New clues to protein structure/function Studies of the interactions involved in protein folding are shedding light on fundamental aspects of protein structure and activity relationships and providing clues about how to engineer proteins with new prop erties, according to speakers at a symposium sponsored by the Divi sion of Biochemical Technology (for merly the Division of Microbial & Biochemical Technology) at the Mi ami Beach meeting of the American Chemical Society. One speaker at the symposium, David E. Wemmer, an assistant chemistry professor at the Univer sity of California, Berkeley, and fac ulty associate at Lawrence Berkeley Laboratory, described research in which apamin, a small, neurotoxic peptide component of honeybee venom, provides a framework to sta bilize the α-helical structure of an other peptide. The research demonstrates that when the amino acids that make up what is known as the S-peptide, a well-characterized segment of the enzyme ribonuclease-A (RNase-A), are incorporated into apamin they take on a structure very similar to their structure in native RNase-A. The S-peptide /apamin hybrid binds to S-protein (the large fragment of RNase-A from which S-peptide was cleaved) and restores the enzyme's activity, Wemmer says. The hybrid also elicits antibodies that recognize both the hybrid and native RNase-A. Apamin is a small, highly stable protein. It contains 18 amino acids. Its stability derives from two disul fide bonds and significant secon dary structure, including an α-helix at the C-terminal end of the protein. In work supported by the Na tional Science Foundation, Wemmer and graduate students Joseph H. B. Pease and Richard W. Storrs creat ed hybrid proteins that consist of the eight N-terminal amino acids of apamin (which include two cyste ine residues) and 12 or 19 residues of S-peptide. The chemists replace two S-peptide amino acid residues with cysteine residues to retain the two disulfide bonds found in apamin. Despite the changes, the first 12
residues of the S-peptide fragment adopt a stable α-helical conforma tion in the hybrid, Wemmer says. Both S - p e p t i d e / a p a m i n h y b r i d s complement S-protein, strongly suggesting that the S-peptide adopts a conformation very similar to its conformation in native RNase-A. Preliminary results with two other peptide/apamin hybrids suggest that these peptide fragments also adopt α-helical structures similar to their native conformations. Such hybrids may prove useful in examining structure-function re lationships for many biologically ac tive sequences, Wemmer says. There is also the possibility that such con structs might provide a route to new vaccines. S-peptide alone, for ex ample, would be degraded in vivo before it could stimulate an immune response. The S-peptide/apamin hy brid possesses sufficient stability to elicit such a response. In the anti body research, Wemmer collaborated with Peter S. Kim of Whitehead In stitute for Biomedical Research. Rudy Baum
Use of environmental expert systems growing Environmental expert systems are increasing rapidly in number, ap plications areas are expanding, and the systems have begun to attain greater acceptability in the environ mental community as decision making tools, says Judith M. Hushon, head of artificial intelligence and information systems at Roy F. Weston Inc., Washington, D.C. Hushon pre sented her assessment at a Division of Chemical Information symposium on environmental expert systems that she organized at the recent American Chemical Society nation al meeting in Miami Beach, Fla. Hushon points out that although the first such systems came out only about five years ago, almost 70 are being used today or are in various stages of development. In addition, she says, "Whereas a number of the early systems took on very limited areas of expertise, such as the oper ation of a sewage treatment plant, the systems are now moving out to tackle siting problems and recom
mendations of complex remedial technology combinations/' She adds, "What is even more important is that expert systems are becoming an accepted vehicle for offering advice for solving environ mental problems. Over the next few years, more complex systems will be developed that share databases and tackle multiple related environ mental problems." Expert systems help solve prob lems in well-defined subject areas based on information provided by experts. To develop a system, a "knowledge engineer" questions ex perts in the field in an effort to identify the kinds of information needed to solve the problems being modeled and how this information is used to derive conclusions. This information is then programed into the system's "knowledge base." A separate "inference engine" pro vides mechanisms for interpreting commands and accessing the knowl edge base to solve problems. Initially, most expert systems were developed on microcomputers, but there has been a steady growth in the number of workstation- and minicomputer-based systems as ex pert systems have grown more so phisticated. IBM PC-ATs and com patibles are still the most common development base. "However," says Hushon, "the limit of 640K of ran dom access memory [on AT-class computers] is causing programers
Hushon: greater acceptability October 9, 1989 C&EN
25
Science/Technology
Environmental expert systems in use for varied applications System
Function
Source
System
Selection of service providers
Model front ends INHEC-1
LABSYS
Selects labs for analysis of environmental samples
Roy F. Weston Inc., EPA
TSDSYS
Selects waste treatment and recycling facilities
Roy F. Weston Inc., EPA
Selection of remedial action technology XUMA Uses chemical data to evaluate hazards and identify disposal alternatives
Nuclear Research Center, Karlsruhe, West Germany
Plan generation Work Assignment/Work Plan Generator
Uses information about a waste site to plan cleanup activities
CDM Federal Systems, EPA
Estimates costs for cleanup of waste sites Determines cost, scheduling of work required for cleanup of waste sites
EPA, CH2M Hill Inc.
CORA
SCEES
Data evaluation CADRE
Permit assistance SEPIC
Evaluates lab data on volatile and semivolatile organics and pesticides
Aid for Evaluating Redevelopment of Industrial Sites
Helps dam gate operators control water flow from reservoirs
Roy F. Weston Inc.
Helps perform environmental impact assessments at airports
ESSA Ltd.
Uses environmental and toxicological data to estimate exposure at redevelopment sites
SENES Consultants
Lockheed, EPA
Toxicity prediction Fish Toxicity Prediction Site ranking DPM
Intelligent Advisors
Permit Writer's Assistant
Assists EPA in issuing water permits for several industry sectors
EPA
Expert System for . . . Environmental Regulations
Helps identify permit regulations and documents
Siemens
WAPRA
Helps EPA review waste analysis plans, screens for potential chemical incompatibilities
EPA
to undertake ingenious solutions to fit their code into this space." Two types of development environments are used in the construction of expert systems: shells and languages. An expert system shell makes it possible to write programs using Englishlike commands, provides a built-in problem-solving paradigm, and provides functions such as screen management and the abil-
Roy F. Weston Inc.
Emergency response Dispatches forest Expert System Dispatch for Forfire control equipest Fire Control ment and crews Resources
Issues permits for on-site private sewage disposal systems
October 9, 1989 C&EN
Risk assessment SCREENER
MEPAS
i
Source
Helps select input parameters for groundwater modeling
CDM Federal Systems, EPA
Canadian Forestry Service
Uses chemical structure to predict aquatic toxicity
Department of Interior
Ranks Department of Defense hazardous waste sites based on potential threats to health and ecology Assesses potential human impacts from Department of Energy sites
Roy F. Weston Inc., U.S. Air Force
Battelle Pacific Northwest Laboratory, Department of Energy
Friupatinn
bUUvdllvll
Note: Includes environmental expert systems currently in use; excludes prototypes, other systems in development. Source: Roy F. Weston Inc.
26
Engineering MUMS
Function
Water Resources Lab Aid
Tutors students in use and calibration of water models
Regulatory evaluation Assists interpretaSmart Reg tion of underground storage tank regulations
ity to access external programs. Shells "exact a price for this functionality, however," she says. "They remove a number of design options from the developer and force expert system development within a rigidly defined environment. They also run more slowly due to the extra translation step." Nevertheless, she adds, "Shells are particularly useful for prototyping
University of Alaska
Geomet
a system to see if a problem can be solved using expert systems technology. The code can be rewritten later if the concept can be proven." The other option is to develop an expert system directly in a highlevel computer language. This may be either a language designed specifically for artificial intelligence applications, such as Prolog or LISP,
or a more generic language such as Cor Fortran. Although expert systems were first demonstrated in practice in the early 1970s, environmental expert systems only began to emerge around 1985. According to Hushon, this was because "the science for dealing with environmental problems is not well understood and there are few absolutely agreed upon methods/' In addition, environmental prob lems frequently require input from experts in several different fields, such as environmental science, civ il and chemical engineering, and toxicology, making the systems more difficult to develop. Now, about 70 environmental expert systems are in existence worldwide—about 50 in the U.S. and 20 in other coun tries, primarily Canada and West Germany. Whereas early environmental ex pert systems tended to tackle small and w e l l - u n d e r s t o o d p r o b l e m s , "there is a trend toward trying to solve more complex problems in areas where there is a higher de gree of uncertainty/' she says. For example, Daniel Greathouse of the Environmental Protection Agency's Risk Reduction Engineering Labo ratory in Cincinnati, Ohio, pointed out in another presentation at the symposium that EPA has increased its support for development of sys tems that address "a broad scope of legal, regulatory, and administrative issues." One example of this, he says, "is the recent approval of a fiveyear research initiative to support development of systems for assistance in the management and implemen tation of Superfund functions." Another reflection of the trend toward increasing complexity, says Hushon, is that expert systems are now being used "to provide 'gut reactions' to problem solutions, just as we ask experts to do. These sys tems will also be used increasingly to deal with incomplete data sets." According to Hushon, acceptance of expert systems by the environ mental community seems to be on the increase. "These types of sys tems are here to stay," she says, "and will play an increasingly im portant role as the demand for smarter systems grows." Stu Borman
Bioengineered tomatoes readied for taste trials The first taste trials on a new type of tomato grown from genetically modified plants will take place in the U.K. in a few months, when British government safety guidelines regulating the event will have been drawn up. The tomatoes are de signed by ICI Seeds to ripen on the vine without becoming soft. A problem commercial growers and retailers face is damage to their produce when tomatoes are ripe. To avoid this happening, and to prolong shelf life, harvesting usu ally takes place when the fruit is still green and firm. The ripening process continues, but the tomatoes generally lack the texture and fla vor of those that ripen on the vine. Softening results partly from a buildup of polygalacturonase, the enzyme that weakens the structure of the tomato's cell walls, as ripening occurs. Working in collaboration with Donald Grierson and his asso ciates at the University of Notting ham's department of physiology and environmental sciences, scientists at ICI Seeds' labs in Jealott's Hill, near London, produced an antisense messenger-RNA from antisense DNA, a reversed replica of the nor mal gene that encodes for polygal acturonase. When present in toma to plants, this RNA reduces output of the enzyme more than 90%. Agrobacterium tumefaciens is used as the vector for transferring the antisense messenger-RNA to cells of the Ailsa Craig variety of tomato plants used in the studies. To date, some 20,000 modified tomatoes grown in specially monitored green houses have been harvested. All will be destroyed following analysis and study, in compliance with the cur rent strict safety guidelines regulat ing research on genetically manip ulated plants. The staff at ICI Seeds believes that if the planned tasting trials are successful, improved strains of ge netically modified tomatoes could become commercially available with in five years. It also foresees that experience gained from the work could be adapted to other crops. Dermot Ο Sullivan
Microelectronics Processing Chemical Engineering Aspects
T
nis clear, easy-to-roiiow reference nils an important gap in the literature—and ties solid state process technology to its fun damental chemical engineering principles. More than 500 pages offer a complete intro duction to the principles behind microelectron ics processing, with an emphasis on siliconbased integrated circuits. Selected aspects of solid state physics are covered as well as proc essing issues. This practical manual will help to master the chemistry and chemical engineering be hind "unit operations" in microelectronic de vice fabrication, including • • • •
bulk crystal growth chemical reactions with surfaces thin-film formation lithography
• semiconductor doping This volume also addresses the correct individ ual steps for designing and carrying out com plicated processes and looks at solutions to problems posed by the extreme purity and cleanliness required. These factors point out the importance of quality control in integrated-circuit manufacture. Microelectronics Processing is an excellent introductory tutorial, with extensive lists of references for further study of individual top ics. It's ideal for academic chemical engineers who want to introduce solid state technology into the curriculum. And it's a perfect desktop resource for industrial scientists in the field, giving "need-to-know" basic information to support the practical techniques used on the job everyday. Dennis W. Hess, Editor, University of California Klavs F. Jensen, Editor, University of Minnesota Advances in Chemistry Series No. 221 523 pages (1989) Clothbound ISBN 0-8412-1475-1 LC 89-6842 U.S. & Canada $49.95 Export $59.95 0 · R · D · Ε · R
F · R · Ο · Μ
American Chemical Society Distribution Office, Dept. 35 1155 Sixteenth St. N.W. Washington, DC 20036 or CALL TOLL FREE
800-227-5558 (in Washington, P.C. 872-4363) and use your credit card! | October 9, 1989 C&EN
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