Design of fast enzymes by optimizing interaction potential in active site

The diffusional encounter between substrate and enzyme, and hence catalytic efficiency, can be enhanced by mutating charged residues on the surface of the enzyme. In this paper we present a simple method for screening such mutations. This is based on our earlier result that electrostatic enhancement of the enzyme-substrate binding rate constant can be accounted for just by the interaction potential within the active site. Assuming that catalytic and structural integrity is maintained, the catalytic efficiency can be optimized by surface charge mutations which lead to stronger interaction potential within the active site. Application of the screening method on superoxide dismutase shows that only charge mutations close to the active site will have practical effect on the catalytic efficiency. This rationalizes a large number of findings obtained in previous simulation and experimental studies.

Rational design of a global inhibitor of the virulence response in Staphylococcus aureus, based in part on localization of the site of inhibition to the receptor-histidine kinase, AgrC

Two-component signaling systems involving receptor-histidine kinases are ubiquitous in bacteria and have been found in yeast and plants. These systems provide the major means by which bacteria communicate with each other and the outside world. Remarkably, very little is known concerning the extracellular ligands that presumably bind to receptor-histidine kinases to initiate signaling. The two-component agr signaling circuit in Staphylococcus aureus is one system where the ligands are known in chemical detail, thus opening the door for detailed structure–activity relationship studies. These ligands are short (8- to 9-aa) peptides containing a thiolactone structure, in which the α-carboxyl group of the C-terminal amino acid is linked to the sulfhydryl group of a cysteine, which is always the fifth amino acid from the C terminus of the peptide. One unique aspect of the agr system is that peptides that activate virulence expression in one group of S. aureus strains also inhibit virulence expression in other groups of S. aureus strains. Herein, it is demonstrated by switching the receptor-histidine kinase, AgrC, between strains of different agr specificity types, that intragroup activation and intergroup inhibition are both mediated by the same group-specific receptors. These results have facilitated the development of a global inhibitor of virulence in S. aureus, which consists of a truncated version of one of the naturally occurring thiolactone peptides.

Identification of a second aryl phosphate-binding site in protein-tyrosine phosphatase 1B: A paradigm for inhibitor design

The structure of the catalytically inactive mutant (C215S) of the human protein-tyrosine phosphatase 1B (PTP1B) has been solved to high resolution in two complexes. In the first, crystals were grown in the presence of bis-(para-phosphophenyl) methane (BPPM), a synthetic high-affinity low-molecular weight nonpeptidic substrate (Km = 16 μM), and the structure was refined to an R-factor of 18.2% at 1.9 Å resolution. In the second, crystals were grown in a saturating concentration of phosphotyrosine (pTyr), and the structure was refined to an R-factor of 18.1% at 1.85 Å. Difference Fourier maps showed that BPPM binds PTP1B in two mutually exclusive modes, one in which it occupies the canonical pTyr-binding site (the active site), and another in which a phosphophenyl moiety interacts with a set of residues not previously observed to bind aryl phosphates. The identification of a second pTyr molecule at the same site in the PTP1B/C215S–pTyr complex confirms that these residues constitute a low-affinity noncatalytic aryl phosphate-binding site. Identification of a second aryl phosphate binding site adjacent to the active site provides a paradigm for the design of tight-binding, highly specific PTP1B inhibitors that can span both the active site and the adjacent noncatalytic site. This design can be achieved by tethering together two small ligands that are individually targeted to the active site and the proximal noncatalytic site.

Negative pH, efflorescent mineralogy, and consequences for environmental restoration at the Iron Mountain Superfund site, California

The Richmond Mine of the Iron Mountain copper deposit contains some of the most acid mine waters ever reported. Values of pH have been measured as low as −3.6, combined metal concentrations as high as 200 g/liter, and sulfate concentrations as high as 760 g/liter. Copious quantities of soluble metal sulfate salts such as melanterite, chalcanthite, coquimbite, rhomboclase, voltaite, copiapite, and halotrichite have been identified, and some of these are forming from negative-pH mine waters. Geochemical calculations show that, under a mine-plugging remediation scenario, these salts would dissolve and the resultant 600,000-m3 mine pool would have a pH of 1 or less and contain several grams of dissolved metals per liter, much like the current portal effluent water. In the absence of plugging or other at-source control, current weathering rates indicate that the portal effluent will continue for approximately 3,000 years. Other remedial actions have greatly reduced metal loads into downstream drainages and the Sacramento River, primarily by capturing the major acidic discharges and routing them to a lime neutralization plant. Incorporation of geochemical modeling and mineralogical expertise into the decision-making process for remediation can save time, save money, and reduce the likelihood of deleterious consequences.

Molecular design of the N-methyl-D-aspartate receptor binding site for phencyclidine and dizolcipine.

The N-methyl-D-aspartate receptor (NMDAR), a pivotal entity for synaptic plasticity and excitotoxicity in the brain, is a target of psychotomimetic drugs such as phencyclidine (PCP) and dizolcipine (MK-801). In contrast, a related glutamate receptor, the alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate/kainate receptor GluR1, is weakly sensitive to these drugs. Three point mutations on GluR1, mimicking homologous residues on the NMDAR, confer the PCP and MK-801 blockade properties that are characteristic of the NMDAR--namely, high potency, voltage dependence, and use dependence. The molecular determinants that specify the PCP block appear confined to the putative M2 transmembrane segment, whereas the sensitivity to MK-801 requires an interplay between residues from M2 and M3. Given the plausible involvement of the NMDAR in the etiology of several neurodegenerative diseases and in excitotoxic neuronal cell death, tailored glutamate receptors with specific properties may be models for designing and screening new drugs targeted to prevent glutamate-mediated neural damage.

Improving urban park design: A comparative and analytical study addressing resources available and components necessary to improve the environmental and economic sustainability of urban parks

Urban parks have long been valued for the environmental, social, and economic benefits they provide. Increasingly, parks are also being recognized as features important for sustainable city design. This Capstone Project will identify, compare, analyze, and discuss means for designing sustainable urban parks. Recommendations for designing sustainable urban parks, based on project results, include: 1) ensure park features will support high levels of human activity; 2) use gravel to construct park trails; 3) purchase playground structures made of recycled materials; 4) plant a high number of perennials in flowerbeds and other vegetated areas; 5) plant climate-appropriate plants in vegetated areas; 6) ensure parks have high levels of plant diversity; and 7) develop future studies further exploring sustainable park design.

Industry Professionals Who Attain Leadership in Energy and Environmental Design (LEED) Accreditation: An Examination of Motivations in Human Resource (HR) Training and Development

Despite the economy, the green building industry continues to grow and drive the demand for environmentally conscious, highly skilled professionals (USGBC 2009). LEED Accredited Professionals (APs) have the knowledge and skills to meet such demand; however, information is limited regarding LEED APs or their motivations and expectations toward prospective employers. The author surveyed a sample of LEED Accredited architects and found a combination of job and personal factors motivated them to attain accreditation. LEED APs value both a competitive salary and commitment to sustainability in prospective employers. To attract, retain, and utilize LEED APs, executives in this industry must reexamine corporate culture, their willingness to pay for credentialing, and the alignment of their reputation with the desires of potential applicants.

Combined simulation-optimization methodology for the design of environmental conscious absorption systems

This work addresses the optimization of ammonia–water absorption cycles for cooling and refrigeration applications with economic and environmental concerns. Our approach combines the capabilities of process simulation, multi-objective optimization (MOO), cost analysis and life cycle assessment (LCA). The optimization task is posed in mathematical terms as a multi-objective mixed-integer nonlinear program (moMINLP) that seeks to minimize the total annualized cost and environmental impact of the cycle. This moMINLP is solved by an outer-approximation strategy that iterates between primal nonlinear programming (NLP) subproblems with fixed binaries and a tailored mixed-integer linear programming (MILP) model. The capabilities of our approach are illustrated through its application to an ammonia–water absorption cycle used in cooling and refrigeration applications.

Quality Management, Environmental Management and Organizational Design in the Hotel Industry: A Qualitative Study

The purpose of this paper is twofold. First, the paper analyzes the relationship between quality management and environmental management and their effects on hotel performance. Second, the article examines the relationship between these two management systems and organizational design. The paper uses an exploratory, qualitative approach based on interviews with managers and experts in the hotel industry. Based on a content analysis of interviews, the results lead to several propositions. Specifically, quality and environmental management influence hotel performance through mediating variables. Moreover, the implementation of quality management facilitates the implementation of environmental management. Furthermore, the implementation of these two management systems is associated with an increase of formalization and decentralization. The paper contributes to the analysis of quality management, environmental management, organizational design and performance in a joint manner, which has not been attempted before in the hotel industry. In addition, it helps extend the findings about these links in manufacturing and service organizations to the hotel industry.

Dating sediments in coastal areas and potential applications for constraining the palaeo-environmental context of an archaeological site at Vohemar

We present an overview on different environmental zones within coastal areas and summarise the physical basis behind the three most important methods that are available to date Holocene coastal sediments. Besides radiocarbon and uranium series dating, Optically Stimulated Luminescence (Osl) has increasingly been applied for dating in coastal settings over the past decade. This is illustrated by a number of case studies showing that Osl can be applied to sediments from almost any kind of coastal environment, covering a potential dating range from some years up to several hundred thousand years. Osl dating may hence be the method of choice for deciphering natural environmental change along coasts as well as the presence and the impact of human occupation in such areas. In addition, we briefly show how and where these dating methods could be applied to constrain the palaeo-environmental context of an archaeological site at Vohemar in north-eastern Madagascar.

Herbert Hoover national historic site, interpretive prospectus (1971) B1; Natural resources management plan (1980) B2; Cultural resources management plan (1981) B3; Annual statement for interpretation and visitor services B4; Snowmobile use, environmental assessment (EA) : environmental impact statement.

Mode of access: Internet.

Los Angeles-Long Beach (LA-2) ocean dredged material disposal site designation : environmental impact statement.

Mode of access: Internet.

Design and evaluation of innovative hazardous waste treatment technologies at McClellan AFB,

Mode of access: Internet.

Draft environmental impact statement, general management plan : Fort Davis National Historic Site, Texas.

"NPS D-45"--P. [3] of cover.

Safety and environmental design considerations in the use of commercial electronic variable-message signage. Final report.

Mode of access: Internet.