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Modeling the antigen combining site of an anti‐dinitrophenyl antibody, ANO2

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Zeitschriftentitel: Protein Science
Personen und Körperschaften: Bassolino‐Klimas, Donna, Bruccoleri, Robert E., Subramaniam, Shankar
In: Protein Science, 1, 1992, 11, S. 1465-1476
Format: E-Article
Sprache: Englisch
veröffentlicht:
Wiley
Schlagwörter:
Molecular Biology
Biochemistry
author_facet Bassolino‐Klimas, Donna
Bruccoleri, Robert E.
Subramaniam, Shankar
Bassolino‐Klimas, Donna
Bruccoleri, Robert E.
Subramaniam, Shankar
author Bassolino‐Klimas, Donna
Bruccoleri, Robert E.
Subramaniam, Shankar
spellingShingle Bassolino‐Klimas, Donna
Bruccoleri, Robert E.
Subramaniam, Shankar
Protein Science
Modeling the antigen combining site of an anti‐dinitrophenyl antibody, ANO2
Molecular Biology
Biochemistry
author_sort bassolino‐klimas, donna
spelling Bassolino‐Klimas, Donna Bruccoleri, Robert E. Subramaniam, Shankar 0961-8368 1469-896X Wiley Molecular Biology Biochemistry http://dx.doi.org/10.1002/pro.5560011108 <jats:title>Abstract</jats:title><jats:p>A model structure has been constructed for a monoclonal anti‐dinitrophenyl antibody. The antibody, ANO2, has been sequenced and cloned (Anglister, J., Frey, T., &amp; McConnell, H.M., 1984, <jats:italic>Biochemistry 23</jats:italic>, 1138–1142). Its amino acid sequence shows striking homology with the anti‐lysozyme Fab fragments HyHel5 (83%) and HyHel10 (73%). Based on this homology, a model for the ANO2 variable heavy and variable light chain framework was constructed using a hybrid of the HyHel5 light chain and the HyHel10 heavy chain backbone, omitting the hypervariable loops. These coordinates were used as scaffolds for the model building of ANO2.</jats:p><jats:p>The CONGEN conformational sampling algorithm (Bruccoleri, R.E. &amp; Karplus, M., 1987, <jats:italic>Biopolymers 26</jats:italic>, 127–196) was used to model the six hypervariable loops that contain the antigen‐combining site. All the possible conformations of the loop backbones were constructed and the best loop structures were selected using a combination of the CHARMM potential energy function and evaluation of the solvent‐accessible surface area of the conformers. The order in which the loops were searched was carried out based on the relative locations of the loops with reference to the framework of the β‐barrel, namely, L2‐H1‐L3‐H2‐H3‐L1. The model structures thus obtained were compared to the high resolution X‐ray structure (Brünger, A.T., Leahy, D.J., Hynes, T.R., &amp; Fox, R.O., 1991, <jats:italic>J. Mol. Biol. 221</jats:italic>, 239–256).</jats:p> Modeling the antigen combining site of an anti‐dinitrophenyl antibody, ANO2 Protein Science
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series Protein Science
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title Modeling the antigen combining site of an anti‐dinitrophenyl antibody, ANO2
title_unstemmed Modeling the antigen combining site of an anti‐dinitrophenyl antibody, ANO2
title_full Modeling the antigen combining site of an anti‐dinitrophenyl antibody, ANO2
title_fullStr Modeling the antigen combining site of an anti‐dinitrophenyl antibody, ANO2
title_full_unstemmed Modeling the antigen combining site of an anti‐dinitrophenyl antibody, ANO2
title_short Modeling the antigen combining site of an anti‐dinitrophenyl antibody, ANO2
title_sort modeling the antigen combining site of an anti‐dinitrophenyl antibody, ano2
topic Molecular Biology
Biochemistry
url http://dx.doi.org/10.1002/pro.5560011108
publishDate 1992
physical 1465-1476
description <jats:title>Abstract</jats:title><jats:p>A model structure has been constructed for a monoclonal anti‐dinitrophenyl antibody. The antibody, ANO2, has been sequenced and cloned (Anglister, J., Frey, T., &amp; McConnell, H.M., 1984, <jats:italic>Biochemistry 23</jats:italic>, 1138–1142). Its amino acid sequence shows striking homology with the anti‐lysozyme Fab fragments HyHel5 (83%) and HyHel10 (73%). Based on this homology, a model for the ANO2 variable heavy and variable light chain framework was constructed using a hybrid of the HyHel5 light chain and the HyHel10 heavy chain backbone, omitting the hypervariable loops. These coordinates were used as scaffolds for the model building of ANO2.</jats:p><jats:p>The CONGEN conformational sampling algorithm (Bruccoleri, R.E. &amp; Karplus, M., 1987, <jats:italic>Biopolymers 26</jats:italic>, 127–196) was used to model the six hypervariable loops that contain the antigen‐combining site. All the possible conformations of the loop backbones were constructed and the best loop structures were selected using a combination of the CHARMM potential energy function and evaluation of the solvent‐accessible surface area of the conformers. The order in which the loops were searched was carried out based on the relative locations of the loops with reference to the framework of the β‐barrel, namely, L2‐H1‐L3‐H2‐H3‐L1. The model structures thus obtained were compared to the high resolution X‐ray structure (Brünger, A.T., Leahy, D.J., Hynes, T.R., &amp; Fox, R.O., 1991, <jats:italic>J. Mol. Biol. 221</jats:italic>, 239–256).</jats:p>
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author Bassolino‐Klimas, Donna, Bruccoleri, Robert E., Subramaniam, Shankar
author_facet Bassolino‐Klimas, Donna, Bruccoleri, Robert E., Subramaniam, Shankar, Bassolino‐Klimas, Donna, Bruccoleri, Robert E., Subramaniam, Shankar
author_sort bassolino‐klimas, donna
container_issue 11
container_start_page 1465
container_title Protein Science
container_volume 1
description <jats:title>Abstract</jats:title><jats:p>A model structure has been constructed for a monoclonal anti‐dinitrophenyl antibody. The antibody, ANO2, has been sequenced and cloned (Anglister, J., Frey, T., &amp; McConnell, H.M., 1984, <jats:italic>Biochemistry 23</jats:italic>, 1138–1142). Its amino acid sequence shows striking homology with the anti‐lysozyme Fab fragments HyHel5 (83%) and HyHel10 (73%). Based on this homology, a model for the ANO2 variable heavy and variable light chain framework was constructed using a hybrid of the HyHel5 light chain and the HyHel10 heavy chain backbone, omitting the hypervariable loops. These coordinates were used as scaffolds for the model building of ANO2.</jats:p><jats:p>The CONGEN conformational sampling algorithm (Bruccoleri, R.E. &amp; Karplus, M., 1987, <jats:italic>Biopolymers 26</jats:italic>, 127–196) was used to model the six hypervariable loops that contain the antigen‐combining site. All the possible conformations of the loop backbones were constructed and the best loop structures were selected using a combination of the CHARMM potential energy function and evaluation of the solvent‐accessible surface area of the conformers. The order in which the loops were searched was carried out based on the relative locations of the loops with reference to the framework of the β‐barrel, namely, L2‐H1‐L3‐H2‐H3‐L1. The model structures thus obtained were compared to the high resolution X‐ray structure (Brünger, A.T., Leahy, D.J., Hynes, T.R., &amp; Fox, R.O., 1991, <jats:italic>J. Mol. Biol. 221</jats:italic>, 239–256).</jats:p>
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spelling Bassolino‐Klimas, Donna Bruccoleri, Robert E. Subramaniam, Shankar 0961-8368 1469-896X Wiley Molecular Biology Biochemistry http://dx.doi.org/10.1002/pro.5560011108 <jats:title>Abstract</jats:title><jats:p>A model structure has been constructed for a monoclonal anti‐dinitrophenyl antibody. The antibody, ANO2, has been sequenced and cloned (Anglister, J., Frey, T., &amp; McConnell, H.M., 1984, <jats:italic>Biochemistry 23</jats:italic>, 1138–1142). Its amino acid sequence shows striking homology with the anti‐lysozyme Fab fragments HyHel5 (83%) and HyHel10 (73%). Based on this homology, a model for the ANO2 variable heavy and variable light chain framework was constructed using a hybrid of the HyHel5 light chain and the HyHel10 heavy chain backbone, omitting the hypervariable loops. These coordinates were used as scaffolds for the model building of ANO2.</jats:p><jats:p>The CONGEN conformational sampling algorithm (Bruccoleri, R.E. &amp; Karplus, M., 1987, <jats:italic>Biopolymers 26</jats:italic>, 127–196) was used to model the six hypervariable loops that contain the antigen‐combining site. All the possible conformations of the loop backbones were constructed and the best loop structures were selected using a combination of the CHARMM potential energy function and evaluation of the solvent‐accessible surface area of the conformers. The order in which the loops were searched was carried out based on the relative locations of the loops with reference to the framework of the β‐barrel, namely, L2‐H1‐L3‐H2‐H3‐L1. The model structures thus obtained were compared to the high resolution X‐ray structure (Brünger, A.T., Leahy, D.J., Hynes, T.R., &amp; Fox, R.O., 1991, <jats:italic>J. Mol. Biol. 221</jats:italic>, 239–256).</jats:p> Modeling the antigen combining site of an anti‐dinitrophenyl antibody, ANO2 Protein Science
spellingShingle Bassolino‐Klimas, Donna, Bruccoleri, Robert E., Subramaniam, Shankar, Protein Science, Modeling the antigen combining site of an anti‐dinitrophenyl antibody, ANO2, Molecular Biology, Biochemistry
title Modeling the antigen combining site of an anti‐dinitrophenyl antibody, ANO2
title_full Modeling the antigen combining site of an anti‐dinitrophenyl antibody, ANO2
title_fullStr Modeling the antigen combining site of an anti‐dinitrophenyl antibody, ANO2
title_full_unstemmed Modeling the antigen combining site of an anti‐dinitrophenyl antibody, ANO2
title_short Modeling the antigen combining site of an anti‐dinitrophenyl antibody, ANO2
title_sort modeling the antigen combining site of an anti‐dinitrophenyl antibody, ano2
title_unstemmed Modeling the antigen combining site of an anti‐dinitrophenyl antibody, ANO2
topic Molecular Biology, Biochemistry
url http://dx.doi.org/10.1002/pro.5560011108