R. Adhikary, W. Yu, M. Oda, T. Chen, R. Walker, R. Stanfield, I. Wilson, J. Zimmermann, F.E. Romesberg, Biochemistry (2015) 54:2085–2093.
In this work, three affinity matured anti-MPTS antibodies (Abs) are characterized via X-ray and spectroscopic studies and the results are discussed in terms of the elasticity, anelasticity, and plasticity of the complexes. We find that the level of plasticity of the Ab-MPTS complexes is correlated with specificity, suggesting that the optimization of protein dynamics may have contributed to affinity maturation.
R. Adhikary, W. Yu, M. Oda, J. Zimmermann, F.E. Romesberg, J. Biol. Chem. (2012) 287:27139-27147.
We report the sequence, thermodynamic, and time-resolved spectroscopic characterization of a panel of eight antibodies (Abs) elicited to a chromophoric antigen (MPTS). Three of the Abs arose from unique germline Abs, while the remaining five comprise two sets of siblings that arose by somatic mutation of a common precursor. By characterizing both flexibility and conformational heterogeneity, we show that point mutations are capable of fixing significant differences in protein dynamics.
J. Zimmermann, F.E. Romesberg, C.L. Brooks III, I.F. Thorpe, J. Phys. Chem. B (2010) 114:7359-7370.
We show that 3PEPS spectroscopy in combination with molecular dynamics simulations can provide a detailed description of protein dynamics for the fluorescein Ab 4−4−20, and how it is evolved for biological function.
J. Zimmermann, M.C. Thielges, W. Yu, F.E. Romesberg, in Protein Engineering Handbook, Vol. 1 (2009) S. Lutz and U.T. Bornscheuer, Eds., Wiley-VCH:Weinheim, 147-186.
We review novel experimental methods to characterize conformational heterogeneity and dynamics in proteins.
M.C. Thielges, J. Zimmermann, W. Yu, M. Oda, F.E. Romesberg, Biochemistry (2008) 47:7237-7247. [June 2008 Hot Article].
We examine a panel of antibodies elicited to the chromophoric antigen fluorescein. On the basis of isothermal titration calorimetry, we select six antibodies that bind fluorescein with diverse binding entropies, suggestive of varying contributions of dynamics to molecular recognition. We find that more than half of all the somatic mutations among the six antibodies are located in positions unlikely to contact fluorescein directly, and using 3PEPS and TG spectroscopy, we find a high level of dynamic diversity among the antibodies.
M.F. Goodman, M.D. Schaarf, F.E. Romesberg, Adv. Immunol. (2007) 94:127-155.
We review the role of activation-induced cytidine deaminase (AID) in the complex process of somatic hypermutation (SHM) and present recent advances in experimental methods to characterize antibody dynamics as a function of SHM to help elucidate the role that the AID-induced mutations play in tailoring molecular recognition.
J. Zimmermann, E.L. Oakman, I.F. Thorpe, X. Shi, P. Abbyad, C.L. Brooks, III, S.G. Boxer, F.E. Romesberg, Proc. Natl. Acad. Sci. USA (2006) 103:13722-13727.
We report the characterization of protein heterogeneity and dynamics as a function of evolution for the antifluorescein antibody 4-4-20. Using nonlinear laser spectroscopy, surface plasmon resonance, and molecular dynamics simulations, we demonstrate that evolution localized the Ab-combining site from a heterogeneous ensemble of conformations to a single conformation by introducing mutations that act cooperatively and over significant distances to rigidify the protein.