roots expressing this fusion protein however showed an increase in nodule number, suggesting that expression of MtLecRK1;1 influences nodulation. The potential role of LecRKs in the legumerhizobia symbiosis is discussed.The lectin-like receptor kinases (LecRKs) are a class of proteins originally described from Arabidopsis (Hervé et al., 1996). They have a structure similar to other plant receptor-like kinases (RLKs; Shiu and Bleecker, 2001;Cock et al., 2002) with an N-terminal targeting signal, a presumably extracellular domain, a single transmembrane (TM)-spanning helix, and a cytosolic kinase domain. The Arabidopsis genome contains over 610 RLKs that have been shown to be monophylogenetic with respect to the kinase domain and most closely related to the fruitfly (Drosophila melanogaster) Pelle and related animal cytoplasmic kinases (Shiu and Bleecker, 2001). In cases in which they have been tested, these kinases have been shown to have specificity for phosphorylation on Ser/Thr residues (Shiu and Bleecker, 2001).The plant RLKs can be grouped into more than 21 structural classes based on their extracellular domains (Shiu and Bleecker, 2001). The LecRKs represent one such class in which the extracellular domain is related to legume lectins. The Arabidopsis genome contains at least 42 LecRK sequences that have been grouped into three classes (A-C) plus an additional nine sequences of related soluble lectins (Barre et al., 2002). Searches in plant databases reveal that LecRK genes are widespread in higher plants, but apart from Arabidopsis (Hervé et al., 1996,...

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“…The stereochemistries of the resulting models were checked using the PROCHECK program (27). Connolly surfaces were calculated using the MOLCAD program (28).…”

mentioning

confidence: 99%

LysM Domains from Pteris ryukyuensis Chitinase-A

Ohnuma

Onaga

Murata

et al. 2008

Journal of Biological Chemistry

108

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The LysM domain probably binds peptidoglycans, but how it does so has yet to be described. For this report, we measured the thermal stabilities of recombinant LysM domains derived from Pteris ryukyuensis chitinase-A (PrChi-A) and monitored their binding to N-acetylglucosamine oligomers ((GlcNAc) n ) using differential scanning calorimetry, isothermal titration calorimetry, and NMR spectroscopy. We thereby characterized certain of the domains' functional and structural features. We observed that the domains are very resistant to thermal denaturation and that this resistance depends on the presence of disulfide bonds. We also show that the stoichiometry of (GlcNAc) n /LysM domain binding is 1:1. (GlcNAc) 5 titration experiments, monitored by NMR spectroscopy, allowed us to identify the domain residues that are critical for (GlcNAc) 5 binding. The binding site is a shallow groove formed by the N-terminal part of helix 1, the loop between strand 1 and helix 1, the C-terminal part of helix 2, and the loop between helix 2 and strand 2. Furthermore, mutagenesis experiments reiterate the critical involvement of Tyr 72 in (GlcNAc) n /LysM domain binding. Ours is the first report describing the physical structure of a LysM oligosaccharide-binding site based on experimental data.Carbohydrates are often the signals that initiate biochemical processes. For example, as a response to pathogenic attacks, plant defense proteins first recognize and then attack the carbohydrate components of the pathogens' cell walls (1). As these defense proteins bind carbohydrates (2), via their noncatalytic carbohydrate-binding modules, their binding mechanisms are physiologically interesting. Many carbohydrate-binding modules have been structurally and/or functionally characterized (3) and, based on these characteristics, are currently grouped into 49 families in the Carbohydrate-Active Enzyme (CAZy) data base (available on the World Wide Web).The LysM domain, which probably binds chitin, a ␤-(134)-linked N-acetylglucosamine oligosaccharide ((GlcNAc) n ), was originally identified as a component of bacterial lysins. This domain is found in many of the enzymes involved in cell wall degradation and is also present in other proteins that are associated with bacterial cell walls (4 -8). Basal level resistance by plants against certain pathogens also appears to involve the recognition of chitin oligosaccharides and related compounds. Recently, a chitin oligosaccharide elicitor receptor was purified, and it contains a LysM domain within its extracellular domain (9). Additionally, certain symbiotic relationships between leguminous plants and rhizobial bacteria appear to be mediated by LysM domain/chitin oligosaccharide interactions. Recent studies have identified a class of proteins that recognize Nod factors, which are the lipochitin oligosaccharide signal molecules secreted by symbiotic bacteria (10 -12). These plant proteins are members of a serine/threonine receptor kinase family and contain extracellular LysM domains. After reviewing the availab...

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MOLCAD — Computer Aided Visualization and Manipulation of Models in Molecular Science

Cited by 49 publications

References 13 publications

Conformational Studies on Five Octasaccharides Isolated from Chondroitin Sulfate Using NMR Spectroscopy and Molecular Modeling

Conformational Studies on Five Octasaccharides Isolated from Chondroitin Sulfate Using NMR Spectroscopy and Molecular Modeling

Characterization of Four Lectin-Like Receptor Kinases Expressed in Roots of Medicago truncatula. Structure, Location, Regulation of Expression, and Potential Role in the Symbiosis with Sinorhizobium meliloti

LysM Domains from Pteris ryukyuensis Chitinase-A

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