Transitions of CDR-L3 Loop Canonical Cluster Conformations on the Micro-to-Millisecond Timescale

Fernández‐Quintero, Monica L.; Math, Barbara A.; Loeffler, Johannes R.; Liedl, Klaus R.

doi:10.3389/fimmu.2019.02652

Cited by 18 publications

(27 citation statements)

References 73 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…This approach removes any bias stemming from a different number of starting clusters in the seeding process and allows us to capture accurate thermodynamic and kinetic properties of the sampled dynamic processes (Bowman et al, 2013 ; Kohlhoff et al, 2014 ). Similar approaches have been reported previously (Noé et al, 2009 ; Nedialkova et al, 2014 ; Biswas et al, 2018 ; Sun et al, 2018 ; Zimmerman et al, 2018 ; Fernández-Quintero et al, 2019a , b , 2020 ; Kahler et al, 2020 ; Kamenik et al, 2020 ).…”

Section: Methodssupporting

confidence: 84%

pH-Induced Local Unfolding of the Phl p 6 Pollen Allergen From cpH-MD

Hofer

Kamenik

Fernández‐Quintero

et al. 2021

Front. Mol. Biosci.

Self Cite

View full text Add to dashboard Cite

Susceptibility to endosomal degradation is a decisive contribution to a protein's immunogenicity. It is assumed that the processing kinetics of structured proteins are inherently linked to their probability of local unfolding. In this study, we quantify the impact of endosomal acidification on the conformational stability of the major timothy grass pollen allergen Phl p 6. We use state of the art sampling approaches in combination with constant pH MD techniques to profile pH-dependent local unfolding events in atomistic detail. Integrating our findings into the current view on type 1 allergic sensitization, we characterize local protein dynamics in the context of proteolytic degradation at neutral and acidic pH for the wild type protein and point mutants with varying proteolytic stability. We analyze extensive simulation data using Markov state models and retrieve highly reliable thermodynamic and kinetic information at varying pH levels. Thereby we capture the impact of endolysosomal acidification on the structure and dynamics of the Phl p 6 mutants. We find that upon protonation at lower pH values, the conformational flexibilities in key areas of the wild type protein, i.e., T-cell epitopes and early proteolytic cleavage sites, increase significantly. A decrease of the pH even leads to local unfolding in otherwise stable secondary structure elements, which is a prerequisite for proteolytic cleavage. This effect is even more pronounced in the destabilized mutant, while no unfolding was observed for the stabilized mutant. In summary, we report detailed structural models which rationalize the experimentally observed cleavage pattern during endosomal acidification.

show abstract

Section: Methodssupporting

confidence: 84%

pH-Induced Local Unfolding of the Phl p 6 Pollen Allergen From cpH-MD

Hofer

Kamenik

Fernández‐Quintero

et al. 2021

Front. Mol. Biosci.

Self Cite

View full text Add to dashboard Cite

show abstract

“…Studies revealed that the high conformational diversity of the CDR loops can be captured by kinetically characterizing the loops as ensembles in solution. For all CDR loops conformational transitions between canonical clusters and additional dominant solution structures have been observed 18 , 27 , 28 . Additionally, these conformational transitions between different CDR loop states occur in the micro-to-millisecond timescale 18 , 27 , 28 , 43 , while the relative V H and V L interdomain dynamics can be captured in the 0.1–10 ns timescale 44 , 45 .…”

Section: Discussionmentioning

confidence: 90%

“…The sampling is accelerated by a history-dependent bias potential, which is constructed in the space of the CVs 64,66,70 . As collective variables, we used a well-established protocol, boosting a linear combination of sine and cosine of the ψ torsion angles of all CDR loops calculated with functions MATHEVAL and COMBINE implemented in PLUMED 2 18,27,43,52,69,71 . As discussed previously the ψ torsion angle captures conformational transitions comprehensively 72 .…”

Section: Methodsmentioning

confidence: 99%

“…Recent studies using molecular dynamics simulations extended the model of static canonical clusters to a characterization of the CDR-L3 and CDR-H3 loops as ensembles in solution by showing that for a given CDR-L3/CDR-H3 loop sequence several conformations should be considered. Besides capturing several conformational transitions between different canonical clusters, other probable CDR-L3 loop structures in solution were identified that are not apparent from X-ray analysis most likely due to crystal packing effects 27 , 28 . Another crucial aspect in antibody structure design is the relative orientation of the two variable domains V H /V L , which influences the shape of the paratope and plays an important role in understanding antigen-specificity 29 , 30 .…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Antibodies exhibit multiple paratope states influencing VH–VL domain orientations

et al. 2020

Self Cite

View full text Add to dashboard Cite

In the last decades, antibodies have emerged as one of the most important and successful classes of biopharmaceuticals. The highest variability and diversity of an antibody is concentrated on six hypervariable loops, also known as complementarity determining regions (CDRs) shaping the antigen-binding site, the paratope. Whereas it was assumed that certain sequences can only adopt a limited set of backbone conformations, in this study we present a kinetic classification of several paratope states in solution. Using molecular dynamics simulations in combination with experimental structural information we capture the involved conformational transitions between different canonical clusters and additional dominant solution structures occurring in the micro-to-millisecond timescale. Furthermore, we observe a strong correlation of CDR loop movements. Another important aspect when characterizing different paratope states is the relative VH/VL orientation and the influence of the distinct CDR loop states on the VH/VL interface. Conformational rearrangements of the CDR loops do not only have an effect on the relative VH/VL orientations, but also influence in some cases the elbow-angle dynamics and shift the respective distributions. Thus, our results show that antibodies exist as several interconverting paratope states, each contributing to the antibody’s properties.

show abstract

“…Previous studies showed the importance of taking the conformational diversity into account when characterizing antibody paratopes and the involved conformational changes upon antigen binding ( Fernández-Quintero et al. 2019a , b , c ). Conformational diversity of proteins, and the pre-existence of a conformational ensemble out of which the functional conformations are selected, has been focus of various studies ( Foote and Milstein, 1994 ; James and Tawfik, 2003 ).…”

Section: Discussionmentioning

confidence: 99%

Conformational selection of allergen-antibody complexes—surface plasticity of paratopes and epitopes

Fernández‐Quintero

Loeffler

Waibl

et al. 2019

Protein Engineering, Design and Selection

View full text Add to dashboard Cite

Antibodies have the ability to bind various types of antigens and to recognize different antibody-binding sites (epitopes) of the same antigen with different binding affinities. Due to the conserved structural framework of antibodies, their specificity to antigens is mainly determined by their antigen-binding site (paratope). Therefore, characterization of epitopes in combination with describing the involved conformational changes of the paratope upon binding is crucial in understanding and predicting antibody-antigen binding. Using molecular dynamics simulations complemented with strong experimental structural information, we investigated the underlying binding mechanism and the resulting local and global surface plasticity in the binding interfaces of distinct antibody-antigen complexes. In all studied allergen-antibody complexes, we clearly observe that experimentally suggested epitopes reveal less plasticity, while non-epitope regions show high surface plasticity. Surprisingly, the paratope shows higher conformational diversity reflected in substantially higher surface plasticity, compared to the epitope. This work allows a visualization and characterization of antibody-antigen interfaces and might have strong implications for antibody-antigen docking and in the area of epitope prediction.

show abstract

Transitions of CDR-L3 Loop Canonical Cluster Conformations on the Micro-to-Millisecond Timescale

Cited by 18 publications

References 73 publications

pH-Induced Local Unfolding of the Phl p 6 Pollen Allergen From cpH-MD

pH-Induced Local Unfolding of the Phl p 6 Pollen Allergen From cpH-MD

Antibodies exhibit multiple paratope states influencing VH–VL domain orientations

Conformational selection of allergen-antibody complexes—surface plasticity of paratopes and epitopes

Contact Info

Product

Resources

About