Optimality of mutation and selection in germinal centers

The population dynamics theory of B cells in a typical germinal center could play an important role in revealing how affinity maturation is achieved. However, the existing models encountered some conflicts with experiments. To resolve these conflicts, we present a coarse-grained model to calculate the B cell population development in affinity maturation, which allows a comprehensive analysis of its parameter space to look for optimal values of mutation rate, selection strength, and initial antibody-antigen binding level that maximize the affinity improvement. With these optimized parameters, the model is compatible with the experimental observations such as the ~100-fold affinity improvements, the number of mutations, the hypermutation rate, and the "all or none" phenomenon. Moreover, we study the reasons behind the optimal parameters. The optimal mutation rate, in agreement with the hypermutation rate in vivo, results from a tradeoff between accumulating enough beneficial mutations and avoiding too many deleterious or lethal mutations. The optimal selection strength evolves as a balance between the need for affinity improvement and the requirement to pass the population bottleneck. These findings point to the conclusion that germinal centers have been optimized by evolution to generate strong affinity antibodies effectively and rapidly. In addition, we study the enhancement of affinity improvement due to B cell migration between germinal centers. These results could enhance our understandings to the functions of germinal centers.Comment: 5 figures in main text, and 4 figures in Supplementary Informatio

High Affinity Antigen Recognition of the Dual Specific Variants of Herceptin Is Entropy-Driven in Spite of Structural Plasticity

The antigen-binding site of Herceptin, an anti-human Epidermal Growth Factor Receptor 2 (HER2) antibody, was engineered to add a second specificity toward Vascular Endothelial Growth Factor (VEGF) to create a high affinity two-in-one antibody bH1. Crystal structures of bH1 in complex with either antigen showed that, in comparison to Herceptin, this antibody exhibited greater conformational variability, also called “structural plasticity”. Here, we analyzed the biophysical and thermodynamic properties of the dual specific variants of Herceptin to understand how a single antibody binds two unrelated protein antigens. We showed that while bH1 and the affinity-improved bH1-44, in particular, maintained many properties of Herceptin including binding affinity, kinetics and the use of residues for antigen recognition, they differed in the binding thermodynamics. The interactions of bH1 and its variants with both antigens were characterized by large favorable entropy changes whereas the Herceptin/HER2 interaction involved a large favorable enthalpy change. By dissecting the total entropy change and the energy barrier for dual interaction, we determined that the significant structural plasticity of the bH1 antibodies demanded by the dual specificity did not translate into the expected increase of entropic penalty relative to Herceptin. Clearly, dual antigen recognition of the Herceptin variants involves divergent antibody conformations of nearly equivalent energetic states. Hence, increasing the structural plasticity of an antigen-binding site without increasing the entropic cost may play a role for antibodies to evolve multi-specificity. Our report represents the first comprehensive biophysical analysis of a high affinity dual specific antibody binding two unrelated protein antigens, furthering our understanding of the thermodynamics that drive the vast antigen recognition capacity of the antibody repertoire

Flexibility and molecular recognition in the immune system

Photon echo spectroscopy has been used to measure the response of three antibody-binding sites to perturbation from electronic excitation of a bound antigen, fluorescein. The three antibodies show motions that range in time scale from tens of femtoseconds to nanoseconds. Relative to the others, one antibody, 4-4-20, possesses a rigid binding site that likely results from a short and inflexible heavy chain complementarity-determining region 3 (HCDR3) loop and a critical Tyr that acts as a “molecular splint,” rigidifying the antigen across its most flexible internal degree of freedom. The remaining two antibodies, 34F10 and 40G4, despite being generated against the same antigen, possess binding sites that are considerably more flexible. The more flexible combining sites likely result from longer HCDR3 loops and a deletion in the light chain complementarity-determining region 1 (LCDR1) that removes the critical Tyr residue. The binding site flexibilities may result in varying mechanisms of antigen recognition including lock-and-key, induced-fit, and conformational selection

Estimation of damped oscillation associated spectra from ultrafast transient absorption spectra

When exciting a complex molecular system with a short optical pulse, all chromophores present in the system can be excited. The resulting superposition of electronically and vibrationally excited states evolves in time, which is monitored with transient absorption spectroscopy. We present a methodology to resolve simultaneously the contributions of the different electronically and vibrationally excited states from the complete data. The evolution of the excited states is described with a superposition of damped oscillations. The amplitude of a damped oscillation cos(ωnt)exp(−γnt) as a function of the detection wavelength constitutes a damped oscillation associated spectrum DOASn(λ) with an accompanying phase characteristic φn(λ). In a case study, the cryptophyte photosynthetic antenna complex PC612 which contains eight bilin chromophores was excited by a broadband optical pulse. Difference absorption spectra from 525 to 715 nm were measured until 1 ns. The population dynamics is described by four lifetimes, with interchromophore equilibration in 0.8 and 7.5 ps. We have resolved 24 DOAS with frequencies between 130 and 1649 cm−1 and with damping rates between 0.9 and 12 ps−1. In addition, 11 more DOAS with faster damping rates were necessary to describe the “coherent artefact.” The DOAS contains both ground and excited state features. Their interpretation is aided by DOAS analysis of simulated transient absorption signals resulting from stimulated emission and ground state bleach

Structural evidence for substrate strain in antibody catalysis

The crystal structure of the Michaelis complex between the Fab fragment of ferrochelatase antibody 7G12 and its substrate mesoporphyrin has been solved to 2.6-Å resolution. The antibody-bound mesoporphyrin clearly adopts a nonplanar conformation and reveals that the antibody catalyzes the porphyrin metallation reaction by straining/distorting the bound substrate toward the transition-state configuration. The crystal structures of the Fab fragment of the germ-line precursor antibody to 7G12 and its complex with the hapten N-methylmesoporphyrin have also been solved. A comparison of these structures with the corresponding structures of the affinity-matured antibody 7G12 reveals the molecular mechanism by which the immune system evolves binding energy to catalyze this reaction

Structural Studies of Catalytic Antibodies

A panel of catalytic antibodies which catalyze ester hydrolysis, transesterification, porphyrin metallation, Diels-Alder, and redox reactions has been selected for crystallographic study. While these examples are only a handful of the catalytic antibodies generated to date, they represent distinct and important aspects of antibody catalysis. Since the first reports of catalysis, a great deal of progress has been made with respect to the scope, selectivity, and efficiency of antibody catalysis and strategies for generating catalytic antibodies. However, it is clear that further progress in the field will benefit greatly from a detailed understanding of the molecular interactions occurring in the combining site. High-resolution crystallographic data should allow the importance of general base catalysis, entropy effects, electrophilic catalysis, and transition-state stabilization to be evaluated. Antibody and enzyme active sites have been shown to share considerable structural and mechanistic similarity, and ongoing structure-function studies of catalytic antibodies may enhance our understanding of the mechanisms and evolution of enzymatic catalysis. Structural studies of antibodies which perform a biological or highly selective reactions should enhance our ability to generate catalysts for important synthetic applications. Finally, the combination of high-resolution crystallographic analysis with rational mutagenesis should provide a basis for engineering antibodies with enhanced properties

Preridiniopsis Kevei SP. nov., A new freshwater dinoflagellate species (peridiniceae, dinophyta) from Hungary

This paper reports results from light and scanning electron microscopic study of a freshwater dinoflagellate considered as a new species for the science, Peridiniopsis keveisp. nov. It was found during the last ten years in different lake, rivers, canals in Hungary and some European countries. it frequently appeared as a water-bloom forming species. The theca morphology and and plate structure analysis of this dinoflagellate established its identity as a new species. P. kevei Grigorszky et Vasas is discussed in the paper in comparsion with related taxa, moreover data about its occurrence and ecology