ArticleBMC structural biology2007
Binding induced conformational changes of proteins correlate with their intrinsic fluctuations: a case study of antibodies.
Article in BMC structural biology, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers.
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55 citing papers in PubMed, 122 citations in OpenAlex.
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- Human IgE monoclonal antibodies define two unusual epitopes trapping dog allergen Can f 1 in different conformations.Protein science : a publication of the Protein Society · 2025Article
- Deep learning of antibody epitopes using positional permutation vectors.Computational and structural biotechnology journal · 2024Article
- Immunoglobulin constant regions provide stabilization to the paratope and enforce epitope specificity.The Journal of biological chemistry · 2024Article
- Efficient Refinement of Complex Structures of Flexible Histone Peptides Using Post-Docking Molecular Dynamics Protocols.International journal of molecular sciences · 2024Article
- The Conformational Contribution to Molecular Complexity and Its Implications for Information Processing in Living Beings and Chemical Artificial Intelligence.Biomimetics (Basel, Switzerland) · 2024Article
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- Electrospray ion beam deposition plus low-energy electron holography as a tool for imaging individual biomolecules.Essays in biochemistry · 2023Article
- Fewer Dimensions, More Structures for Improved Discrete Models of Dynamics of Free versus Antigen-Bound Antibody.Biomolecules · 2022Article
- Low-energy electron holography imaging of conformational variability of single-antibody molecules from electrospray ion beam deposition.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Investigation of major amino acid residues of anti-norfloxacin monoclonal antibodies responsible for binding with fluoroquinolones.Scientific reports · 2021Article
- Normal Mode Analysis of KRas4B Reveals Partner Specific Dynamics.The journal of physical chemistry. B · 2021Article
- In vitro and in vivo inhibition of malaria parasite infection by monoclonal antibodies against Plasmodium falciparum circumsporozoite protein (CSP).Scientific reports · 2021Article
- Structural Analysis of Anti-Hapten Antibodies to Identify Long-Range Structural Movements Induced by Hapten Binding.Frontiers in molecular biosciences · 2021Article
- The Allosteric Effect in Antibody-Antigen Recognition.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Structural Aspects of the Allergen-Antibody Interaction.Frontiers in immunology · 2020Review
- Article
- In Silico Methods in Antibody Design.Antibodies (Basel, Switzerland) · 2018Review
- Local and global anatomy of antibody-protein antigen recognition.Journal of molecular recognition : JMR · 2018Article
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Authors and funding
1 author at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundHow antibodies recognize and bind to antigens can not be totally explained by rigid shape and electrostatic complimentarity models. Alternatively, pre-existing equilibrium hypothesis states that the native state of an antibody is not defined by a single rigid conformation but instead with an ensemble of similar conformations that co-exist at equilibrium. Antigens bind to one of the preferred conformations making this conformation more abundant shifting the equilibrium.
resultsHere, two antibodies, a germline antibody of 36-65 Fab and a monoclonal antibody, SPE7 are studied in detail to elucidate the mechanism of antibody-antigen recognition and to understand how a single antibody recognizes different antigens. An elastic network model, Anisotropic Network Model (ANM) is used in the calculations. Pre-existing equilibrium is not restricted to apply to antibodies. Intrinsic fluctuations of eight proteins, from different classes of proteins, such as enzymes, binding and transport proteins are investigated to test the suitability of the method. The intrinsic fluctuations are compared with the experimentally observed ligand induced conformational changes of these proteins. The results show that the intrinsic fluctuations obtained by theoretical methods correlate with structural changes observed when a ligand is bound to the protein. The decomposition of the total fluctuations serves to identify the different individual modes of motion, ranging from the most cooperative ones involving the overall structure, to the most localized ones.
conclusionResults suggest that the pre-equilibrium concept holds for antibodies and the promiscuity of antibodies can also be explained this hypothesis: a limited number of conformational states driven by intrinsic motions of an antibody might be adequate to bind to different antigens.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.