Behavioral model synthesis with Cones

The Cones synthesis system for automatic generation of VLSI implementations is discussed. Named for the cones in sequential logic, Cones takes behavioral models written in C and produces gate-level implementations in technologies such as standard cells and programmable logic arrays or programmable logic devices. The overall design is produced faster, more efficiently, and with fewer errors. Designers are free to concentrate on functions, instead of on the details of the implementation technology     

The additivity of substrate fragments in enzyme-ligand binding

BACKGROUND: Enzymes have evolved to recognise their target substrates with exquisite selectivity and specificity. Whether fragments of the substrate--perhaps never available to the evolving enzyme--are bound in the same manner as the parent substrate addresses the fundamental basis of specificity. An understanding of the relative contributions of individual portions of ligand molecules to the enzyme-binding interaction may offer considerable insight into the principles of substrate recognition. RESULTS: We report 12 crystal structures of Escherichia coli thymidylate synthase in complexes with available fragments of the substrate (dUMP), both with and without the presence of a cofactor analogue. The structures display considerable fidelity of binding mode and interactions. These complexes reveal several interesting features: the cofactor analogue enhances the localisation of substrate and substrate fragments near the reactive thiol; the ribose moiety reduces local disorder through additional specific enzyme-ligand interactions; the pyrimidine has multiple roles, ranging from stereospecificity to mechanistic competence; and the glycosidic linkage has an important role in the formation of a covalent attachment between substrate and enzyme. CONCLUSIONS: The requirements of ligand-protein binding can be understood in terms of the binding of separate fragments of the ligand. Fragments which are subsystems of the natural substrate for the enzyme confer specific contributions to the binding affinity, orientation or electrostatics of the enzymatic mechanism. This ligand-binding analysis provides a complementary method to the more prevalent approaches utilising site-directed mutagenesis. In addition, these observations suggest a modular approach for rational drug design utilising chemical fragments.     

Domain flexibility in retroviral proteases: structural implications for drug resistant mutations

Rigid body rotation of five domains and movements within their interfacial joints provide a rational context for understanding why HIV protease mutations that arise in drug resistant strains are often spatially removed from the drug or substrate binding sites. Domain motions associated with substrate binding in the retroviral HIV-1 and SIV proteases are identified and characterized. These motions are in addition to closure of the flaps and result from rotations of approximately 6-7 degrees at primarily hydrophobic interfaces. A crystal structure of unliganded SIV protease (incorporating the point mutation Ser 4 His to stabilize the protease against autolysis) was determined to 2.0 A resolution in a new space group, P3221. The structure is in the most "open" conformation of any retroviral protease so far examined, with six residues of the flaps disordered. Comparison of this and unliganded HIV structures, with their respective liganded structures by difference distance matrixes identifies five domains of the protease dimer that move as rigid bodies against one another: one terminal domain encompassing the N- and C-terminal beta sheet of the dimer, two core domains containing the catalytic aspartic acids, and two flap domains. The two core domains rotate toward each other on substrate binding, reshaping the binding pocket. We therefore show that, for enzymes, mutations at interdomain interfaces that favor the unliganded form of the target active site will increase the off-rate of the inhibitor, allowing the substrate greater access for catalysis. This offers a mechanism of resistance to competitive inhibitors, especially when the forward enzymatic reaction rate exceeds the rate of substrate dissociation.     

Kalman-extended genetic algorithm for search in nonstationaryenvironments with noisy fitness evaluations

In basic genetic algorithm (GA) applications, the fitness of a solution takes a value that is certain and unchanging. This formulation does not work for ongoing searches for better solutions in a nonstationary environment in which expected solution fitness changes with time in unpredictable ways, or for fitness evaluations corrupted by noise. In such cases, the estimated fitness has an associated uncertainty. The uncertainties due to environmental changes (process noise) and to noisy evaluations (observation noise) can be reduced, at least temporarily, by re-evaluating existing solutions. The Kalman formulation provides a formal mechanism for treating uncertainty in GA. It provides the mechanics for determining the estimated fitness and uncertainty when a new solution is generated and evaluated for the first time. It also provides the mechanics for updating the estimated fitness and uncertainty after an existing solution is re-evaluated and for increasing the uncertainty with the passage of time. A Kalman-extended GA (KGA) is developed to determine when to generate a new individual, and when to re-evaluate an existing one and which to re-evaluate. This KGA is applied to the problem of maintaining a network configuration with minimized message loss, with mobile nodes and stochastic transmission. As the nodes move, the optimal network changes, but information contained within the population of solutions allows efficient discovery of better-adapted solutions. The sensitivity of the KGA to several control parameters is explored     

Ergonomic design of ticket barriers for use by the travelling public

This paper describes a two-stage study of the performance and acceptability of automatic ticket barriers. The aim of the research was to provide information to both manufacturers and transport operators to aid them in specifying equipment which would meet requirements for security and passenger flow and at the same time be acceptable, convenient and safe for use by passengers.

Stage one consisted of field studies at three railway stations and a laboratory evaluation of five types of ticket barrier. The field studies were undertaken to record and identify the characteristics of users and the type and frequency of problems they encountered. The laboratory trials consisted of objective and subjective evaluations of the four barriers by selected classes of user. Stage two consisted of a detailed study of certain features of barrier design, identified in stage one, including the type and speed of ticket checking, barrier dimensions and equipment for luggage handling. Results of the research have enabled design recommendations to be drawn up for use in the specification of future ticket barrier design.     

Quantum fast Fourier transform using multilevel atoms

We propose an implementation of the quantum fast Fourier transform algorithm in an entangled system of multilevel atoms. The Fourier transform occurs naturally in the unitary time evolution of energy eigenstates and is used to define an alternative wave-packet basis for quantum information in the atom. A change of basis from energy levels to wave packets amounts to a discrete quantum Fourier transform within each atom. The algorithm then reduces to a series of conditional phase transforms between two entangled atoms in mixed energy and wave-packet bases. We show how to implement such transforms using wave-packet control of the internal states of the ions in the linear ion-trap scheme for quantum computing.     

Family of G protein {alpha} chains: amphipathic analysis and predicted structure of functional domains

The G proteins transduce hormonal and other signals into regulationof enzymes such as adenylyl cyclase and retinal cGMP phosphodiesterase.Each G protein contains an subunit that binds and hydrolyzesguanine nucleotides and interacts with ß subunitsand specific receptor and effector proteins. Amphipathic andsecondary structure analysis of the primary sequences of fivedifferent chains (bovine _s, _t1 and _t2, mouse _i, and rat _o)predicted the secondary structure of a composite chain (_avg).The chains contain four short regions of sequence homologousto regions in the GDP binding domain of bacterial elongationfactor Tu (EF-Tu). Similarities between the predicted secondarystructures of these regions in _avg and the known secondary structureof EF-Tu allowed us to construct a three-dimensional model ofthe GDP binding domain of _avg. Identification of the GDP bindingdomain of _avg defined three additional domains in the compositepolypeptide. The first includes the amino terminal 41 residuesof _avg, with a predicted am phipathic helical structure; thisdomain may control binding of the chains to the ßcomplex. The second domain, containing predicted ßstrands and helices, several of which are strongly amphipathic,probably contains sequences responsible for interaction of chains with effector enzymes. The predicted structure of thethird domain, containing the carhoxy terminal 100 amino acids,is predominantly ß sheet with an amphipathic helixat the carboxy terminus. We propose that this domain is reponsiblefor receptor binding. Our model should help direct further experimentsinto the structure and function of the G protein chain.     

Systemic inflammatory load in humans is suppressed by consumption of two formulations of dried,encapsulated juice concentrate

Chronic inflammation contributes to an increased risk for developing chronic conditions such as cardiovascular disease, diabetes, and cancer. A high “inflammatory load” is defined as elevated inflammation markers in blood or other tissues. We evaluated several markers of systemic inflammation from healthy adults and tested the hypothesis that two formulations of encapsulated fruit and vegetable juice powder concentrate with added berry powders (FVB) or without (FV) could impact markers of inflammatory load. Using a double‐blind, placebo‐controlled approach, 117 subjects were randomly assigned to receive placebo, FV, or FVB capsules. Blood was drawn at baseline and after 60 d of capsule consumption. We measured inflammatory markers (high sensitivity C‐Reactive Protein, Monocyte Chemotactic Protein‐1, Macrophage Inflammatory Protein 1‐β, and Regulated upon Activation, Normal T cell Expressed and Secreted), superoxide dismutase, and micronutrients (β‐carotene, vitamin C, and vitamin E). Results showed Monocyte Chemotactic Protein‐1, Macrophage Inflammatory Protein 1‐β, and RANTES levels were significantly reduced and superoxide dismutase and micronutrient levels were significantly increased in subjects consuming both FV and FVB, relative to placebo. Data suggest a potential health benefit by consuming either formulation of the encapsulated juice concentrates through their anti‐inflammatory properties.     

Inactivity of N229A thymidylate synthase due to water-mediated effects: isolating a late stage in methyl transfer

Mutation of thymidylate synthase N229(177) to alanine results in an essentially inactive enzyme, yet it leads to formation of a stable ternary complex. The kinetics of N229(177)A show that kcat for Escherichia coli is reduced by 200-fold while the Km for dUMP is increased 200-fold and the Km for folate increased by tenfold versus the wild-type enzyme. The crystal structures of N229(177)A in complex with dUMP and CB3717, and in complex with dUMP alone are determined at 2.4 A, and 2.5 A resolution. These structures identify the covalently bound ternary complex and show how N229(177)A traps an intermediate, and so becomes inactive in a later step of the reaction. Since the smaller alanine side-chain at N229(177)A does not directly sterically impair binding of ligands, the structures implicate, and place quantitative limits on the involvement of the structured water network in the active site of thymidylate synthase in both catalysis and in determining the binding affinity for dUMP (in contrast, the N229(177)V mutation in Lactobacillus casei has minimal effect on activity).