scholarly journals Antibodies exhibit multiple paratope states influencing VH–VL domain orientations

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Monica L. Fernández-Quintero ◽  
Nancy D. Pomarici ◽  
Barbara A. Math ◽  
Katharina B. Kroell ◽  
Franz Waibl ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Structural Information ◽  
Conformational Transitions ◽  
Antigen Binding ◽  
Antigen Binding Site ◽  
Solution Structures ◽  
Conformational Rearrangements ◽  
Complementarity Determining Regions ◽  
Dynamics Simulations

Abstract 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.

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

2019 ◽  
Vol 32 (11) ◽  
pp. 513-523
Author(s):  
Monica L Fernández-Quintero ◽  
Johannes R Loeffler ◽  
Franz Waibl ◽  
Anna S Kamenik ◽  
Florian Hofer ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Structural Information ◽  
High Surface ◽  
Epitope Prediction ◽  
Antigen Binding ◽  
Antigen Binding Site ◽  
Surface Plasticity ◽  
Structural Framework ◽  
Dynamics Simulations

Abstract 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.

Antigen exposure leads to rigidification of germline antibody combining site

2014 ◽  
Vol 12 (03) ◽  
pp. 1450006 ◽  
Author(s):  
Jasmita Gill ◽  
Praapti Jayaswal ◽  
Dinakar M. Salunke
Keyword(s):  
Molecular Dynamics ◽  
Immune Complexes ◽  
Structural State ◽  
Bound States ◽  
Mechanistic Model ◽  
Conformational Transitions ◽  
Affinity Maturation ◽  
Antigen Binding ◽  
Dynamics Simulations ◽  
Antigen Release

Immune complexes involving diverse antigens and corresponding antibodies were analyzed for mapping conformational transitions of an antibody before antigen binding, upon antigen binding and after antigen release. Molecular dynamics simulations of the two comprehensive datasets consisting of the antigen-free and antigen-bound structures of the germline antibodies 36-65 and BBE6.12H3 provided mechanistic model of antigen encounter by primary antibodies. While native germline antibodies exhibit substantial mobility in the antigen-combining sites, their antigen-bound states exhibit relatively rigid conformations, even in the absence of the antigen suggesting preservation of the structural state after antigen release. It is proposed that acquired rigidity by a germline antibody upon antigen binding may be the first step in affinity maturation in favor of that antigen.

Use of Molecular Dynamics Simulations in Structure-Based Drug Discovery

2019 ◽  
Vol 25 (31) ◽  
pp. 3339-3349 ◽  
Author(s):  
Indrani Bera ◽  
Pavan V. Payghan
Keyword(s):  
Molecular Dynamics ◽  
Drug Discovery ◽  
Molecular Dynamics Simulations ◽  
Drug Target ◽  
Structural Information ◽  
Drug Binding ◽  
Structure Based Drug Design ◽  
Drug Designing ◽  
Target Binding ◽  
Dynamics Simulations

Background: Traditional drug discovery is a lengthy process which involves a huge amount of resources. Modern-day drug discovers various multidisciplinary approaches amongst which, computational ligand and structure-based drug designing methods contribute significantly. Structure-based drug designing techniques require the knowledge of structural information of drug target and drug-target complexes. Proper understanding of drug-target binding requires the flexibility of both ligand and receptor to be incorporated. Molecular docking refers to the static picture of the drug-target complex(es). Molecular dynamics, on the other hand, introduces flexibility to understand the drug binding process. Objective: The aim of the present study is to provide a systematic review on the usage of molecular dynamics simulations to aid the process of structure-based drug design. Method: This review discussed findings from various research articles and review papers on the use of molecular dynamics in drug discovery. All efforts highlight the practical grounds for which molecular dynamics simulations are used in drug designing program. In summary, various aspects of the use of molecular dynamics simulations that underline the basis of studying drug-target complexes were thoroughly explained. Results: This review is the result of reviewing more than a hundred papers. It summarizes various problems that use molecular dynamics simulations. Conclusion: The findings of this review highlight how molecular dynamics simulations have been successfully implemented to study the structure-function details of specific drug-target complexes. It also identifies the key areas such as stability of drug-target complexes, ligand binding kinetics and identification of allosteric sites which have been elucidated using molecular dynamics simulations.

scholarly journals Elucidating Solution Structures of Cyclic Peptides Using Molecular Dynamics Simulations

2021 ◽  
Vol 121 (4) ◽  
pp. 2292-2324
Author(s):  
Jovan Damjanovic ◽  
Jiayuan Miao ◽  
He Huang ◽  
Yu-Shan Lin
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Cyclic Peptides ◽  
Solution Structures ◽  
Dynamics Simulations

scholarly journals The answer lies in the energy: how simple atomistic molecular dynamics simulations may hold the key to epitope prediction on the fully glycosylated SARS-CoV-2 spike protein

2020 ◽  
Author(s):  
Stefano Serapian ◽  
Filippo Marchetti ◽  
Alice Triveri ◽  
Giulia Morra ◽  
Massimiliano Meli ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Structural Information ◽  
Epitope Prediction ◽  
Spike Protein ◽  
Cell Infection ◽  
Monosaccharide Residue ◽  
Decomposition Approach ◽  
S Protein ◽  
Dynamics Simulations

AbstractBetacoronavirus SARS-CoV-2 is posing a major threat to human health and its diffusion around the world is having dire socioeconomical consequences. Thanks to the scientific community’s unprecedented efforts, the atomic structure of several viral proteins has been promptly resolved. As the crucial mediator of host cell infection, the heavily glycosylated trimeric viral Spike protein (S) has been attracting the most attention and is at the center of efforts to develop antivirals, vaccines, and diagnostic solutions.Herein, we use an energy-decomposition approach to identify antigenic domains and antibody binding sites on the fully glycosylated S protein. Crucially, all that is required by our method are unbiased atomistic molecular dynamics simulations; no prior knowledge of binding properties or ad hoc combinations of parameters/measures extracted from simulations is needed. Our method simply exploits the analysis of energy interactions between all intra-protomer aminoacid and monosaccharide residue pairs, and cross-compares them with structural information (i.e., residueresidue proximity), identifying potential immunogenic regions as those groups of spatially contiguous residues with poor energetic coupling to the rest of the protein.Our results are validated by several experimentally confirmed structures of the S protein in complex with anti- or nanobodies. We identify poorly coupled sub-domains: on the one hand this indicates their role in hosting (several) epitopes, and on the other hand indicates their involvement in large functional conformational transitions. Finally, we detect two distinct behaviors of the glycan shield: glycans with stronger energetic coupling are structurally relevant and protect underlying peptidic epitopes; those with weaker coupling could themselves be poised for antibody recognition. Predicted Immunoreactive regions can be used to develop optimized antigens (recombinant subdomains, synthetic (glyco)peptidomimetics) for therapeutic applications.

scholarly journals Comment on ‘Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size’

2019 ◽  
Author(s):  
Vytautas Gapsys ◽  
Bert L. de Groot
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Size Dependence ◽  
Conformational Transitions ◽  
Human Hemoglobin ◽  
Order Of Magnitude ◽  
The Stability ◽  
Dynamics Simulations ◽  
T State

AbstractA recent molecular dynamics investigation into the stability of hemoglobin concluded that the unliganded protein is only stable in the T state when a solvent box is used in the simulations that is ten times larger than what is usually employed. Here, we express three main concerns about that study. In addition, we show that with an order of magnitude more statistics, the reported box size dependence is not reproducible. Overall, no significant effects on the kinetics or thermodynamics of conformational transitions were observed.

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