Anchor Side Chains of Short Peptide Fragments Trigger Ligand-Exchange of Class II MHC Molecules

Class II MHC molecules display peptides on the cell surface for the surveillance by CD4+ T cells. To ensure that these ligands accurately reflect the content of the intracellular MHC loading compartment, a complex processing pathway has evolved that delivers only stable peptide/MHC complexes to the surface. As additional safeguard, MHC molecules quickly acquire a ‘non-receptive’ state once they have lost their ligand. Here we show now that amino acid side chains of short peptides can bypass these safety mechanisms by triggering the reversible ligand-exchange. The catalytic activity of dipeptides such as Tyr-Arg was stereo-specific and could be enhanced by modifications addressing the conserved H-bond network near the P1 pocket of the MHC molecule. It affected both antigen-loading and ligand-release and strictly correlated with reported anchor preferences of P1, the specific target site for the catalytic side chain of the dipeptide. The effect was evident also in CD4+ T cell assays, where the allele-selective influence of the dipeptides translated into increased sensitivities of the antigen-specific immune response. Molecular dynamic calculations support the hypothesis that occupation of P1 prevents the ‘closure’ of the empty peptide binding site into the non-receptive state. During antigen-processing and -presentation P1 may therefore function as important “sensor” for peptide-load. While it regulates maturation and trafficking of the complex, on the cell surface, short protein fragments present in blood or lymph could utilize this mechanism to alter the ligand composition on antigen presenting cells in a catalytic way

Model for the Peptide-Free Conformation of Class II MHC Proteins

Background: Major histocompatibility complex proteins are believed to undergo significant conformational changes concomitant with peptide binding, but structural characterization of these changes has remained elusive. Methodology/Principal Findings: Here we use molecular dynamics simulations and experimental probes of protein conformation to investigate the peptide-free state of class II MHC proteins. Upon computational removal of the bound peptide from HLA-DR1-peptide complex, the a50-59 region folded into the P1-P4 region of the peptide binding site, adopting the same conformation as a bound peptide. Strikingly, the structure of the hydrophobic P1 pocket is maintained by engagement of the side chain of Phe a54. In addition, conserved hydrogen bonds observed in crystal structures between the peptide backbone and numerous MHC side chains are maintained between the a51-55 region and the rest of the molecule. The model for the peptide-free conformation was evaluated using conformationally-sensitive antibody and superantigen probes predicted to show no change, moderate change, or dramatic changes in their interaction with peptide-free DR1 and peptide-loaded DR1. The binding observed for these probes is in agreement with the movements predicted by the model. Conclusion/Significance: This work presents a molecular model for peptide-free class II MHC proteins that can help to interpret the conformational changes known to occur within the protein during peptide binding and release, and ca

Strengthening the morphological study of informal settlements

Methods of articulating the morphological structure of slums can have considerable potential in better planning for site-specific design or policy responses for these areas in the contemporary city. Although urban morphology traditionally studies landscapes as stratified residues with distinct divisions between lot and boundary, built and unbuilt, the authors find these definitions insufficient to address the complexity of slum morphology. Through this article, the authors’ identify that morphological analysis of informal settlements needs to be sensitive to the dynamics and the absence (or blurring) of physical boundaries. By analyzing the spatial impact of social, economic, and political factors, situational and site factors, building typologies, and configurations of circulation space, an attempt to articulate the morphological structure of slums is made. Aiming to overcome the current polarization in the literature between the formal and informal city, this article adds to the ongoing research on the study of challenges within contemporary cities, by providing new methodologies for studying the morphology of slum urbanization and shaping planning practice

Evolution and clinical impact of co-occurring genetic alterations in advanced-stage EGFR-mutant lung cancers

A widespread approach to modern cancer therapy is to identify a single oncogenic driver gene and target its mutant-protein product (for example, EGFR-inhibitor treatment in EGFR-mutant lung cancers). However, genetically driven resistance to targeted therapy limits patient survival. Through genomic analysis of 1,122 EGFR-mutant lung cancer cell-free DNA samples and whole-exome analysis of seven longitudinally collected tumor samples from a patient with EGFR-mutant lung cancer, we identified critical co-occurring oncogenic events present in most advanced-stage EGFR-mutant lung cancers. We defined new pathways limiting EGFR-inhibitor response, including WNT/β-catenin alterations and cell-cycle-gene (CDK4 and CDK6) mutations. Tumor genomic complexity increases with EGFR-inhibitor treatment, and co-occurring alterations in CTNNB1 and PIK3CA exhibit nonredundant functions that cooperatively promote tumor metastasis or limit EGFR-inhibitor response. This study calls for revisiting the prevailing single-gene driver-oncogene view and links clinical outcomes to co-occurring genetic alterations in patients with advanced-stage EGFR-mutant lung cancer

In-situ density and temperature measurements of vibrationally-excited hydrogen molecules in ion source plasmas

The role of highly vibrationally-excited hydrogen molecules has been postulated to be of great importance in H/sup /minus// ion sources. However the difficulty of making in-situ measurements has led to a paucity of direct determinations of these species within the plasma of these sources. Recently, vacuum-ultraviolet (VUV) laser absorption spectroscopy has been used to measure the H/sub 2/ rovibrational populations up to v/prime//prime/ = 5 and J/prime//prime/ = 8 in a medium-power hydrogen plasma. This work extends those measurements to v/prime//prime/ = 8 and to J/prime//prime/ = 13. The populations of the vibrational levels still appear to be almost Boltzmann. The theoretically predicted plateau is not observed up to the detection limit. The dependence of several vibrational levels on discharge current and filling pressure is shown. 15 refs., 4 figs

Measurement Of H And H 2 Populations In-Situ In A Low-Temperature Plasma By Vacuum-Ultraviolet Laser-Absorption Spectroscopy

A new technique, vacuum-ultraviolet laser-absorption spectroscopy, has been developed to quantitatively determine the absolute density of H and H/sub 2/ within a plasma. The technique is particularly well suited to measurement in a plasma, where high charged particle and photon background complicate other methods of detection. The high selectivity and sensitivity of the technique allows for the measurement of the rotational-vibrational state distribution of H/sub 2/ as well as the translational temperature of the atoms and molecules. The technique has been used to study both pulsed and continuous H/sup /minus// ion-source plasma discharges. H/sub 2/ state distributions in a multicusp ''volume'' H/sup /minus// ion- source plasma show a high degree of internal excitation, with levels up to v = 5 and J = 8 being observed. The method is applicable for a very wide range of plasma conditions. Emission measurements from excited states of H are also reported. 17 refs., 9 figs