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Rigidity Emerges during Antibody Evolution in Three Distinct Antibody Systems: Evidence from QSFR Analysis of Fab Fragments.

Li T, Tracka MB, Uddin S, Casas-Finet J, Jacobs DJ, Livesay DR - PLoS Comput. Biol. (2015)

Bottom Line: The effects of somatic mutations that transform polyspecific germline (GL) antibodies to affinity mature (AM) antibodies with monospecificity are compared among three GL-AM Fab pairs.We have previously established that the DCM can be robustly applied across a series of antibody fragments (VL to Fab), and subsequently, the DCM was combined with molecular dynamics (MD) simulations to similarly characterize five thermostabilizing scFv mutants.Applied to three disparate antibody systems changes in QSFR quantities indicate that the VH domain is typically rigidified, whereas the VL domain and CDR L2 loop become more flexible during affinity maturation.

View Article: PubMed Central - PubMed

Affiliation: Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina, United States of America.

ABSTRACT
The effects of somatic mutations that transform polyspecific germline (GL) antibodies to affinity mature (AM) antibodies with monospecificity are compared among three GL-AM Fab pairs. In particular, changes in conformational flexibility are assessed using a Distance Constraint Model (DCM). We have previously established that the DCM can be robustly applied across a series of antibody fragments (VL to Fab), and subsequently, the DCM was combined with molecular dynamics (MD) simulations to similarly characterize five thermostabilizing scFv mutants. The DCM is an ensemble based statistical mechanical approach that accounts for enthalpy/entropy compensation due to network rigidity, which has been quite successful in elucidating conformational flexibility and Quantitative Stability/Flexibility Relationships (QSFR) in proteins. Applied to three disparate antibody systems changes in QSFR quantities indicate that the VH domain is typically rigidified, whereas the VL domain and CDR L2 loop become more flexible during affinity maturation. The increase in CDR H3 loop rigidity is consistent with other studies in the literature. The redistribution of conformational flexibility is largely controlled by nonspecific changes in the H-bond network, although certain Arg to Asp salt bridges create highly localized rigidity increases. Taken together, these results reveal an intricate flexibility/rigidity response that accompanies affinity maturation.

No MeSH data available.


Related in: MedlinePlus

Structures of the three Fab fragments bound with antigens (fluorescein, CD3 and hapten, respectively) are shown.H and L chains are colored in cyan and green, respectively; epitope is colored in orange.
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pcbi.1004327.g002: Structures of the three Fab fragments bound with antigens (fluorescein, CD3 and hapten, respectively) are shown.H and L chains are colored in cyan and green, respectively; epitope is colored in orange.

Mentions: Three GL-AM antibody pairs including anti-fluorescein, anti-CD3 T-cell receptor and esterase catalytic antibodies were compiled for rigidity/flexibility analysis. For each pair we compare the AM sequence to the GL sequence via sequence alignments (Fig 1). The numbers of mutations located in the Fab and CDRs with respect to the GL sequence are 12/6, 9/6 and 9/5 for FA, CA and EA, respectively, indicating that 50% or more of the mutations occur in CDRs. Fig 2 shows the binding modes of the antigens in their AM antibodies. It is noted that antigen fluorescein and hapten 5-(para-nitrophenyl phosphonate)-pentanoic acid are located in similar sub-regions of the binding site, which facilitate them to interact directly with the CDR-H3 and CDR-L3 loops. Similarly, one epitope loop of antigen CD3 inserts into the same sub-regions, while others make contact with CDR-H1 and CDR-H2 loops. S1 Fig summaries the changes of amino acid propensity during affinity maturation. An apparent trend is that charged residues are favorable in the mature sequences while polar residues are unfavorable (S5 Table).


Rigidity Emerges during Antibody Evolution in Three Distinct Antibody Systems: Evidence from QSFR Analysis of Fab Fragments.

Li T, Tracka MB, Uddin S, Casas-Finet J, Jacobs DJ, Livesay DR - PLoS Comput. Biol. (2015)

Structures of the three Fab fragments bound with antigens (fluorescein, CD3 and hapten, respectively) are shown.H and L chains are colored in cyan and green, respectively; epitope is colored in orange.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4489365&req=5

pcbi.1004327.g002: Structures of the three Fab fragments bound with antigens (fluorescein, CD3 and hapten, respectively) are shown.H and L chains are colored in cyan and green, respectively; epitope is colored in orange.
Mentions: Three GL-AM antibody pairs including anti-fluorescein, anti-CD3 T-cell receptor and esterase catalytic antibodies were compiled for rigidity/flexibility analysis. For each pair we compare the AM sequence to the GL sequence via sequence alignments (Fig 1). The numbers of mutations located in the Fab and CDRs with respect to the GL sequence are 12/6, 9/6 and 9/5 for FA, CA and EA, respectively, indicating that 50% or more of the mutations occur in CDRs. Fig 2 shows the binding modes of the antigens in their AM antibodies. It is noted that antigen fluorescein and hapten 5-(para-nitrophenyl phosphonate)-pentanoic acid are located in similar sub-regions of the binding site, which facilitate them to interact directly with the CDR-H3 and CDR-L3 loops. Similarly, one epitope loop of antigen CD3 inserts into the same sub-regions, while others make contact with CDR-H1 and CDR-H2 loops. S1 Fig summaries the changes of amino acid propensity during affinity maturation. An apparent trend is that charged residues are favorable in the mature sequences while polar residues are unfavorable (S5 Table).

Bottom Line: The effects of somatic mutations that transform polyspecific germline (GL) antibodies to affinity mature (AM) antibodies with monospecificity are compared among three GL-AM Fab pairs.We have previously established that the DCM can be robustly applied across a series of antibody fragments (VL to Fab), and subsequently, the DCM was combined with molecular dynamics (MD) simulations to similarly characterize five thermostabilizing scFv mutants.Applied to three disparate antibody systems changes in QSFR quantities indicate that the VH domain is typically rigidified, whereas the VL domain and CDR L2 loop become more flexible during affinity maturation.

View Article: PubMed Central - PubMed

Affiliation: Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina, United States of America.

ABSTRACT
The effects of somatic mutations that transform polyspecific germline (GL) antibodies to affinity mature (AM) antibodies with monospecificity are compared among three GL-AM Fab pairs. In particular, changes in conformational flexibility are assessed using a Distance Constraint Model (DCM). We have previously established that the DCM can be robustly applied across a series of antibody fragments (VL to Fab), and subsequently, the DCM was combined with molecular dynamics (MD) simulations to similarly characterize five thermostabilizing scFv mutants. The DCM is an ensemble based statistical mechanical approach that accounts for enthalpy/entropy compensation due to network rigidity, which has been quite successful in elucidating conformational flexibility and Quantitative Stability/Flexibility Relationships (QSFR) in proteins. Applied to three disparate antibody systems changes in QSFR quantities indicate that the VH domain is typically rigidified, whereas the VL domain and CDR L2 loop become more flexible during affinity maturation. The increase in CDR H3 loop rigidity is consistent with other studies in the literature. The redistribution of conformational flexibility is largely controlled by nonspecific changes in the H-bond network, although certain Arg to Asp salt bridges create highly localized rigidity increases. Taken together, these results reveal an intricate flexibility/rigidity response that accompanies affinity maturation.

No MeSH data available.


Related in: MedlinePlus