Antibody protein structure
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Antibody Protein Structure: Insights and Advances
Introduction to Antibody Structure
Antibodies, also known as immunoglobulins, are crucial components of the immune system, capable of binding to a vast array of antigens. They share a common basic structure across species, yet exhibit significant diversity to recognize numerous antigens5. This diversity is achieved through variations in their covalent structures, which are superimposed on a relatively constant basic configuration9.
Advances in Antibody Structure Prediction
AlphaFold2 and AI in Structure Prediction
The field of protein structure prediction has seen revolutionary advancements with the introduction of AlphaFold2, which combines artificial intelligence with evolutionary information to predict protein structures with high accuracy. This has significant implications for antibodies, as accurate structural models are essential for predicting biophysical properties and designing effective antibodies1.
Specialized Tools for Antibody Structure Prediction
Several specialized tools have been developed to predict antibody structures, leveraging the advances in AI. For instance, ImmuneBuilder is a set of deep learning models designed to predict the structures of antibodies, nanobodies, and T-cell receptors with high accuracy and speed. ImmuneBuilder's ABodyBuilder2, for example, predicts CDR-H3 loops with an RMSD of 2.81Å, outperforming AlphaFold-Multimer while being significantly faster2.
Structural Features of Antibody-Antigen Interactions
Antibody-Peptide Recognition
Antibodies recognize antigens through specific binding sites, often targeting linear epitopes of proteins. These interactions are characterized by a broad range of peptide conformations and varying degrees of secondary structure. Antibody-peptide interfaces typically have lower buried surface areas and fewer hydrogen bonds compared to antibody-protein antigen complexes, but they exhibit higher binding energy per buried interface area due to a greater proportion of hydrophobic residues and higher shape complementarity3.
H3 Loop: A Critical Binding Region
The H3 loop of antibodies is particularly challenging to model and is often the most critical region for antigen binding. Accurate prediction of the H3 loop structure is essential for understanding antibody specificity and function. Various computational approaches have been developed to improve the accuracy of H3 loop structure prediction4.
Applications in Structural Biology
Antibodies in Protein Structure Determination
Antibodies are invaluable tools in structural biology, aiding in the determination of challenging protein structures through techniques like X-ray crystallography and electron microscopy. They can be engineered to recognize specific 3D conformations of target proteins, facilitating the study of protein dynamics and interactions6.
Flexibility and Dynamics of Antibodies
Traditional methods like X-ray crystallography often provide static views of protein structures. However, techniques such as individual-particle electron tomography (IPET) have revealed the dynamic nature of antibodies, showing a range of conformations and flexibility. This understanding of antibody dynamics is crucial for comprehending their functional mechanisms7.
Conclusion
The study of antibody protein structures has made significant strides with the advent of AI-driven prediction tools and advanced structural biology techniques. These advancements not only enhance our understanding of antibody-antigen interactions but also pave the way for the rational design of therapeutic antibodies. As the field continues to evolve, the integration of computational and experimental approaches will be key to unlocking the full potential of antibodies in biomedicine.
Sources and full results
Most relevant research papers on this topic
Challenges in antibody structure prediction
Protein structure models are crucial for accurate biophysical property predictions, but careful review is crucial to avoid structural inaccuracies and improve antibody design.
ImmuneBuilder: Deep-Learning models for predicting the structures of immune proteins
ImmuneBuilder deep learning models accurately predict the structures of immune proteins, improving accuracy and speed compared to AlphaFold2, making it a valuable tool for understanding immune system function.
Rigorous Journal
Highly CitedStructural Features of Antibody-Peptide Recognition
Antibody-peptide complexes show similar structural features to antibody-protein antigen complexes, but with lower buried surface areas and fewer hydrogen bonds, potentially impacting vaccine design and immunotherapy.
Antibody H3 Structure Prediction
Computerized H3 structure prediction is crucial for accurate antibody binding site modeling and drug development, aiding rational design procedures.
Rigorous JournalAntibody structure.
Antibodies have a unique basic structure, but their molecular modifications create a large variety of immunoglobulin classes and distinct combining specificities, affecting immune reactions.
Application of antihelix antibodies in protein structure determination
Antihelix antibodies can be expanded for structural studies by transplanting their epitopes to proteins with different structures and sequences, enabling accurate and efficient protein structure determination.
3D Structural Fluctuation of IgG1 Antibody Revealed by Individual Particle Electron Tomography
Individual-particle electron tomography (IPET) reveals the 3D conformational flexibility of IgG1 antibody particles, potentially aiding in understanding protein dynamics and functions.
Highly CitedCrystal structures of an antibody to a peptide and its complex with peptide antigen at 2.8 A.
The crystal structures of an antibody to a peptide and its complex with peptide antigen reveal that the antibody binds to conformationally altered forms of myohemerythrin or apo-myohemerythrin, with minor side chain and main chain rearrangements.
Highly CitedANTIBODY STRUCTURE AND MOLECULAR IMMUNOLOGY *
Molecular immunology has revolutionized immunological thought by linking antibody structure to antigen specificity and enabling experiments to test our arguments.
Highly CitedThe structure of an antigenic determinant in a protein
Synthetic peptides can generate antibodies that interact with regions of the protein not immunogenic or generally accessible when the protein is the immunogen.
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