Effects of the protein environment on the structure and energetics of active sites of metalloenzymes. ONIOM study of methane monooxygenase and ribonucleotide reductase.

As the first application of our recently developed ONIOM2(QM:MM) and ONIOM3(QM:QM:MM) codes to the metalloenzymes with a large number of protein residues, two members of the non-heme protein family, methane monooxygenause and ribonucleotide reductase, have been chosen. The "active-site + four alpha-helical fragments" model was adopted which includes about 1000 atoms from 62 residues around the Fe-centered spheres. Comparison of the active-site geometries of MMOH and R2 units optimized with this model with those obtained with the "active site only" (with only 39-46 atoms) model and the X-ray results clearly demonstrates the crucial role of the active site-protein interaction in the enzymatic activities.     

New insights into the metal ion–peptide hydroxamate interactions: Metal complexes of primary hydroxamic acid derivatives of common dipeptides in aqueous solution

Complex formation of primary dipeptide hydroxamic acids, L-Ala-L-AlaNHOH and L-Ala-L-SerNHOH, as well as the corresponding Z-protected ones, Z-L-Ala-L-AlaNHOH and Z-L-Ala-L-SerNHOH (Z = benzyloxycarbonyl), with iron(III), aluminium(III), nickel(II), copper(II) and zinc(II) was studied in aqueous solution by pH-potentiometric and spectroscopic (UV–Vis, EPR, CD, ¹H NMR) methods. The exclusive formation of [O,O] chelated hydroxamate complexes was found with iron(III) and aluminium(III) with all the ligands. Formation of linkage isomers with the involvement of either [O,O] hydroxamate or [NH₂,CO] chelates was detected both in the zinc(II)-L-Ala-L-AlaNHOH and -L-Ala-L-SerNHOH systems. Upon increasing the pH, none of these chelating sets are capable of preventing the hydrolysis of the metal ion. The formation of stable complexes was found in the nickel(II) and copper(II) systems above pH ∼ 6 with a [NH₂, N_amide, N_hydrox.] binding mode after deprotonation and coordination of the peptide amide and the hydroxamate group. With an excess of copper(II), the formation of trinuclear [Cu₃H_xL₂]^x+4 type (x = −4 to −6) complexes as the major species was also detected. Blocking the terminal amino group in the Z-protected ligands results in a dramatic decrease of the nickel(II) and zinc(II) binding strengths, and insoluble complexes with copper(II). No indication was found for the role of the hydroxyl group of the serine moiety in metal ion binding.     

Involutes: the geometry of chemical waves rotating in annular membranes

According to earlier theories certain parts of a chemical wave front propagating in a 2-D excitable medium with a convex obstacle should be involutes of that obstacle. The present paper discusses a special case where self-sustained chemical waves are rotating around a central obstacle in an annular 2-D excitable region. A simple geometrical model of wave propagation based on the Fermat principle (minimum propagation time) is suggested. Applying this model it is shown that the wave fronts in the case of an annular excitable region should be purely involutes of the central obstacle in the asymptotic state. This theory is supported by experiments in a novel membrane reactor where a catalyst of the Belousov-Zhabotinsky reaction is fixed on a porous membrane combined with a gel medium. Involutes of circular and triangular obstacles are observed experimentally. Deviations from the ideal involute geometry are explained by inhomogeneities in the membrane. (c) 1995 American Institute of Physics.     

High-frequency enhancement by an optical system for superresolution of temporally restricted objects

A system for superresolution of temporally restricted objects allows one to transmit ultrawideband optical signals (objects) through a narrow aperture. Such a system was proposed, improved, and implemented for one- and two-dimensional objects. Implementing frequency-plane enhancement in this system provides the ability of spatial filtering of ultrawideband objects. A method for spatial filtering in a system for superresolution of temporally restricted objects by use of a generalized Dammann grating is suggested. An experimental demonstration of high-frequency enhancement (high-pass filtering) of one-dimensional objects is presented.     

Note on asynchronous exponential growth for structured population models

In the present note we show asynchronous exponential growth for important age- and size-structured population models.     

Data Perturbations of Matrices of Pairwise Comparisons

This paper deals with data perturbations of pairwise comparison matrices (PCM). Transitive and symmetrically reciprocal (SR) matrices are defined. Characteristic polynomials and spectral properties of certain SR perturbations of transitive matrices are presented. The principal eigenvector components of some of these PCMs are given in explicit form. Results are applied to PCMs occurring in various fields of interest, such as in the analytic hierarchy process (AHP) to the paired comparison matrix entries of which are positive numbers, in the dynamic input–output analysis to the matrix of economic growth elements of which might become both positive and negative and in vehicle system dynamics to the input spectral density matrix whose entries are complex numbers.     

Nucleotides Induced Changes in Skeletal Muscle Myosin by DSC,TMDSC and EPR

Electron paramagnetic resonance (EPR, ST-EPR) and differential scanning calorimetry(DSC) were used in conventional and temperature modulated mode to study internal motions and energetics of myosin in skeletal muscle fibres in different states of the actomyosin ATPase cycle. Psoas muscle fibres from rabbit were spin-labelled with an isothiocyanate-based probe molecule at the reactive sulfhydryl site (Cys-707) of the catalytic domain of myosin. In the presence of nucleotides (ATP, ADP, AMP⋅PNP) and ATP or ADP plus orthovanadate, the conventional EPR spectra showed changes in the ordering of the probe molecules in fibres. In MgADP state a new distribution appeared; ATP plus orthovanadate increased the orientational disorder of myosin heads, a random population of spin labels was superimposed on the ADP-like spectrum. In the complex DSC pattern, higher transition referred to the head region of myosin. The enthalpy of the thermal unfolding depended on the nucleotides, the conversion from a strongly attached state of myosin to actin to a weakly binding state was accompanied with an increase of the transition temperature which was due to the change of the affinity of nucleotide binding to myosin. This was more pronounced in TMDSC mode, indicating that the strong-binding state and rigor state differ energetically from each other. The different transition temperatures indicated alterations in the internal microstructure of myosin head region The monoton decreasing TMDSC heat capacities show that C _p of biological samples should not be temperature independent. This revised version was published online in August 2006 with corrections to the Cover Date.