The rigidity of a structural bridge on HLA-I binding groove explains its differential outcome in cancer immune response.

The tremendous success of immune checkpoint blockade (ICB) therapy has raised the great demand for the development of predictive biomarkers. A recent cancer genomic study suggested that human leukocyte antigen (HLA)-B*44:02 and HLA-B*15:01 alleles may act as potential biomarkers for ICB therapies, however, the underlying molecular mechanisms remain largely elusive. Here, we investigated the molecular origins of differential responses to ICB therapies for four representative HLA alleles: HLA-B*44:02, HLA-B*15:01, HLA-B*07:02, and HLA-B*53:01, using extensive all-atom molecular dynamics simulations. We first demonstrated that the relatively more rigid peptide-binding groove of HLA-B*15:01, than those in the other three HLA alleles, may result in challenges in its recognition with T-cell receptors. Specifically, the "bridge" structure in HLA-B*15:01 is stabilized through both intramolecular electrostatic interactions between the HLA residues and intermolecular interactions between the HLA and the antigenic peptide. These observations were further confirmed by in silico mutagenesis studies, as well as simulations of several other HLA-B*15:01-peptide complexes. By contrast, the "bridge" structure is either completely absent in HLA-B*44:02 or easily perturbed in HLA-B*07:02 and HLA-B*53:01. Our findings provide detailed structural and mechanistic insights into how HLA genotype influences ICB responses and may have important implications for developing immune markers.

Structural basis of BAM-mediated outer membrane ß-barrel protein assembly.

The outer membrane structure is common in Gram-negative bacteria, mitochondria and chloroplasts, and contains outer membrane ß-barrel proteins (OMPs) that are essential interchange portals of materials1-3. All known OMPs share the antiparallel ß-strand topology4, implicating a common evolutionary origin and conserved folding mechanism. Models have been proposed for bacterial ß-barrel assembly machinery (BAM) to initiate OMP folding5,6; however, mechanisms by which BAM proceeds to complete OMP assembly remain unclear. Here we report intermediate structures of BAM assembling an OMP substrate, EspP, demonstrating sequential conformational dynamics of BAM during the late stages of OMP assembly, which is further supported by molecular dynamics simulations. Mutagenic in vitro and in vivo assembly assays reveal functional residues of BamA and EspP for barrel hybridization, closure and release. Our work provides novel insights into the common mechanism of OMP assembly.

Molecular Details of the PH Domain of ACAP1BAR-PH Protein Binding to PIP-Containing Membrane.

ACAP1 proteins were previously reported to specifically bind PIP2-containing cell membranes and form well-structured protein lattices in order to conduct membrane tubulation. We carried out molecular dynamics simulations to characterize orientation of the PH domains with respect to the BAR domains inside the protein dimer. Followed by molecular dynamics simulations, we present a comprehensive orientation analysis of PH domain under different states including unbound and bound with lipids. We have examined two binding pockets on the PH domain and present PMF profiles of the two pockets to account for their preference to PIP2 lipids. Combining orientation analysis and studies of binding pockets, our simulations results reveal valuable molecular basis for protein-lipid interactions of ACAP1 proteins during membrane remodeling process.