Differential geometric analysis of alterations in MH α‐helices

Antigen presenting cells present processed peptides via their major histocompatibility (MH) complex to the T cell receptors (TRs) of T cells. If a peptide is immunogenic, a signaling cascade can be triggered within the T cell. However, the binding of different peptides and/or different TRs to MH is also known to influence the spatial arrangement of the MH α‐helices which could itself be an additional level of T cell regulation. In this study, we introduce a new methodology based on differential geometric parameters to describe MH deformations in a detailed and comparable way. For this purpose, we represent MH α‐helices by curves. On the basis of these curves, we calculate in a first step the curvature and torsion to describe each α‐helix independently. In a second step, we calculate the distribution parameter and the conical curvature of the ruled surface to describe the relative orientation of the two α‐helices. On the basis of four different test sets, we show how these differential geometric parameters can be used to describe changes in the spatial arrangement of the MH α‐helices for different biological challenges. In the first test set, we illustrate on the basis of all available crystal structures for (TR)/pMH complexes how the binding of TRs influences the MH helices. In the second test set, we show a cross evaluation of different MH alleles with the same peptide and the same MH allele with different peptides. In the third test set, we present the spatial effects of different TRs on the same peptide/MH complex. In the fourth test set, we illustrate how a severe conformational change in an α‐helix can be described quantitatively. Taken together, we provide a novel structural methodology to numerically describe subtle and severe alterations in MH α‐helices for a broad range of applications. © 2013 Wiley Periodicals, Inc.     

The Ligand‐Based Quintuple Bond‐Shortening Concept and Some of Its Limitations

Herein, the ligand‐based concept of shortening quintuple bonds and some of its limitations are reported. In dichromium–diguanidinato complexes, the length of the quintuple bond can be influenced by the substituent at the central carbon atom of the used ligand. The guanidinato ligand with a 2,6‐dimethylpiperidine backbone was found to be the optimal ligand. The reduction of its chromium(II) chloride–ate complex gave a quintuply bonded bimetallic complex with a Cr? Cr distance of 1.7056 (12) Å. Its metal–metal distance, the shortest observed in any stable compound yet, is of essentially the same length as that of the longest alkane C? C bond (1.704 (4) Å). Both molecules, the alkane and the Cr complex, are of remarkable stability. Furthermore, an unsupported Cr^I dimer with an effective bond order (EBO) of 1.25 between the two metal atoms, indicated by CASSCF/CASPT2 calculations, was isolated as a by‐product. The formation of this by‐product indicates that with a certain bulk of the guanidinato ligand, other coordination isomers become relevant. Over‐reduction takes place, and a chromium–arene sandwich complex structurally related to the classic dibenzene chromium complex was observed, even when bulkier substituents are introduced at the central carbon atom of the used guanidinato ligand.     

The Role of 2,6‐Diaminopyridine Ligands in the Isolation of an Unprecedented,Low‐Valent Tin Complex

Stabilization of the central atom in an oxidation state of zero through coordination of neutral ligands is a common bonding motif in transition‐metal chemistry. However, the stabilization of main‐group elements in an oxidation state of zero by neutral ligands is rare. Herein, we report that the transamination reaction of the DAMPY ligand system (DAMPY=2,6‐[ArNH‐CH₂]₂(NC₅H₃) (Ar=C₆H₃‐2,6‐iPr₂)) with Sn[N(SiMe₃)₂]₂ produces the DIMPYSn complex (DIMPY=(2,6‐[ArN?CH]₂(NC₅H₃)) with the Sn atom in a formal oxidation state of zero. This is the first example of a tin compound stabilized in a formal oxidation state of zero by only one donor molecule. Furthermore, three related low‐valent Sn^II complexes, including a [DIMPYSn^IICl]⁺[SnCl₃]^? ion pair, a bisstannylene DAMPY{Sn^II[N(SiMe₃)₂]₂}₂, and the enamine complex MeDIMPYSn^II, were isolated. Experimental results and the conclusions drawn are also supported by theoretical studies at the density functional level of theory and ¹¹⁹Sn Mössbauer spectroscopy.     

Targeting the Substrate Binding Site of E. coli Nitrile Reductase QueF by Modeling,Substrate and Enzyme Engineering

Nitrile reductase QueF catalyzes the reduction of 2‐amino‐5‐cyanopyrrolo[2,3‐d]pyrimidin‐4‐one (preQ₀) to 2‐amino‐5‐aminomethylpyrrolo[2,3‐d]pyrimidin‐4‐one (preQ₁) in the biosynthetic pathway of the hypermodified nucleoside queuosine. It is the only enzyme known to catalyze a reduction of a nitrile to its corresponding primary amine and could therefore expand the toolbox of biocatalytic reactions of nitriles. To evaluate this new oxidoreductase for application in biocatalytic reactions, investigation of its substrate scope is prerequisite. We report here an investigation of the active site binding properties and the substrate scope of nitrile reductase QueF from Escherichia coli. Screenings with simple nitrile structures revealed high substrate specificity. Consequently, binding interactions of the substrate to the active site were identified based on a new homology model of E. coli QueF and modeled complex structures of the natural and non‐natural substrates. Various structural analogues of the natural substrate preQ₀ were synthesized and screened with wild‐type QueF from E. coli and several active site mutants. Two amino acid residues Cys190 and Asp197 were shown to play an essential role in the catalytic mechanism. Three non‐natural substrates were identified and compared to the natural substrate regarding their specific activities by using wild‐type and mutant nitrile reductase.     

Polymorphs of the Gadolinite-Type Borates ZrB2O5 and HfB2O5 Under Extreme Pressure

Based on the results from previous high-pressure experiments on the gadolinite-type mineral datolite, CaBSiO₄(OH), the behavior of the isostructural borates β-HfB₂O₅ and β-ZrB₂O₅ have been studied by synchrotron-based in situ high-pressure single-crystal X-ray diffraction experiments. On compression to 120 GPa, both borate layer-structures are preserved. Additionally, at ≈114 GPa, the formation of a second phase can be observed in both compounds. The new high-pressure modification γ-ZrB₂O₅ features a rearrangement of the corner-sharing BO₄ tetrahedra, while still maintaining the four- and eight-membered rings. The new phase γ-HfB₂O₅ contains ten-membered rings including the rare structural motif of edge-sharing BO₄ tetrahedra with exceptionally short B−O and B⋅⋅⋅B distances. For both structures, unusually high coordination numbers are found for the transition metal cations, with ninefold coordinated Hf⁴⁺, and tenfold coordinated Zr⁴⁺, respectively. These findings remarkably show the potential of cold compression as a low-energy pathway to discover metastable structures that exhibit new coordinations and structural motifs.     

Stereospecific Formal [3+2] Dipolar Cycloaddition of Cyclopropanes with Nitrosoarenes: An Approach to Isoxazolidines

The MgBr₂‐catalyzed formal [3+2] cycloaddition of donor–acceptor activated cyclopropanes with nitrosoarenes offers a novel approach to various structurally diverse isoxazolidines. The reactions, which are experimentally easy to conduct, occur with complete stereospecificity and perfect control of regioselectivity. Product isoxazolidines can be readily transformed into α‐amino lactones by reductive or decarboxylative N? O cleavage and subsequent lactonisation, and the N‐aryl bond cleavage is also possible under oxidative conditions.