Functional Consequences of Complementarity-determining Region Deactivation in a Multifunctional Anti-nucleic Acid Antibody

Kim, Hye-Jin; Roh, Jooho; Seo, Youngsil; Kim, Minjae; Jun, Hye-Ryeong; Pham, Dinh‐Chuong; Kwon, Myung-Hee

doi:10.1074/jbc.m113.508499

Cited by 7 publications

(5 citation statements)

References 33 publications

(44 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The far‐UV CD spectra (190–240 nm) for the six scFvs (Fig. d) showed the scFvs were predominantly β‐sheets, as expected for typical members of the immunoglobulin family, including scFvs (Supplementary Table SVI) (Blanco‐Toribio et al, ; Glaven et al, ; Gregoire et al, ; Lee et al, ; Song et al, ). The scFv‐2D10 (PDB ID‐ 4H0H) crystal structure showed the presence of 4% helical and 47% beta sheet secondary structures (Tapryal et al, ), whereas the CD data for the scFv‐2D10 in our hands retrieved 3.4, 5, and 9% helical and 40, 38, and 27% beta sheet structures from CDSSTR, CONTIN, and GOR4, respectively (Supplementary Table SVI).…”

Section: Resultssupporting

confidence: 59%

Computational de novo design of antibodies binding to a peptide with high affinity

Poosarla¹,

Li²,

Goh

et al. 2017

Biotech & Bioengineering

View full text Add to dashboard Cite

Antibody drugs play a critical role in infectious diseases, cancer, autoimmune diseases, and inflammation. However, experimental methods for the generation of therapeutic antibodies such as using immunized mice or directed evolution remain time consuming and cannot target a specific antigen epitope. Here, we describe the application of a computational framework called OptMAVEn combined with molecular dynamics to de novo design antibodies. Our reference system is antibody 2D10, a single-chain antibody (scFv) that recognizes the dodecapeptide DVFYPYPYASGS, a peptide mimic of mannose-containing carbohydrates. Five de novo designed scFvs sharing less than 75% sequence similarity to all existing natural antibody sequences were generated using OptMAVEn and their binding to the dodecapeptide was experimentally characterized by biolayer interferometry and isothermal titration calorimetry. Among them, three scFvs show binding affinity to the dodecapeptide at the nM level. Critically, these de novo designed scFvs exhibit considerably diverse modeled binding modes with the dodecapeptide. The results demonstrate the potential of OptMAVEn for the de novo design of thermally and conformationally stable antibodies with high binding affinity to antigens and encourage the targeting of other antigen targets in the future.

show abstract

Section: Resultssupporting

confidence: 59%

Computational de novo design of antibodies binding to a peptide with high affinity

Poosarla¹,

Li²,

Goh

et al. 2017

Biotech & Bioengineering

View full text Add to dashboard Cite

show abstract

“…Here, we aimed to elucidate the function of both classes of cell surface HSPGs and CSPGs as true endocytic receptors for a basic recombinant anti-nucleic acid antibody (3D8 single-chain variable fragment (scFv); pI value, 9.15) that is internalized by a variety of living cells. Previous studies suggest involvement of HSPGs in 3D8 scFv endocytosis, although evidence is scant 22 , 23 . Given that both HS and CS are highly negatively charged GAGs (due to acidic sugar residues and/or modification by sulfate groups), we were motivated to study whether both HSPGs and CSPGs function as true endocytic receptors for 3D8 scFv (used as a basic model macromolecule).…”

Section: Introductionmentioning

confidence: 99%

Heparan sulfate proteoglycans (HSPGs) and chondroitin sulfate proteoglycans (CSPGs) function as endocytic receptors for an internalizing anti-nucleic acid antibody

Park

Kim

et al. 2017

Sci Rep

Self Cite

View full text Add to dashboard Cite

A subset of monoclonal anti-DNA autoantibodies enters a variety of living cells. Here, we aimed to identify the endocytic receptors recognized by an internalizing anti-nucleic acid autoantibody, the 3D8 single-chain variable fragment (scFv). We found that cell surface binding and internalization of 3D8 scFv were inhibited markedly in soluble heparan sulfate (HS)/chondroitin sulfate (CS)-deficient or -removed cells and in the presence of soluble HS and CS. 3D8 scFv colocalized intracellularly with either HS proteoglycans (HSPGs) or CSPGs in HeLa cells. 3D8 scFv was co-endocytosed and co-precipitated with representative individual HSPG and CSPG molecules: syndecan-2 (a transmembrane HSPG), glypican-3 (a glycosylphosphatidylinositol (GPI)-anchored HSPG); CD44 (a transmembrane CSPG); and brevican (a GPI-anchored CSPG). Collected data indicate that 3D8 scFv binds to the negatively charged sugar chains of both HSPGs and CSPGs and is then internalized along with these molecules, irrespective of how these proteoglycans are associated with the cell membrane. This is the first study to show that anti-DNA antibodies enter cells via both HSPGs and CSPGs simultaneously. The data may aid understanding of endocytic receptors that bind anti-DNA autoantibodies. The study also provides insight into potential cell membrane targets for macromolecular delivery.

show abstract

“…The assay was performed in the presence or absence of heparin. Heparin competes with the m3D8 for DNA-binding sites and inhibits its DNA hydrolyzing activity (Lee et al, 2013); if the DNA hydrolyzing activities of m3D8 and ck3D8 are inhibited by heparin, false-positives caused by contamination during the protein preparation can be ruled out. The DNA hydrolyzing activity of ck3D8 was comparable to that of m3D8 and was completely blocked by the soluble competitor, heparin (Fig.…”

Section: Resultsmentioning

confidence: 99%

Generation of a chickenized catalytic anti-nucleic acid antibody by complementarity-determining region grafting

Roh

Byun

Seo

et al. 2015

Molecular Immunology

Self Cite

View full text Add to dashboard Cite

Functional Consequences of Complementarity-determining Region Deactivation in a Multifunctional Anti-nucleic Acid Antibody

Cited by 7 publications

References 33 publications

Computational de novo design of antibodies binding to a peptide with high affinity

Computational de novo design of antibodies binding to a peptide with high affinity

Heparan sulfate proteoglycans (HSPGs) and chondroitin sulfate proteoglycans (CSPGs) function as endocytic receptors for an internalizing anti-nucleic acid antibody

Generation of a chickenized catalytic anti-nucleic acid antibody by complementarity-determining region grafting

Contact Info

Product

Resources

About