1
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Marini-Rapoport O, Fernández-Quintero ML, Keswani T, Zong G, Shim J, Pedersen LC, Mueller GA, Patil SU. Defining the cross-reactivity between peanut allergens Ara h 2 and Ara h 6 using monoclonal antibodies. Clin Exp Immunol 2024; 216:25-35. [PMID: 38346116 PMCID: PMC10929694 DOI: 10.1093/cei/uxae005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 12/08/2023] [Accepted: 02/09/2024] [Indexed: 03/13/2024] Open
Abstract
In peanut allergy, Arachis hypogaea 2 (Ara h 2) and Arachis hypogaea 6 (Ara h 6) are two clinically relevant peanut allergens with known structural and sequence homology and demonstrated cross-reactivity. We have previously utilized X-ray crystallography and epitope binning to define the epitopes on Ara h 2. We aimed to quantitatively characterize the cross-reactivity between Ara h 2 and Ara h 6 on a molecular level using human monoclonal antibodies (mAbs) and structural characterization of allergenic epitopes. We utilized mAbs cloned from Ara h 2 positive single B cells isolated from peanut-allergic, oral immunotherapy-treated patients to quantitatively analyze cross-reactivity between recombinant Ara h 2 (rAra h 2) and Ara h 6 (rAra h 6) proteins using biolayer interferometry and indirect inhibitory ELISA. Molecular dynamics simulations assessed time-dependent motions and interactions in the antibody-antigen complexes. Three epitopes-conformational epitopes 1.1 and 3, and the sequential epitope KRELRNL/KRELMNL-are conserved between Ara h 2 and Ara h 6, while two more conformational and three sequential epitopes are not. Overall, mAb affinity was significantly lower to rAra h 6 than it was to rAra h 2. This difference in affinity was primarily due to increased dissociation of the antibodies from rAra h 6, a phenomenon explained by the higher conformational flexibility of the Ara h 6-antibody complexes in comparison to Ara h 2-antibody complexes. Our results further elucidate the cross-reactivity of peanut 2S albumins on a molecular level and support the clinical immunodominance of Ara h 2.
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Affiliation(s)
- Orlee Marini-Rapoport
- Harvard University, Cambridge, MA, USA
- Food Allergy Center, Massachusetts General Hospital, Boston, MA, USA
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA
| | | | - Tarun Keswani
- Food Allergy Center, Massachusetts General Hospital, Boston, MA, USA
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Guangning Zong
- National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Jane Shim
- Food Allergy Center, Massachusetts General Hospital, Boston, MA, USA
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Lars C Pedersen
- National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Geoffrey A Mueller
- National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Sarita U Patil
- Food Allergy Center, Massachusetts General Hospital, Boston, MA, USA
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA
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2
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Fischer AL, Tichy A, Kokot J, Hoerschinger VJ, Wild RF, Riccabona JR, Loeffler JR, Waibl F, Quoika PK, Gschwandtner P, Forli S, Ward AB, Liedl KR, Zacharias M, Fernández-Quintero ML. The Role of Force Fields and Water Models in Protein Folding and Unfolding Dynamics. J Chem Theory Comput 2024; 20:2321-2333. [PMID: 38373307 PMCID: PMC10938642 DOI: 10.1021/acs.jctc.3c01106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 01/29/2024] [Accepted: 01/29/2024] [Indexed: 02/21/2024]
Abstract
Protein folding is a fascinating, not fully understood phenomenon in biology. Molecular dynamics (MD) simulations are an invaluable tool to study conformational changes in atomistic detail, including folding and unfolding processes of proteins. However, the accuracy of the conformational ensembles derived from MD simulations inevitably relies on the quality of the underlying force field in combination with the respective water model. Here, we investigate protein folding, unfolding, and misfolding of fast-folding proteins by examining different force fields with their recommended water models, i.e., ff14SB with the TIP3P model and ff19SB with the OPC model. To this end, we generated long conventional MD simulations highlighting the perks and pitfalls of these setups. Using Markov state models, we defined kinetically independent conformational substates and emphasized their distinct characteristics, as well as their corresponding state probabilities. Surprisingly, we found substantial differences in thermodynamics and kinetics of protein folding, depending on the combination of the protein force field and water model, originating primarily from the different water models. These results emphasize the importance of carefully choosing the force field and the respective water model as they determine the accuracy of the observed dynamics of folding events. Thus, the findings support the hypothesis that the water model is at least equally important as the force field and hence needs to be considered in future studies investigating protein dynamics and folding in all areas of biophysics.
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Affiliation(s)
- Anna-Lena
M. Fischer
- Institute
for General, Inorganic and Theoretical Chemistry, Center for Molecular
Biosciences Innsbruck (CMBI), University
of Innsbruck, A-6020 Innsbruck, Austria
| | - Anna Tichy
- Institute
for General, Inorganic and Theoretical Chemistry, Center for Molecular
Biosciences Innsbruck (CMBI), University
of Innsbruck, A-6020 Innsbruck, Austria
| | - Janik Kokot
- Institute
for General, Inorganic and Theoretical Chemistry, Center for Molecular
Biosciences Innsbruck (CMBI), University
of Innsbruck, A-6020 Innsbruck, Austria
| | - Valentin J. Hoerschinger
- Institute
for General, Inorganic and Theoretical Chemistry, Center for Molecular
Biosciences Innsbruck (CMBI), University
of Innsbruck, A-6020 Innsbruck, Austria
| | - Robert F. Wild
- Institute
for General, Inorganic and Theoretical Chemistry, Center for Molecular
Biosciences Innsbruck (CMBI), University
of Innsbruck, A-6020 Innsbruck, Austria
| | - Jakob R. Riccabona
- Institute
for General, Inorganic and Theoretical Chemistry, Center for Molecular
Biosciences Innsbruck (CMBI), University
of Innsbruck, A-6020 Innsbruck, Austria
| | - Johannes R. Loeffler
- Institute
for General, Inorganic and Theoretical Chemistry, Center for Molecular
Biosciences Innsbruck (CMBI), University
of Innsbruck, A-6020 Innsbruck, Austria
| | - Franz Waibl
- Department
of Chemistry and Applied Biosciences, ETH
Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Patrick K. Quoika
- Center
for Protein Assemblies (CPA), Physics Department, Chair of Theoretical
Biophysics, Technical University of Munich, D-80333 Munich, Germany
| | | | - Stefano Forli
- Department
of Integrative Structural and Computational Biology, Scripps Research Institute, La
Jolla, California 92037, United States
| | - Andrew B. Ward
- Department
of Integrative Structural and Computational Biology, Scripps Research Institute, La
Jolla, California 92037, United States
| | - Klaus R. Liedl
- Institute
for General, Inorganic and Theoretical Chemistry, Center for Molecular
Biosciences Innsbruck (CMBI), University
of Innsbruck, A-6020 Innsbruck, Austria
| | - Martin Zacharias
- Center
for Protein Assemblies (CPA), Physics Department, Chair of Theoretical
Biophysics, Technical University of Munich, D-80333 Munich, Germany
| | - Monica L. Fernández-Quintero
- Institute
for General, Inorganic and Theoretical Chemistry, Center for Molecular
Biosciences Innsbruck (CMBI), University
of Innsbruck, A-6020 Innsbruck, Austria
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3
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Heigl T, Netzer MA, Zanetti L, Ganglberger M, Fernández-Quintero ML, Koschak A. Characterization of two pathological gating-charge substitutions in Cav1.4 L-type calcium channels. Channels (Austin) 2023; 17:2192360. [PMID: 36943941 PMCID: PMC10038055 DOI: 10.1080/19336950.2023.2192360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 03/14/2023] [Indexed: 03/23/2023] Open
Abstract
Cav1.4 L-type calcium channels are predominantly expressed at the photoreceptor terminals and in bipolar cells, mediating neurotransmitter release. Mutations in its gene, CACNA1F, can cause congenital stationary night-blindness type 2 (CSNB2). Due to phenotypic variability in CSNB2, characterization of pathological variants is necessary to better determine pathological mechanism at the site of action. A set of known mutations affects conserved gating charges in the S4 voltage sensor, two of which have been found in male CSNB2 patients. Here, we describe two disease-causing Cav1.4 mutations with gating charge neutralization, exchanging an arginine 964 with glycine (RG) or arginine 1288 with leucine (RL). In both, charge neutralization was associated with a reduction channel expression also reflected in smaller ON gating currents. In RL channels, the strong decrease in whole-cell current densities might additionally be explained by a reduction of single-channel currents. We further identified alterations in their biophysical properties, such as a hyperpolarizing shift of the activation threshold and an increase in slope factor of activation and inactivation. Molecular dynamic simulations in RL substituted channels indicated water wires in both, resting and active, channel states, suggesting the development of omega (ω)currents as a new pathological mechanism in CSNB2. This sum of the respective channel property alterations might add to the differential symptoms in patients beside other factors, such as genomic and environmental deviations.
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Affiliation(s)
- Thomas Heigl
- University of Innsbruck, Institute of Pharmacy, Pharmacology and Toxicology, Innsbruck, Austria
| | - Michael A. Netzer
- University of Innsbruck, Institute of Pharmacy, Pharmacology and Toxicology, Innsbruck, Austria
| | - Lucia Zanetti
- University of Innsbruck, Institute of Pharmacy, Pharmacology and Toxicology, Innsbruck, Austria
| | - Matthias Ganglberger
- University of Innsbruck, Institute of Pharmacy, Pharmacology and Toxicology, Innsbruck, Austria
| | - Monica L. Fernández-Quintero
- Institute of General, Inorganic and Theoretical Chemistry, Center for Chemistry and Biomedicine, University of Innsbruck, Innsbruck, Austria
- Division of Pharmacology and Toxicology, Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | - Alexandra Koschak
- University of Innsbruck, Institute of Pharmacy, Pharmacology and Toxicology, Innsbruck, Austria
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4
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Tang X, Kokot J, Waibl F, Fernández-Quintero ML, Kamenik AS, Liedl KR. Addressing Challenges of Macrocyclic Conformational Sampling in Polar and Apolar Solvents: Lessons for Chameleonicity. J Chem Inf Model 2023; 63:7107-7123. [PMID: 37943023 PMCID: PMC10685455 DOI: 10.1021/acs.jcim.3c01123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 10/24/2023] [Accepted: 10/24/2023] [Indexed: 11/10/2023]
Abstract
We evaluated a workflow to reliably sample the conformational space of a set of 47 peptidic macrocycles. Starting from SMILES strings, we use accelerated molecular dynamics simulations to overcome high energy barriers, in particular, the cis-trans isomerization of peptide bonds. We find that our approach performs very well in polar solvents like water and dimethyl sulfoxide. Interestingly, the protonation state of a secondary amine in the ring only slightly influences the conformational ensembles of our test systems. For several of the macrocycles, determining the conformational distribution in chloroform turns out to be considerably more challenging. Especially, the choice of partial charges crucially influences the ensembles in chloroform. We address these challenges by modifying initial structures and the choice of partial charges. Our results suggest that special care has to be taken to understand the configurational distribution in apolar solvents, which is a key step toward a reliable prediction of membrane permeation of macrocycles and their chameleonic properties.
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Affiliation(s)
- Xuechen Tang
- Department
of General, Inorganic and Theoretical Chemistry, University of Innsbruck, A-6020 Innsbruck, Austria
| | - Janik Kokot
- Department
of General, Inorganic and Theoretical Chemistry, University of Innsbruck, A-6020 Innsbruck, Austria
| | - Franz Waibl
- Department
of General, Inorganic and Theoretical Chemistry, University of Innsbruck, A-6020 Innsbruck, Austria
- Department
of Chemistry and Applied Biosciences, ETH
Zürich, 8093 Zürich, Switzerland
| | | | - Anna S. Kamenik
- Department
of General, Inorganic and Theoretical Chemistry, University of Innsbruck, A-6020 Innsbruck, Austria
| | - Klaus R. Liedl
- Department
of General, Inorganic and Theoretical Chemistry, University of Innsbruck, A-6020 Innsbruck, Austria
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5
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Hoerschinger V, Waibl F, Pomarici ND, Loeffler JR, Deane CM, Georges G, Kettenberger H, Fernández-Quintero ML, Liedl KR. PEP-Patch: Electrostatics in Protein-Protein Recognition, Specificity, and Antibody Developability. J Chem Inf Model 2023; 63:6964-6971. [PMID: 37934909 PMCID: PMC10685443 DOI: 10.1021/acs.jcim.3c01490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/14/2023] [Accepted: 10/16/2023] [Indexed: 11/09/2023]
Abstract
The electrostatic properties of proteins arise from the number and distribution of polar and charged residues. Electrostatic interactions in proteins play a critical role in numerous processes such as molecular recognition, protein solubility, viscosity, and antibody developability. Thus, characterizing and quantifying electrostatic properties of a protein are prerequisites for understanding these processes. Here, we present PEP-Patch, a tool to visualize and quantify the electrostatic potential on the protein surface in terms of surface patches, denoting separated areas of the surface with a common physical property. We highlight its applicability to elucidate protease substrate specificity and antibody-antigen recognition and predict heparin column retention times of antibodies as an indicator of pharmacokinetics.
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Affiliation(s)
- Valentin
J. Hoerschinger
- Department
of General, Inorganic and Theoretical Chemistry, and Center for Molecular
Biosciences Innsbruck (CMBI), University
of Innsbruck, 6020 Innsbruck, Austria
| | - Franz Waibl
- Department
of General, Inorganic and Theoretical Chemistry, and Center for Molecular
Biosciences Innsbruck (CMBI), University
of Innsbruck, 6020 Innsbruck, Austria
| | - Nancy D. Pomarici
- Department
of General, Inorganic and Theoretical Chemistry, and Center for Molecular
Biosciences Innsbruck (CMBI), University
of Innsbruck, 6020 Innsbruck, Austria
| | - Johannes R. Loeffler
- Department
of General, Inorganic and Theoretical Chemistry, and Center for Molecular
Biosciences Innsbruck (CMBI), University
of Innsbruck, 6020 Innsbruck, Austria
| | - Charlotte M. Deane
- Department
of Statistics, University of Oxford, Oxford OX1 2JD, United Kingdom
| | - Guy Georges
- Roche
Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, Penzberg 82377, Germany
| | - Hubert Kettenberger
- Roche
Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, Penzberg 82377, Germany
| | - Monica L. Fernández-Quintero
- Department
of General, Inorganic and Theoretical Chemistry, and Center for Molecular
Biosciences Innsbruck (CMBI), University
of Innsbruck, 6020 Innsbruck, Austria
| | - Klaus R. Liedl
- Department
of General, Inorganic and Theoretical Chemistry, and Center for Molecular
Biosciences Innsbruck (CMBI), University
of Innsbruck, 6020 Innsbruck, Austria
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6
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Zeindl R, Franzmann AL, Fernández-Quintero ML, Seidler CA, Hoerschinger VJ, Liedl KR, Tollinger M. Structural Basis of the Immunological Cross-Reactivity between Kiwi and Birch Pollen. Foods 2023; 12:3939. [PMID: 37959058 PMCID: PMC10649968 DOI: 10.3390/foods12213939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 10/25/2023] [Accepted: 10/26/2023] [Indexed: 11/15/2023] Open
Abstract
Allergies related to kiwi consumption have become a growing health concern, with their prevalence on the rise. Many of these allergic reactions are attributed to cross-reactivity, particularly with the major allergen found in birch pollen. This cross-reactivity is associated with proteins belonging to the pathogenesis-related class 10 (PR-10) protein family. In our study, we determined the three-dimensional structures of the two PR-10 proteins in gold and green kiwi fruits, Act c 8 and Act d 8, using nuclear magnetic resonance (NMR) spectroscopy. The structures of both kiwi proteins closely resemble the major birch pollen allergen, Bet v 1, providing a molecular explanation for the observed immunological cross-reactivity between kiwi and birch pollen. Compared to Act d 11, however, a kiwi allergen that shares the same architecture as PR-10 proteins, structural differences are apparent. Moreover, despite both Act c 8 and Act d 8 containing multiple cysteine residues, no disulfide bridges are present within their structures. Instead, all the cysteines are accessible on the protein's surface and exposed to the surrounding solvent, where they are available for reactions with components of the natural food matrix. This structural characteristic sets Act c 8 and Act d 8 apart from other kiwi proteins with a high cysteine content. Furthermore, we demonstrate that pyrogallol, the most abundant phenolic compound found in kiwi, binds into the internal cavities of these two proteins, albeit with low affinity. Our research offers a foundation for further studies aimed at understanding allergic reactions associated with this fruit and exploring how interactions with the natural food matrix might be employed to enhance food safety.
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Affiliation(s)
- Ricarda Zeindl
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020 Innsbruck, Austria; (R.Z.); (A.L.F.)
| | - Annika L. Franzmann
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020 Innsbruck, Austria; (R.Z.); (A.L.F.)
| | - Monica L. Fernández-Quintero
- Institute of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020 Innsbruck, Austria; (M.L.F.-Q.); (C.A.S.); (K.R.L.)
| | - Clarissa A. Seidler
- Institute of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020 Innsbruck, Austria; (M.L.F.-Q.); (C.A.S.); (K.R.L.)
| | - Valentin J. Hoerschinger
- Institute of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020 Innsbruck, Austria; (M.L.F.-Q.); (C.A.S.); (K.R.L.)
| | - Klaus R. Liedl
- Institute of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020 Innsbruck, Austria; (M.L.F.-Q.); (C.A.S.); (K.R.L.)
| | - Martin Tollinger
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020 Innsbruck, Austria; (R.Z.); (A.L.F.)
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7
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Fernández-Quintero ML, Pomarici ND, Fischer ALM, Hoerschinger VJ, Kroell KB, Riccabona JR, Kamenik AS, Loeffler JR, Ferguson JA, Perrett HR, Liedl KR, Han J, Ward AB. Structure and Dynamics Guiding Design of Antibody Therapeutics and Vaccines. Antibodies (Basel) 2023; 12:67. [PMID: 37873864 PMCID: PMC10594513 DOI: 10.3390/antib12040067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/10/2023] [Accepted: 10/13/2023] [Indexed: 10/25/2023] Open
Abstract
Antibodies and other new antibody-like formats have emerged as one of the most rapidly growing classes of biotherapeutic proteins. Understanding the structural features that drive antibody function and, consequently, their molecular recognition is critical for engineering antibodies. Here, we present the structural architecture of conventional IgG antibodies alongside other formats. We emphasize the importance of considering antibodies as conformational ensembles in solution instead of focusing on single-static structures because their functions and properties are strongly governed by their dynamic nature. Thus, in this review, we provide an overview of the unique structural and dynamic characteristics of antibodies with respect to their antigen recognition, biophysical properties, and effector functions. We highlight the numerous technical advances in antibody structure prediction and design, enabled by the vast number of experimentally determined high-quality structures recorded with cryo-EM, NMR, and X-ray crystallography. Lastly, we assess antibody and vaccine design strategies in the context of structure and dynamics.
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Affiliation(s)
- Monica L. Fernández-Quintero
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Nancy D. Pomarici
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Anna-Lena M. Fischer
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Valentin J. Hoerschinger
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Katharina B. Kroell
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Jakob R. Riccabona
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Anna S. Kamenik
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Johannes R. Loeffler
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - James A. Ferguson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Hailee R. Perrett
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Klaus R. Liedl
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Julianna Han
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Andrew B. Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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8
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Rappazzo CG, Fernández-Quintero ML, Mayer A, Wu NC, Greiff V, Guthmiller JJ. Defining and Studying B Cell Receptor and TCR Interactions. J Immunol 2023; 211:311-322. [PMID: 37459189 PMCID: PMC10495106 DOI: 10.4049/jimmunol.2300136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 04/15/2023] [Indexed: 07/20/2023]
Abstract
BCRs (Abs) and TCRs (or adaptive immune receptors [AIRs]) are the means by which the adaptive immune system recognizes foreign and self-antigens, playing an integral part in host defense, as well as the emergence of autoimmunity. Importantly, the interaction between AIRs and their cognate Ags defies a simple key-in-lock paradigm and is instead a complex many-to-many mapping between an individual's massively diverse AIR repertoire, and a similarly diverse antigenic space. Understanding how adaptive immunity balances specificity with epitopic coverage is a key challenge for the field, and terms such as broad specificity, cross-reactivity, and polyreactivity remain ill-defined and are used inconsistently. In this Immunology Notes and Resources article, a group of experimental, structural, and computational immunologists define commonly used terms associated with AIR binding, describe methodologies to study these binding modes, as well as highlight the implications of these different binding modes for therapeutic design.
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Affiliation(s)
| | | | - Andreas Mayer
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Nicholas C. Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Victor Greiff
- Department of Immunology, University of Oslo and Oslo University Hospital, 0372 Oslo, Norway
| | - Jenna J. Guthmiller
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
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9
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Martin GM, Fernández-Quintero ML, Lee WH, Pholcharee T, Eshun-Wilson L, Liedl KR, Pancera M, Seder RA, Wilson IA, Ward AB. Structural basis of epitope selectivity and potent protection from malaria by PfCSP antibody L9. Nat Commun 2023; 14:2815. [PMID: 37198165 PMCID: PMC10192352 DOI: 10.1038/s41467-023-38509-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 05/04/2023] [Indexed: 05/19/2023] Open
Abstract
A primary objective in malaria vaccine design is the generation of high-quality antibody responses against the circumsporozoite protein of the malaria parasite, Plasmodium falciparum (PfCSP). To enable rational antigen design, we solved a cryo-EM structure of the highly potent anti-PfCSP antibody L9 in complex with recombinant PfCSP. We found that L9 Fab binds multivalently to the minor (NPNV) repeat domain, which is stabilized by a unique set of affinity-matured homotypic, antibody-antibody contacts. Molecular dynamics simulations revealed a critical role of the L9 light chain in integrity of the homotypic interface, which likely impacts PfCSP affinity and protective efficacy. These findings reveal the molecular mechanism of the unique NPNV selectivity of L9 and emphasize the importance of anti-homotypic affinity maturation in protective immunity against P. falciparum.
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Affiliation(s)
- Gregory M Martin
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Monica L Fernández-Quintero
- Department of General, Inorganic, and Theoretical Chemistry, Center for Chemistry and Biomedicine, The University of Innsbruck; Innrain 80-82/III, 6020, Innsbruck, Austria
| | - Wen-Hsin Lee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Tossapol Pholcharee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Department of Biochemistry, University of Oxford, Oxford, OX1 3DR, UK
| | - Lisa Eshun-Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Klaus R Liedl
- Department of General, Inorganic, and Theoretical Chemistry, Center for Chemistry and Biomedicine, The University of Innsbruck; Innrain 80-82/III, 6020, Innsbruck, Austria
| | - Marie Pancera
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Robert A Seder
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA.
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10
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Pomarici ND, Cacciato R, Kokot J, Fernández-Quintero ML, Liedl KR. Evolution of the Immunoglobulin Isotypes-Variations of Biophysical Properties among Animal Classes. Biomolecules 2023; 13:801. [PMID: 37238671 PMCID: PMC10216798 DOI: 10.3390/biom13050801] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/03/2023] [Accepted: 05/05/2023] [Indexed: 05/28/2023] Open
Abstract
The adaptive immune system arose around 500 million years ago in jawed fish, and, since then, it has mediated the immune defense against pathogens in all vertebrates. Antibodies play a central role in the immune reaction, recognizing and attacking external invaders. During the evolutionary process, several immunoglobulin isotypes emerged, each having a characteristic structural organization and dedicated function. In this work, we investigate the evolution of the immunoglobulin isotypes, in order to highlight the relevant features that were preserved over time and the parts that, instead, mutated. The residues that are coupled in the evolution process are often involved in intra- or interdomain interactions, meaning that they are fundamental to maintaining the immunoglobulin fold and to ensuring interactions with other domains. The explosive growth of available sequences allows us to point out the evolutionary conserved residues and compare the biophysical properties among different animal classes and isotypes. Our study offers a general overview of the evolution of immunoglobulin isotypes and advances the knowledge of their characteristic biophysical properties, as a first step in guiding protein design from evolution.
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Affiliation(s)
| | | | | | - Monica L. Fernández-Quintero
- Department of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
| | - Klaus R. Liedl
- Department of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
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11
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Lechable M, Tang X, Siebert S, Feldbacher A, Fernández-Quintero ML, Breuker K, Juliano CE, Liedl KR, Hobmayer B, Hartl M. High Intrinsic Oncogenic Potential in the Myc-Box-Deficient Hydra Myc3 Protein. Cells 2023; 12:cells12091265. [PMID: 37174665 PMCID: PMC10177328 DOI: 10.3390/cells12091265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/17/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023] Open
Abstract
The proto-oncogene myc has been intensively studied primarily in vertebrate cell culture systems. Myc transcription factors control fundamental cellular processes such as cell proliferation, cell cycle control and stem cell maintenance. Myc interacts with the Max protein and Myc/Max heterodimers regulate thousands of target genes. The genome of the freshwater polyp Hydra encodes four myc genes (myc1-4). Previous structural and biochemical characterization showed that the Hydra Myc1 and Myc2 proteins share high similarities with vertebrate c-Myc, and their expression patterns suggested a function in adult stem cell maintenance. In contrast, an additional Hydra Myc protein termed Myc3 is highly divergent, lacking the common N-terminal domain and all conserved Myc-boxes. Single cell transcriptome analysis revealed that the myc3 gene is expressed in a distinct population of interstitial precursor cells committed to nerve- and gland-cell differentiation, where the Myc3 protein may counteract the stemness actions of Myc1 and Myc2 and thereby allow the implementation of a differentiation program. In vitro DNA binding studies showed that Myc3 dimerizes with Hydra Max, and this dimer efficiently binds to DNA containing the canonical Myc consensus motif (E-box). In vivo cell transformation assays in avian fibroblast cultures further revealed an unexpected high potential for oncogenic transformation in the conserved Myc3 C-terminus, as compared to Hydra Myc2 or Myc1. Structure modeling of the Myc3 protein predicted conserved amino acid residues in its bHLH-LZ domain engaged in Myc3/Max dimerization. Mutating these amino acid residues in the human c-Myc (MYC) sequence resulted in a significant decrease in its cell transformation potential. We discuss our findings in the context of oncogenic transformation and cell differentiation, both relevant for human cancer, where Myc represents a major driver.
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Affiliation(s)
- Marion Lechable
- Institute of Zoology, University of Innsbruck, 6020 Innsbruck, Austria
- Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020 Innsbruck, Austria
| | - Xuechen Tang
- Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020 Innsbruck, Austria
- Institute of Inorganic and Theoretical Chemistry, University of Innsbruck, 6020 Innsbruck, Austria
| | - Stefan Siebert
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
| | - Angelika Feldbacher
- Institute of Zoology, University of Innsbruck, 6020 Innsbruck, Austria
- Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020 Innsbruck, Austria
| | - Monica L Fernández-Quintero
- Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020 Innsbruck, Austria
- Institute of Inorganic and Theoretical Chemistry, University of Innsbruck, 6020 Innsbruck, Austria
| | - Kathrin Breuker
- Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020 Innsbruck, Austria
- Institute of Organic Chemistry, University of Innsbruck, 6020 Innsbruck, Austria
| | - Celina E Juliano
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
| | - Klaus R Liedl
- Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020 Innsbruck, Austria
- Institute of Inorganic and Theoretical Chemistry, University of Innsbruck, 6020 Innsbruck, Austria
| | - Bert Hobmayer
- Institute of Zoology, University of Innsbruck, 6020 Innsbruck, Austria
- Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020 Innsbruck, Austria
| | - Markus Hartl
- Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020 Innsbruck, Austria
- Institute of Biochemistry, University of Innsbruck, 6020 Innsbruck, Austria
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12
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Seitter H, Obkircher J, Grabher P, Hartl J, Zanetti L, Lux UT, Fotakis G, Fernández-Quintero ML, Kaserer T, Koschak A. A novel calcium channel Cavβ 2 splice variant with unique properties predominates in the retina. J Biol Chem 2023; 299:102972. [PMID: 36738788 PMCID: PMC10074810 DOI: 10.1016/j.jbc.2023.102972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 01/15/2023] [Accepted: 01/17/2023] [Indexed: 02/05/2023] Open
Abstract
Cavβ subunits are essential for surface expression of voltage-gated calcium channel complexes and crucially modulate biophysical properties like voltage-dependent inactivation. Here, we describe the discovery and characterization of a novel Cavβ2 variant with distinct features that predominates in the retina. We determined spliced exons in retinal transcripts of the Cacnb2 gene, coding for Cavβ2, by RNA-Seq data analysis and quantitative PCR. We cloned a novel Cavβ2 splice variant from mouse retina, which we are calling β2i, and investigated biophysical properties of calcium currents with this variant in a heterologous expression system as well as its intrinsic membrane interaction when expressed alone. Our data showed that β2i predominated in the retina with expression in photoreceptors and bipolar cells. Furthermore, we observed that the β2i N-terminus exhibited an extraordinary concentration of hydrophobic residues, a distinct feature not seen in canonical variants. The biophysical properties resembled known membrane-associated variants, and β2i exhibited both a strong membrane association and a propensity for clustering, which depended on hydrophobic residues in its N-terminus. We considered available Cavβ structure data to elucidate potential mechanisms underlying the observed characteristics but resolved N-terminus structures were lacking and thus, precluded clear conclusions. With this description of a novel N-terminus variant of Cavβ2, we expand the scope of functional variation through N-terminal splicing with a distinct form of membrane attachment. Further investigation of the molecular mechanisms underlying the features of β2i could provide new angles on the way Cavβ subunits modulate Ca2+ channels at the plasma membrane.
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Affiliation(s)
- Hartwig Seitter
- Department of Pharmacology and Toxicology, Institute of Pharmacy, University of Innsbruck, Innsbruck, Austria.
| | - Jana Obkircher
- Department of Pharmacology and Toxicology, Institute of Pharmacy, University of Innsbruck, Innsbruck, Austria
| | - Patricia Grabher
- Department of Pharmacology and Toxicology, Institute of Pharmacy, University of Innsbruck, Innsbruck, Austria
| | - Julia Hartl
- Department of Pharmacology and Toxicology, Institute of Pharmacy, University of Innsbruck, Innsbruck, Austria
| | - Lucia Zanetti
- Department of Pharmacology and Toxicology, Institute of Pharmacy, University of Innsbruck, Innsbruck, Austria
| | - Uwe Thorsten Lux
- Department of Biology, Animal Physiology/Neurobiology, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Georgios Fotakis
- Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Teresa Kaserer
- Department of Pharmaceutical Chemistry, Institute of Pharmacy, University of Innsbruck, Innsbruck, Austria
| | - Alexandra Koschak
- Department of Pharmacology and Toxicology, Institute of Pharmacy, University of Innsbruck, Innsbruck, Austria.
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13
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Török F, Tezcan K, Filippini L, Fernández-Quintero ML, Zanetti L, Liedl KR, Drexel RS, Striessnig J, Ortner NJ. Germline de novo variant F747S extends the phenotypic spectrum of CACNA1D Ca2+ channelopathies. Hum Mol Genet 2023; 32:847-859. [PMID: 36208199 PMCID: PMC9941835 DOI: 10.1093/hmg/ddac248] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 09/22/2022] [Accepted: 09/30/2022] [Indexed: 11/14/2022] Open
Abstract
Germline gain-of-function missense variants in the pore-forming Cav1.3 α1-subunit (CACNA1D gene) confer high risk for a severe neurodevelopmental disorder with or without endocrine symptoms. Here, we report a 4-week-old new-born with the novel de novo missense variant F747S with a so far not described prominent jittering phenotype in addition to symptoms previously reported for CACNA1D mutations including developmental delay, elevated aldosterone level and transient hypoglycemia. We confirmed the pathogenicity of this variant in whole-cell patch-clamp experiments with wild-type and F747S mutant channels heterologously expressed together with α2δ1 and cytosolic β3 or membrane-bound β2a subunits. Mutation F747S caused the quantitatively largest shift in the voltage dependence of activation (-28 mV) reported so far for CACNA1D germline mutations. It also shifted inactivation to more negative voltages, slowed the time course of current inactivation and slowed current deactivation upon repolarization with both co-expressed β-subunits. In silico modelling and molecular docking, simulations revealed that this gain-of-function phenotype can be explained by formation of a novel inter-domain hydrogen bond between mutant residues S747 (IIS6) with N1145 (IIIS6) stabilizing selectively the activated open channel state. F747S displayed 2-6-fold increased sensitivity for the L-type Ca2+ channel blocker isradipine compared to wild type. Our data confirm the pathogenicity of the F747S variant with very strong gain-of-function gating changes, which may contribute to the novel jittering phenotype. Increased sensitivity for isradipine suggests this drug for potential symptomatic off-label treatment for carriers of this mutation.
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Affiliation(s)
- Ferenc Török
- Department of Pharmacology and Toxicology, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck 6020, Austria
| | - Kamer Tezcan
- Department of Genetics, Kaiser Permanente, Sacramento, CA 95825, USA
| | - Ludovica Filippini
- Department of Pharmacology and Toxicology, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck 6020, Austria
| | - Monica L Fernández-Quintero
- Department of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck 6020, Austria
| | - Lucia Zanetti
- Department of Pharmacology and Toxicology, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck 6020, Austria
| | - Klaus R Liedl
- Department of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck 6020, Austria
| | - Raphaela S Drexel
- Department of Pharmacology and Toxicology, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck 6020, Austria
| | - Jörg Striessnig
- Department of Pharmacology and Toxicology, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck 6020, Austria
| | - Nadine J Ortner
- Department of Pharmacology and Toxicology, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck 6020, Austria
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14
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Seidler CA, Kokot J, Fernández-Quintero ML, Liedl KR. Structural Characterization of Nanobodies during Germline Maturation. Biomolecules 2023; 13:380. [PMID: 36830754 PMCID: PMC9953242 DOI: 10.3390/biom13020380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/27/2023] [Accepted: 02/14/2023] [Indexed: 02/22/2023] Open
Abstract
Camelid heavy-chain antibody variable domains (VHH), nanobodies, are the smallest-known functional antibody fragments with high therapeutic potential. In this study, we investigate a VHH binding to hen egg-white lysozyme (HEL). We structurally and dynamically characterized the conformational diversity of four VHH variants to elucidate the antigen-binding process. For two of these antibodies, not only are the dissociation constants known, but also the experimentally determined crystal structures of the VHH in complex with HEL are available. We performed well-tempered metadynamics simulations in combination with molecular dynamics simulations to capture a broad conformational space and to reconstruct the thermodynamics and kinetics of conformational transitions in the antigen-binding site, the paratope. By kinetically characterizing the loop movements of the paratope, we found that, with an increase in affinity, the state populations shift towards the binding competent conformation. The contacts contributing to antigen binding, and those who contribute to the overall stability, show a clear trend towards less variable but more intense contacts. Additionally, these investigated nanobodies clearly follow the conformational selection paradigm, as the binding competent conformation pre-exists within the structural ensembles without the presence of the antigen.
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Affiliation(s)
| | | | - Monica L. Fernández-Quintero
- Department of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020 Innsbruck, Austria
| | - Klaus R. Liedl
- Department of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020 Innsbruck, Austria
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15
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Fernández-Quintero ML, Pelizzari S, El Ghaleb Y, Heiss MC, Liedl KR, Flucher BE. Voltage-dependent transitions between resting and activated states of the four Cav1.1 voltage sensors observed in MD simulation. Biophys J 2023; 122:106a. [PMID: 36782458 DOI: 10.1016/j.bpj.2022.11.758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023] Open
Affiliation(s)
| | - Simone Pelizzari
- Institute of Physiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Yousra El Ghaleb
- Institute of Physiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Martin C Heiss
- Institute of Physiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Klaus R Liedl
- Department of General, Inorganic and Theoretical Chemistry, Medical University of Innsbruck, Innsbruck, Austria
| | - Bernhard E Flucher
- Department of Physiology and Medical Physics, Medical University of Innsbruck, Innsbruck, Austria
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16
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Abstract
Advances in structural biology and the exponential increase in the amount of high-quality experimental structural data available in the Protein Data Bank has motivated numerous studies to tackle the grand challenge of predicting protein structures. In 2020 AlphaFold2 revolutionized the field using a combination of artificial intelligence and the evolutionary information contained in multiple sequence alignments. Antibodies are one of the most important classes of biotherapeutic proteins. Accurate structure models are a prerequisite to advance biophysical property predictions and consequently antibody design. Specialized tools used to predict antibody structures based on different principles have profited from current advances in protein structure prediction based on artificial intelligence. Here, we emphasize the importance of reliable protein structure models and highlight the enormous advances in the field, but we also aim to increase awareness that protein structure models, and in particular antibody models, may suffer from structural inaccuracies, namely incorrect cis-amide bonds, wrong stereochemistry or clashes. We show that these inaccuracies affect biophysical property predictions such as surface hydrophobicity. Thus, we stress the importance of carefully reviewing protein structure models before investing further computing power and setting up experiments. To facilitate the assessment of model quality, we provide a tool "TopModel" to validate structure models.
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Affiliation(s)
| | - Janik Kokot
- Department of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Franz Waibl
- Department of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Anna-Lena M. Fischer
- Department of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Patrick K. Quoika
- Center for Protein Assemblies (CPA), Physics Department, Chair of Theoretical Biophysics, Technical University of Munich, Garching, Germany
| | | | - Klaus R. Liedl
- CONTACT Klaus R. Liedl Department of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
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17
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Fernández-Quintero ML, Ljungars A, Waibl F, Greiff V, Andersen JT, Gjølberg TT, Jenkins TP, Voldborg BG, Grav LM, Kumar S, Georges G, Kettenberger H, Liedl KR, Tessier PM, McCafferty J, Laustsen AH. Assessing developability early in the discovery process for novel biologics. MAbs 2023; 15:2171248. [PMID: 36823021 PMCID: PMC9980699 DOI: 10.1080/19420862.2023.2171248] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 01/18/2023] [Indexed: 02/25/2023] Open
Abstract
Beyond potency, a good developability profile is a key attribute of a biological drug. Selecting and screening for such attributes early in the drug development process can save resources and avoid costly late-stage failures. Here, we review some of the most important developability properties that can be assessed early on for biologics. These include the influence of the source of the biologic, its biophysical and pharmacokinetic properties, and how well it can be expressed recombinantly. We furthermore present in silico, in vitro, and in vivo methods and techniques that can be exploited at different stages of the discovery process to identify molecules with liabilities and thereby facilitate the selection of the most optimal drug leads. Finally, we reflect on the most relevant developability parameters for injectable versus orally delivered biologics and provide an outlook toward what general trends are expected to rise in the development of biologics.
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Affiliation(s)
- Monica L. Fernández-Quintero
- Center for Molecular Biosciences Innsbruck (CMBI), Department of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Anne Ljungars
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Franz Waibl
- Center for Molecular Biosciences Innsbruck (CMBI), Department of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Victor Greiff
- Department of Immunology, University of Oslo, Oslo, Norway
| | - Jan Terje Andersen
- Department of Immunology, University of Oslo, Oslo University Hospital Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine and Department of Pharmacology, University of Oslo, Oslo, Norway
| | | | - Timothy P. Jenkins
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Bjørn Gunnar Voldborg
- National Biologics Facility, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Lise Marie Grav
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Sandeep Kumar
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceuticals Inc, Ridgefield, CT, USA
| | - Guy Georges
- Roche Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany
| | - Hubert Kettenberger
- Roche Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany
| | - Klaus R. Liedl
- Center for Molecular Biosciences Innsbruck (CMBI), Department of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Peter M. Tessier
- Department of Chemical Engineering, Pharmaceutical Sciences and Biomedical Engineering, Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan, USA
| | - John McCafferty
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
- Maxion Therapeutics, Babraham Research Campus, Cambridge, UK
| | - Andreas H. Laustsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
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18
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Pomarici ND, Fernández-Quintero ML, Quoika PK, Waibl F, Bujotzek A, Georges G, Liedl KR. Bispecific antibodies-effects of point mutations on CH3-CH3 interface stability. Protein Eng Des Sel 2022; 35:6873150. [PMID: 36468666 PMCID: PMC9741699 DOI: 10.1093/protein/gzac012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 10/19/2022] [Accepted: 10/19/2022] [Indexed: 12/12/2022] Open
Abstract
A new format of therapeutic proteins is bispecific antibodies, in which two different heavy chains heterodimerize to obtain two different binding sites. Therefore, it is crucial to understand and optimize the third constant domain (CH3-CH3) interface to favor heterodimerization over homodimerization, and to preserve the physicochemical properties, as thermal stability. Here, we use molecular dynamics simulations to investigate the dissociation process of 19 CH3-CH3 crystal structures that differ from each other in few point mutations. We describe the dissociation of the dimeric interface as a two-steps mechanism. As confirmed by a Markov state model, apart from the bound and the dissociated state, we observe an additional intermediate state, which corresponds to an encounter complex. The analysis of the interdomain contacts reveals key residues that stabilize the interface. We expect that our results will improve the understanding of the CH3-CH3 interface interactions and thus advance the developability and design of new antibodies formats.
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Affiliation(s)
- Nancy D Pomarici
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
| | - Monica L Fernández-Quintero
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
| | - Patrick K Quoika
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria,Center for Protein Assemblies (CPA), Department of Physics, Chair of Theoretical Biophysics, Technical University of Munich, Ernst-Otto-Fischer-Str. 8, 85748, Garching, Germany
| | - Franz Waibl
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
| | - Alexander Bujotzek
- Roche Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Penzberg, Nonnenwald 2, Penzberg, 82377, Germany
| | - Guy Georges
- Roche Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Penzberg, Nonnenwald 2, Penzberg, 82377, Germany
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19
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Hofer F, Fischer AL, Kamenik AS, Waibl F, Fernández-Quintero ML, Liedl KR. pH-dependent structural diversity of profilin allergens determines thermal stability. Front Allergy 2022; 3:1007000. [PMID: 36324331 PMCID: PMC9618696 DOI: 10.3389/falgy.2022.1007000] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 09/20/2022] [Indexed: 11/05/2022] Open
Abstract
The family of profilin allergens is a common class of proteins found in plants, viruses and various eukaryotes including mammals. Profilins are characterized by an evolutionary conserved structural fold, which is responsible for their cross-reactive nature of Immunoglobulin E (IgE) antibodies. Despite their high overall structural similarity, they exhibit substantial differences in their biophysical properties, such as thermal and pH stability. To understand the origin of these functional differences of Amb a 8, Art v 4 and Bet v 2, we performed constant pH molecular dynamics simulation in combination with Gaussian accelerated MD simulations. Depending on the respective protonation at different pH levels, we find distinct differences in conformational flexibility, which are consistent with experimentally determined melting temperatures. These variations in flexibility are accompanied by ensemble shifts in the conformational landscape and quantified and localized by residue-wise B-factors and dihedral entropies. These findings strengthen the link between flexibility of profilin allergens and their thermal stability. Thus, our results clearly show the importance of considering protonation dependent conformational ensembles in solution to elucidate biophysical differences between these structurally similar allergens.
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20
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El Ghaleb Y, Ortner NJ, Posch W, Fernández-Quintero ML, Tuinte WE, Monteleone S, Draheim HJ, Liedl KR, Wilflingseder D, Striessnig J, Tuluc P, Flucher BE, Campiglio M. Calcium current modulation by the γ1 subunit depends on alternative splicing of CaV1.1. J Gen Physiol 2022; 154:e202113028. [PMID: 35349630 PMCID: PMC9037348 DOI: 10.1085/jgp.202113028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 03/08/2022] [Indexed: 01/01/2023] Open
Abstract
The skeletal muscle voltage-gated calcium channel (CaV1.1) primarily functions as a voltage sensor for excitation-contraction coupling. Conversely, its ion-conducting function is modulated by multiple mechanisms within the pore-forming α1S subunit and the auxiliary α2δ-1 and γ1 subunits. In particular, developmentally regulated alternative splicing of exon 29, which inserts 19 amino acids in the extracellular IVS3-S4 loop of CaV1.1a, greatly reduces the current density and shifts the voltage dependence of activation to positive potentials outside the physiological range. We generated new HEK293 cell lines stably expressing α2δ-1, β3, and STAC3. When the adult (CaV1.1a) and embryonic (CaV1.1e) splice variants were expressed in these cells, the difference in the voltage dependence of activation observed in muscle cells was reproduced, but not the reduced current density of CaV1.1a. Only when we further coexpressed the γ1 subunit was the current density of CaV1.1a, but not that of CaV1.1e, reduced by >50%. In addition, γ1 caused a shift of the voltage dependence of inactivation to negative voltages in both variants. Thus, the current-reducing effect of γ1, unlike its effect on inactivation, is specifically dependent on the inclusion of exon 29 in CaV1.1a. Molecular structure modeling revealed several direct ionic interactions between residues in the IVS3-S4 loop and the γ1 subunit. However, substitution of these residues by alanine, individually or in combination, did not abolish the γ1-dependent reduction of current density, suggesting that structural rearrangements in CaV1.1a induced by inclusion of exon 29 may allosterically empower the γ1 subunit to exert its inhibitory action on CaV1.1 calcium currents.
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Affiliation(s)
- Yousra El Ghaleb
- Institute of Physiology, Department of Physiology and Medical Physics, Medical University Innsbruck, Innsbruck, Austria
| | - Nadine J. Ortner
- Department of Pharmacology and Toxicology, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Wilfried Posch
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Wietske E. Tuinte
- Institute of Physiology, Department of Physiology and Medical Physics, Medical University Innsbruck, Innsbruck, Austria
| | - Stefania Monteleone
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Henning J. Draheim
- Boehringer Ingelheim Pharma GmbH & Co KG, CNS Research, Biberach an der Riss, Germany
| | - Klaus R. Liedl
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Doris Wilflingseder
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Jörg Striessnig
- Department of Pharmacology and Toxicology, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Petronel Tuluc
- Department of Pharmacology and Toxicology, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Bernhard E. Flucher
- Institute of Physiology, Department of Physiology and Medical Physics, Medical University Innsbruck, Innsbruck, Austria
| | - Marta Campiglio
- Institute of Physiology, Department of Physiology and Medical Physics, Medical University Innsbruck, Innsbruck, Austria
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21
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Fernández-Quintero ML, Fischer ALM, Kokot J, Waibl F, Seidler CA, Liedl KR. The influence of antibody humanization on shark variable domain (VNAR) binding site ensembles. Front Immunol 2022; 13:953917. [PMID: 36177031 PMCID: PMC9514858 DOI: 10.3389/fimmu.2022.953917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 08/15/2022] [Indexed: 11/13/2022] Open
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22
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Waibl F, Fernández-Quintero ML, Wedl FS, Kettenberger H, Georges G, Liedl KR. Comparison of hydrophobicity scales for predicting biophysical properties of antibodies. Front Mol Biosci 2022; 9:960194. [PMID: 36120542 PMCID: PMC9475378 DOI: 10.3389/fmolb.2022.960194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 08/09/2022] [Indexed: 11/13/2022] Open
Abstract
While antibody-based therapeutics have grown to be one of the major classes of novel medicines, some antibody development candidates face significant challenges regarding expression levels, solubility, as well as stability and aggregation, under physiological and storage conditions. A major determinant of those properties is surface hydrophobicity, which promotes unspecific interactions and has repeatedly proven problematic in the development of novel antibody-based drugs. Multiple computational methods have been devised for in-silico prediction of antibody hydrophobicity, often using hydrophobicity scales to assign values to each amino acid. Those approaches are usually validated by their ability to rank potential therapeutic antibodies in terms of their experimental hydrophobicity. However, there is significant diversity both in the hydrophobicity scales and in the experimental methods, and consequently in the performance of in-silico methods to predict experimental results. In this work, we investigate hydrophobicity of monoclonal antibodies using hydrophobicity scales. We implement several scoring schemes based on the solvent-accessibility and the assigned hydrophobicity values, and compare the different scores and scales based on their ability to predict retention times from hydrophobic interaction chromatography. We provide an overview of the strengths and weaknesses of several commonly employed hydrophobicity scales, thereby improving the understanding of hydrophobicity in antibody development. Furthermore, we test several datasets, both publicly available and proprietary, and find that the diversity of the dataset affects the performance of hydrophobicity scores. We expect that this work will provide valuable guidelines for the optimization of biophysical properties in future drug discovery campaigns.
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Affiliation(s)
- Franz Waibl
- Department of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | | | - Florian S. Wedl
- Department of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Hubert Kettenberger
- Large Molecule Research, Roche Pharma Research and Early Development, Roche Innovation Center Munich, Penzberg, Germany
| | - Guy Georges
- Large Molecule Research, Roche Pharma Research and Early Development, Roche Innovation Center Munich, Penzberg, Germany
| | - Klaus R. Liedl
- Department of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
- *Correspondence: Klaus R. Liedl,
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23
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Führer S, Unterhauser J, Zeindl R, Eidelpes R, Fernández-Quintero ML, Liedl KR, Tollinger M. The Structural Flexibility of PR-10 Food Allergens. Int J Mol Sci 2022; 23:ijms23158252. [PMID: 35897827 PMCID: PMC9330593 DOI: 10.3390/ijms23158252] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 07/22/2022] [Accepted: 07/23/2022] [Indexed: 12/18/2022] Open
Abstract
PR-10 proteins constitute a major cause of food allergic reactions. Birch-pollen-related food allergies are triggered by the immunologic cross-reactivity of IgE antibodies with structurally homologous PR-10 proteins that are present in birch pollen and various food sources. While the three-dimensional structures of PR-10 food allergens have been characterized in detail, only a few experimental studies have addressed the structural flexibility of these proteins. In this study, we analyze the millisecond-timescale structural flexibility of thirteen PR-10 proteins from prevalent plant food sources by NMR relaxation-dispersion spectroscopy, in a comparative manner. We show that all the allergens in this study have inherently flexible protein backbones in solution, yet the extent of the structural flexibility appears to be strikingly protein-specific (but not food-source-specific). Above-average flexibility is present in the two short helices, α1 and α2, which form a V-shaped support for the long C-terminal helix α3, and shape the internal ligand-binding cavity, which is characteristic for PR-10 proteins. An in-depth analysis of the NMR relaxation-dispersion data for the PR-10 allergen from peanut reveals the presence of at least two subglobal conformational transitions on the millisecond timescale, which may be related to the release of bound low-molecular-weight ligands from the internal cavity.
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Affiliation(s)
- Sebastian Führer
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria; (S.F.); (J.U.); (R.Z.); (R.E.)
| | - Jana Unterhauser
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria; (S.F.); (J.U.); (R.Z.); (R.E.)
| | - Ricarda Zeindl
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria; (S.F.); (J.U.); (R.Z.); (R.E.)
| | - Reiner Eidelpes
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria; (S.F.); (J.U.); (R.Z.); (R.E.)
| | - Monica L. Fernández-Quintero
- Department of General, Inorganic and Theoretical Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria; (M.L.F.-Q.); (K.R.L.)
| | - Klaus R. Liedl
- Department of General, Inorganic and Theoretical Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria; (M.L.F.-Q.); (K.R.L.)
| | - Martin Tollinger
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria; (S.F.); (J.U.); (R.Z.); (R.E.)
- Correspondence: ; Tel.: +43-512-504-57730
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24
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Waibl F, Kraml J, Hoerschinger VJ, Hofer F, Kamenik AS, Fernández-Quintero ML, Liedl KR. Grid inhomogeneous solvation theory for cross-solvation in rigid solvents. J Chem Phys 2022; 156:204101. [PMID: 35649837 DOI: 10.1063/5.0087549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Grid Inhomogeneous Solvation Theory (GIST) has proven useful to calculate localized thermodynamic properties of water around a solute. Numerous studies have leveraged this information to enhance structure-based binding predictions. We have recently extended GIST toward chloroform as a solvent to allow the prediction of passive membrane permeability. Here, we further generalize the GIST algorithm toward all solvents that can be modeled as rigid molecules. This restriction is inherent to the method and is already present in the inhomogeneous solvation theory. Here, we show that our approach can be applied to various solvent molecules by comparing the results of GIST simulations with thermodynamic integration (TI) calculations and experimental results. Additionally, we analyze and compare a matrix consisting of 100 entries of ten different solvent molecules solvated within each other. We find that the GIST results are highly correlated with TI calculations as well as experiments. For some solvents, we find Pearson correlations of up to 0.99 to the true entropy, while others are affected by the first-order approximation more strongly. The enthalpy-entropy splitting provided by GIST allows us to extend a recently published approach, which estimates higher order entropies by a linear scaling of the first-order entropy, to solvents other than water. Furthermore, we investigate the convergence of GIST in different solvents. We conclude that our extension to GIST reliably calculates localized thermodynamic properties for different solvents and thereby significantly extends the applicability of this widely used method.
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Affiliation(s)
- Franz Waibl
- Center for Molecular Biosciences Innsbruck, Department of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, Innsbruck, Austria
| | - Johannes Kraml
- Center for Molecular Biosciences Innsbruck, Department of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, Innsbruck, Austria
| | - Valentin J Hoerschinger
- Center for Molecular Biosciences Innsbruck, Department of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, Innsbruck, Austria
| | - Florian Hofer
- Center for Molecular Biosciences Innsbruck, Department of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, Innsbruck, Austria
| | - Anna S Kamenik
- Center for Molecular Biosciences Innsbruck, Department of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, Innsbruck, Austria
| | - Monica L Fernández-Quintero
- Center for Molecular Biosciences Innsbruck, Department of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, Innsbruck, Austria
| | - Klaus R Liedl
- Center for Molecular Biosciences Innsbruck, Department of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, Innsbruck, Austria
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25
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Werner ER, Fernández-Quintero ML, Hulo N, Golderer G, Sailer S, Lackner K, Werner-Felmayer G, Liedl KR, Watschinger K. Essential role of a conserved aspartate for the enzymatic activity of plasmanylethanolamine desaturase. Cell Mol Life Sci 2022; 79:214. [PMID: 35347434 PMCID: PMC8960569 DOI: 10.1007/s00018-022-04238-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 03/07/2022] [Accepted: 03/08/2022] [Indexed: 11/30/2022]
Abstract
Plasmalogens are an abundant class of glycerophospholipids in the mammalian body, with special occurrence in the brain and in immune cell membranes. Plasmanylethanolamine desaturase (PEDS1) is the final enzyme of plasmalogen biosynthesis, which introduces the characteristic 1-O-alk-1′-enyl double bond. The recent sequence identification of PEDS1 as transmembrane protein 189 showed that its protein sequence is related to a special class of plant desaturases (FAD4), with whom it shares a motif of 8 conserved histidines, which are essential for the enzymatic activity. In the present work, we wanted to gain more insight into the sequence–function relationship of this enzyme and mutated to alanine additional 28 amino acid residues of murine plasmanylethanolamine desaturase including those 20 residues, which are also totally conserved—in addition to the eight-histidine-motif—among the animal PEDS1 and plant FAD4 plant desaturases. We measured the enzymatic activity by transient transfection of tagged murine PEDS1 expression clones to a PEDS1-deficient human HAP1 cell line by monitoring of labeled plasmalogens formed from supplemented 1-O-pyrenedecyl-sn-glycerol in relation to recombinant protein expression. Surprisingly, only a single mutation, namely aspartate 100, led to a total loss of PEDS1 activity. The second strongest impact on enzymatic activity had mutation of phenylalanine 118, leaving only 6% residual activity. A structural model obtained by homology modelling to available structures of stearoyl-CoA reductase predicted that this aspartate 100 residue interacts with histidine 96, and phenylalanine 118 interacts with histidine 187, both being essential histidines assumed to be involved in the coordination of the di-metal center of the enzyme.
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Affiliation(s)
- Ernst R Werner
- Institute of Biological Chemistry, Biocenter, Medical University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria
| | - Monica L Fernández-Quintero
- Department of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria
| | - Nicolas Hulo
- Institute of Genetics and Genomics of Geneva, University of Geneva, 1, rue Michel Servet, 1211, Geneva 4, Switzerland
| | - Georg Golderer
- Institute of Biological Chemistry, Biocenter, Medical University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria
| | - Sabrina Sailer
- Institute of Biological Chemistry, Biocenter, Medical University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria
| | - Katharina Lackner
- Institute of Biological Chemistry, Biocenter, Medical University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria
| | - Gabriele Werner-Felmayer
- Institute of Biological Chemistry, Biocenter, Medical University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria
| | - Klaus R Liedl
- Department of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria
| | - Katrin Watschinger
- Institute of Biological Chemistry, Biocenter, Medical University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria.
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26
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Fernández-Quintero ML, Quoika PK, Wedl FS, Seidler CA, Kroell KB, Loeffler JR, Pomarici ND, Hoerschinger VJ, Bujotzek A, Georges G, Kettenberger H, Liedl KR. Corrigendum: Comparing Antibody Interfaces to Inform Rational Design of New Antibody Formats. Front Mol Biosci 2022; 9:864654. [PMID: 35242816 PMCID: PMC8886232 DOI: 10.3389/fmolb.2022.864654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 01/31/2022] [Indexed: 11/18/2022] Open
Affiliation(s)
- Monica L Fernández-Quintero
- Department of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Patrick K Quoika
- Department of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Florian S Wedl
- Department of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Clarissa A Seidler
- Department of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Katharina B Kroell
- Department of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Johannes R Loeffler
- Department of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Nancy D Pomarici
- Department of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Valentin J Hoerschinger
- Department of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Alexander Bujotzek
- Roche Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany
| | - Guy Georges
- Roche Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany
| | - Hubert Kettenberger
- Roche Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany
| | - Klaus R Liedl
- Department of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
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27
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Guthmiller JJ, Han J, Utset HA, Li L, Lan LYL, Henry C, Stamper CT, McMahon M, O'Dell G, Fernández-Quintero ML, Freyn AW, Amanat F, Stovicek O, Gentles L, Richey ST, de la Peña AT, Rosado V, Dugan HL, Zheng NY, Tepora ME, Bitar DJ, Changrob S, Strohmeier S, Huang M, García-Sastre A, Liedl KR, Bloom JD, Nachbagauer R, Palese P, Krammer F, Coughlan L, Ward AB, Wilson PC. Broadly neutralizing antibodies target a haemagglutinin anchor epitope. Nature 2022; 602:314-320. [PMID: 34942633 PMCID: PMC8828479 DOI: 10.1038/s41586-021-04356-8] [Citation(s) in RCA: 65] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 12/15/2021] [Indexed: 11/09/2022]
Abstract
Broadly neutralizing antibodies that target epitopes of haemagglutinin on the influenza virus have the potential to provide near universal protection against influenza virus infection1. However, viral mutants that escape broadly neutralizing antibodies have been reported2,3. The identification of broadly neutralizing antibody classes that can neutralize viral escape mutants is critical for universal influenza virus vaccine design. Here we report a distinct class of broadly neutralizing antibodies that target a discrete membrane-proximal anchor epitope of the haemagglutinin stalk domain. Anchor epitope-targeting antibodies are broadly neutralizing across H1 viruses and can cross-react with H2 and H5 viruses that are a pandemic threat. Antibodies that target this anchor epitope utilize a highly restricted repertoire, which encodes two public binding motifs that make extensive contacts with conserved residues in the fusion peptide. Moreover, anchor epitope-targeting B cells are common in the human memory B cell repertoire and were recalled in humans by an oil-in-water adjuvanted chimeric haemagglutinin vaccine4,5, which is a potential universal influenza virus vaccine. To maximize protection against seasonal and pandemic influenza viruses, vaccines should aim to boost this previously untapped source of broadly neutralizing antibodies that are widespread in the human memory B cell pool.
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Affiliation(s)
- Jenna J Guthmiller
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL, USA.
| | - Julianna Han
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Henry A Utset
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL, USA
| | - Lei Li
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL, USA
| | | | - Carole Henry
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL, USA
- Moderna Inc., Cambridge, MA, USA
| | | | - Meagan McMahon
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - George O'Dell
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Monica L Fernández-Quintero
- Center for Molecular Biosciences Innsbruck, Department of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Alec W Freyn
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Moderna Inc., Cambridge, MA, USA
| | - Fatima Amanat
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Olivia Stovicek
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL, USA
| | - Lauren Gentles
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Sara T Richey
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Alba Torrents de la Peña
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Victoria Rosado
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Haley L Dugan
- Committee on Immunology, University of Chicago, Chicago, IL, USA
| | - Nai-Ying Zheng
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL, USA
| | - Micah E Tepora
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL, USA
| | - Dalia J Bitar
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL, USA
| | - Siriruk Changrob
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL, USA
| | - Shirin Strohmeier
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Min Huang
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Klaus R Liedl
- Center for Molecular Biosciences Innsbruck, Department of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Jesse D Bloom
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Microbiology, University of Washington, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Raffael Nachbagauer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Moderna Inc., Cambridge, MA, USA
| | - Peter Palese
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lynda Coughlan
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
- Center for Vaccine Development and Global Health (CVD), University of Maryland School of Medicine, Baltimore, MD, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.
| | - Patrick C Wilson
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL, USA.
- Committee on Immunology, University of Chicago, Chicago, IL, USA.
- Drukier Institute for Children's Health, Department of Pediatrics, Weill Cornell Medicine, New York, NY, USA.
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28
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Fernández-Quintero ML, Kroell KB, Grunewald LJ, Fischer ALM, Riccabona JR, Liedl KR. CDR loop interactions can determine heavy and light chain pairing preferences in bispecific antibodies. MAbs 2022; 14:2024118. [PMID: 35090383 PMCID: PMC8803122 DOI: 10.1080/19420862.2021.2024118] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
As the current biotherapeutic market is dominated by antibodies, the design of different antibody formats, like bispecific antibodies, is critical to the advancement of the field. In contrast to monovalent antibodies, which consist of two identical antigen-binding sites, bispecific antibodies can target two different epitopes by containing two different antigen-binding sites. Thus, the rise of new formats as successful therapeutics has reignited the interest in advancing and facilitating the efficient production of bispecific antibodies. Here, we investigate the influence of point mutations in the antigen-binding site, the paratope, on heavy and light chain pairing preferences by using molecular dynamics simulations. In agreement with experiments, we find that specific residues in the antibody variable domain (Fv), i.e., the complementarity-determining region (CDR) L3 and H3 loops, determine heavy and light chain pairing preferences. Excitingly, we observe substantial population shifts in CDR-H3 and CDR-L3 loop conformations in solution accompanied by a decrease in bispecific IgG yield. These conformational changes in the CDR3 loops induced by point mutations also influence all other CDR loop conformations and consequentially result in different CDR loop states in solution. However, besides their effect on the obtained CDR loop ensembles, point mutations also lead to distinct interaction patterns in the VH-VL interface. By comparing the interaction patterns among all investigated variants, we observe specific contacts in the interface that drive heavy and light chain pairing. Thus, these findings have broad implications in the field of antibody engineering and design because they provide a mechanistic understanding of antibody interfaces, by identifying critical factors driving the pairing preferences, and thus can help to advance the design of bispecific antibodies.
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Affiliation(s)
- Monica L Fernández-Quintero
- Department of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Katharina B Kroell
- Department of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Lukas J Grunewald
- Department of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Anna-Lena M Fischer
- Department of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Jakob R Riccabona
- Department of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Klaus R Liedl
- Department of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
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Fernández-Quintero ML, Quoika PK, Wedl FS, Seidler CA, Kroell KB, Loeffler JR, Pomarici ND, Hoerschinger VJ, Bujotzek A, Georges G, Kettenberger H, Liedl KR. Comparing Antibody Interfaces to Inform Rational Design of New Antibody Formats. Front Mol Biosci 2022; 9:812750. [PMID: 35155578 PMCID: PMC8826573 DOI: 10.3389/fmolb.2022.812750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 01/10/2022] [Indexed: 11/13/2022] Open
Abstract
As the current biotherapeutic market is dominated by antibodies, the design of different antibody formats, like bispecific antibodies and other new formats, represent a key component in advancing antibody therapy. When designing new formats, a targeted modulation of pairing preferences is key. Several existing approaches are successful, but expanding the repertoire of design possibilities would be desirable. Cognate immunoglobulin G antibodies depend on homodimerization of the fragment crystallizable regions of two identical heavy chains. By modifying the dimeric interface of the third constant domain (CH3-CH3), with different mutations on each domain, the engineered Fc fragments form rather heterodimers than homodimers. The first constant domain (CH1-CL) shares a very similar fold and interdomain orientation with the CH3-CH3 dimer. Thus, numerous well-established design efforts for CH3-CH3 interfaces, have also been applied to CH1-CL dimers to reduce the number of mispairings in the Fabs. Given the high structural similarity of the CH3-CH3 and CH1-CL domains we want to identify additional opportunities in comparing the differences and overlapping interaction profiles. Our vision is to facilitate a toolkit that allows for the interchangeable usage of different design tools from crosslinking the knowledge between these two interface types. As a starting point, here, we use classical molecular dynamics simulations to identify differences of the CH3-CH3 and CH1-CL interfaces and already find unexpected features of these interfaces shedding new light on possible design variations. Apart from identifying clear differences between the similar CH3-CH3 and CH1-CL dimers, we structurally characterize the effects of point-mutations in the CH3-CH3 interface on the respective dynamics and interface interaction patterns. Thus, this study has broad implications in the field of antibody engineering as it provides a structural and mechanistical understanding of antibody interfaces and thereby presents a crucial aspect for the design of bispecific antibodies.
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Affiliation(s)
- Monica L. Fernández-Quintero
- Department of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Patrick K. Quoika
- Department of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Florian S. Wedl
- Department of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Clarissa A. Seidler
- Department of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Katharina B. Kroell
- Department of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Johannes R. Loeffler
- Department of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Nancy D. Pomarici
- Department of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Valentin J. Hoerschinger
- Department of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Alexander Bujotzek
- Roche Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany
| | - Guy Georges
- Roche Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany
| | - Hubert Kettenberger
- Roche Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany
| | - Klaus R. Liedl
- Department of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
- *Correspondence: Klaus R. Liedl,
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30
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Waibl F, Kraml J, Fernández-Quintero ML, Loeffler JR, Liedl KR. Explicit solvation thermodynamics in ionic solution: extending grid inhomogeneous solvation theory to solvation free energy of salt-water mixtures. J Comput Aided Mol Des 2022; 36:101-116. [PMID: 35031880 PMCID: PMC8907097 DOI: 10.1007/s10822-021-00429-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 10/28/2021] [Indexed: 12/03/2022]
Abstract
Hydration thermodynamics play a fundamental role in fields ranging from the pharmaceutical industry to environmental research. Numerous methods exist to predict solvation thermodynamics of compounds ranging from small molecules to large biomolecules. Arguably the most precise methods are those based on molecular dynamics (MD) simulations in explicit solvent. One theory that has seen increased use is inhomogeneous solvation theory (IST). However, while many applications require accurate description of salt-water mixtures, no implementation of IST is currently able to estimate solvation properties involving more than one solvent species. Here, we present an extension to grid inhomogeneous solvation theory (GIST) that can take salt contributions into account. At the example of carbazole in 1 M NaCl solution, we compute the solvation energy as well as first and second order entropies. While the effect of the first order ion entropy is small, both the water-water and water-ion entropies contribute strongly. We show that the water-ion entropies are efficiently approximated using the Kirkwood superposition approximation. However, this approach cannot be applied to the water-water entropy. Furthermore, we test the quantitative validity of our method by computing salting-out coefficients and comparing them to experimental data. We find a good correlation to experimental salting-out constants, while the absolute values are overpredicted due to the approximate second order entropy. Since ions are frequently used in MD, either to neutralize the system or as a part of the investigated process, our method greatly extends the applicability of GIST. The use-cases range from biopharmaceuticals, where many assays require high salt concentrations, to environmental research, where solubility in sea water is important to model the fate of organic substances.
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Affiliation(s)
- Franz Waibl
- Department of General, Inorganic, and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria
| | - Johannes Kraml
- Department of General, Inorganic, and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria
| | - Monica L Fernández-Quintero
- Department of General, Inorganic, and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria
| | - Johannes R Loeffler
- Department of General, Inorganic, and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria
| | - Klaus R Liedl
- Department of General, Inorganic, and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria.
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31
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El Ghaleb Y, Fernández-Quintero ML, Monteleone S, Tuluc P, Campiglio M, Liedl KR, Flucher BE. Ion-pair interactions between voltage-sensing domain IV and pore domain I regulate Ca V1.1 gating. Biophys J 2021; 120:4429-4441. [PMID: 34506774 PMCID: PMC8553663 DOI: 10.1016/j.bpj.2021.09.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 07/29/2021] [Accepted: 09/02/2021] [Indexed: 11/21/2022] Open
Abstract
The voltage-gated calcium channel CaV1.1 belongs to the family of pseudo-heterotetrameric cation channels, which are built of four structurally and functionally distinct voltage-sensing domains (VSDs) arranged around a common channel pore. Upon depolarization, positive gating charges in the S4 helices of each VSD are moved across the membrane electric field, thus generating the conformational change that prompts channel opening. This sliding helix mechanism is aided by the transient formation of ion-pair interactions with countercharges located in the S2 and S3 helices within the VSDs. Recently, we identified a domain-specific ion-pair partner of R1 and R2 in VSD IV of CaV1.1 that stabilizes the activated state of this VSD and regulates the voltage dependence of current activation in a splicing-dependent manner. Structure modeling of the entire CaV1.1 in a membrane environment now revealed the participation in this process of an additional putative ion-pair partner (E216) located outside VSD IV, in the pore domain of the first repeat (IS5). This interdomain interaction is specific for CaV1.1 and CaV1.2 L-type calcium channels. Moreover, in CaV1.1 it is sensitive to insertion of the 19 amino acid peptide encoded by exon 29. Whole-cell patch-clamp recordings in dysgenic myotubes reconstituted with wild-type or E216 mutants of GFP-CaV1.1e (lacking exon 29) showed that charge neutralization (E216Q) or removal of the side chain (E216A) significantly shifted the voltage dependence of activation (V1/2) to more positive potentials, suggesting that E216 stabilizes the activated state. Insertion of exon 29 in the GFP-CaV1.1a splice variant strongly reduced the ionic interactions with R1 and R2 and caused a substantial right shift of V1/2, whereas no further shift of V1/2 was observed on substitution of E216 with A or Q. Together with our previous findings, these results demonstrate that inter- and intradomain ion-pair interactions cooperate in the molecular mechanism regulating VSD function and channel gating in CaV1.1.
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Affiliation(s)
- Yousra El Ghaleb
- Department of Physiology and Medical Physics, Institute of Physiology, Medical University Innsbruck, Innsbruck, Austria
| | - Monica L Fernández-Quintero
- Department of Physiology and Medical Physics, Institute of Physiology, Medical University Innsbruck, Innsbruck, Austria; Department of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck
| | - Stefania Monteleone
- Department of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck; Evotec (UK) Ltd., Abingdon, Oxfordshire, United Kingdom
| | - Petronel Tuluc
- Department of Pharmacology and Toxicology, Institute of Pharmacy and Center for Molecular Biosciences, University of Innsbruck, Innsbruck, Austria
| | - Marta Campiglio
- Department of Physiology and Medical Physics, Institute of Physiology, Medical University Innsbruck, Innsbruck, Austria
| | - Klaus R Liedl
- Department of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck
| | - Bernhard E Flucher
- Department of Physiology and Medical Physics, Institute of Physiology, Medical University Innsbruck, Innsbruck, Austria.
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32
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Fernández-Quintero ML, Kroell KB, Bacher LM, Loeffler JR, Quoika PK, Georges G, Bujotzek A, Kettenberger H, Liedl KR. Germline-Dependent Antibody Paratope States and Pairing Specific V H-V L Interface Dynamics. Front Immunol 2021; 12:675655. [PMID: 34447370 PMCID: PMC8382685 DOI: 10.3389/fimmu.2021.675655] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 06/24/2021] [Indexed: 11/13/2022] Open
Abstract
Antibodies have emerged as one of the fastest growing classes of biotherapeutic proteins. To improve the rational design of antibodies, we investigate the conformational diversity of 16 different germline combinations, which are composed of 4 different kappa light chains paired with 4 different heavy chains. In this study, we systematically show that different heavy and light chain pairings strongly influence the paratope, interdomain interaction patterns and the relative VH-VL interface orientations. We observe changes in conformational diversity and substantial population shifts of the complementarity determining region (CDR) loops, resulting in distinct dominant solution structures and differently favored canonical structures. Additionally, we identify conformational changes in the structural diversity of the CDR-H3 loop upon different heavy and light chain pairings, as well as upon changes in sequence and structure of the neighboring CDR loops, despite having an identical CDR-H3 loop amino acid sequence. These results can also be transferred to all CDR loops and to the relative VH-VL orientation, as certain paratope states favor distinct interface angle distributions. Furthermore, we directly compare the timescales of sidechain rearrangements with the well-described transition kinetics of conformational changes in the backbone of the CDR loops. We show that sidechain flexibilities are strongly affected by distinct heavy and light chain pairings and decipher germline-specific structural features co-determining stability. These findings reveal that all CDR loops are strongly correlated and that distinct heavy and light chain pairings can result in different paratope states in solution, defined by a characteristic combination of CDR loop conformations and VH-VL interface orientations. Thus, these results have broad implications in the field of antibody engineering, as they clearly show the importance of considering paired heavy and light chains to understand the antibody binding site, which is one of the key aspects in the design of therapeutics.
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Affiliation(s)
- Monica L Fernández-Quintero
- Department of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Katharina B Kroell
- Department of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Lisa M Bacher
- Department of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Johannes R Loeffler
- Department of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Patrick K Quoika
- Department of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Guy Georges
- Roche Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany
| | - Alexander Bujotzek
- Roche Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany
| | - Hubert Kettenberger
- Roche Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany
| | - Klaus R Liedl
- Department of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
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33
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El Ghaleb Y, Schneeberger PE, Fernández-Quintero ML, Geisler SM, Pelizzari S, Polstra AM, van Hagen JM, Denecke J, Campiglio M, Liedl KR, Stevens CA, Person RE, Rentas S, Marsh ED, Conlin LK, Tuluc P, Kutsche K, Flucher BE. CACNA1I gain-of-function mutations differentially affect channel gating and cause neurodevelopmental disorders. Brain 2021; 144:2092-2106. [PMID: 33704440 PMCID: PMC8422349 DOI: 10.1093/brain/awab101] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 01/05/2021] [Accepted: 01/06/2021] [Indexed: 12/11/2022] Open
Abstract
T-type calcium channels (Cav3.1 to Cav3.3) regulate low-threshold calcium spikes, burst firing and rhythmic oscillations of neurons and are involved in sensory processing, sleep, and hormone and neurotransmitter release. Here, we examined four heterozygous missense variants in CACNA1I, encoding the Cav3.3 channel, in patients with variable neurodevelopmental phenotypes. The p.(Ile860Met) variant, affecting a residue in the putative channel gate at the cytoplasmic end of the IIS6 segment, was identified in three family members with variable cognitive impairment. The de novo p.(Ile860Asn) variant, changing the same amino acid residue, was detected in a patient with severe developmental delay and seizures. In two additional individuals with global developmental delay, hypotonia, and epilepsy, the variants p.(Ile1306Thr) and p.(Met1425Ile), substituting residues at the cytoplasmic ends of IIIS5 and IIIS6, respectively, were found. Because structure modelling indicated that the amino acid substitutions differentially affect the mobility of the channel gate, we analysed possible effects on Cav3.3 channel function using patch-clamp analysis in HEK293T cells. The mutations resulted in slowed kinetics of current activation, inactivation, and deactivation, and in hyperpolarizing shifts of the voltage-dependence of activation and inactivation, with Cav3.3-I860N showing the strongest and Cav3.3-I860M the weakest effect. Structure modelling suggests that by introducing stabilizing hydrogen bonds the mutations slow the kinetics of the channel gate and cause the gain-of-function effect in Cav3.3 channels. The gating defects left-shifted and increased the window currents, resulting in increased calcium influx during repetitive action potentials and even at resting membrane potentials. Thus, calcium toxicity in neurons expressing the Cav3.3 variants is one likely cause of the neurodevelopmental phenotype. Computer modelling of thalamic reticular nuclei neurons indicated that the altered gating properties of the Cav3.3 disease variants lower the threshold and increase the duration and frequency of action potential firing. Expressing the Cav3.3-I860N/M mutants in mouse chromaffin cells shifted the mode of firing from low-threshold spikes and rebound burst firing with wild-type Cav3.3 to slow oscillations with Cav3.3-I860N and an intermediate firing mode with Cav3.3-I860M, respectively. Such neuronal hyper-excitability could explain seizures in the patient with the p.(Ile860Asn) mutation. Thus, our study implicates CACNA1I gain-of-function mutations in neurodevelopmental disorders, with a phenotypic spectrum ranging from borderline intellectual functioning to a severe neurodevelopmental disorder with epilepsy.
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Affiliation(s)
- Yousra El Ghaleb
- Institute of Physiology, Medical University Innsbruck, Innsbruck 6020, Austria
| | - Pauline E Schneeberger
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg 20251, Germany
| | - Monica L Fernández-Quintero
- Institute of Physiology, Medical University Innsbruck, Innsbruck 6020, Austria
- Institute of Theoretical Chemistry, University of Innsbruck, Innsbruck 6020, Austria
| | - Stefanie M Geisler
- Department of Pharmacology, University of Innsbruck, Innsbruck 6020, Austria
| | - Simone Pelizzari
- Institute of Physiology, Medical University Innsbruck, Innsbruck 6020, Austria
| | - Abeltje M Polstra
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, 1012 WX, The Netherlands
| | - Johanna M van Hagen
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, 1012 WX, The Netherlands
| | - Jonas Denecke
- Department of Pediatrics, University Medical Center Hamburg-Eppendorf, Hamburg 20251, Germany
| | - Marta Campiglio
- Institute of Physiology, Medical University Innsbruck, Innsbruck 6020, Austria
| | - Klaus R Liedl
- Institute of Theoretical Chemistry, University of Innsbruck, Innsbruck 6020, Austria
| | - Cathy A Stevens
- Department of Pediatrics, University of Tennessee College of Medicine, Chattanooga, TN 37403, USA
| | | | - Stefan Rentas
- Division of Genomic Diagnostics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Eric D Marsh
- Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Laura K Conlin
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Petronel Tuluc
- Department of Pharmacology, University of Innsbruck, Innsbruck 6020, Austria
| | - Kerstin Kutsche
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg 20251, Germany
| | - Bernhard E Flucher
- Institute of Physiology, Medical University Innsbruck, Innsbruck 6020, Austria
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Dayal A, Fernández-Quintero ML, Liedl KR, Grabner M. Pore mutation N617D in the skeletal muscle DHPR blocks Ca 2+ influx due to atypical high-affinity Ca 2+ binding. eLife 2021; 10:63435. [PMID: 34061024 PMCID: PMC8184209 DOI: 10.7554/elife.63435] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 05/28/2021] [Indexed: 11/13/2022] Open
Abstract
Skeletal muscle excitation-contraction (EC) coupling roots in Ca2+-influx-independent inter-channel signaling between the sarcolemmal dihydropyridine receptor (DHPR) and the ryanodine receptor (RyR1) in the sarcoplasmic reticulum. Although DHPR Ca2+ influx is irrelevant for EC coupling, its putative role in other muscle-physiological and developmental pathways was recently examined using two distinct genetically engineered mouse models carrying Ca2+ non-conducting DHPRs: DHPR(N617D) (Dayal et al., 2017) and DHPR(E1014K) (Lee et al., 2015). Surprisingly, despite complete block of DHPR Ca2+-conductance, histological, biochemical, and physiological results obtained from these two models were contradictory. Here, we characterize the permeability and selectivity properties and henceforth the mechanism of Ca2+ non-conductance of DHPR(N617). Our results reveal that only mutant DHPR(N617D) with atypical high-affinity Ca2+ pore-binding is tight for physiologically relevant monovalent cations like Na+ and K+. Consequently, we propose a molecular model of cooperativity between two ion selectivity rings formed by negatively charged residues in the DHPR pore region.
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Affiliation(s)
- Anamika Dayal
- Department of Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Klaus R Liedl
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Manfred Grabner
- Department of Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
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35
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Abstract
The rise of antibodies as a promising and rapidly growing class of biotherapeutic proteins has motivated numerous studies to characterize and understand antibody structures. In the past decades, the number of antibody crystal structures increased substantially, which revolutionized the atomistic understanding of antibody functions. Even though numerous static structures are known, various biophysical properties of antibodies (i.e., specificity, hydrophobicity and stability) are governed by their dynamic character. Additionally, the importance of high-quality structures in structure–function relationship studies has substantially increased. These structure–function relationship studies have also created a demand for precise homology models of antibody structures, which allow rational antibody design and engineering when no crystal structure is available. Here, we discuss various aspects and challenges in antibody design and extend the paradigm of describing antibodies with only a single static structure to characterizing them as dynamic ensembles in solution.
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Affiliation(s)
- Monica L Fernández-Quintero
- Department of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Guy Georges
- Roche Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany
| | - Janos M Varga
- Department of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Klaus R Liedl
- Department of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
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36
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Quoika PK, Fernández-Quintero ML, Podewitz M, Hofer F, Liedl KR. Implementation of the Freely Jointed Chain Model to Assess Kinetics and Thermodynamics of Thermosensitive Coil-Globule Transition by Markov States. J Phys Chem B 2021; 125:4898-4909. [PMID: 33942614 PMCID: PMC8154620 DOI: 10.1021/acs.jpcb.1c01946] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
![]()
We revived and implemented
a method developed by Kuhn in 1934,
originally only published in German, that is, the so-called “freely
jointed chain” model. This approach turned out to be surprisingly
useful for analyzing state-of-the-art computer simulations of the
thermosensitive coil–globule transition of N-Isopropylacrylamide 20-mer. Our atomistic computer simulations are
orders of magnitude longer than those of previous studies and lead
to a reliable description of thermodynamics and kinetics at many different
temperatures. The freely jointed chain model provides a coordinate
system, which allows us to construct a Markov state model of the conformational
transitions. Furthermore, this guarantees a reliable reconstruction
of the kinetics in back-and-forth directions. In addition, we obtain
a description of the high diversity and variability of both conformational
states. Thus, we gain a detailed understanding of the coil–globule
transition. Surprisingly, conformational entropy turns out to play
only a minor role in the thermodynamic balance of the process. Moreover,
we show that the radius of gyration is an unexpectedly unsuitable
coordinate to comprehend the transition kinetics because it does not
capture the high conformational diversity within the different states.
Consequently, the approach presented here allows for an exhaustive
description and resolution of the conformational ensembles of arbitrary
linear polymer chains.
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Affiliation(s)
- Patrick K Quoika
- Institute of General, Inorganic and Theoretical Chemistry, and Centre of Molecular Biosciences University of Innsbruck, A-6020 Innsbruck, Austria
| | - Monica L Fernández-Quintero
- Institute of General, Inorganic and Theoretical Chemistry, and Centre of Molecular Biosciences University of Innsbruck, A-6020 Innsbruck, Austria
| | - Maren Podewitz
- Institute of General, Inorganic and Theoretical Chemistry, and Centre of Molecular Biosciences University of Innsbruck, A-6020 Innsbruck, Austria
| | - Florian Hofer
- Institute of General, Inorganic and Theoretical Chemistry, and Centre of Molecular Biosciences University of Innsbruck, A-6020 Innsbruck, Austria
| | - Klaus R Liedl
- Institute of General, Inorganic and Theoretical Chemistry, and Centre of Molecular Biosciences University of Innsbruck, A-6020 Innsbruck, Austria
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Fernández-Quintero ML, Seidler CA, Quoika PK, Liedl KR. Shark Antibody Variable Domains Rigidify Upon Affinity Maturation-Understanding the Potential of Shark Immunoglobulins as Therapeutics. Front Mol Biosci 2021; 8:639166. [PMID: 33959632 PMCID: PMC8093575 DOI: 10.3389/fmolb.2021.639166] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 03/17/2021] [Indexed: 12/22/2022] Open
Abstract
Sharks and other cartilaginous fish are the phylogenetically oldest living organisms that have antibodies as part of their adaptive immune system. As part of their humoral adaptive immune response, they produce an immunoglobulin, the so-called immunoglobulin new antigen receptor (IgNAR), a heavy-chain only antibody. The variable domain of an IgNAR, also known as V NAR , binds the antigen as an independent soluble domain. In this study, we structurally and dynamically characterized the affinity maturation mechanism of the germline and somatically matured (PBLA8) V NAR to better understand their function and their applicability as therapeutics. We observed a substantial rigidification upon affinity maturation, which is accompanied by a higher number of contacts, thereby contributing to the decrease in flexibility. Considering the static x-ray structures, the observed rigidification is not obvious, as especially the mutated residues undergo conformational changes during the simulation, resulting in an even stronger network of stabilizing interactions. Additionally, the simulations of the V NAR in complex with the hen egg-white lysozyme show that the V NAR antibodies evidently follow the concept of conformational selection, as the binding-competent state already preexisted even without the presence of the antigen. To have a more detailed description of antibody-antigen recognition, we also present here the binding/unbinding mechanism between the hen egg-white lysozyme and both the germline and matured V NAR s. Upon maturation, we observed a substantial increase in the resulting dissociation-free energy barrier. Furthermore, we were able to kinetically and thermodynamically describe the binding process and did not only identify a two-step binding mechanism, but we also found a strong population shift upon affinity maturation toward the native binding pose.
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Affiliation(s)
- Monica L Fernández-Quintero
- Department of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Clarissa A Seidler
- Department of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Patrick K Quoika
- Department of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Klaus R Liedl
- Department of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
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Loeffler JR, Fernández-Quintero ML, Waibl F, Quoika PK, Hofer F, Schauperl M, Liedl KR. Conformational Shifts of Stacked Heteroaromatics: Vacuum vs. Water Studied by Machine Learning. Front Chem 2021; 9:641610. [PMID: 33842433 PMCID: PMC8032969 DOI: 10.3389/fchem.2021.641610] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 03/08/2021] [Indexed: 11/13/2022] Open
Abstract
Stacking interactions play a crucial role in drug design, as we can find aromatic cores or scaffolds in almost any available small molecule drug. To predict optimal binding geometries and enhance stacking interactions, usually high-level quantum mechanical calculations are performed. These calculations have two major drawbacks: they are very time consuming, and solvation can only be considered using implicit solvation. Therefore, most calculations are performed in vacuum. However, recent studies have revealed a direct correlation between the desolvation penalty, vacuum stacking interactions and binding affinity, making predictions even more difficult. To overcome the drawbacks of quantum mechanical calculations, in this study we use neural networks to perform fast geometry optimizations and molecular dynamics simulations of heteroaromatics stacked with toluene in vacuum and in explicit solvation. We show that the resulting energies in vacuum are in good agreement with high-level quantum mechanical calculations. Furthermore, we show that using explicit solvation substantially influences the favored orientations of heteroaromatic rings thereby emphasizing the necessity to include solvation properties starting from the earliest phases of drug design.
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Affiliation(s)
- Johannes R Loeffler
- Center of Molecular Biosciences Innsbruck, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Monica L Fernández-Quintero
- Center of Molecular Biosciences Innsbruck, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Franz Waibl
- Center of Molecular Biosciences Innsbruck, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Patrick K Quoika
- Center of Molecular Biosciences Innsbruck, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Florian Hofer
- Center of Molecular Biosciences Innsbruck, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Michael Schauperl
- Center of Molecular Biosciences Innsbruck, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Klaus R Liedl
- Center of Molecular Biosciences Innsbruck, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
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Fernández-Quintero ML, El Ghaleb Y, Tuluc P, Campiglio M, Liedl KR, Flucher BE. Structural determinants of voltage-gating properties in calcium channels. eLife 2021; 10:e64087. [PMID: 33783354 PMCID: PMC8099428 DOI: 10.7554/elife.64087] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 03/29/2021] [Indexed: 12/20/2022] Open
Abstract
Voltage-gated calcium channels control key functions of excitable cells, like synaptic transmission in neurons and the contraction of heart and skeletal muscles. To accomplish such diverse functions, different calcium channels activate at different voltages and with distinct kinetics. To identify the molecular mechanisms governing specific voltage sensing properties, we combined structure modeling, mutagenesis, and electrophysiology to analyze the structures, free energy, and transition kinetics of the activated and resting states of two functionally distinct voltage sensing domains (VSDs) of the eukaryotic calcium channel CaV1.1. Both VSDs displayed the typical features of the sliding helix model; however, they greatly differed in ion-pair formation of the outer gating charges. Specifically, stabilization of the activated state enhanced the voltage dependence of activation, while stabilization of resting states slowed the kinetics. This mechanism provides a mechanistic model explaining how specific ion-pair formation in separate VSDs can realize the characteristic gating properties of voltage-gated cation channels.
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Affiliation(s)
- Monica L Fernández-Quintero
- Department of Physiology and Medical Physics, Medical University InnsbruckInnsbruckAustria
- Department of General, Inorganic and Theoretical Chemistry, University of InnsbruckInnsbruckAustria
| | - Yousra El Ghaleb
- Department of Physiology and Medical Physics, Medical University InnsbruckInnsbruckAustria
| | - Petronel Tuluc
- Department of Pharmacology and Toxicology, Institute of Pharmacy and Center for Molecular Biosciences, University of InnsbruckInnsbruckAustria
| | - Marta Campiglio
- Department of Physiology and Medical Physics, Medical University InnsbruckInnsbruckAustria
| | - Klaus R Liedl
- Department of General, Inorganic and Theoretical Chemistry, University of InnsbruckInnsbruckAustria
| | - Bernhard E Flucher
- Department of Physiology and Medical Physics, Medical University InnsbruckInnsbruckAustria
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40
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Fernández-Quintero ML, Kroell KB, Hofer F, Riccabona JR, Liedl KR. Mutation of Framework Residue H71 Results in Different Antibody Paratope States in Solution. Front Immunol 2021; 12:630034. [PMID: 33737932 PMCID: PMC7960778 DOI: 10.3389/fimmu.2021.630034] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 01/20/2021] [Indexed: 12/13/2022] Open
Abstract
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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Affiliation(s)
- Monica L Fernández-Quintero
- Department of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Katharina B Kroell
- Department of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Florian Hofer
- Department of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Jakob R Riccabona
- Department of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Klaus R Liedl
- Department of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
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41
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Abstract
In the past decade, the relevance of antibodies as therapeutics has increased substantially. Therefore, structural and functional characterization, in particular of the complementarity-determining regions (CDRs), is crucial to the design and engineering of antibodies with unique binding properties. Various studies have focused on classifying the CDR loops into a small set of main-chain conformations to facilitate antibody design by assuming that certain sequences can only adopt a limited number of conformations. Here, we present a kinetic classification of CDR loop structures as ensembles in solution. Using molecular dynamics simulations in combination with strong experimental structural information, we observe conformational transitions between canonical clusters and additional dominant solution structures in the micro-to-millisecond timescale for all CDR loops, independent of length and sequence composition. Besides identifying all relevant conformations in solution, our results revealed that various canonical cluster medians actually belong to the same kinetic minimum. Additionally, we reconstruct the kinetics and probabilities of the conformational transitions between canonical clusters, and thereby extend the model of static canonical structures to reveal a dynamic conformational ensemble in solution as a new paradigm in the field of antibody structure design. Abbreviations: CDR: Complementary-determining region; Fv: Antibody variable fragment; PCCA: Perron cluster analysis; tICA: Time-lagged independent component analysis; VH: Heavy chain variable region; VL: Light chain variable region
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Affiliation(s)
- Monica L Fernández-Quintero
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Martin C Heiss
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Nancy D Pomarici
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Barbara A Math
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Klaus R Liedl
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
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Hofer F, Kamenik AS, Fernández-Quintero ML, Kraml J, Liedl KR. pH-Induced Local Unfolding of the Phl p 6 Pollen Allergen From cpH-MD. Front Mol Biosci 2021; 7:603644. [PMID: 33511157 PMCID: PMC7835895 DOI: 10.3389/fmolb.2020.603644] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 12/10/2020] [Indexed: 11/13/2022] Open
Abstract
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.
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Fernández-Quintero ML, Kroell KB, Heiss MC, Loeffler JR, Quoika PK, Waibl F, Bujotzek A, Moessner E, Georges G, Liedl KR. Surprisingly Fast Interface and Elbow Angle Dynamics of Antigen-Binding Fragments. Front Mol Biosci 2020; 7:609088. [PMID: 33330636 PMCID: PMC7732698 DOI: 10.3389/fmolb.2020.609088] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 10/21/2020] [Indexed: 12/14/2022] Open
Abstract
Fab consist of a heavy and light chain and can be subdivided into a variable (V H and V L ) and a constant region (C H 1 and C L ). The variable region contains the complementarity-determining region (CDR), which is formed by six hypervariable loops, shaping the antigen binding site, the paratope. Apart from the CDR loops, both the elbow angle and the relative interdomain orientations of the V H -V L and the C H 1-C L domains influence the shape of the paratope. Thus, characterization of the interface and elbow angle dynamics is essential to antigen specificity. We studied nine antigen-binding fragments (Fab) to investigate the influence of affinity maturation, antibody humanization, and different light-chain types on the interface and elbow angle dynamics. While the CDR loops reveal conformational transitions in the micro-to-millisecond timescale, both the interface and elbow angle dynamics occur on the low nanosecond timescale. Upon affinity maturation, we observe a substantial rigidification of the V H and V L interdomain and elbow-angle flexibility, reflected in a narrower and more distinct distribution. Antibody humanization describes the process of grafting non-human CDR loops onto a representative human framework. As the antibody framework changes upon humanization, we investigated if both the interface and the elbow angle distributions are changed or shifted. The results clearly showed a substantial shift in the relative V H -V L distributions upon antibody humanization, indicating that different frameworks favor distinct interface orientations. Additionally, the interface and elbow angle dynamics of five antibody fragments with different light-chain types are included, because of their strong differences in elbow angles. For these five examples, we clearly see a high variability and flexibility in both interface and elbow angle dynamics, highlighting the fact that Fab interface orientations and elbow angles interconvert between each other in the low nanosecond timescale. Understanding how the relative interdomain orientations and the elbow angle influence antigen specificity, affinity, and stability has broad implications in the field of antibody modeling and engineering.
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Affiliation(s)
- Monica L. Fernández-Quintero
- Center for Molecular Biosciences Innsbruck (CMBI), Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Katharina B. Kroell
- Center for Molecular Biosciences Innsbruck (CMBI), Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Martin C. Heiss
- Center for Molecular Biosciences Innsbruck (CMBI), Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Johannes R. Loeffler
- Center for Molecular Biosciences Innsbruck (CMBI), Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Patrick K. Quoika
- Center for Molecular Biosciences Innsbruck (CMBI), Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Franz Waibl
- Center for Molecular Biosciences Innsbruck (CMBI), Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Alexander Bujotzek
- Roche Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany
| | - Ekkehard Moessner
- Roche Pharma Research and Early Development, Large Molecular Research, Roche Innovation Center Zurich, Schlieren, Switzerland
| | - Guy Georges
- Roche Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany
| | - Klaus R. Liedl
- Center for Molecular Biosciences Innsbruck (CMBI), Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
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Waibl F, Fernández-Quintero ML, Kamenik AS, Kraml J, Hofer F, Kettenberger H, Georges G, Liedl KR. Conformational Ensembles of Antibodies Determine Their Hydrophobicity. Biophys J 2020; 120:143-157. [PMID: 33220303 PMCID: PMC7820740 DOI: 10.1016/j.bpj.2020.11.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 10/23/2020] [Accepted: 11/10/2020] [Indexed: 12/11/2022] Open
Abstract
A major challenge in the development of antibody biotherapeutics is their tendency to aggregate. One root cause for aggregation is exposure of hydrophobic surface regions to the solvent. Many current techniques predict the relative aggregation propensity of antibodies via precalculated scales for the hydrophobicity or aggregation propensity of single amino acids. However, those scales cannot describe the nonadditive effects of a residue’s surrounding on its hydrophobicity. Therefore, they are inherently limited in their ability to describe the impact of subtle differences in molecular structure on the overall hydrophobicity. Here, we introduce a physics-based approach to describe hydrophobicity in terms of the hydration free energy using grid inhomogeneous solvation theory (GIST). We apply this method to assess the effects of starting structures, conformational sampling, and protonation states on the hydrophobicity of antibodies. Our results reveal that high-quality starting structures, i.e., crystal structures, are crucial for the prediction of hydrophobicity and that conformational sampling can compensate errors introduced by the starting structure. On the other hand, sampling of protonation states only leads to good results when combined with high-quality structures, whereas it can even be detrimental otherwise. We conclude by pointing out that a single static homology model may not be adequate for predicting hydrophobicity.
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Affiliation(s)
- Franz Waibl
- Department of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Monica L Fernández-Quintero
- Department of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Anna S Kamenik
- Department of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Johannes Kraml
- Department of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Florian Hofer
- Department of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Hubert Kettenberger
- Roche Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany
| | - Guy Georges
- Roche Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany
| | - Klaus R Liedl
- Department of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria.
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45
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Fernández-Quintero ML, Pomarici ND, Math BA, Kroell KB, Waibl F, Bujotzek A, Georges G, Liedl KR. Antibodies exhibit multiple paratope states influencing V H-V L domain orientations. Commun Biol 2020; 3:589. [PMID: 33082531 PMCID: PMC7576833 DOI: 10.1038/s42003-020-01319-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 09/23/2020] [Indexed: 11/17/2022] Open
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.
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Affiliation(s)
- Monica L Fernández-Quintero
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, A-6020, Innsbruck, Austria
| | - Nancy D Pomarici
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, A-6020, Innsbruck, Austria
| | - Barbara A Math
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, A-6020, Innsbruck, Austria
| | - Katharina B Kroell
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, A-6020, Innsbruck, Austria
| | - Franz Waibl
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, A-6020, Innsbruck, Austria
| | - Alexander Bujotzek
- Roche Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany
| | - Guy Georges
- Roche Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany
| | - Klaus R Liedl
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, A-6020, Innsbruck, Austria.
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Fernández-Quintero ML, Loeffler JR, Bacher LM, Waibl F, Seidler CA, Liedl KR. Local and Global Rigidification Upon Antibody Affinity Maturation. Front Mol Biosci 2020; 7:182. [PMID: 32850970 PMCID: PMC7426445 DOI: 10.3389/fmolb.2020.00182] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 07/13/2020] [Indexed: 01/03/2023] Open
Abstract
During the affinity maturation process the immune system produces antibodies with higher specificity and activity through various rounds of somatic hypermutations in response to an antigen. Elucidating the affinity maturation process is fundamental in understanding immunity and in the development of biotherapeutics. Therefore, we analyzed 10 pairs of antibody fragments differing in their specificity and in distinct stages of affinity maturation using metadynamics in combination with molecular dynamics (MD) simulations. We investigated differences in flexibility of the CDR-H3 loop and global changes in plasticity upon affinity maturation. Among all antibody pairs we observed a substantial rigidification in flexibility and plasticity reflected in a substantial decrease of conformational diversity. To visualize and characterize these findings we used Markov-states models to reconstruct the kinetics of CDR-H3 loop dynamics and for the first time provide a method to define and localize surface plasticity upon affinity maturation.
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Affiliation(s)
- Monica L Fernández-Quintero
- Center for Molecular Biosciences Innsbruck, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Johannes R Loeffler
- Center for Molecular Biosciences Innsbruck, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Lisa M Bacher
- Center for Molecular Biosciences Innsbruck, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Franz Waibl
- Center for Molecular Biosciences Innsbruck, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Clarissa A Seidler
- Center for Molecular Biosciences Innsbruck, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Klaus R Liedl
- Center for Molecular Biosciences Innsbruck, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
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47
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Fernández-Quintero ML, Pomarici ND, Loeffler JR, Seidler CA, Liedl KR. T-Cell Receptor CDR3 Loop Conformations in Solution Shift the Relative Vα-Vβ Domain Distributions. Front Immunol 2020; 11:1440. [PMID: 32733478 PMCID: PMC7360859 DOI: 10.3389/fimmu.2020.01440] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 06/03/2020] [Indexed: 12/12/2022] Open
Abstract
T-cell receptors are an important part in the adaptive immune system as they are responsible for detecting foreign proteins presented by the major histocompatibility complex (MHC). The affinity is predominantly determined by structure and sequence of the complementarity determining regions (CDRs), of which the CDR3 loops are responsible for peptide recognition. We present a kinetic classification of T-cell receptor CDR3 loops with different loop lengths into canonical and non-canonical solution structures. Using molecular dynamics simulations, we do not only sample available X-ray structures, but we also observe a substantially broader CDR3 loop ensemble with various distinct kinetic minima in solution. Our results strongly imply, that for given CDR3 loop sequences several canonical structures have to be considered to characterize the conformational diversity of these loops. Our suggested dominant solution structures could extend the repertoire of available canonical clusters by including kinetic minimum structures present in solution. Thus, the CDR3 loops need to be characterized as conformational ensembles in solution. Furthermore, the conformational changes of the CDR3 loops follow the paradigm of conformational selection, because the experimentally determined binding competent state is present within this ensemble of pre-existing conformations without the presence of the antigen. We also identify strong correlations between the CDR3 loops and include combined state descriptions. Additionally, we observe a strong dependency of the CDR3 loop conformations on the relative Vα-Vβ interdomain orientations, revealing that certain CDR3 loop states favor specific interface orientations.
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MESH Headings
- Adaptive Immunity
- Animals
- Antigens/metabolism
- Complementarity Determining Regions/chemistry
- Complementarity Determining Regions/genetics
- Complementarity Determining Regions/metabolism
- Crystallography, X-Ray
- Histocompatibility Antigens/metabolism
- Humans
- Molecular Dynamics Simulation
- Peptides/metabolism
- Protein Binding
- Protein Conformation
- Protein Domains/genetics
- Receptors, Antigen, T-Cell, alpha-beta/chemistry
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/metabolism
- Structure-Activity Relationship
- T-Cell Antigen Receptor Specificity
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Affiliation(s)
| | | | | | | | - Klaus R. Liedl
- Center for Molecular Biosciences Innsbruck (CMBI), Department of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
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Abstract
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The
use of fragments to biophysically characterize a protein binding
pocket and determine the strengths of certain interactions is a computationally
and experimentally commonly applied approach. Almost all drug like
molecules contain at least one aromatic moiety forming stacking interactions
in the binding pocket. In computational drug design, the strength
of stacking and the resulting optimization of the aromatic core or
moiety is usually calculated using high level quantum mechanical approaches.
However, as these calculations are performed in a vacuum, solvation
properties are neglected. We close this gap by using Grid Inhomogeneous
Solvation Theory (GIST) to describe the properties of individual heteroaromatics
and complexes and thereby estimate the desolvation penalty. In our
study, we investigated the solvation free energies of heteroaromatics
frequently occurring in drug design projects in complex with truncated
side chains of phenylalanine, tyrosine, and tryptophan. Furthermore,
we investigated the properties of drug-fragments crystallized in a
fragment-based lead optimization approach investigating PDE-10-A.
We do not only find good correlation for the estimated desolvation
penalty and the experimental binding free energy, but our calculations
also allow us to predict prominent interaction sites. We highlight
the importance of including the desolvation penalty of the respective
heteroaromatics in stacked complexes to explain the gain or loss in
affinity of potential lead compounds.
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Affiliation(s)
- Johannes R Loeffler
- Institute of General, Inorganic and Theoretical Chemistry, and Center of Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Tyrol, Austria
| | - Monica L Fernández-Quintero
- Institute of General, Inorganic and Theoretical Chemistry, and Center of Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Tyrol, Austria
| | - Michael Schauperl
- Institute of General, Inorganic and Theoretical Chemistry, and Center of Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Tyrol, Austria
| | - Klaus R Liedl
- Institute of General, Inorganic and Theoretical Chemistry, and Center of Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Tyrol, Austria
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Fernández-Quintero ML, Seidler CA, Liedl KR. T-Cell Receptor Variable β Domains Rigidify During Affinity Maturation. Sci Rep 2020; 10:4472. [PMID: 32161287 PMCID: PMC7066139 DOI: 10.1038/s41598-020-61433-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 01/30/2020] [Indexed: 11/17/2022] Open
Abstract
We investigated T-cell receptor variable β chains binding to the superantigen staphylococcal enterotoxin C3 (SEC 3) with structure information in different stages of affinity maturation. Metadynamics in combination with molecular dynamics simulations allow to access the micro-to-millisecond timescale and reveal a strong effect of energetically significant mutations on the flexibility of the antigen-binding site. The observed changes in dynamics of the complementarity determining region (CDR) loops, especially the CDR 2, and HV 4 loop on this specific pathway of affinity maturation are reflected in their structural diversity, thermodynamics of conformations and kinetics of structural transitions. In addition, this affinity maturation pathway follows the concept of conformational selection, because even without the presence of the antigen the binding competent state is present in this pre-existing ensemble of conformations. In all stages of this affinity maturation process we observe a link between specificity and reduced flexibility.
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Affiliation(s)
- Monica L Fernández-Quintero
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, A-6020, Innsbruck, Austria
| | - Clarissa A Seidler
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, A-6020, Innsbruck, Austria
| | - Klaus R Liedl
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, A-6020, Innsbruck, Austria.
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Fernández-Quintero ML. Structural Determinants of Voltage-Gated Calcium Channel Gating Properties. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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