CD1 molecules present lipid antigens for recognition by T-cell receptors (TCRs). Although a reasonably detailed picture of the CD1-lipid-TCR interaction exists, the initial steps regarding lipid loading onto and exchange between CD1 proteins remain elusive. The hydrophobic nature of lipids and the fact that CD1 molecules are unable to extract lipids from membranes raise the need for the assistance of helper proteins in lipid trafficking. However, the experimental study of this traffic in the endosomal compartments at which it occurs is so challenging that computational studies can help provide mechanistic insight into the associated processes. Here we present a multifaceted computational approach to obtain dynamic structural data on the human CD1d isotype. Conformational dynamics analysis shows an intrinsic flexibility associated with the protein architecture. Electrostatic properties together with molecular dynamics results for CD1d complexes with several lipids and helper proteins unravel the high dynamic plasticity of the antigen-binding site that is crucially favoured by acidic pH and the presence of helper proteins. Adaptive immune responses critically depend on interactions between T-cell receptors (TCRs) and antigen-presenting molecules on the surface of antigen-presenting cells. In mammals, peptide-presenting major histocompatibility complex (MHC) classes I and II and lipid-presenting cluster of differentiation 1 (CD1) are the main antigen-presenting molecules. The generation and loading of peptides onto MHC-I and MHC-II proteins and the molecular mechanisms associated with MHC-mediated responses are well understood 1-4. However, the knowledge of lipid antigen presentation is far less complete. Since the essential review by Barral and Brenner in 5 , considerable progress in the understanding of the processing and presentation of lipid antigens has been achieved 6-8. In particular, the mechanisms of T-cell activation through CD1-lipid-TCR interactions have emerged and even though important gaps remain, a detailed picture of lipid antigen display to TCRs is available 1,6-8. However, the initial steps regarding the loading onto and exchange between CD1 proteins remain elusive. CD1 molecules are MHC-I-like glycoproteins organised early according to sequence homology into two groups: group 1 is composed of CD1a, CD1b, CD1c, and CD1e and group 2 is composed of the single member CD1d 9. Of these five CD1 isotypes, ad are transmembrane proteins that present lipid antigens to TCRs at the cell surface, while CD1e remains intracellular, is the only CD1 member that exists in soluble form and can apparently function as a lipid transfer protein (LTP) 10. Mammals express CD1 molecules, humans express the five isoforms, and only CD1d is expressed in humans and mice. The common antigen-presenting function of MHC-I and CD1 proteins underlies their similar structure and the existence of antigen-binding clefts (Fig. 1a), cellular pathways and overall modes of TCR interaction. However, the distinct physicochemical nature of p...