Analysis of Enzyme Structure and Activity by Protein Engineering

Structure-activity relationships of enzymes can now be analyzed for the first time by the systematic alteration of protein structure. Recent developments in the chemical synthesis of DNA fragments and recombinant DNA technology enable the facile modification of proteins by highly specific mutagenesis of their genes. Kinetic analysis of the mutant enzymes combined with high-resolution structural data from protein X-ray crystallography allow direct measurements on the relationships between structure and function. In particular, the strength and nature of enzyme-substrate interactions and their detailed roles in catalysis and specificity can now be studied. We have developed such analysis of enzyme structure-function by site-directed mutagenesis of the tyrosyl-tRNA synthetase from Bacillus stearothermophilus, concentrating so far on the subtle role of hydrogen bonding in both substrate specificity and catalysis. We find that the energetics of tyrosine and ATP binding must be analyzed in terms of an exchange reaction with solvent water. Based on this idea and structural data, we have engineered an enzyme of improved enzyme-substrate affinity, and there thus appear to be real prospects of engineering proteins of new specificities, activities, and structural properties. We are also using protein engineering to gather direct information on the nature of enzyme catalysis. For example, we find the catalysis of formation of Tyr-AMP from Tyr and ATP is due largely to electrostatic and hydrogen bonding interactions that are stronger in the transition state than in the ground state—a “strain” mechanism rather than acid-base or covalent catalysis.     

Staggered ladder spectra

We exactly solve a Fokker-Planck equation by determining its eigenvalues and eigenfunctions: we construct nonlinear second-order differential operators which act as raising and lowering operators, generating ladder spectra for the odd- and even-parity states. The ladders are staggered: the odd-even separation differs from even-odd. The Fokker-Planck equation corresponds, in the limit of weak damping, to a generalized Ornstein-Uhlenbeck process where the random force depends upon position as well as time. The process describes damped stochastic acceleration, and exhibits anomalous diffusion at short times and a stationary non-Maxwellian momentum distribution.     

Perturbation Theory for a Stochastic Process with Ornstein-Uhlenbeck Noise

The Ornstein-Uhlenbeck process may be used to generate a noise signal with a finite correlation time. If a one-dimensional stochastic process is driven by such a noise source, it may be analysed by solving a Fokker-Planck equation in two dimensions. In the case of motion in the vicinity of an attractive fixed point, it is shown how the solution of this equation can be developed as a power series. The coefficients are determined exactly by using algebraic properties of a system of annihilation and creation operators.     

A pulsed, optically-pumped rubidium laser at high pump intensity

A rubidium laser operating at 795 nm is optically pumped by a pulsed titanium sapphire laser to investigate the dynamics of Diode Pumped Alkali Lasers (DPALs). Linear scaling of output intensity for longitudinal excitation at intensities of 1.3-43 kW/cm² and as much as 32 times threshold is observed. The slope efficiency depends directly on the number of absorbed photons for alkali concentrations of 0.8-2.0 × 10¹³ atoms/cm³ with no evidence for second order kinetics. The effective absorption cross section is reduced in part by the broad spectral width of the pump source relative to the pressure broadened lineshape. Spin orbit relaxation between the pumped and upper laser levels is sufficiently fast at 550 Torr of methane to prevent bottlenecking at all but the highest intensities. Comparison of laser characteristics with a quasi-two level analytic model suggests performance near the ideal steady-state limit, with the exception of modest mode matching.     

Determination of elastic strain fields and geometrically necessary dislocation distributions near nanoindents using electron back scatter diffraction

The deformation around a 500-nm deep Berkovich indent in a large grained Fe sample has been studied using high resolution electron back scatter diffraction (EBSD). EBSD patterns were obtained in a two-dimensional map around the indent on the free surface. A cross-correlation-based analysis of small shifts in many sub-regions of the EBSD patterns was used to determine the variation of elastic strain and lattice rotations across the map at a sensitivity of ～±10^?4. Elastic strains were smaller than lattice rotations, with radial strains found to be compressive and hoop strains tensile as expected. Several analyses based on Nye's dislocation tensor were used to estimate the distribution of geometrically necessary dislocations (GNDs) around the indent. The results obtained using different assumed dislocation geometries, optimisation routines and different contributions from the measured lattice rotation and strain fields are compared. Our favoured approach is to seek a combination of GND types which support the six measurable (of a possible nine) gradients of the lattice rotations after correction for the 10 measurable elastic strain gradients, and minimise the total GND line energy using an L¹ optimisation method. A lower bound estimate for the noise on the GND density determination is ～±10¹² m^?2 for a 200-nm step size, and near the indent densities as high as 10¹⁵ m^?2 were measured. For comparison, a Hough-based analysis of the EBSD patterns has a much higher noise level of ～±10¹⁴m^?2 for the GND density.     

Variable-range projection model for turbulence-driven collisions

We discuss the relative speeds DeltaV of inertial particles suspended in a highly turbulent gas when the Stokes number, a dimensionless measure of their inertia, is large. We identify a mechanism giving rise to the distribution P(DeltaV) approximately exp(-C|DeltaV|(4/3)) (for some constant C). Our conclusions are supported by numerical simulations, and by the analytical solution of a model equation of motion. The results determine the rate of collisions between suspended particles. They are relevant to the hypothesized mechanism for formation of planets by aggregation of dust particles in circumstellar nebula.     

Two polymorphs of 20‐desmethyl‐β‐carotene

Two polymorphs of 20‐desmethyl‐β‐carotene (systematic name: 20‐nor‐β,β‐carotene), C₃₉H₅₄, in monoclinic and triclinic space groups, were formed in the same vial by recrystallization from pyridine and water. Each polymorph crystallizes with the complete molecule as the asymmetric unit, and the two polymorphs show differing patterns of disorder. The β end rings of both polymorphs have the 6‐s‐cis conformation, and are twisted out of the plane of the polyene chain by angles of −53.2 (8) and 47.3 (8)° for the monoclinic polymorph, and −43.6 (3) and 56.1 (3)° for the triclinic polymorph. The cyclohexene end groups are in the half‐chair conformation, but the triclinic polymorph shows disorder of one ring. Overlay of the molecules shows that they differ in the degree of nonplanarity of the polyene chains and the angles of twist of the end rings. The packing arrangements of the two polymorphs are quite different, with the monoclinic polymorph showing short intermolecular contacts of the disordered methyl groups with adjacent polyene chain atoms, and the triclinic polymorph showing π–π stacking interactions of the almost parallel polyene chains. The determination of the crystal structures of the two title polymorphs of 20‐desmethyl‐β‐carotene allows information to be gained regarding the structural effects on the polyene chain, as well as on the end groups, versus that of the parent compound β‐carotene. The absence of the methyl group is known to have an impact on various functions of the title compound.     

Light-emitting iridium complexes with tridentate ligands

Once the Cinderella amongst the Platinum Group Metals at the Photochemistry Ball, iridium has become of intense interest since the beginning of the decade. Complexes of iridium(III) can be prepared that are highly luminescent, with emission wavelengths tuneable over the whole of the visible region. Whilst most studies have focused on tris-bidentate complexes, a rich and varied chemistry is also possible using tridentate ligands. In this review, we discuss the synthesis and excited-state properties of such complexes, exploring in particular how the number of cyclometallating carbon atoms in the coordination sphere of the metal ion influences the luminescence. Moving from [IrN6]3+ to [IrN3X3] coordination via [IrN5X]2+ and cis/trans-[IrN4X2]+ complexes, where N is a heterocyclic nitrogen and X is an anionic ligand or cyclometallated carbon, a whole range of luminescence efficiencies are encountered, ranging from the barely detectable to room temperature quantum yields approaching unity. We consider the extent to which these profound differences, arising as a result of subtle changes in molecular structure, can be rationalised in terms of the nature of the frontier orbitals.