Z.F. Zhang

Shear fracture and fragmentation mechanisms of bulk metallic glasses

Zr- and Co-based bulk metallic glasses display completely different failure modes under compressive loading. Zr-based metallic glasses always fail in a pure shear mode, whereas Co-based metallic glasses often break into small particles or powder, exhibiting a fragmentation mode. The difference in the failure modes for the two glassy alloys indicates that different mechanisms control the fracture processes, which can be described by a combined effect of surface energy γ, cleavage strength σ0, fragmentation coefficient Fn and fracture mode factor α = τ0/σ0.

Molecular basis of the substrate specificity and the catalytic mechanism of citramalate synthase from Leptospira interrogans

Leptospira interrogans is the causative agent for leptospirosis, a zoonotic disease of global importance. In contrast with most other micro-organisms, L. interrogans employs a pyruvate pathway to synthesize isoleucine and LiCMS (L. interrogans citramalate synthase) catalyses the first reaction of the pathway which converts pyruvate and acetyl-CoA into citramalate, thus making it an attractive target for the development of antibacterial agents. We report here the crystal structures of the catalytic domain of LiCMS and its complexes with substrates, and kinetic and mutagenesis studies of LiCMS, which together reveal the molecular basis of the high substrate specificity and the catalytic mechanism of LiCMS. The catalytic domain consists of a TIM barrel flanked by an extended C-terminal region. It forms a homodimer in the crystal structure, and the active site is located at the centre of the TIM barrel near the C-terminal ends of the beta-strands and is composed of conserved residues of the beta-strands of one subunit and the C-terminal region of the other. The substrate specificity of LiCMS towards pyruvate against other alpha-oxo acids is dictated primarily by residues Leu(81), Leu(104) and Tyr(144), which form a hydrophobic pocket to accommodate the C(2)-methyl group of pyruvate. The catalysis follows the typical aldol condensation reaction, in which Glu(146) functions as a catalytic base to activate the methyl group of acetyl-CoA to form an enolated acetyl-CoA intermediate and Arg(16) as a general acid to stabilize the intermediate.

Anisotropic compressive properties of iron subjected to single-pass equal-channel angular pressing

The anisotropic compressive properties and shear deformation mechanism of iron subjected to equal-channel angular pressing (ECAP) with single-pass have been investigated. It was found that the anisotropic compressive properties can be attributed to the effect of the ECAP shear plane. It is suggested that the ECAP shear plane induced by the first pass of ECAP is a relatively weak plane in terms of resisting subsequent shear deformation.

Atypical OmpR/PhoB Subfamily Response Regulator GlnR of Actinomycetes Functions as a Homodimer, Stabilized by the Unphosphorylated Conserved Asp-focused Charge Interactions

Background: Orphan response transcription factor GlnR regulates nitrogen metabolism in important actinomycetes. Results: GlnR has no typical “phosphorylation pocket,” where the only conserved Asp is unphosphorylated but is essential for functional homodimerization. Conclusion: Actinomycete GlnR is an atypical response regulator functioning as a homodimer. Significance: Conserved Asp-focused charge interactions of actinomycete GlnR are probably the mechanism that stabilizes the homodimer for physiological function. The OmpR/PhoB subfamily protein GlnR of actinomycetes is an orphan response regulator that globally coordinates the expression of genes related to nitrogen metabolism. Biochemical and genetic analyses reveal that the functional GlnR from Amycolatopsis mediterranei is unphosphorylated at the potential phosphorylation Asp50 residue in the N-terminal receiver domain. The crystal structure of this receiver domain demonstrates that it forms a homodimer through the α4-β5-α5 dimer interface highly similar to the phosphorylated typical response regulator, whereas the so-called “phosphorylation pocket” is not conserved, with its space being occupied by an Arg52 from the β3-α3 loop. Both in vitro and in vivo experiments confirm that GlnR forms a functional homodimer via its receiver domain and suggest that the charge interactions of Asp50 with the highly conserved Arg52 and Thr9 in the receiver domain may be crucial in maintaining the proper conformation for homodimerization, as also supported by molecular dynamics simulations of the wild type GlnR versus the deficient mutant GlnR(D50A). This model is backed by the distinct phenotypes of the total deficient GlnR(R52A/T9A) double mutant versus the single mutants of GlnR (i.e. D50N, D50E, R52A and T9A), which have only minor effects upon both dimerization and physiological function of GlnR in vivo, albeit their DNA binding ability is weakened compared with that of the wild type. By integrating the supportive data of GlnRs from the model Streptomyces coelicolor and the pathogenic Mycobacterium tuberculosis, we conclude that the actinomycete GlnR is atypical with respect to its unphosphorylated conserved Asp residue being involved in the critical Arg/Asp/Thr charge interactions, which is essential for maintaining the biologically active homodimer conformation.

Nature of shear flow lines in equal-channel angular-pressed metals and alloys

The nature of shear flow lines in equal-channel angular-pressed (ECAPed) metals has been investigated experimentally and theoretically. Experimental results indicate that, for metals pressed in a right-angle die, the shear flow lines often have an angle of ∼27° with respect to the extrusion direction. It is suggested that the shear flow lines are composed of a group of elongated grains with an elongation direction that deviates slightly from that of the shear flow lines.

Molecular basis of the inhibitor selectivity and insights into the feedback inhibition mechanism of citramalate synthase from Leptospira interrogans

LiCMS (Leptospira interrogans citramalate synthase) catalyses the first reaction of the isoleucine biosynthesis pathway in L. interrogans, the pathogen of leptospirosis. The catalytic reaction is regulated through feedback inhibition by its end product isoleucine. To understand the molecular basis of the high selectivity of the inhibitor and the mechanism of feedback inhibition, we determined the crystal structure of LiCMSC (C-terminal regulatory domain of LiCMS) in complex with isoleucine, and performed a biochemical study of the inhibition of LiCMS using mutagenesis and kinetic methods. LiCMSC forms a dimer of dimers in both the crystal structure and solution and the dimeric LiCMSC is the basic functional unit. LiCMSC consists of six beta-strands forming two anti-parallel beta-sheets and two alpha-helices and assumes a betaalphabeta three-layer sandwich structure. The inhibitor isoleucine is bound in a pocket at the dimer interface and has both hydrophobic and hydrogen-bonding interactions with several conserved residues of both subunits. The high selectivity of LiCMS for isoleucine over leucine is primarily dictated by the residues, Tyr430, Leu451, Tyr454, Ile458 and Val468, that form a hydrophobic pocket to accommodate the side chain of the inhibitor. The binding of isoleucine has inhibitory effects on the binding of both the substrate, pyruvate, and coenzyme, acetyl-CoA, in a typical pattern of K-type inhibition. The structural and biochemical data from the present study together suggest that the binding of isoleucine affects the binding of the substrate and coenzyme at the active site, possibly via conformational change of the dimer interface of the regulatory domain, leading to inhibition of the catalytic reaction.

Structural Insights into Mitochondrial Antiviral Signaling Protein (MAVS)-Tumor Necrosis Factor Receptor-associated Factor 6 (TRAF6) Signaling

Background: MAVS recruits TRAF6 to activate RLR antiviral signaling. Results: T6BM2 of MAVS is essential for TRAF6 binding and downstream signaling. Conclusion: T6BM2-mediated TRAF6 binding is required for MAVS-related antiviral response. Significance: This work provides a structural understanding of the MAVS-TRAF6 antiviral signaling. In response to viral infection, cytosolic retinoic acid-inducible gene I-like receptors sense viral RNA and promote oligomerization of mitochondrial antiviral signaling protein (MAVS), which then recruits tumor necrosis factor receptor-associated factor (TRAF) family proteins, including TRAF6, to activate an antiviral response. Currently, the interaction between MAVS and TRAF6 is only partially understood, and atomic details are lacking. Here, we demonstrated that MAVS directly interacts with TRAF6 through its potential TRAF6-binding motif 2 (T6BM2; amino acids 455–460). Further, we solved the crystal structure of MAVS T6BM2 in complex with the TRAF6 TRAF_C domain at 2.95 Å resolution. T6BM2 of MAVS binds to the canonical adaptor-binding groove of the TRAF_C domain. Structure-directed mutational analyses in vitro and in cells revealed that MAVS binding to TRAF6 via T6BM2 instead of T6BM1 is essential but not sufficient for an optimal antiviral response. Particularly, a MAVS mutant Y460E retained its TRAF6-binding ability as predicted but showed significantly impaired signaling activity, highlighting the functional importance of this tyrosine. Moreover, these observations were further confirmed in MAVS−/− mouse embryonic fibroblast cells. Collectively, our work provides a structural basis for understanding the MAVS-TRAF6 antiviral response.

On the determination of Burgers vectors of type B dislocations in an Al70Co15Ni15 decagonal quasicrystal by convergent-beam electron diffraction

Abstract Type B dislocations with Burgers vectors parallel to the twofold axes of the Al70Co15Ni15 decagonal quasicrystal were studied by means of electron diffraction contrast imaging and defocus convergent-beam electron diffraction techniques. Two kinds of Burgers vector of the type B dislocations were determined, both being parallel to a twofold axis A2P of the decagonal quasicrystal. The components |b∥| of the Burgers vector b = 〈00 1 0 [sbnd] 1 0〉 in physical space and the component |bperp| of the Burgers vector in complementary space are 0.186 and 0:115 nm respectively, with a ratio T of 1.618. The components for b = 〈0 1 0 [sbnd]11〉 are 0.302 and 0.071 nm with a ratio τ3 of 4.235.

Friction Stir Welding of SiCp/Al Composite and 2024 Al Alloy

6 mm thick SiCp/2009Al composite and 2024Al-T351 alloy plates were successfully joined by friction stir welding (FSW) with and without the tool pin offsetting to the 2024Al side (denoted as NOS and OS samples, respectively), producing defect-free joints. The SiC particles from the composite were distributed along a ring structure in the nugget and the volume fraction of the SiC particles decreased as the tool pin offset to the 2024Al side. The Al-clad layer on the 2024Al plate was aggregated on the retreating side of the nugget after FSW. For the OS sample, the Al formed a layer along the nugget boundary. The strength of the NOS sample reached up to 85% of the 2024Al alloy with the joint failing in the heat affected zone on the 2024Al side. The strength of the OS samples was 47% of the 2024Al alloy due to the aggregated Al layer on the retreating side of the nugget which decreased the strength of the joint.

Subdomain II of α-Isopropylmalate Synthase Is Essential for Activity: INFERRING A MECHANISM OF FEEDBACK INHIBITION*

Background: Isopropylmalate synthases (IPMSs) with and without a regulatory domain were found. Results: IPMS subdomain II is essential for activities and likely involved in acetyl-CoA binding-mediated conformation transition. Conclusion: The N-terminal domain and the two subdomains comprise the complete and independently functional catalytic module of IPMS. Significance: The IPMS catalytic module was defined and characterized, which inferred a probable feedback inhibition mechanism. The committed step of leucine biosynthesis, converting acetyl-CoA and α-ketoisovalerate into α-isopropylmalate, is catalyzed by α-isopropylmalate synthase (IPMS), an allosteric enzyme subjected to feedback inhibition by the end product l-leucine. We characterized the short form IPMS from Leptospira biflexa (LbIPMS2), which exhibits a catalytic activity comparable with that of the long form IPMS (LbIPMS1) and has a similar N-terminal domain followed by subdomain I and subdomain II but lacks the whole C-terminal regulatory domain. We found that partial deletion of the regulatory domain of LbIPMS1 resulted in a loss of about 50% of the catalytic activity; however, when the regulatory domain was deleted up to Arg-385, producing a protein that is almost equivalent to the intact LbIPMS2, about 90% of the activity was maintained. Moreover, in LbIPMS2 or LbIPMS1, further deletion of several residues from the C terminus of subdomain II significantly impaired or completely abolished the catalytic activity, respectively. These results define a complete and independently functional catalytic module of IPMS consisting of both the N-terminal domain and the two subdomains. Structural comparison of LbIPMS2 and the Mycobacterium tuberculosis IPMS revealed two different conformations of subdomain II that likely represent two substrate-binding states related to cooperative catalysis. The biochemical and structural analyses together with the previously published hydrogen-deuterium exchange data led us to propose a conformation transition mechanism for feedback inhibition mediated by subdomains I and II that might associated with alteration of the binding affinity toward acetyl-CoA.