A Proton Magnetic Resonance Study of the Association of Lysozyme with Monosaccharide Inhibitors

It has been shown that the acetamido methyl protons of N-acetyl-d-glucosamine undergo a chemical shift to higher fields in their proton magnetic resonance spectrum when the inhibitor is bound to lysozyme. The observed chemical shift in the presence of the enzyme is different for the agr- and ß-anomeric forms of 2-acetamido-2-deoxy-d-glucopyranose indicating either a difference in the affinity of the anomeric forms for lysozyme or different magnetic environments for the methyl protons in their enzyme-bound state. That the agr- and ß-anomeric forms of GlcAc bind to lysozyme in a competitive fashion was indicated by observing the proton magnetic resonance spectra in the presence of 2-acetamido-d3-2-deoxy-agr-d-glucopyranose. The methyl glycosides, methyl-agr-GlcAc and methyl-ß-GlcAc, were also shown to bind competitively with both anomers of GlcAc. Quantitative analysis of the chemical shift data observed for the association of GlcAc with lysozyme was complicated by the mutarotation of GlcAc between its agr- and ß-anomeric forms. However, in the case of the methyl glucosides, where the conformation of each anomer is frozen, it was possible to analyze the chemical shift data in a straightforward manner, and the dissociation constant as well as the chemical shift of the acetamido methyl protons of the enzyme-inhibitor complex was determined for both anomers. The results indicate that the two anomers of methyl-GlcAc bind to lysozyme with slightly different affinities but that the acetamido methyl groups of both anomers experience identical magnetic environments in the enzyme-inhibitor complex

NMR studies of the phosphotransfer domain of the histidine kinase CheA from Escherichia coli: assignments, secondary structure, general fold, and backbone dynamics

Multidimensional heteronuclear NMR techniques were applied to study the phosphotransfer domain, residues 1 - 134, of the histidine kinase CheA, from Escherichia coli, which contains the site of autophosphorylation, His48. Assignments of the backbone amide groups and side chain patons are nearly complete. Our studies show that this protein fragment consists of five a-helices (A-E)connected by turns. Analysis of NOE distance restraints provided by two-dimensional (2D) ^1H-^1H and three-dimensional (3D) ^(15)N-edited NOESY spectra using model building and structure calculations indicates that the five helices form an antiparallel helix bundle with near-neighbor connectivity. The amino-tenninal four helices are proposed to be arranged in a right-handed manner with helix E packing against helices C and D. From ideal hydrophobic helical packing and structure calculations, the site of autophosphorylation, His48, is nearly fully exposed to the solvent. We measured the NMR relaxation properties of the backbone ^(15)N nuclei using inverse detected two-dimensional NMR spectroscopy. The protein backbone dynamics studies show that CheA1-134 is formed into a tight and compact structure with very limited flexibilities both in helices and turns. Structural implications of titration and phosphorylation experiments are briefly discussed

Phosphotransfer and CheY-Binding Domains of the Histidine Autokinase CheA Are Joined by a Flexible Linker

Multidimensional heteronuclear NMR techniques were applied to study a protein fragment of the histidine autokinase CheA from Escherichia coli. This fragment (CheA_(1-233)) contains the phosphotransfer domain and the CheY-binding domain joined by a linker region. Comparison of chemical shift and NOE cross-peak patterns indicates that the structures of the two domains in CheA_(1-233) remain nearly the same as in the two individual domain fragments, CheA1-134 and CheA_(124-257). Relaxation properties of the backbone ^(15)N nuclei were measured to study the rotational correlations of the two domains and properties of the linker region. Dynamics data were analyzed both by an isotropic motional model and an anisotropic motional model. The experimental T_1 and T_2 values, the derived rotational correlation times, and motional anisotropy are significantly different for the two domains, indicating the two domains reorient independently and the linker region is highly flexible. Dynamics data of CheA_(1-233) were also compared with those of CheA_(1-134). Our studies show that flexible domain linkers and extended and flexible terminal polypeptide chains can have significant effects on the motional properties of the adjacent structured regions. These observations suggest a model for the graded regulation of CheA autophosphorylation activity. In this model, the various activity states of the receptor are generated by controlling the access of the mean position of the kinase domain to the phosphotransfer domain. This would then modulate the diffusional encounter rate of the domains and hence activity over a wide and graded range of values

Overview of mathematical approaches used to model bacterial chemotaxis II: bacterial populations

We review the application of mathematical modeling to understanding the behavior of populations of chemotactic bacteria. The application of continuum mathematical models, in particular generalized Keller–Segel models, is discussed along with attempts to incorporate the microscale (individual) behavior on the macroscale, modeling the interaction between different species of bacteria, the interaction of bacteria with their environment, and methods used to obtain experimentally verified parameter values. We allude briefly to the role of modeling pattern formation in understanding collective behavior within bacterial populations. Various aspects of each model are discussed and areas for possible future research are postulated

From least action in electrodynamics to magnetomechanical energy -- a review

The equations of motion for electromechanical systems are traced back to the fundamental Lagrangian of particles and electromagnetic fields, via the Darwin Lagrangian. When dissipative forces can be neglected the systems are conservative and one can study them in a Hamiltonian formalism. The central concepts of generalized capacitance and inductance coefficients are introduced and explained. The problem of gauge independence of self-inductance is considered. Our main interest is in magnetomechanics, i.e. the study of systems where there is exchange between mechanical and magnetic energy. This throws light on the concept of magnetic energy, which according to the literature has confusing and peculiar properties. We apply the theory to a few simple examples: the extension of a circular current loop, the force between parallel wires, interacting circular current loops, and the rail gun. These show that the Hamiltonian, phase space, form of magnetic energy has the usual property that an equilibrium configuration corresponds to an energy minimum.Comment: 29 pages, 9 figures, 65 reference

Ontologies in Quantitative Biology: A Basis for Comparison, Integration, and Discovery

As biology is becoming a data-driven discipline, ontologies become increasingly important for systematically capturing the existing knowledge. This essay discusses current trends and how ontologies can also be used for discovery

Ultraviolet Difference Spectral Studies on Concanavalin A

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/65204/1/j.1432-1033.1970.tb01116.x.pd