Cuboid and grid representations of the T–cell receptor geometries.

<p>(A) Localisation of the considered Vα and Vβ variable domains within the ternary TCR:pMHC complex. A TCR consists of two chains, the α and the β chain (blue and red). Each chain is partitioned into two domains, the constant domain (Cα and Cβ shown transparently) and a variable domain (Vα and Vβ, here surrounded by cuboids). The Vα and Vβ domains form the binding interface to the major histocompatibility complex (MHC) molecule (green) presenting an antigenic peptide (magenta) to the TCR. This work focuses on the variable domains. (B) Superimposition of the TCR variable domains. (i) The TCR structures were superimposed on the Vα domains leading to displaced Vβ domains. (ii) Cuboids were placed around the superimposed Vα and Vβ domains. This unified description of the different domains allows a quantitative analysis of the displacement. (C) Preparation of the cuboid placement templates. Vα (blue) and Vβ (red) domains of the structure 2bnu are used as reference structure. Both chains are surrounded with cuboids of the size of their spatial extent. Residues considered for superimposition are determined in an iterative process (unused residues are depicted transparently). These residues are used to compute the angular displacement of the Vβ domain relative to the Vα domain. (D) Center of Rotation (CoR). (i) Different geometries of (only three for clearness) β-cuboid geometries (red), superimposed on the α-cuboids (blue). (ii) Grids were fit into the β-cuboids. (iii) For each grid point <i>i</i>, the sum of pairwise distances and the variance was computed according to Formula 2. (iv) The residues at the center of rotation (CoR, green sphere) were investigated. For most of the structures, a conserved pair hydrogen bond interaction between the α and the β chain is located directly at the CoR. These hydrogen bonds are established by conserved Q residues.</p

Exceptional structural examples of the center of rotation.

<p>Region around the Center of Rotation (CoR), the Vα domain is shown in blue and the Vβ domain in red. Hydrogen atoms were added for the end-groups of the interacting amino acids. The average center of rotation is drawn as an orange sphere and the interacting residues are shown in licorice representation. CoR stabilizing interactions are drawn as a green line. For these six structures the highly conserved Q-Q interaction between the α and the β chains is replaced by the following residues (shown in licorice style): (A, D-F) αK (PDB-IDs: 1bd2, 3qiu, 3qiw, 3qjh), (B) βR (PDB-ID: 2esv), (C) αW (PDB-ID: 3gsn).</p

All TCR structures used for the analysis.

<p>^a) Species: h = <i>homo sapiens</i>, m = <i>mus musculus</i>.</p><p>^b) Bound state: u = unbound, 1 = MHCI, 2 = MHCII, s = superantigen. More detailed information is available in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004244#pcbi.1004244.s002" target="_blank">S1 Table</a>.</p><p>^c) Structure 2xn9 and 2icw are not considered as MHC II bound TCRs, since the TCRs only contact the super-antigens.</p><p>^d) WT with solubility mutations acc. to ref. [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004244#pcbi.1004244.ref063" target="_blank">63</a>]. More detailed information is available in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004244#pcbi.1004244.s003" target="_blank">S2 Table</a>.</p><p>All TCR structures used for the analysis.</p

Pairwise Euler Angle Distances [°] of the bound and free 2C TCR variants.

<p>The structures were superimposed to the α variable domains. All Euler angle distances are given in degrees in respect to averaged geometries of all biological units. Unlike other 2C T7 variants (m6, T7-wt-s, m13) the m67 variant (underlined) affiliates to cluster (C) 6 occupied by the 2C wt TCRs bound to a different ligand. The two clusters are emphasized by bold typesetting.</p><p>^a) Cluster affiliation.</p><p>^b) Subtypes.</p><p>^c) Ligands: U = unbound, <i>K</i>E = H2-K1^b+EQYKFYSV, <i>K</i>S = H2-K1^b+SIYRYYG, <i>L</i>Q = H2-L^d+QLSPFPFDL. The ligand main type (MHC) is indicated by the first letter in italics.</p><p>^d) MHC mutation: (F9Y)(V12T)(I23T).</p><p>Pairwise Euler Angle Distances [°] of the bound and free 2C TCR variants.</p

Pairwise Euler Angle Distances [°] of the bound and free 1G4 TCR variants.

<p>The structures were superimposed to the α variable domains. All Euler angle distances given in degrees. Averaged angle distances: inter unbound: 2.5°, Inter bound (bold): 2.1°, bound vs. unbound (underlined): 8.0°.</p><p>^a) Subtypes: W = wild type, V = AV-wt, A = c5c1, B = c49c50, C = c58c62, D = C58c61</p><p>^b) Ligands: u = unbound, v = SLLMWITQV+HLA-A*0201, c = SLLMWITQC+HLA-A*0201.</p><p>Pairwise Euler Angle Distances [°] of the bound and free 1G4 TCR variants.</p

Conservation at the CoR position.

<p>Relative (and absolute) Frequency of the AA at the α or β CoR position, based on an multiple sequence alignments of all functional variable TCR gene segments alleles of the α (342 sequences) or β (164 sequences) locus obtained from the IMGT/Gene-DB [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004244#pcbi.1004244.ref061" target="_blank">61</a>].</p><p>^a) amino acid type</p><p>Conservation at the CoR position.</p

Geometry clusters of pMHC bound TCRs.

<p>Pairwise Euler-angle distances (EAD) were determined for all pMHC-bound TCR structures according to Formula 1. The distance matrix was hierarchically clustered using the Ward update formula. We identified six significant clusters, using a bootstrapping approach [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004244#pcbi.1004244.ref058" target="_blank">58</a>]. Notably, in most of the cases, TCRs of the same type occur in the same cluster. Upper panel: Clustering dendrogram with bootstrapping results (au = approximately unbiased, bp = bootstrapping probability). Left panel: TCR types occurring within a cluster. Right/lower panel: PDB identifiers and corresponding TCR names. Central panel: Pairwise Euler-angle distances (EAD). The color key is provided in the bottom of the figure.</p

Amber-Compatible Parametrization Procedure for Peptide-like Compounds: Application to 1,4- and 1,5-Substituted Triazole-Based Peptidomimetics

Peptidomimetics are molecules of particular interest in the context of drug design and development. They are proteolytically and metabolically more stable than their natural peptide counterparts but still offer high specificity toward their biological targets. In recent years, 1,4- and 1,5-disubstituted 1,2,3-triazole-based peptidomimetics have emerged as promising lead compounds for the design of various inhibitory and tumor-targeting molecules as well as for the synthesis of peptide analogues. The growing popularity of triazole-based peptidomimetics and a constantly broadening range of their application generated a demand for elaborate theoretical investigations by classical molecular dynamics simulations and molecular docking. Despite this rising interest, accurate and coherent force field parameters for triazole-based peptidomimetics are still lacking. Here, we report the first complete set of parameters dedicated to this group of compounds, named TZLff. This parametrization is compatible with the latest version of the AMBER force field (ff14SB) and can be readily applied for the modeling of pure triazole-based peptidomimetics as well as natural peptide sequences containing one or more triazole-based modifications in their backbone. The parameters were optimized to reproduce HF/6-31G* electrostatic potentials as well as MP2/cc-pVTZ equilibrium Hessian matrices and conformational potential energy surfaces through the use of a genetic algorithm-based search and least-squares fitting. Following the standards of AMBER, we introduce residue building units, thus allowing the user to define any given sequence of triazole-based peptidomimetics. Validation of the parameter set against ab initio- and NMR-based reference systems shows that we obtain fairly accurate results, which properly capture the conformational features of triazole-based peptidomimetics. The successful and efficient parametrization strategy developed in this work is general enough to be applied in a straightforward manner for parametrization of other peptidomimetics and, potentially, any polymeric assemblies

Sequential Inactivation of Gliotoxin by the <i>S</i>‑Methyltransferase TmtA

The epipolythiodioxopiperazine (ETP) gliotoxin mediates toxicity via its reactive thiol groups and thereby contributes to virulence of the human pathogenic fungus <i>Aspergillus fumigatus</i>. Self-intoxication of the mold is prevented either by reversible oxidation of reduced gliotoxin or by irreversible conversion to bis­(methylthio)­gliotoxin. The latter is produced by the <i>S</i>-methyltransferase TmtA and attenuates ETP biosynthesis. Here, we report the crystal structure of TmtA in complex with <i>S</i>-(5′-adenosyl)-l-homocysteine. TmtA features one substrate and one cofactor binding pocket per protein, and thus, bis-thiomethylation of gliotoxin occurs sequentially. Molecular docking of substrates and products into the active site of TmtA reveals that gliotoxin forms specific interactions with the protein surroundings, and free energy calculations indicate that methylation of the C10a-SH group precedes alkylation of the C3-SH site. Altogether, TmtA is well suited to selectively convert gliotoxin and to control its biosynthesis, suggesting that homologous enzymes serve to regulate the production of their toxic natural sulfur compounds in a similar manner

NS3-4A protease domain of PDB structure with co-crystallized ligand CPX (yellow) 32 and a second ligand, SCH 446211 (light blue), taken from the superimposed PDB structure 30

The protease binding pocket from structure is shown as a transparent surface patch. The residues V36 and T54 are depicted as stick-and-ball models, located in the parallel β-strands β1 and β3 of an anti-parallel β-sheet (dark blue).<p><b>Copyright information:</b></p><p>Taken from "Molecular basis of telaprevir resistance due to V36 and T54 mutations in the NS3-4A protease of the hepatitis C virus"</p><p>http://genomebiology.com/2008/9/1/R16</p><p>Genome Biology 2008;9(1):R16-R16.</p><p>Published online 23 Jan 2008</p><p>PMCID:PMC2395260.</p><p></p