Well-Tempered Metadynamics as a Tool for Characterizing Multi-Component, Crystalline Molecular Machines

Ilott, Andrew J.; Pałucha, S.; Hodgkinson, Paul; Wilson, Mark R.

doi:10.1021/jp4045995

Cited by 22 publications

(19 citation statements)

References 82 publications

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“…As enhanced sampling technique, we chose metadynamics as it allows to focus the enhanced sampling on predefined collective variables (CV). 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 .…”

Section: Methodsmentioning

confidence: 99%

Antibodies exhibit multiple paratope states influencing VH–VL domain orientations

et al. 2020

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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.

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Section: Methodsmentioning

confidence: 99%

Antibodies exhibit multiple paratope states influencing VH–VL domain orientations

et al. 2020

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“…This leads to an accelerated sampling allowing the system to escape deep energy minima. Well-tempered metadynamics (48) adapts the height of the Gaussian functions with simulation time. Various collective variables (CV) have been tested to achieve a better description of the conformational space.…”

Section: Methodsmentioning

confidence: 99%

Characterizing the Diversity of the CDR-H3 Loop Conformational Ensembles in Relationship to Antibody Binding Properties

et al. 2019

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We present an approach to assess antibody CDR-H3 loops according to their dynamic properties using molecular dynamics simulations. We selected six antibodies in three pairs differing substantially in their individual promiscuity respectively specificity. For two pairs of antibodies crystal structures are available in different states of maturation and used as starting structures for the analyses. For a third pair we chose two antibody CDR sequences obtained from a synthetic library and predicted the respective structures. For all three pairs of antibodies we performed metadynamics simulations to overcome the limitations in conformational sampling imposed by high energy barriers. Additionally, we used classic molecular dynamics simulations to describe nano- to microsecond flexibility and to estimate up to millisecond kinetics of captured conformational transitions. The methodology represents the antibodies as conformational ensembles and allows comprehensive analysis of structural diversity, thermodynamics of conformations and kinetics of structural transitions. Referring to the concept of conformational selection we investigated the link between promiscuity and flexibility of the antibodies' binding interfaces. The obtained detailed characterization of the binding interface clearly indicates a link between structural flexibility and binding promiscuity for this set of antibodies.

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“…As enhanced sampling technique, we chose metadynamics as it allows to focus the enhanced sampling on predefined collective variables (CV). The sampling is accelerated by a history-dependent bias potential, which is constructed in the space of the CVs (33,35,39). As collective variables, we used a well-established protocol, boosting a linear combination of sine and cosine of the y torsion angles of all CDR loops calculated with functions MATHEVAL and COMBINE implemented in PLUMED 2 (13,38,(40)(41)(42)(43).…”

Section: Metadynamics Simulationsmentioning

confidence: 99%

Mutation of Framework Residue H71 Results in Different Antibody Paratope States in Solution

et al. 2021

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Characterizing and understanding the antibody binding interface have become a pre-requisite for rational antibody design and engineering. The antigen-binding site is formed by six hypervariable loops, known as the complementarity determining regions (CDRs) and by the relative interdomain orientation (VH–VL). Antibody CDR loops with a certain sequence have been thought to be limited to a single static canonical conformation determining their binding properties. However, it has been shown that antibodies exist as ensembles of multiple paratope states, which are defined by a characteristic combination of CDR loop conformations and interdomain orientations. In this study, we thermodynamically and kinetically characterize the prominent role of residue 71H (Chothia nomenclature), which does not only codetermine the canonical conformation of the CDR-H2 loop but also results in changes in conformational diversity and population shifts of the CDR-H1 and CDR-H3 loop. As all CDR loop movements are correlated, conformational rearrangements of the heavy chain CDR loops also induce conformational changes in the CDR-L1, CDR-L2, and CDR-L3 loop. These overall conformational changes of the CDR loops also influence the interface angle distributions, consequentially leading to different paratope states in solution. Thus, the type of residue of 71H, either an alanine or an arginine, not only influences the CDR-H2 loop ensembles, but co-determines the paratope states in solution. Characterization of the functional consequences of mutations of residue 71H on the paratope states and interface orientations has broad implications in the field of antibody engineering.

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Well-Tempered Metadynamics as a Tool for Characterizing Multi-Component, Crystalline Molecular Machines

Cited by 22 publications

References 82 publications

Antibodies exhibit multiple paratope states influencing VH–VL domain orientations

Antibodies exhibit multiple paratope states influencing VH–VL domain orientations

Characterizing the Diversity of the CDR-H3 Loop Conformational Ensembles in Relationship to Antibody Binding Properties

Mutation of Framework Residue H71 Results in Different Antibody Paratope States in Solution

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