Viperin: a multifunctional, interferon-inducible protein that regulates virus replication.

Viperin is an interferon-inducible protein that inhibits the replication of a variety of viruses by apparently diverse mechanisms. In some circumstances, it also plays a role in intracellular signaling pathways. Its expression in mitochondria, revealed by infection with human cytomegalovirus, also affects cellular metabolic pathways. We review here the current status of our understanding of this unusual molecule.

Human cytomegalovirus directly induces the antiviral protein viperin to enhance infectivity.

Viperin is an interferon-inducible protein that is directly induced in cells by human cytomegalovirus (HCMV) infection. Why HCMV would induce viperin, which has antiviral activity, is unknown. We show that HCMV-induced viperin disrupts cellular metabolism to enhance the infectious process. Viperin interaction with the viral protein vMIA resulted in viperin relocalization from the endoplasmic reticulum to the mitochondria. There, viperin interacted with the mitochondrial trifunctional protein that mediates ß-oxidation of fatty acids to generate adenosine triphosphate (ATP). This interaction with viperin, but not with a mutant lacking the viperin iron-sulfur cluster-binding motif, reduced cellular ATP generation, which resulted in actin cytoskeleton disruption and enhancement of infection. This function of viperin, which was previously attributed to vMIA, suggests that HCMV has coopted viperin to facilitate the infectious process.

Peptide binding to MHC class I and II proteins: new avenues from new methods.

Major histocompatibility complex (MHC) class I and II proteins have been in the focus of interest for immunologists, biochemists, cell biologists, and structural biologists for decades. With dozens of entries in the Protein Data Bank, their crystal structures are now sufficiently well understood, while their dynamic properties such as peptide binding and intracellular trafficking and their immunological (as well as non-immunological) functions are still being intensely investigated. In recent years, new methods and technologies have emerged to detect and characterize the conformational changes and intermediate states that accompany peptide binding and exchange by MHC proteins. These techniques have delivered more detailed information and allowed us to compare the molecular mechanisms of peptide selection between MHC class I and II proteins, suggesting both similarities and differences. Here, we review these recent achievements and suggest avenues for further work.

Tapasin edits peptides on MHC class I molecules by accelerating peptide exchange.

The endoplasmic reticulum (ER) protein tapasin is essential for the loading of high-affinity peptides onto MHC class I molecules. It mediates peptide editing, i.e. the binding of peptides of successively higher affinity until class I molecules pass ER quality control and exit to the cell surface. The molecular mechanism of action of tapasin is unknown. We describe here the reconstitution of tapasin-mediated peptide editing on class I molecules in the lumen of microsomal membranes. We find that in a competitive situation between high- and low-affinity peptides, tapasin mediates the binding of the high-affinity peptide to class I by accelerating the dissociation of the peptide from an unstable intermediate of the binding reaction.

Flexibility of the MHC class II peptide binding cleft in the bound, partially filled, and empty states: a molecular dynamics simulation study.

Major histocompatibility (MHC) Class II cell surface proteins present antigenic peptides to the immune system. Class II structures in complex with peptides but not in the absence of peptide are known. Comparative molecular dynamics (MD) simulations of a Class II protein (HLA-DR3) with and without CLIP (invariant chain-associated protein) peptide were performed starting from the CLIP-bound crystal structure. Depending on the protonation of acidic residues in the P6 peptide-binding pocket the simulations stayed overall close to the start structure. The simulations without CLIP showed larger conformational fluctuations especially of alpha-helices flanking the binding cleft. Largest fluctuations without CLIP were observed in a helical segment near the peptide C-terminus binding region matching a segment recognized by antibodies specific for empty Class II proteins. Simulations on a Val86Tyr mutation that fills the peptide N-terminus binding P1 pocket or of a complex with a CLIP fragment (dipeptide) bound to P1 showed an unexpected long range effect. In both simulations the mobility not only of P1 but also of the entire binding cleft was reduced compared to simulations without CLIP. It correlates with the experimental finding that the CLIP fragment binding to P1 is sufficient to prevent antibody recognition specific for the empty form at a site distant from P1. The results suggest a mechanism how a local binding event of small peptides or of an exchange factor near P1 may promote peptide binding and exchange through a long range stabilization of the whole binding cleft in a receptive (near bound) conformation.