HLA3DB: comprehensive annotation of peptide/HLA complexes enables blind structure prediction of T cell epitopes.

The class I proteins of the major histocompatibility complex (MHC-I) display epitopic peptides derived from endogenous proteins on the cell surface for immune surveillance. Accurate modeling of peptides bound to the human MHC, HLA, has been mired by conformational diversity of the central peptide residues, which are critical for recognition by T cell receptors. Here, analysis of X-ray crystal structures within our curated database (HLA3DB) shows that pHLA complexes encompassing multiple HLA allotypes present a discrete set of peptide backbone conformations. Leveraging these backbones, we employ a regression model trained on terms of a physically relevant energy function to develop a comparative modeling approach for nonamer pHLA structures named RepPred. Our method outperforms the top pHLA modeling approach by up to 19% in structural accuracy, and consistently predicts blind targets not included in our training set. Insights from our work may be applied towards predicting antigen immunogenicity, and receptor cross-reactivity.

Crowding-induced membrane remodeling: Interplay of membrane tension, polymer density, architecture.

The plasma membrane hosts a wide range of biomolecules, mainly proteins and carbohydrates, that mediate cellular interactions with its environment. The crowding of such biomolecules regulates cellular morphologies and cellular trafficking. Recent discoveries have shown that the structure and density of cell surface polymers and hence the signaling machinery change with the state of the cell, especially in cancer progression. The alterations in membrane-attached glycocalyx and glycosylation of proteins and lipids are common features of cancer cells. The overexpression of glycocalyx polymers, such as mucin and hyaluronan, strongly correlates with cancer metastasis. Here, we present a mesoscale biophysics-based model that accounts for the shape regulation of membranes by crowding of membrane-attached biopolymer-glycocalyx and actin networks. Our computational model is based on the dynamically triangulated Monte Carlo model for membranes and coarse-grained representations of polymer chains. The model allows us to investigate the crowding-induced shape transformations in cell membranes in a tension- and graft polymer density-dependent manner. Our results show that the number of membrane protrusions and their shape depend on membrane tension, with higher membrane tension inducing more tubular protrusions than the vesicular shapes formed at low tension at high surface coverage of polymers. The shape transformations occur above the threshold density predicted by the polymer brush theory, but this threshold also depends on the membrane tension. Increasing the size of the polymer, either by changing the length or by adding side chains, is shown to increase the crowding-induced curvature. The effect of crowding is more prominent for flexible polymers than for semiflexible rigid polymers. We also present an extension of the model that incorporates properties of the actin-like filament networks and demonstrate how tubular structures can be generated by biopolymer crowding on the cytosolic side of cell membranes.

Dimerization and structure formation of colloids via capillarity at curved fluid interfaces.

Capillary interactions are ubiquitous between colloids trapped at fluid interfaces. Generally, colloids in fluid interfaces have pinned, undulated contact lines that distort the interface around them. To minimize the area, and therefore the energy of these distortions, colloids interact and assemble in a manner that depends on the shape of the host interface. On curved interfaces, capillary interactions direct isolated colloid motion along deviatoric curvature gradients. This directed motion relies on the leading order, long-ranged quadrupolar distortions made by the colloids' undulated pinned contact lines. Here we study pair interactions and dimer formation of colloids on non-uniformly curved fluid interfaces. Pair interaction energies are inferred to be order of 104kBT, and interacting forces are of order 10-1 pN for 10 micron particles adsorbed on interfaces formed around a 250 micron micropost. We compare experiments to analysis for the pair interaction energy, and identify criteria for dimers to form. We also study the formation of trapped structures by multiple particles to discern the influence of the underlying interface shape and the contact line undulations. By comparison to Monte Carlo simulations with potentials of interactions based on analysis, we find that higher order terms in the distortion fields generated by the particles play a major role in the structure formation on the curved interface. These interactions are determined by the particle's contact line and the host interface shape, and can be used to assemble particles independent of their material properties.