Bioinformatics in molecular immunology laboratories demonstrated: Modeling an anti-CMV scFv antibody

Heng, Chua Kek; Othman, Rofina Yasmin

doi:10.6026/97320630001118

Cited by 7 publications

(2 citation statements)

References 25 publications

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“…The Swiss-Pdb Viewer is used to evaluate the predicted structure. The Ramachandran plot (bottom, right) shows how good the values of the dihedral angles agree with the values of allowed conformations themenschwerpunkt SWISS-MODEL, ranging from mutations, chimeric enzymes to active sites and factor-receptor complexes [54][55][56][57][58][59][60][61][62][63][64][65][66][67][68][69]. The resulting structures can be visualized at the Pdb-Viewer in several representations such as balls-and-sticks or as ribbon (showing secondary structure elements) and the molecular surface can be calculated.…”

Section: Discussionmentioning

confidence: 99%

Homology Modelling: Eine Übersicht über die Methode am Beispiel der Strukturbestimmung vom Diabetes Antigen GAD 65

Wiltgen

Tilz

2009

Wien Med Wochenschr

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This introductory paper describes the basic principles and clinical applications of the protein 3D structure prediction by homology modelling. The paper mainly addresses physicians and medical chemists. Because many proteins are of immediate clinical importance, the determination of their structures is crucial for molecular medicine. In homology modelling, a protein sequence with unknown structure is aligned with sequences of known protein structures. By exploiting structural information from the known configurations, the new structure can be predicted. The necessary condition for successful homology modelling is a sufficient similarity between the protein sequences. Because in the near future for every protein family at least one member with a known structure will be available, the importance and applicability of homology modelling is steadily increasing. We demonstrate the principles of homology modelling on hand of the Glutamic Acid Decarboxylase (GAD 65) structure prediction, which is a typical autoantigen involved in Diabetes Mellitus Type 1.

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Section: Discussionmentioning

confidence: 99%

Homology Modelling: Eine Übersicht über die Methode am Beispiel der Strukturbestimmung vom Diabetes Antigen GAD 65

Wiltgen

Tilz

2009

Wien Med Wochenschr

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“…To develop a novel biosensor for overused fluoroquinolones antibiotics, we envisioned utilization of the phage-display selection of a single-chain variable-fragment (scFv) library for the discovery of a general or specific recognition module for antibiotics. Recombinant scFv is a small (∼25 kDa) protein composed of antibody variable heavy (V H ) and light (V L ) chains that are connected by a peptide linker . The key advantages of using an scFv as the recognition element are its excellent selectivity to antigen and low operation cost; further, target-specific scFv clones can be easily selected from an scFv library by phage display , .…”

Section: Introductionmentioning

confidence: 99%

Pharmacophore-Based Strategy for the Development of General and Specific scFv Biosensors for Abused Antibiotics

Young

Lee

et al. 2010

Bioconjugate Chem.

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We developed fluorescent biosensor systems that are either general or selective to fluoroquinolone antibiotics by using a single-chain variable-fragment (scFv) as a recognition element. The selectivity of these biosensors to fluoroquinolone antibiotics was rationally tuned through the structural modification on the pharmacophore of fluoroquinolone antibiotics and the subsequent selection of scFv receptor modules against these antibiotics-based antigens using phage display. The resulting A2 and F9 scFv's bound to their representative antigen with a moderate affinity (K(D) in micromolar range as determined by surface plasmon resonance). A2 is a specific binder for enrofloxacin and did not cross-react with other fluoroquinolone antibiotics including structurally similar ciprofloxacin, while F9 is a general fluoroquinolone binder that likely bound to the antigen at the common pyridone-carboxylic acid pharmacophore. These scFv-based receptors were successfully applied to the development of one-step fluorescent biosensor which can detect fluoroquinolone antibiotics at concentrations below the level suggested in animal drug application guidelines. The strategy described in this report can be applied to developing convenient field biosensors that can qualitatively detect overused/misused antibiotics in the livestock drinking water.

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Modeling the three-dimensional structures of an unbound single-chain variable fragment (scFv) and its hypothetical complex with a Corynespora cassiicola toxin, cassiicolin

et al. 2010

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Rubber trees infected with a host-specific cassiicolin toxin often experience considerable leaf fall, which in turn results in loss of crop productivity. It was recently revealed that cassiicolin-specific single-chain variable fragments (scFv) can successfully reduce the toxic effects of cassiicolin. However, the detailed mechanism of antibody action remains poorly understood. The primary sequence of the newly sequenced cassiicolin-specific scFv was highly homologous to several members of single-chain antibodies in the 14B7 family. In this study, with the aid of homology modeling, the three-dimensional structure of cassiicolin-specific scFv was elucidated, and was found to exhibit a characteristic immunoglobulin fold that mainly consists of β sheets. Additionally, molecular docking between the modeled scFv antibody and the available three-dimensional crystal structure of cassiicolin toxin was also performed. The predicted structural complex and the change in accessible surface area between the toxin and the scFv antibody upon complexation reveal the potential role of certain complementarity determining region (CDR) amino acid residues in the formation of the complex. These computational results suggest that mutagenesis experiments that are aimed at validating the model and improving the binding affinity of cassiicolin-specific scFv antibodies for the toxin should be performed.

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Bioinformatics in molecular immunology laboratories demonstrated: Modeling an anti-CMV scFv antibody

Cited by 7 publications

References 25 publications

Homology Modelling: Eine Übersicht über die Methode am Beispiel der Strukturbestimmung vom Diabetes Antigen GAD 65

Homology Modelling: Eine Übersicht über die Methode am Beispiel der Strukturbestimmung vom Diabetes Antigen GAD 65

Pharmacophore-Based Strategy for the Development of General and Specific scFv Biosensors for Abused Antibiotics

Modeling the three-dimensional structures of an unbound single-chain variable fragment (scFv) and its hypothetical complex with a Corynespora cassiicola toxin, cassiicolin

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