Microcalorimetric indications for ligand binding as a function of the protein for galactoside-specific plant and avian lectins

The process cascade leading to the final accommodation of the carbohydrate ligand in the lectin’s binding site comprises enthalpic and entropic contributions of the binding partners and solvent molecules. With emphasis on lactose, N-acetyllactosamine, and thiodigalactoside as potent inhibitors of binding of galactoside-specific lectins, the question was addressed to what extent these parameters are affected as a function of the protein. The microcalorimetric study of carbohydrate association to the galectin from chicken liver (CG-16) and the agglutinin from Viscum album (VAA) revealed enthalpy–entropy compensation with evident protein type-dependent changes for N-acetyllactosamine. Reduction of the entropic penalty by differential flexibility of loops or side chains and/or solvation properties of the protein will have to be reckoned with to assign a molecular cause to protein type-dependent changes in thermodynamic parameters for lectins sharing the same monosaccharide specificity.

Generation of a Manganese Specific Restriction Endonuclease with Nicking Activity

A typical feature of type II restriction endonucleases (REases) is their obligate sequence specificity and requirement for Mg2+ during catalysis. R.KpnI is an exception. Unlike most other type II REases, the active site of this enzyme can accommodate Mg2+, Mn2+, Ca2+, or Zn2+ and cleave DNA. The enzyme belongs to the HNH superfamily of nucleases and is characterized by the presence of a beta beta alpha-Me finger motif. Residues D148, H149, and Q175 together form the HNH active site and are essential for Mg2+ binding and catalysis. The unique ability of the enzyme to cleave DNA in the presence of different metal ions is exploited to generate mutants that are specific to one particular metal ion. We describe the generation of a Mn2+-dependent sequence specific endonuclease, defective in DNA cleavage with Mg2+ and other divalent metal ions. In the engineered mutant, only Mn2+ is selectively bound at the active site, imparting Mn2+-mediated cleavage. The mutant is impaired in concerted double-stranded DNA cleavage, leading to accumulation of nicked intermediates. The nicking activity of the mutant enzyme is further enhanced by altered reaction conditions. The active site fluidity of R Eases allowing flexible accommodation of catalytic cofactors thus forms a basis for engineering selective metal ion-dependent REase additionally possessing nicking activity.

Softening and dynamic recrystallization in magnesium single crystals during c-axis compression

Commercial purity (99.8%) magnesium single crystals were subjected to plane strain compression (PSC) along the c-axis at 200 and 370 degrees C and a constant strain rate of 10(-3) s(-1). Extension was confined to the < 1 1 (2) over bar 0 > direction and the specimens were strained up to a logarithmic true strain of -1. The initial rapid increase in flow stress was followed by significant work softening at different stresses and comparable strains of about -0.05 related to macroscopic twinning events. The microstructure of the specimen after PSC at 200 degrees C was characterized by a high density of {1 0 (1) over bar 1} and {1 0 (1) over bar 3} compression twins, some of which were recrystallized. After PSC at 370 degrees C, completely recrystallized twin bands were the major feature of the observed microstructure. All new grains in these bands retained the same c-axis orientation of their compression twin hosts. The basal plane in these grains was randomly rotated around the c-axis, forming a fiber texture component. The obtained results are discussed with respect to the mechanism of recrystallization, the specific character of the boundaries between new grains and the initial matrix, and the importance of the dynamically recrystallized bands for strain accommodation in these deformed magnesium single crystals. (C) 2011 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Extent of Structural Asymmetry in Homodimeric Proteins: Prevalence and Relevance

Most homodimeric proteins have symmetric structure. Although symmetry is known to confer structural and functional advantage, asymmetric organization is also observed. Using a non-redundant dataset of 223 high-resolution crystal structures of biologically relevant homodimers, we address questions on the prevalence and significance of asymmetry. We used two measures to quantify global and interface asymmetry, and assess the correlation of several molecular and structural parameters with asymmetry. We have identified rare cases (11/223) of biologically relevant homodimers with pronounced global asymmetry. Asymmetry serves as a means to bring about 2:1 binding between the homodimer and another molecule; it also enables cellular signalling arising from asymmetric macromolecular ligands such as DNA. Analysis of these cases reveals two possible mechanisms by which possible infinite array formation is prevented. In case of homodimers associating via non-topologically equivalent surfaces in their tertiary structures, ligand-dependent mechanisms are used. For stable dimers binding via large surfaces, ligand-dependent structural change regulates polymerisation/depolymerisation; for unstable dimers binding via smaller surfaces that are not evolutionarily well conserved, dimerisation occurs only in the presence of the ligand. In case of homodimers associating via interaction surfaces with parts of the surfaces topologically equivalent in the tertiary structures, steric hindrance serves as the preventive mechanism of infinite array. We also find that homodimers exhibiting grossly symmetric organization rarely exhibit either perfect local symmetry or high local asymmetry. Binding of small ligands at the interface does not cause any significant variation in interface asymmetry. However, identification of biologically relevant interface asymmetry in grossly symmetric homodimers is confounded by the presence of similar small magnitude changes caused due to artefacts of crystallisation. Our study provides new insights regarding accommodation of asymmetry in homodimers.

Odd-even effect in the elastic modulii of alpha,omega-Alkanedicarboxylic acids

Nanoindentation studies on alpha,omega-alkanedicarboxylic acids reveal that the elastic modulus, E, shows an odd-even alternation in exactly the same manner as the melting temperature, T-m. The results are consistent with the hypothesis that the strained molecular conformations in the odd diacids are the reasons for these alternations in T-m. The same packing features that lower T-m in the odd acids lead to easy accommodation of the deformation during nanoindentation and hence their low E.

Al based ultra-fine eutectic with high room temperature plasticity and elevated temperature strength

Developments of aluminum alloys that can retain strength at and above 250 degrees C present a significant challenge. In this paper we report an ultrafine scale Al-Fe-Ni eutectic alloy with less than 3.5 aa transition metals that exhibits room temperature ultimate tensile strength of similar to 400 MPa with a tensile ductility of 6-8%. The yield stress under compression at 300 degrees C was found to be 150 MPa. We attribute it to the refinement of the microstructure that is achieved by suction casting in copper mold. The characterization using scanning and transmission electron microscopy (SEM and TEM) reveals an unique composite structure that contains the Al-Al3Ni rod eutectic with spacing of similar to 90 nm enveloped by a lamellar eutectic of Al-Al9FeNi (similar to 140 nm). Observation of subsurface deformation under Vickers indentation using bonded interface technique reveals the presence of extensive shear banding during deformation that is responsible for the origin of ductility. The dislocation configuration in Al-Al3Ni eutectic colony indicates accommodation of plasticity in alpha-Al with dislocation accumulation at the alpha-Al/Al3Ni interface boundaries. In contrast the dislocation activities in the intermetallic lamellae are limited and contain set of planner dislocations across the plates. We present a detailed analysis of the fracture surface to rationalize the origin of the high strength and ductility in this class of potentially promising cast alloy. (C) 2015 Elsevier B.V. All rights reserved.

Surface motions and intraplate continental deformation in Alaska driven by mantle flow

The degree to which the lithosphere and mantle are coupled and contribute to surface deformation beneath continental regions remains a fundamental question in the field of geodynamics. Here we use a new approach with a surface deformation field constrained by GPS, geologic, and seismicity data, together with a lithospheric geodynamic model, to solve for tractions inferred to be generated by mantle convection that (1) drive extension within interior Alaska generating southward directed surface motions toward the southern convergent plate boundary, (2) result in accommodation of the relative motions between the Pacific and North America in a comparatively small zone near the plate boundary, and (3) generate the observed convergence within the North American plate interior in the Mackenzie mountains in northwestern Canada. The evidence for deeper mantle influence on surface deformation beneath a continental region suggests that this mechanism may be an important contributing driver to continental plate assemblage and breakup.