Crystal structure determination of anti‐DNA Fab A52

Stanfield, Robyn L.; Eilat, Dan

doi:10.1002/prot.24514

Cited by 8 publications

(10 citation statements)

References 42 publications

(46 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…A careful examination of the X-ray crystal structure revealed 19 sulfate ions, and one forms a salt bridge between the side chain of ArgH98 in chain B and that of LysH50 in chain D in the other crystal unit, as shown in Fig. 4a (Stanfield and Eilat, 2014). In the asymmetric unit of A52 crystal structure, there is another antibody molecule, chains C and D. Interestingly, the side chain of ArgH98 in chain D forms another salt bridge with the side chain of HisL189 (HisA194 as the PDB residue number) in chain A in the other crystal unit across another sulfate ion, as shown in Fig.…”

Section: Resultsmentioning

confidence: 99%

“…Although the antigen of the A52 antibody is known to be either single-stranded or double-stranded DNA, no complex structure is available. Only a few structures of antibodies that bind to DNA are available (Stanfield and Eilat, 2014), such as that of the DNA-1 antibody (Tanner et al ., 2001), which adopts multiple conformations in the apo-state (Schuermann et al ., 2005). If the A52 antibody has similar properties to the DNA-1 antibody, then our free energy landscape consisting of several stable structures may capture the structural properties of the A52 antibody in the apo-state.…”

Section: Resultsmentioning

confidence: 99%

“…The crystal structure of A52 (PDBID 4m61, Stanfield and Eilat, 2014), which contains two similar Fab domains, was obtained from the Protein Data Bank (Berman et al ., 2007), and the Fab domain of chains A and B was used for modeling. The initial structure of the CDR-H3 loop was taken from our previous model (Shirai et al ., 2014), which had been built with the MODELLER program (Sali and Blundell, 1993), followed by energy minimization with the myPresto/cosgene program (Fukunishi et al ., 2003).…”

Section: Methodsmentioning

confidence: 99%

See 2 more Smart Citations

Revisiting antibody modeling assessment for CDR-H3 loop

Nishimura

Kamiya

Nakamura

2016

Protein Engineering, Design and Selection

View full text Add to dashboard Cite

The antigen-binding site of antibodies, also known as complementarity-determining region (CDR), has hypervariable sequence properties. In particular, the third CDR loop of the heavy chain, CDR-H3, has such variability in its sequence, length, and conformation that ordinary modeling techniques cannot build a high-quality structure. At Stage 2 of the Second Antibody Modeling Assessment (AMA-II) held in 2013, the model structures of the CDR-H3 loops were submitted by the seven modelers and were critically assessed. After our participation in AMA-II, we rebuilt one of the long CDR-H3 loops with 13 residues (A52 antibody) by a more precise method, using enhanced conformational sampling with the explicit water model, as compared to our previous method employed at AMA-II. The current stable models obtained from the free energy landscape at 300 K include structures similar to the X-ray crystal structures. Those models were not built in our previous work at AMA-II. The current free energy landscape suggested that the CDR-H3 loop structures in the crystal are not stable in solution, but they are stabilized by the crystal packing effect.

show abstract

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Revisiting antibody modeling assessment for CDR-H3 loop

Nishimura

Kamiya

Nakamura

2016

Protein Engineering, Design and Selection

View full text Add to dashboard Cite

show abstract

“…In this introductory article we describe the organization of AMA‐II, summarize the main features of the benchmark structures, provide an overview of the assessment, outline the evaluation criteria, highlight relevant results, and reflect on current challenges in antibody modeling and future directions of the field. The articles that follow in this special issue discuss the benchmark structures, including four short reports on structures relevant to the assessment, assess the quality of the models generated by the participant groups, and expand on each modeling method and the corresponding lessons learned by each participant group …”

Section: Introductionmentioning

confidence: 99%

Second antibody modeling assessment (AMA‐II)

et al. 2014

View full text Add to dashboard Cite

To assess the state of the art in antibody 3D modeling, 11 unpublished high-resolution x-ray Fab crystal structures from diverse species and covering a wide range of antigen-binding site conformations were used as a benchmark to compare Fv models generated by seven structure prediction methodologies. The participants included: Accerlys Inc, Chemical Computer Group (CCG), Schrodinger, Jeff Gray's lab at John Hopkins University, Macromoltek, Astellas Pharma/Osaka University and Prediction of ImmunoGlobulin Structure (PIGS). The sequences of benchmark structures were submitted to the modelers and PIGS, and a set of models were generated for each structure. We provide here an overview of the organization, participants and main results of this second antibody modeling assessment (AMA-II). Also, we compare the results with the first antibody assessment published in this journal (Almagro et al., 2011;79:3050).

show abstract

“…Both properties apply to the structures of the AMAII set, which have all been crystallized in the unbound state and, with the sole exception of anti‐DNA Fab A52 (PDB ID 4M61; Ref. ), are protein binding. The predicted HL value for Ab01 (−57.17°) lies between the two reference structure values of −57.61° (4MA3_BA) and −51.82° (4MA3_HL) but leans toward the more “conservative” end of the range of HL.…”

Section: Resultsmentioning

confidence: 99%

Prediction of VH–VL domain orientation for antibody variable domain modeling

Bujotzek¹,

Dunbar

Lipsmeier

et al. 2015

Proteins

View full text Add to dashboard Cite

The antigen-binding site of antibodies forms at the interface of their two variable domains, VH and VL, making VH-VL domain orientation a factor that codetermines antibody specificity and affinity. Preserving VH-VL domain orientation in the process of antibody engineering is important in order to retain the original antibody properties, and predicting the correct VH-VL orientation has also been recognized as an important factor in antibody homology modeling. In this article, we present a fast sequence-based predictor that predicts VH-VL domain orientation with Q(2) values ranging from 0.54 to 0.73 on the evaluation set. We describe VH-VL orientation in terms of the six absolute ABangle parameters that have recently been proposed as a means to separate the different degrees of freedom of VH-VL domain orientation. In order to assess the impact of adjusting VH-VL orientation according to our predictions, we use the set of antibody structures of the recently published Antibody Modeling Assessment (AMA) II study. In comparison to the original AMAII homology models, we find an improvement in the accuracy of VH-VL orientation modeling, which also translates into an improvement in the average root-mean-square deviation with regard to the crystal structures.

show abstract

Crystal structure determination of anti‐DNA Fab A52

Cited by 8 publications

References 42 publications

Revisiting antibody modeling assessment for CDR-H3 loop

Revisiting antibody modeling assessment for CDR-H3 loop

Second antibody modeling assessment (AMA‐II)

Prediction of VH–VL domain orientation for antibody variable domain modeling

Contact Info

Product

Resources

About