{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T05:24:43Z","timestamp":1786944283818,"version":"build-2736575974"},"reference-count":44,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T00:00:00Z","timestamp":1786924800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Immunol."],"abstract":"<jats:sec>\n                    <jats:title>Introduction<\/jats:title>\n                    <jats:p>CD40L (CD154) is a homotrimeric member of the TNF superfamily protein expressed on activated CD4+ T cells whose interaction with CD40 is required for class-switch recombination, somatic hypermutation, and B cell terminal differentiation. Loss-of-function mutations in gene CD40LG cause X-linked hyper-IgM syndrome type 1 (HIGM1), characterized by recurrent infections, lack of IgG, IgA and IgE, and near-normal or elevated IgM.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>We implemented computational strategies to describe the structure and dynamics of the CD40L-CD40 complex for the native protein and three missense variants not previously characterized at the molecular level: A123E, S222F and G257R. Two independent 300 ns simulations were run per system in explicit solvent at 300\u00a0K and 0.15 M NaCl. In addition, we evaluated the energetics and electrostatics of the complex using continuum solvent models, such as molecular mechanics-Poisson-Boltzmann Surface Area (MM-PBSA) and Adaptive Poisson-Boltzmann Solver (APBS).<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We found that A123E caused a moderate, energetically coherent reduction in binding affinity consistent with partial loss of function. S222F caused the largest reduction in binding free energy (weakest binder by MM-PBSA) along with an increase of the CD40L-CD40 contact area, consistent with a geometrically expanded but energetically disrupted interface where the aromatic side chain offsets paradoxically favorable electrostatic reorganization. G257R maintained near-native binding free energies but reduced the trimeric contact area by 20-22%, and increased the radius of gyration of CD40L, consistent with structural loosening of the homotrimer that we predict could uncouple binding competence from signaling competence, with potential effects on CD40 receptor mobility and mechanotransduction at the immunological synapse that remain to be tested experimentally.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Discussion<\/jats:title>\n                    <jats:p>These findings may offer a structural basis for the clinical heterogeneity of HIGM1 and illustrate what computational approaches can contribute to the interpretation of CD40LG variants, including novel variants identified in Latin American patients where experimental validation is rarely available.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.3389\/fimmu.2026.1861005","type":"journal-article","created":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T04:36:20Z","timestamp":1786941380000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Computational analysis of CD40L missense variants A123E, S222F, and G257R predicts altered CD40 binding and trimeric stability in X-linked hyper-IgM syndrome"],"prefix":"10.3389","volume":"17","author":[{"given":"Mar\u00eda Guadalupe","family":"Vel\u00e1squez-Ortiz","sequence":"first","affiliation":[{"name":"Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnolog\u00eda, Universidad Nacional Aut\u00f3noma de M\u00e9xico","place":["Cuernavaca, Morelos, Mexico"]},{"name":"Posgrado en Ciencias Biol\u00f3gicas, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Unidad de Posgrado, Ciudad Universitaria","place":["Coyoac\u00e1n, Mexico City, Mexico"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eduardo","family":"Jard\u00f3n-Valadez","sequence":"additional","affiliation":[{"name":"Departamento de Recursos de la Tierra, Universidad Aut\u00f3noma Metropolitana","place":["Estado de M\u00e9xico, Mexico"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ra\u00fal Fernando","family":"Reyes-Huerta","sequence":"additional","affiliation":[{"name":"Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnolog\u00eda, Universidad Nacional Aut\u00f3noma de M\u00e9xico","place":["Cuernavaca, Morelos, Mexico"]},{"name":"Doctorado en Ciencias Biom\u00e9dicas, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Unidad de Posgrado, Ciudad Universitaria","place":["Coyoac\u00e1n, Mexico City, Mexico"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jovani","family":"Catal\u00e1n-Dibene","sequence":"additional","affiliation":[{"name":"Division of Biomedical Sciences, School of Medicine, University of California","place":["Riverside, Riverside, CA, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laura","family":"Berr\u00f3n-Ruiz","sequence":"additional","affiliation":[{"name":"Laboratorio de Inmunodeficiencias, Instituto Nacional de Pediatr\u00eda","place":["Coyoac\u00e1n, Mexico City, Mexico"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gabriela","family":"L\u00f3pez-Herrera","sequence":"additional","affiliation":[{"name":"Laboratorio de Inmunodeficiencias, Instituto Nacional de Pediatr\u00eda","place":["Coyoac\u00e1n, Mexico City, Mexico"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David Eduardo","family":"Meza-S\u00e1nchez","sequence":"additional","affiliation":[{"name":"Red de Apoyo a la Investigaci\u00f3n, Universidad Nacional Aut\u00f3noma de M\u00e9xico-Instituto Nacional de Ciencias M\u00e9dicas y Nutrici\u00f3n Salvador Zubir\u00e1n","place":["Mexico City, Mexico"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jos\u00e9 Luis","family":"Maravillas-Montero","sequence":"additional","affiliation":[{"name":"Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnolog\u00eda, Universidad Nacional Aut\u00f3noma de M\u00e9xico","place":["Cuernavaca, Morelos, Mexico"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,8,17]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","DOI":"10.1016\/j.pharmthera.2020.107709","article-title":"Molecular basis and therapeutic implications of Cd40\/Cd40l immune checkpoint","volume":"219","author":"Tang","year":"2021","journal-title":"Pharmacol Ther"},{"key":"B2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1600-065X.2009.00782.x","article-title":"Molecular mechanism and function of Cd40\/Cd40l engagement in the immune system","volume":"229","author":"Elgueta","year":"2009","journal-title":"Immunol Rev"},{"key":"B3","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.94.5.1931","article-title":"Functional Cd40 ligand is expressed on human vascular endothelial cells, smooth muscle cells, and macrophages: Implications for Cd40-Cd40 ligand signaling in atherosclerosis","volume":"94","author":"Mach","year":"1997","journal-title":"Proc Natl Acad Sci U S A"},{"key":"B4","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M112.427583","article-title":"Cysteine-rich domain 1 of Cd40 mediates receptor self-assembly","volume":"288","author":"Smulski","year":"2013","journal-title":"J Biol Chem"},{"key":"B5","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M110.208215","article-title":"Crystallographic and mutational analysis of the Cd40-Cd154 complex and its implications for receptor activation","volume":"286","author":"An","year":"2011","journal-title":"J Biol Chem"},{"key":"B6","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2022.840767","article-title":"Variants disrupting Cd40l transmembrane domain and atypical X-linked hyper-Igm syndrome: A case report with leishmaniasis and review of the literature","volume":"13","author":"Palterer","year":"2022","journal-title":"Front Immunol"},{"key":"B7","doi-asserted-by":"publisher","DOI":"10.1007\/s10875-021-01182-5","article-title":"Cd40 ligand deficiency in Latin America: Clinical, immunological, and genetic characteristics","volume":"42","author":"Franca","year":"2022","journal-title":"J ClinImmunol"},{"key":"B8","doi-asserted-by":"publisher","first-page":"62","DOI":"10.1111\/j.1749-6632.2011.06289.x","article-title":"Advances in primary immunodeficiency diseases in Latin America: Epidemiology, research, and perspectives","volume":"1250","author":"Errante","year":"2012","journal-title":"Ann N Y Acad Sci"},{"key":"B9","doi-asserted-by":"publisher","DOI":"10.1007\/s10875-006-9052-0","article-title":"Primary immunodeficiency diseases in Latin America: The second report of the Lagid registry","volume":"27","author":"Leiva","year":"2007","journal-title":"J ClinImmunol"},{"key":"B10","article-title":"An\u00e1lisis fenot\u00edpico y molecular de pacientes mexicanos con s\u00edndrome de hiper-Igm","author":"Alem\u00e1n-L\u00f3pez","year":"2016"},{"key":"B11","doi-asserted-by":"publisher","DOI":"10.1016\/j.clim.2023.109692","article-title":"Advanced computational analysis of Cd40lg variants in atypical X-linked hyper-Igm syndrome","volume":"253","author":"Pazhanisamy","year":"2023","journal-title":"Clin Immunol"},{"key":"B12","doi-asserted-by":"publisher","DOI":"10.1038\/361541a0","article-title":"Cd40 ligand mutations in X-linked immunodeficiency with hyper-Igm","volume":"361","author":"DiSanto","year":"1993","journal-title":"Nature"},{"key":"B13","doi-asserted-by":"publisher","DOI":"10.1046\/j.1365-2249.2003.02184.x","article-title":"Three novel mutations reflect the variety of defects causing phenotypically diverse X-linked hyper-Igm syndrome","volume":"133","author":"Lopez-Granados","year":"2003","journal-title":"Clin Exp Immunol"},{"key":"B14","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-021-03819-2","article-title":"Highly accurate protein structure prediction with Alphafold","volume":"596","author":"Jumper","year":"2021","journal-title":"Nature"},{"key":"B15","doi-asserted-by":"publisher","DOI":"10.1016\/0263-7855(96)00018-5","article-title":"Vmd: Visual molecular dynamics","volume":"14","author":"Humphrey","year":"1996","journal-title":"J Mol Graph"},{"key":"B16","doi-asserted-by":"publisher","first-page":"583","DOI":"10.1038\/s41586-021-03819-2","article-title":"Highly Accurate Protein Structure Prediction with Alphafold","volume":"596","author":"Jumper","year":"2021","journal-title":"Nature"},{"key":"B17","doi-asserted-by":"publisher","first-page":"D609","DOI":"10.1093\/nar\/gkae1010","article-title":"UniProt: The Universal Protein Knowledgebase in 2025","volume":"53","year":"2025","journal-title":"Nucleic Acids Research"},{"key":"B18","doi-asserted-by":"publisher","first-page":"583","DOI":"10.1038\/s41586-021-03819-2","article-title":"Highly Accurate Protein Structure Prediction with Alphafold","volume":"596","author":"Jumper","year":"2021","journal-title":"Nature"},{"key":"B19","doi-asserted-by":"publisher","first-page":"D609","DOI":"10.1093\/nar\/gkae1010","article-title":"UniProt: The Universal Protein Knowledgebase in 2025","volume":"53","year":"2025","journal-title":"Nucleic Acids Research"},{"key":"B20","doi-asserted-by":"publisher","first-page":"D980","DOI":"10.1093\/nar\/gkt1113","article-title":"ClinVar: Public Archive of Relationships among Sequence Variation and Human Phenotype","volume":"42","author":"Landrum","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"B21","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.23354","article-title":"Charmm36 all-atom additive protein force field: Validation based on comparison to Nmr data","volume":"34","author":"Huang","year":"2013","journal-title":"J Comput Chem"},{"key":"B22","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.4067","article-title":"Charmm36m: An improved force field for folded and intrinsically disordered proteins","volume":"14","author":"Huang","year":"2017","journal-title":"Nat Methods"},{"key":"B23","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.20289","article-title":"Scalable molecular dynamics with Namd","volume":"26","author":"Phillips","year":"2005","journal-title":"J Comput Chem"},{"key":"B24","doi-asserted-by":"publisher","DOI":"10.1063\/1.470117","article-title":"A smooth particle mesh Ewald method","volume":"103","author":"Essmann","year":"1995","journal-title":"J Chem Phys"},{"key":"B25","doi-asserted-by":"publisher","DOI":"10.1016\/0021-9991(77)90098-5","article-title":"Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of N-alkanes","volume":"23","author":"Ryckaert","year":"1977","journal-title":"J Comput Phys"},{"key":"B26","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.1c00645","article-title":"Gmx_Mmpbsa: A new tool to perform end-state free energy calculations with Gromacs","volume":"17","author":"Valdes-Tresanco","year":"2021","journal-title":"J Chem Theory Comput"},{"key":"B27","doi-asserted-by":"publisher","DOI":"10.1021\/ct0500904","article-title":"Evaluating the accuracy of the quasiharmonic approximation","volume":"1","author":"Chang","year":"2005","journal-title":"J Chem Theory Comput"},{"key":"B28","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.181342398","article-title":"Electrostatics of nanosystems: Application to microtubules and the ribosome","volume":"98","author":"Baker","year":"2001","journal-title":"Proc Natl Acad Sci USA"},{"key":"B29","doi-asserted-by":"publisher","DOI":"10.1529\/biophysj.104.040964","article-title":"How optimal are the binding energetics of Barnase and Barstar","volume":"87","author":"Wang","year":"2004","journal-title":"Biophys J"},{"key":"B30","doi-asserted-by":"publisher","DOI":"10.1517\/17460441.2015.1032936","article-title":"The Mm\/Pbsa and Mm\/Gbsa methods to estimate ligand-binding affinities","volume":"10","author":"Genheden","year":"2015","journal-title":"Expert Opin Drug Discov"},{"key":"B31","doi-asserted-by":"publisher","DOI":"10.1038\/nchembio746","article-title":"C3-symmetric peptide scaffolds are functional mimetics of trimeric Cd40l","volume":"1","author":"Fournel","year":"2005","journal-title":"Nat Chem Biol"},{"key":"B32","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0007334","article-title":"Nanoparticle-delivered multimeric soluble Cd40l DNA combined with toll-like receptor agonists as a treatment for melanoma","volume":"4","author":"Stone","year":"2009","journal-title":"PloS One"},{"key":"B33","doi-asserted-by":"publisher","first-page":"313","DOI":"10.1016\/j.immuni.2018.01.008","article-title":"B cell receptor and Cd40 signaling are rewired for synergistic induction of the C-Myc transcription factor in germinal center B cells","volume":"48","author":"Luo","year":"2018","journal-title":"Immunity"},{"key":"B34","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.immunol.26.021607.090248","article-title":"Mechanism and regulation of class switch recombination","volume":"26","author":"Stavnezer","year":"2008","journal-title":"Annu Rev Immunol"},{"key":"B35","doi-asserted-by":"publisher","DOI":"10.1016\/j.immuni.2013.04.009","article-title":"Transcriptional regulation of germinal center B and plasma cell fates by dynamical control of Irf4","volume":"38","author":"Ochiai","year":"2013","journal-title":"Immunity"},{"key":"B36","doi-asserted-by":"publisher","DOI":"10.1016\/j.jaci.2006.01.043","article-title":"Defects of class-switch recombination","volume":"117","author":"Notarangelo","year":"2006","journal-title":"J Allergy Clin Immunol"},{"key":"B37","doi-asserted-by":"publisher","DOI":"10.1093\/protein\/gzm004","article-title":"The structural basis of hyper Igm deficiency - Cd40l mutations","volume":"20","author":"Thusberg","year":"2007","journal-title":"Protein Eng Des Sel"},{"key":"B38","doi-asserted-by":"publisher","DOI":"10.1016\/j.ccell.2014.11.001","article-title":"Conformation of the human immunoglobulin G2 hinge imparts superagonistic properties to immunostimulatory anticancer antibodies","volume":"27","author":"White","year":"2015","journal-title":"Cancer Cell"},{"key":"B39","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-022-05673-2","article-title":"Reducing affinity as a strategy to boost immunomodulatory antibody agonism","volume":"614","author":"Yu","year":"2023","journal-title":"Nature"},{"key":"B40","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.96.4.1421","article-title":"Specificities of Cd40 signaling: Involvement of Traf2 in Cd40-induced Nf-Kappab activation and intercellular adhesion molecule-1 up-regulation","volume":"96","author":"Lee","year":"1999","journal-title":"Proc Natl Acad Sci USA"},{"key":"B41","doi-asserted-by":"publisher","first-page":"4","DOI":"10.1177\/1753425917739681","article-title":"Prospects for modulating the Cd40\/Cd40l pathway in the therapy of the hyper-Igm syndrome","volume":"24","author":"Meng","year":"2018","journal-title":"Innate Immun"},{"key":"B42","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.adl5815","article-title":"Mechanotransduction governs Cd40 function and underlies X-linked hyper-Igm syndrome","volume":"10","author":"Choi","year":"2024","journal-title":"Sci Adv"},{"key":"B43","doi-asserted-by":"publisher","DOI":"10.1007\/s10875-013-9980-4","article-title":"First report of the hyper-Igm syndrome registry of the Latin American Society for Immunodeficiencies: Novel mutations, unique infections, and outcomes","volume":"34","author":"Cabral-Marques","year":"2014","journal-title":"J ClinImmunol"},{"key":"B44","doi-asserted-by":"publisher","first-page":"28","DOI":"10.1007\/s10875-024-01822-6","article-title":"The latin american society for immunodeficiencies registry","volume":"45","author":"Seminario","year":"2024","journal-title":"J ClinImmunol"}],"container-title":["Frontiers in Immunology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fimmu.2026.1861005\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T04:36:25Z","timestamp":1786941385000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fimmu.2026.1861005\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,8,17]]},"references-count":44,"alternative-id":["10.3389\/fimmu.2026.1861005"],"URL":"https:\/\/doi.org\/10.3389\/fimmu.2026.1861005","relation":{},"ISSN":["1664-3224"],"issn-type":[{"value":"1664-3224","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,8,17]]},"article-number":"1861005"}}