Integral membrane proteins are ubiquitous in biological cellular and subcellular membranes. Despite their significance to cell function, isolation of membrane proteins from their hydrophobic lipid environment and further characterization remains a challenge. To obtain insights into membrane proteins, computational approaches such as docking or self-assembly simulations have been used; however, the promise of these approaches has been limited due to the computational cost. Here we present a new approach called Protein AssociatioN Energy Landscape (PANEL) that provides an extensive and converged data set for all possible conformations of membrane protein associations using a combination of stochastic sampling and equilibration simulations. The PANEL method samples the rotational space around both interacting proteins to obtain the comprehensive interaction energy landscape. We demonstrate the versatility of the PANEL method using two distinct applications: (a) dimerization of claudin-5 tight junction proteins in phospholipid bilayer membrane and (b) dimer and trimer formation of the Outer membrane protein F (OmpF) in the lipopolysaccharide-rich bacterial outer membrane. Both applications required only a fraction of simulation cost compared to self-assembly simulations. The method is robust as it can capture changes in protein–protein conformations caused by point mutations. Moreover, the method is versatile and independent of the molecular resolution (atomistic or coarse grain) or the choice of force field employed to compute the pair-interaction energies. The PANEL method is implemented in easy-to-use scripts that are available for download for general use by the scientific community to characterize any pair of interacting integral membrane proteins.

Post-translational lipid modification of integral membrane proteins is recognized as a key mechanism to modulate protein–protein and membrane–protein associations. Despite numerous reports of lipid-modified proteins, molecular-level understanding of the influence of lipid-modification of key membrane proteins remains elusive. This study focuses on the lipid modification of one such proteinclaudin-5, a critical component of the blood–brain barrier tight junctions. Claudin-5 proteins are responsible for regulating the size and charge-selective permeability at the blood–brain interface. Palmitoylation of the claudin family of proteins is implicated in influencing the tight junction permeability in prior experimental studies. Here, we investigate the impact of palmitoylation on claudin-5 self-assembly using multiscale molecular simulations. To elucidate protein–membrane interactions, we used three model membrane compositions (endoplasmic reticulum, cholesterol-enriched endoplasmic reticulum, and plasma membrane) that mimic the complexity of cell organelles encountered by a typical membrane protein in its secretion pathway. The results show that palmitoylation enhances protein’s affinity for cholesterol-rich domains in a membrane, and it can elicit a site-specific response based on the location of the palmitoyl chain on the protein. Also, in claudin-5 self-assembly, palmitoylation restricts specific protein–protein conformations. Overall, this study demonstrates the significance of post-translational lipid modification of proteins in cellular and subcellular membranes, and the impact palmitoylation can have on critical cellular functions of the protein.

The selectivity of the blood–brain barrier (BBB) is primarily maintained by tight junctions (TJs), which act as gatekeepers of the paracellular space by blocking blood-borne toxins, drugs, and pathogens from entering the brain. The BBB presents a significant challenge in designing neurotherapeutics, so a comprehensive understanding of the TJ architecture can aid in the design of novel therapeutics. Unraveling the intricacies of TJs with conventional experimental techniques alone is challenging, but recently developed computational tools can provide a valuable molecular-level understanding of TJ architecture. We employed the computational methods toolkit to investigate claudin-5, a highly expressed TJ protein at the BBB interface. Our approach started with the prediction of claudin-5 structure, evaluation of stable dimer conformations and nanoscale assemblies, followed by the impact of lipid environments, and posttranslational modifications on these claudin-5 assemblies. These led to the study of TJ pores and barriers and finally understanding of ion and small molecule transport through the TJs. Some of these in silico, molecular-level findings, will need to be corroborated by future experiments. The resulting understanding can be advantageous towards the eventual goal of drug delivery across the BBB. This review provides key insights gleaned from a series of state-of-the-art nanoscale simulations (or computational nanoscopy studies) performed on the TJ architecture.

Members of the claudin family impart unique paracellular selectivity to tight junctions.However, the structure-function relationship between claudin's strand architecture and the paracellular charge-and size-selectivity is not well-understood. This work examines the molecular assembly of claudin-5, a barrier-forming protein, and claudin-15, a channel-forming protein, to determine their structural and functional properties.We adopt a bottom-up approach starting from claudin monomers to build the molecular architecture of the tight junction strands. First, we investigated the cis assembly of claudin-5 and -15 dimers using the Protein Association Energy Landscape method.Out of the millions of dimer conformations, we narrowed down key cis claudin-5 and -15 dimer conformations that were thermodynamically and kinetically stable. Second, we performed the trans assembly of dimers to identify the tetrameric building blocks that serve as the repeat units for strand formation. Finally, the strand assembly of the tetrameric repeat units showed fundamentally distinct strand architectures. In claudin-5, the cis and trans interactions seal the paracellular space, while in claudin-15, the gaps in the paracellular space lead to pore formation. This detailed study suggests that each member of the claudin family is unique and requires systematic molecular-level analysis for determining the strand architecture.

Systematic approach to predicting selectivity of paracellular pores for biomimetic applications.