Despite the progress in structural biology over the last decades, it is still challenging to determine the structure of the transmembrane domains (TMDs) of integral membrane proteins. The work of this thesis has focused on two groups of integral membrane proteins: Toll-like receptors (TLRs) and polysaccharide co-polymerases (PCPs). TLRs are single transmembrane-spanning receptors responsible for recognizing a vast number of exogenous pathogens derived from bacteria, viruses and fungi. Upon ligand binding to the extracellular ectodomains (ECDs), TLRs dimerize and conformational changes are transmitted to the TMDs and intracellular domains to initiation of inflammatory signaling pathways. Overstimulation or dysregulation of the TLR-associated pathways can lead to a number of diseases including sepsis, cancer and rheumatoid arthritis. Although there is extensive structural information available for the dimeric extracellular and intracellular soluble domains, little is known about the TMD assemblies. Clarifying the structure of the TMDs, as it is described in this thesis, should help to further the understanding of the molecular mechanisms of signaling, and hence provide new starting points for therapeutic immunomodulation. Wzz is a PCP1 protein found in the bacterial inner membrane and is involved in the regulation of the O-antigen (Oag) chain length of lipopolysaccharides (LPSs), essential for the virulence of many gram-negative pathogens. All Wzz proteins are comprised of a large periplasmic domain, two transmembrane helices and a short cytosolic domain. Although several experimental oligomeric structures are available for the periplasmic domains of Wzz, the in vivo oligomerization state and transmembrane architecture of Wzz is unclear. Work towards a better understanding is described here and it may help to clarify the mechanism of Oag regulation, and in the future may contribute to new antimicrobial strategies. A multiscale simulation approach has been carried out to investigate the self-assembly of modelled TLR and Wzz TMDs within lipid membrane environments. Upon assembly, interfacial TMD arrangements were assessed to provide structural insights into key residues and motifs that may drive association. In addition, cryo-electron microscopy data for a novel dodecameric structure for Wzz were incorporated into this approach. The dynamics of various oligomers of the full-length Wzz within a lipid membrane environment were investigated via simulations. This work provided new insights into the role of TMDs in the activation and function of TLRs and led to the development of a new model for the mechanism of function of Wzz, as well as providing predictions on which oligomerization state is most likely to represent the in vivo state.