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May 3 - 4, 2005 Meeting Agenda

April 29, 2005

 

FIFRA SCIENTIFIC ADVISORY PANEL (SAP)

OPEN MEETING

MAY 3-4, 2005

FIFRA SAP WEB SITE https://www.epa.gov/scipoly/sap/

OPP Docket Telephone: (703) 305-5805

Docket Number: OPP-2005-0060

 

TSCA INVENTORY NOMENCLATURE FOR ENZYMES AND PROTEINS

 

TUESDAY, MAY 3, 2005

Holiday Inn – Rosslyn at Key Bridge

1900 North Fort Myer Drive
Arlington , Virginia 22209
Telephone: (703) 807-2000

8:30 AM Introduction and Identification of Panel Members – Steven Heeringa, Ph.D., FIFRA SAP Session Chair

8:45 AM Administrative Procedures by Designated Federal Official – Paul Lewis, Ph.D.

8:50 AM Welcome – Clifford Gabriel, Ph.D., Director, Office of Science Coordination and Policy, EPA

8:55 AM Opening Remarks – Mr. Charles Auer, Director, Office of Pollution Prevention and Toxics, EPA

9:00 AM Introduction – Mr. Neil Patel, Associate Director, Economics, Environment and Technology Division, Office of Pollution Prevention and Toxics, EPA

9:10 AM Background on TSCA Inventory – Greg Fritz, Ph.D., Chemist, Economics, Environment and Technology Division, Office of Pollution Prevention and Toxics, EPA

9:40 AM Agency’s Proposed Approach for Enzyme Identification on the TSCA Inventory - Mark Segal, Ph.D., Senior Microbiologist, Risk Assessment Division, Office of Pollution Prevention and Toxics, EPA

10:20 AM BREAK

10:30 AM Public Comments

 

EPA is proposing the use of four data elements (function, sequence, source, and processing) for comprehensively listing and distinguishing among enzymes on the TSCA Inventory. The following questions are intended to help the Agency make a final decision on how enzymes will be listed on the Inventory in the future.

Function

The function of an enzyme refers to its catalytic activity. Internationally-accepted nomenclature conventions of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB) describe and categorize enzymes based on their function. The NC-IUBMB assigns enzymes an Enzyme Committee (EC) code number based on the specific reaction(s) catalyzed by the enzyme, the nature of the bond involved, and the substrate acted upon. EPA intends to incorporate function into TSCA Inventory enzyme listings by using these EC codes and the systematic name for the specific catalytic activity. In the questions below, please identify the scientific merit for using function information to differentiate among enzymes and identify what level of detail regarding function would be scientifically appropriate for this purpose.

1.While the Agency recognizes the practical, historical advantages of using function to describe enzymes, in the context of the Agency’s need for unique and unambiguous naming, what is the scientific rationale for identifying an enzyme based on the chemical reaction(s) it catalyzes?

2. How precise is the IUBMB EC categorizing system for describing enzyme function? For example, in addition to the EC function category to which an enzyme belongs, what additional information about enzyme structure and/or chemical properties, if any, would be gained by a more detailed functional description that included

• enzyme reaction conditions (e.g., pH range, reaction temperature range)?
• non-catalytic enzyme functions that are not represented by EC codes (e.g., binding properties)?
• other additional information about function that could be used to differentiate enzymes (please specify what would be of value)?

3. The Agency is trying to gauge the probable comprehensiveness of enzyme catalytic function descriptions for subsequent enzyme reporting.

a. How common are multifunctional enzymes?

b. How frequently are new catalytic functions for existing enzymes discovered?

c. How good are existing models to assess the likelihood that an enzyme may have several catalytic functions?

• What information is required to utilize such models?

 

12:30 PM LUNCH

1:30 PM Panel Discussion

Sequence The amino acid sequence of an enzyme is known as its primary structure. It is a systematic representation of the linear sequence of amino acids that are connected via amide bonds to form a polypeptide. In the questions below, please consider what scientific support there is for using sequence information to differentiate among enzymes and what level of detail would be scientifically appropriate for this purpose.

4. What information about an enzyme could be gained by identifying it based on its amino acid sequence?

5. The Agency is trying to assess the expected amount of variation in an enzyme amino acid sequence due to various causes in spite of current quality control standards.

a. How much and what type of variation (including substitutions, deletions, and additions) can be expected in the amino acid sequence of an enzyme produced in multiple batches that will arise due to unintended differences in production conditions? Estimate a percentage, number of residues, or other quantifiable measure of variation.

b. How much and what type of variation (including substitutions, deletions, and additions) can be expected in the amino acid sequence of an enzyme within a given sample of a single production batch due to individual-level variation in an enzyme-producing population? Estimate a percentage, number of residues, or other quantifiable measure of variation.

c. How much and what type of variation (including substitutions, deletions, and additions) can be expected in the amino acid sequence of an enzyme across multiple samples collected over time (e.g., in microbial cultures stored for extended periods) due to changes in an enzyme-producing population? Estimate a percentage, number of residues, or other quantifiable measure of variation.

 

i..Over what time scale will such variation arise? That is, is there a predictable relationship between the amount of variation and the length of time in culture?

ii. What kinds of changes might occur to an enzyme preparation if naturally occurring variants become the dominant component (e.g., changes in rates of activity, reactions catalyzed, substrate range, response to environmental conditions)?

iii.Have any enzymes in commerce or research been known to change in amino acid sequence over time? Have any been known to remain unchanged in amino acid sequence for a year/decade or longer? 

• EPA is trying to judge whether a scientifically appropriate level of maximum permissible overall amino acid sequence variation could be determined when identifying a specific enzyme.
  • What types of differences may exist among enzyme variants that differ by a single amino acid change? What types of differences may exist among enzyme variants that differ in amino acid composition by 0.5%? 1%? 10%? etc.?
  • How much does the region of the enzyme in which the variation occurs matter? For example, how important are changes in the amino acid sequence of the active site versus the rest of the molecule? Are there other regions of the enzyme that are considered important, i.e., where sequence is generally conserved?

d. How important are deletions and/or excisions in determining differences between enzymes?

• How easy would it be for a typical enzyme manufacturer to determine the location of the active site or other specific regions mentioned in 6b?

 

3:00 PM BREAK

3:15 PM Panel Discussion (continued)

 

• EPA wants to assess the efficacy of existing sequencing technologies.
  • How accurate and reproducible are readily available amino acid sequencing techniques and instrumentation?
  • How accurate and reproducible are readily available nucleotide sequencing techniques and instrumentation?
  • Does the accuracy of the result depend on the choice of method?
  • How rapidly are sequencing techniques improving or new techniques being developed?
  • How reliably can one predict the amino acid sequence of the final gene product based on the nucleotide sequence?
     
• What additional information would be gained, if any, by a more detailed structural description that included in addition to amino acid sequence:
  • glycosylation sites (and the composition of these carbohydrate moieties),
  • coenzymes (prosthetic groups),
  • cofactors, and/or
  • other post-translational modifications to residues of the amino acid chain?

 

4 :30 PMADJOURNMENT

FIFRA SCIENTIFIC ADVISORY PANEL (SAP)

OPEN MEETING

MAY 4, 2005

FIFRA SAP WEB SITE https://www.epa.gov/scipoly/sap/

OPP Docket Telephone: (703) 305-5805

Docket Number: OPP-2005-0060

 

TSCA INVENTORY NOMENCLATURE FOR ENZYMES AND PROTEINS

 

WEDNESDAY, MAY 4, 2005

Holiday Inn – Rosslyn at Key Bridge

1900 North Fort Myer Drive
Arlington , Virginia 22209
Telephone: (703) 807-2000

8:30 AM Introduction and Identification of Panel Members – Steven Heeringa, Ph.D., FIFRA SAP Session Chair

8:35 AM Administrative procedures by Designated Federal Official – Paul Lewis, Ph.D.

8:40 AM Follow-up from Previous Day’s Discussion - Mark Segal, Ph.D., Senior Microbiologist, Risk Assessment Division, Office of Pollution Prevention and Toxics, EPA

9:00 AM Panel Discussion (continued)

 Source The source of an enzyme refers to (1) the organism from which the gene encoding the enzyme was derived, i.e., the original source and(2) the organism or manufacturing platform (e.g., tissue culture) in which the enzyme is produced, i.e., the production source. In the questions below, please consider what scientific support there is for using source information to differentiate among enzymes and what level of detail would be scientifically appropriate for this purpose.   What information about an enzyme’s structure could be gained by knowing the original source of the enzyme? the production source of the enzyme? If original source information were used as an identification element to discriminate among enzymes, what level of taxonomic specificity (e.g., family, genus, species, subspecies, population, biovar, culture line) would be most scientifically appropriate to use for each of the following categories? What if production source information were used? (Note: EPA recognizes that taxonomic revisions may change the names of particular organisms and can utilize mechanisms for normalizing organism nomenclature, but that consideration does not need to be addressed by the panel.)

• plants
• animals
• fungi
• bacteria
• other micro-organisms

10:30 AM BREAK

• How could source be described if taxonomic names were inappropriate because either the original or production source were artificial? Examples of such new technologies could include enzymes produced/developed through gene splicing or ex vivo chemical synthesis.
• What information about an enzyme’s structure could be gained by additional details about source including:
  • the particular tissue or organ of a given source organism from which they were derived (e.g., swine pancreatic tissue vs. swine salivary glands)?
  • the chemical, geographic, and/or environmental conditions from which source organisms were isolated (e.g., soil, water, feces, etc.)?
  • manipulations of the enzymes original source prior to gene transfer (e.g., through rDNA technology, radiation treatment, altered rearing conditions, etc.)?

d. manipulations of an enzymes production source prior to and/or following gene transfer?

e. other relevant aspects of source that are not mentioned (please specify what would be of value).

12:00 PM LUNCH

1 :00 PM Panel Discussion (continued)

• Processing
  
• The processing of an enzyme refers to procedures used to isolate the enzyme from the production organism or manufacturing platform, procedures used to purify the enzyme, and/or any chemical reactions to which the enzyme is subjected to produce the final enzyme product. In the questions below, please consider what scientific support there is for using certain processing information to differentiate among enzymes and identify the level of detail that would be scientifically appropriate for this purpose.

13 . What information about an enzyme’s structure could be gained by knowing which of certain processing techniques were used in its production?

14. EPA anticipates that certain processing techniques may be so routine and/or chemically inconsequential that their reporting would be unnecessary, while other processing techniques would have significant effects on the chemical structure and/or properties of an enzyme. The Agency is trying to assess how practical it would be to create a list of processing techniques that need not be included as part of enzyme identity.

• What processing techniques are used in the isolation and purification of enzymes?
• Which processing techniques could change the chemical structure of the enzyme? Which could change chemical properties that would indicate an underlying structural change?
• Describe the chemical or structural changes expected to occur from the use of the processing techniques identified in 14(b).
• Which processing techniques would not be expected to cause any structural changes to the enzyme? Which would not be expected to cause any chemical property changes?

3:00 AM BREAK

3 :15 PM Panel Discussion (continued)

• EPA is trying to anticipate whether inclusion of processing in enzyme identity will increase in importance as a result of future advances in enzyme production.
  • What new processing techniques are being developed?
  • How might these techniques change an enzyme’s chemical structure or properties?
  • How frequently are new processing techniques for enzymes adopted?
    
• Other/General Questions:

 

• Aside from function, sequence, source, and processing, are any other data elements crucial for enzyme identification?
  
• Are there any special considerations that should be taken into account when identifying enzymes with multiple, non-identical subunits? For example,
  • when only one subunit is modified?
  • when a modified enzyme is a component of an enzyme complex?
  • when a multi-functional, multi-component enzyme performs a sequence of reactions?
  • when an enzyme has another non-catalytic function, e.g., a binding site?
  • under any other circumstances?
    
• Although EPA believes that all four identification elements are critical for enzyme identification for TSCA purposes, the Agency is trying to judge their relative importance.
  • Do any data elements warrant greater emphasis than others because differences in those data element(s) reflect more significant differences in an enzyme’s physical and/or chemical properties than the others do?
  • If data for sequence, source, and processing were the same for two enzymes (at the level of detail you have determined to be appropriate in the questions above), what additional information about chemical structure and/or properties would be provided by distinguishing the enzymes based on function?
  • If data for function, sequence, and processing were the same for two enzymes (at the level of detail you have determined to be appropriate in the questions above), what additional information about chemical structure and/or properties would be provided by distinguishing the enzymes based on (1) original source and (2) production source?
  • If data for function, sequence, and source were the same for two enzymes (at the level of detail you have determined to be appropriate in the questions above), what additional information about chemical structure and/or properties would be provided by distinguishing the enzymes based on processing?

 

5 :00 PMADJOURNMENT

 

Please be advised that agenda times are approximate. For further information, please contact the Designated Federal Official for this meeting, Paul Lewis via telephone: (202) 564-8450; fax: (202) 564-8382; or email: lewis.paul@epa.gov

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