ABGEN: A Knowledge-Based Automated Approach for Antibody Structure Modeling

Mandal, Chhabinath; Kingery, B. D.; Anchin, Jerry M.; Subramaniam, Shankar; Linthicum, D. Scott

doi:10.1038/nbt0396-323

Cited by 50 publications

(31 citation statements)

References 17 publications

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“…Modeling Studies-Predictions of the three-dimensional structures of AdK, full-length LdCyP, and its truncated version were made by knowledge-based homology modeling using InsightII 98.0 of MSI (Biosym Technologies, San Diego, CA), ABGEN (34), and our in house package of MODELYN and ANALYN (35) in UNIX as well as in the Microsoft Windows environment. Energy minimization and molecular dynamics were performed with the InsightII 98.0/Discover package using the cff91 force field on a Silicon Graphics OCTANE work station.…”

Section: Methodsmentioning

confidence: 99%

A Single-domain Cyclophilin from Leishmania donovaniReactivates Soluble Aggregates of Adenosine Kinase by Isomerase-independent Chaperone Function

Chakraborty¹,

Das²,

Datta³

et al. 2002

Journal of Biological Chemistry

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Disaggregation and reactivation of aggregated proteins by chaperones is well established. However, little is known regarding such kind of function of single-domain small cyclophilins (CyPs). Here we demonstrate that, with increasing concentrations, fully active adenosine kinase (AdK) of Leishmania donovani tends to form soluble aggregates, resulting in inactivation. Using this inactive enzyme as the substrate, it is shown that a CyP from L. donovani (LdCyP) alone can cause complete disaggregation, leading to reactivation of the enzyme. The reactivating ability of LdCyP remains unaffected even in the presence of cyclosporin A and macromolecular crowding agents. The reactivation occurs noncatalytically and is reversible. A truncated LdCyP, devoid of 88 amino acids from the N terminus, is found to be required in near stoichiometric proportion to reactivate AdK, suggesting essentiality of the C-terminal region. Gel filtration and light-scattering experiments together with protein cross-linking studies revealed that both full-length LdCyP and the truncated form directly interact with AdK and convert oligomeric forms of the enzyme to monomeric state. Homology modeling studies suggest that the exposed hydrophobic residues of LdCyP, by interacting with solvent-accessible hydrophobic surface of AdK, pull apart its aggregated inactive oligomers to functional monomers. Clearly, the results are consistent with the interpretation that the higher efficiency of the truncated LdCyP is most likely due to increased exposure of the hydrophobic residues on its surface. These observations, besides establishing L. donovani AdK as one of the model enzymes to study aggregation-disaggregation of proteins, raise the possibility that single-domain small CyPs, under physiological conditions, may regulate the activity of aggregation-prone proteins by ensuring their disaggregation.

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Section: Methodsmentioning

confidence: 99%

A Single-domain Cyclophilin from Leishmania donovaniReactivates Soluble Aggregates of Adenosine Kinase by Isomerase-independent Chaperone Function

Chakraborty¹,

Das²,

Datta³

et al. 2002

Journal of Biological Chemistry

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“…The published X-ray crystallographic structures of human and T. gondii AdK were used as reference templates [20,22]. Prediction of the three-dimensional structure of LdAdK was done by knowledge-based homology modelling using the InsightII 98.0 of MSI (Biosym Technologies, San Diego, CA, U.S.A.), ABGEN [32] and our in-house package of MODELYN and ANALYN [33] in UNIX as well as in the Microsoft Windows environment. Energy minimization and molecular dynamics were performed with the InsightII 98.0/Discover package using a CFF91 forcefield on a Silicon Graphics ® OCTANE workstation.…”

Section: Modelling Studiesmentioning

confidence: 99%

Mutational analysis of the active-site residues crucial for catalytic activity of adenosine kinase from Leishmania donovani

Datta

Das

Sen

et al. 2005

Biochemical Journal

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Leishmania donovani adenosine kinase (LdAdK) plays a pivotal role in scavenging of purines from the host. Exploiting interspecies homology and structural co-ordinates of the enzyme from other sources, we generated a model of LdAdK that led us to target several amino acid residues (namely Gly-62, Arg-69, Arg-131 and Asp-299). Replacement of Gly-62 with aspartate caused a drastic reduction in catalytic activity, with decreased affinity for either substrate. Asp-299 was found to be catalytically indispensable. Mutation of either Arg-131 or Arg-69 caused a significant reduction in k cat . R69A (Arg-69 → Ala) and R131A mutants exhibited unaltered K m for either substrate, whereas ATP K m for R69K increased 6-fold. Importance of both of the arginine residues was reaffirmed by the R69K/R131A double mutant, which exhibited approx. 0.5 % residual activity with a large increase in ATP K m . Phenylglyoxal, which inhibits the wild-type enzyme, also inactivated the arginine mutants to different extents. Adenosine protected both of the Arg-69 mutants, but not the R131A variant, from inactivation. Binding experiments revealed that the AMPbinding property of R69K or R69A and D299A mutants remained largely unaltered, but R131A and R69K/R131A mutants lost their AMP binding ability significantly. The G62D mutant did not bind AMP at all. Free energy calculations indicated that Arg-69 and Arg-131 are functionally independent. Thus, apart from the mandatory requirement of flexibility around the diglycyl (Gly-61-Gly-62) motif, our results identified Asp-299 and Arg-131 as key catalytic residues, with the former functioning as the proton abstractor from the 5 -OH of adenosine, while the latter acts as a bidentate electrophile to stabilize the negative charge on the leaving group during the phosphate transfer. Moreover, the positive charge distribution of Arg-69 probably helps in maintaining the flexibility of the α-3 helix needed for proper domain movement. These findings provide the first comprehensive biochemical evidence implicating the mechanistic roles of the functionally important residues of this chemotherapeutically exploitable enzyme.

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“…The original and the additional rules are in the upper and the lower half, respectively. They can provide identi¢cation of the CDR-H3 conformations from only the amino acid sequences, and they should be useful when antibody structural models are constructed [16,17].…”

Section: H3-rulesmentioning

confidence: 99%

H3‐rules: identification of CDR‐H3 structures in antibodies

Shirai¹,

Kidera²,

Nakamura³

1999

FEBS Letters

163

182

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For the third complementarity determining region of the antibody heavy chain (CDR-H3), we propose the`H3-rules', which should identify the tertiary structure from the amino acid sequence of the CDR-H3 segment. A total of 100 CDR-H3 segments from well-determined crystal structures were analyzed. Distinctive relationships between the structures and the sequences were revealed from 55 segments, and the rules were examined for the other 45 segments and were verified. In some antibodies, basic residues at specific positions were revealed to be notable signals, with their ability to form salt bridges and to assume conformations inconsistent with the rules.z 1999 Federation of European Biochemical Societies.

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ABGEN: A Knowledge-Based Automated Approach for Antibody Structure Modeling

Cited by 50 publications

References 17 publications

A Single-domain Cyclophilin from Leishmania donovaniReactivates Soluble Aggregates of Adenosine Kinase by Isomerase-independent Chaperone Function

A Single-domain Cyclophilin from Leishmania donovaniReactivates Soluble Aggregates of Adenosine Kinase by Isomerase-independent Chaperone Function

Mutational analysis of the active-site residues crucial for catalytic activity of adenosine kinase from Leishmania donovani

H3‐rules: identification of CDR‐H3 structures in antibodies

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