http://gcat.davidson.edu/GcatWiki/api.php?action=feedcontributions&feedformat=atom&user=Eric.sawyer 2026-05-20T07:21:58Z User contributions MediaWiki 1.28.2 http://gcat.davidson.edu/GcatWiki/index.php?title=User:Eric.sawyer&diff=8450 2009-06-11T01:27:42Z

<p>Eric.sawyer: </p> <hr /> <div>I am a high school student at Central High School, class of 2010. I am interested in chemistry and biology, and have enjoyed the laboratory and research opportunities at my school. My past independent research has been in the areas of evolutionary biology, genetics/bioinformatics, and microbiology. I enjoy science and plan to pursue a career in research with a PhD in a chemical or biological field. With respect to the 2009 iGEM project my role is to work with physical and virtual protein modeling, in addition to helping with the overall project. I was invited to participate in the project by Dr. Eckdahl, whom I have known for some time and whose son is best friends with my little brother. I am experienced in or acquainted with general microbiological techniques and some genetics techniques such as PCR, electrophoresis, and transformation and am eager to learn more this summer. I also have a strong general biology and chemistry background, so I manage to generally keep up!</div>

Eric.sawyer http://gcat.davidson.edu/GcatWiki/index.php?title=How_do_signal_sequences/peptides_work_in_bacteria,_and_how_can_we_use_them%3F&diff=8448 2009-06-10T20:58:26Z

<p>Eric.sawyer: /* Questions That Need Addressed */</p> <hr /> <div>== What are signal sequences? ==<br /> Signal sequences are &quot;leader&quot; amino acids on the amino end of a polypeptide. They are recognized by soluble signal recognition proteins and docking proteins that facilitate the attachment of the ribosome-peptide complex to the cell membrane and the translocation of the polypeptide. The signal sequence is cleaved off of the preprotein by a signal peptidase that recognizes the signal sequence's 3-D conformation rather than sequence. The remaining &quot;mature&quot; protein then passes through the cell membrane. As of January 2008 no inhibitors of the signal pepsidase cleavage process have been described. Signal sequences are restricted to general rules about amino acid placement. The signal sequence itself, from amino to carboxy terminus, is described as follows: the positively-charged &quot;n-region&quot; of roughly 1-5 amino acids, the &quot;core&quot; or &quot;h-region&quot; of about 7-15 hydrophobic amino acids, and lastly the cleavage or carboxy-terminal of principally hydrophilic but rarely charged amino acids. Following the carboxy end of the signal sequence are the amino acids of the mature protein that will ultimately be transported across the designated membrane. Of important note is the (-3,-1)-rule, which states that the amino acids in the -1 and -3 positions must be uncharged and small in size (usually alanine). -3 and -1 refer to three amino acids and one amino acid, respectively, from the mature protein's first amino acid to the amino terminus of the signal sequence.<br /> <br /> == How can we use signal sequences in our project? ==<br /> Signal sequences would allow us to remove the FSL from the protein. We would have to insert a signal sequence that ''E. coli'' can recognize between the FSL and the wild type peptide sequence. This would potentially allow us to remove the entire FSL and signal sequence from the protein before it is fully translated.<br /> <br /> == Questions That Need Addressed ==<br /> #Will using this technique require that the reporter protein be excreted from the cell (which would pose a problem for antibiotic resistance proteins)?<br /> #What are some examples of the use of signal sequences in ''E. coli'', both in nature and the lab?<br /> #What are the length constraints for signal sequences?<br /> #How often is the signal sequence found in the ''E. coli'' genome, and will this pose a problem?<br /> #Are signal sequences adaptable to different proteins (ie could we insert one before GFP)?<br /> #How are signal peptidases regulated by ''E. coli''?<br /> #Is this the mechanism by which ''E. coli'' excretes proteins into its extracellular space?<br /> #Will adding the FSL disable the signal sequence? The literature suggests that the amino end must carry an amino acid-generated positive charge. This may not be possible because the FSL must be on the amino end of the signal sequence in order to be removed.<br /> <br /> == References ==<br /> #[http://www.jbc.org/cgi/reprint/266/2/1326 Leader chemical constraints, MOST RELEVANT, full text]<br /> #[http://www.springerlink.com/content/hg2kq7t800m3v833/ Highly relevant but partial paper--is there any chance of getting the full text for free?]<br /> #[http://peds.oxfordjournals.org/cgi/reprint/10/1/1.pdf General information and predicting cleavage sites]</div>

Eric.sawyer http://gcat.davidson.edu/GcatWiki/index.php?title=How_do_signal_sequences/peptides_work_in_bacteria,_and_how_can_we_use_them%3F&diff=8435 2009-06-10T19:56:05Z

<p>Eric.sawyer: </p> <hr /> <div>== What are signal sequences? ==<br /> Signal sequences are &quot;leader&quot; amino acids on the amino end of a polypeptide. They are recognized by soluble signal recognition proteins and docking proteins that facilitate the attachment of the ribosome-peptide complex to the cell membrane and the translocation of the polypeptide. The signal sequence is cleaved off of the preprotein by a signal peptidase that recognizes the signal sequence's 3-D conformation rather than sequence. The remaining &quot;mature&quot; protein then passes through the cell membrane. As of January 2008 no inhibitors of the signal pepsidase cleavage process have been described. Signal sequences are restricted to general rules about amino acid placement. The signal sequence itself, from amino to carboxy terminus, is described as follows: the positively-charged &quot;n-region&quot; of roughly 1-5 amino acids, the &quot;core&quot; or &quot;h-region&quot; of about 7-15 hydrophobic amino acids, and lastly the cleavage or carboxy-terminal of principally hydrophilic but rarely charged amino acids. Following the carboxy end of the signal sequence are the amino acids of the mature protein that will ultimately be transported across the designated membrane. Of important note is the (-3,-1)-rule, which states that the amino acids in the -1 and -3 positions must be uncharged and small in size (usually alanine). -3 and -1 refer to three amino acids and one amino acid, respectively, from the mature protein's first amino acid to the amino terminus of the signal sequence.<br /> <br /> == How can we use signal sequences in our project? ==<br /> Signal sequences would allow us to remove the FSL from the protein. We would have to insert a signal sequence that ''E. coli'' can recognize between the FSL and the wild type peptide sequence. This would potentially allow us to remove the entire FSL and signal sequence from the protein before it is fully translated.<br /> <br /> == Questions That Need Addressed ==<br /> #Will using this technique require that the reporter protein be excreted from the cell (which would pose a problem for antibiotic resistance proteins)?<br /> #What are some examples of the use of signal sequences in ''E. coli'', both in nature and the lab?<br /> #What are the length constraints for signal sequences?<br /> #How often is the signal sequence found in the ''E. coli'' genome, and will this pose a problem?<br /> #Are signal sequences adaptable to different proteins (ie could we insert one before GFP)?<br /> #How are signal peptidases regulated by ''E. coli''?<br /> #Is this the mechanism by which ''E. coli'' excretes proteins into its extracellular space?<br /> <br /> == References ==<br /> #[http://www.jbc.org/cgi/reprint/266/2/1326 Leader chemical constraints, MOST RELEVANT, full text]<br /> #[http://www.springerlink.com/content/hg2kq7t800m3v833/ Highly relevant but partial paper--is there any chance of getting the full text for free?]<br /> #[http://peds.oxfordjournals.org/cgi/reprint/10/1/1.pdf General information and predicting cleavage sites]</div>

Eric.sawyer http://gcat.davidson.edu/GcatWiki/index.php?title=How_do_signal_sequences/peptides_work_in_bacteria,_and_how_can_we_use_them%3F&diff=8434 2009-06-10T19:46:36Z

<p>Eric.sawyer: </p> <hr /> <div>== What are signal sequences? ==<br /> Signal sequences are &quot;leader&quot; amino acids on the amino end of a polypeptide. They are recognized by soluble signal recognition proteins and docking proteins that facilitate the attachment of the ribosome-peptide complex to the cell membrane and the translocation of the polypeptide. The signal sequence is cleaved off of the preprotein by a signal peptidase that recognizes the signal sequence's 3-D conformation rather than sequence. The remaining &quot;mature&quot; protein then passes through the cell membrane. As of January 2008 no inhibitors of the signal pepsidase cleavage process have been described. Signal sequences are restricted to general rules about amino acid placement. The signal sequence itself, from amino to carboxy terminus, is described as follows: the positively-charged &quot;n-region&quot; of roughly 1-5 amino acids, the &quot;core&quot; or &quot;h-region&quot; of about 7-15 hydrophobic amino acids, and lastly the cleavage or carboxy-terminal of principally hydrophilic but rarely charged amino acids. Following the carboxy end of the signal sequence are the amino acids of the mature protein that will ultimately be transported across the designated membrane. Of important note is the (-3,-1)-rule, which states that the amino acids in the -1 and -3 positions must be uncharged and small in size (usually alanine). -3 and -1 refer to three amino acids and one amino acid, respectively, from the mature protein's first amino acid to the amino terminus of the signal sequence.<br /> <br /> == How can we use signal sequences in our project? ==<br /> Signal sequences would allow us to remove the FSL from the protein. We would have to insert a signal sequence that ''E. coli'' can recognize between the FSL and the wild type peptide sequence. This would potentially allow us to remove the entire FSL and signal sequence from the protein before it is fully translated.<br /> <br /> == Questions That Need Addressed ==<br /> #Will using this technique require that the reporter protein be excreted from the cell (which would pose a problem for antibiotic resistance proteins)?<br /> #What are some examples of the use of signal sequences in ''E. coli'', both in nature and the lab?<br /> #What are the length constraints for signal sequences?<br /> #How often is the signal sequence found in the ''E. coli'' genome, and will this pose a problem?<br /> #Are signal sequences adaptable to different proteins (ie could we insert one before GFP)?<br /> #How are signal peptidases regulated by ''E. coli''?<br /> #Is this the mechanism by which ''E. coli'' excretes proteins into its extracellular space?</div>

Eric.sawyer http://gcat.davidson.edu/GcatWiki/index.php?title=Missouri_Western/Davidson_iGEM2009&diff=8433 2009-06-10T19:13:41Z

<p>Eric.sawyer: /* iGEM 2009 Project */</p> <hr /> <div>This space will be used starting April, 2009 for brainstorming and a shared whiteboard space.<br /> <br /> [http://gcat.davidson.edu/GcatWiki/index.php/Davidson_Missouri_W/Davidson_Protocols Davidson Lab Protocols] &lt;br&gt;<br /> [http://gcat.davidson.edu/GcatWiki/index.php/Davidson_Missouri_W/MWSU_protocols MWSU Lab Protocols] &lt;br&gt;<br /> [http://gcat.davidson.edu/sybr-u/bmc.html BioMath Connections Page] &lt;br&gt;<br /> [http://gcat.davidson.edu/GCATalog-r2.2/GCATalog.htm GCAT-alog Freezer Stocks]&lt;br&gt;<br /> &lt;center&gt;<br /> == MWSU-Davidson 2009 iGEM team photo ==<br /> [[Image:iGEMTeam2009.png|250px|]]&lt;br&gt;<br /> == The Davidson College part of the 2009 iGEM Team ==<br /> [[Image:DavidsonTeam2009.png|429px|]]<br /> &lt;/center&gt;<br /> <br /> = [[iGEM 2009 Project]] =<br /> <br /> <br /> We need to learn more about these topics:<br /> &lt;center&gt;'''Biology-based'''&lt;/center&gt;<br /> <br /> #[[How do signal sequences/peptides work in bacteria, and how can we use them?]]<br /> #[[Plasmid Creation]]<br /> #[[What is msDNA?]] <br /> #[[How is msDNA normally produced?]] Olivia/Alyndria<br /> #[[How many copies are carried per cell?]] Alyndria<br /> #[[What would we need to do to turn this into a BioBrick device?]] Romina<br /> #[[ How could we swap out msDNA sequences?]] Shamita<br /> #[[What role can physical modeling of protein structure play in our project?]]<br /> #[[What role can physical modeling of proteins play in our project? Eric Sawyer]]<br /> #[[What other cool reporters are there? (Discrete On/Off or Continuous) Bryce Szczepanik]]<br /> #[[Can we use promoter strength/opposite directions to subtract? Clif Davis]]<br /> #[[Can we use suppressor tRNAs to encode logical operators (suppressor suppressor logic, SSL)?]]<br /> #[[How is msDNA stored in E. coli?]] Olivia<br /> #[[What is the sequence of bacterial reverse transcriptase and can we clone that gene?]] Shamita<br /> #[[Can we redesign the normal msDNA pathway to produce new segments of DNA of our choosing?]] All<br /> #[[What are other available reverse transcriptases?]] Leland<br /> #[[What other math problems (e.g. NP- complete) are accessible to us? Annie Siya Sun]]<br /> #[[What is the relationship between 3-SAT and map coloring? Ashley Schnoor]]<br /> #[[What activators are there that turn on a promoter without any help?]]<br /> #[[Can we use protein interactions to compute? (Post-translation, proteases, quaternary structure) Will Vernon]]<br /> #[[Could we do something with clocks/counting?]]<br /> #[[Could we have/use multiple synthetic organelles in a cell?]]<br /> #[[What ideas from previous iGEM teams are useful to us?]]<br /> #[[Examples of Metabolic Pathways in E.coli]]<br /> <br /> <br /> &lt;center&gt;'''Math-based'''&lt;/center&gt;<br /> #[[Can we get bacteria to solve a problem large enough to challenge a person?]]<br /> #[[What interesting challenges or problems does origami offer?]]<br /> #[[Can we produce a series of increasingly difficult goals that might be possible to produce in the lab?]]<br /> #[[What has been done before and how can we improve upon that?]]<br /> #[[We can perform some pilot experiments using synthesized DNA and later switch to msDNA (maybe).]]<br /> #[[Can we address the Boolean Satisfiability (SAT) problem with a bacterial computer?]]<br /> #[[How has 3SAT been addressed with a DNA computer? Can we use those methods?]]<br /> <br /> #Can we get bacteria to solve a problem large enough to challenge a computer (probably not, but it is fun to think about)?<br /> #[[What are some linear algebra applications for DNA origami?]]<br /> #[[How can we use origami to solve 3-SAT problems?]]<br /> <br /> &lt;center&gt;'''Behavior-based'''&lt;/center&gt;<br /> #[[What constructs are we testing?]]<br /> #[[What school districts do we have access to?]]<br /> #[[Where is the Synthetic Biology page we want high school teachers to use after the survey?]]<br /> #[[Do you need any more input from the veterans before the survey is ready?]]<br /> <br /> <br /> &lt;center&gt;'''Solving The 3SAT Problem Using Suppressor Logic'''&lt;/center&gt;<br /> #[[Can we solve a 3-SAT problem with supressor logic?]]<br /> <br /> <br /> &lt;center&gt;'''Hin/Hix System'''&lt;/center&gt;<br /> Here is a link to the animation of the Hin/Hix system created by the &quot;E. HOP living computer project folks. <br /> [http://www.bio.davidson.edu/people/kahaynes/FAMU_talk/Living_computer.swf Hin/Hix Animation] &lt;br&gt;</div>

Eric.sawyer http://gcat.davidson.edu/GcatWiki/index.php?title=What_role_can_physical_modeling_of_proteins_play_in_our_project%3F_Eric_Sawyer&diff=8314 2009-06-08T20:41:01Z

<p>Eric.sawyer: </p> <hr /> <div>== Advantages of Protein Modeling in General ==<br /> # An amino acid sequence alone does not describe the secondary, tertiary, and quaternary structures of a protein that provide functionality.<br /> # &quot;Seeing&quot; a protein increases understanding.<br /> <br /> == Advantages of Physical Modeling over 2D Computer Modeling ==<br /> # Comprehensive view and feel of protein secondary/tertiary/quaternary structure.<br /> # Demonstrate the interactions between enzyme and substrate<br /> # Universal--does not require knowledge of computer commands specific to a program<br /> # 2D imaging is dependent on learners' spacial visualization ability<br /> # Appeals to tactile learners<br /> <br /> == Feasibility ==<br /> Rapid prototyping--the computer guided construction of 3 dimensional objects--allows autonomous assembly of complex structures. XYZ coordinate data from the popular molecular viewer, Rasmol, can be used to guide the production of these models. Our connection with the SMART Program through the Milwaukee School of Engineering gives us access to these technologies. The number of proteins we can reasonably expect Milwaukee to produce models of on budget may be limited to very few. The <br /> [http://www.3dmoleculardesigns.com/quote.asp cost of model production] varies greatly, including about $600 for a simple, 5-inch, backbone model to quite possibly in excess of $1000 for larger, more complex models. The balance between cost and usefulness to the project is important to consider.<br /> <br /> == How can we use physical modeling in our research? ==<br /> Harris, et al (2009) (below) found that physical modeling in conjunction with computer-based imaging improved student understanding of complex protein concepts better than computer modeling alone. Students used physical models to assist them in answering application-, analysis-, and synthesis-type questions. '''Understanding and utilizing physical modeling could help us choose proper sites for adding or removing amino acids from a protein, and compare the wild type and modified protein.''' It would also allow us to understand substrate-enzyme interactions, and how changes to either would affect functionality. Additionally, one or more physical models would be a good addition to our display at iGEM in the fall.<br /> <br /> == References/Additional Reading ==<br /> # [http://www.lifescied.org/cgi/content/abstract/8/1/29 Study of Advantages of Using Physical Modeling in Educational Applications (web)]<br /> # [http://gcat.davidson.edu/GcatWiki/images/3/33/Molecular_Modeling_and_Student_Learning.pdf Study of Advantages of Using Physical Modeling in Educational Applications (PDF for download)]</div>

Eric.sawyer http://gcat.davidson.edu/GcatWiki/index.php?title=What_role_can_physical_modeling_of_proteins_play_in_our_project%3F_Eric_Sawyer&diff=8313 2009-06-08T19:27:01Z

<p>Eric.sawyer: /* Feasibility */</p> <hr /> <div>=== Advantages of Protein Modeling in General ===<br /> # An amino acid sequence alone does not describe the secondary, tertiary, and quaternary structures of a protein that provide functionality.<br /> # &quot;Seeing&quot; a protein increases understanding.<br /> <br /> === Advantages of Physical Modeling over 2D Computer Modeling ===<br /> # Comprehensive view and feel of protein secondary/tertiary/quaternary structure.<br /> # Demonstrate the interactions between enzyme and substrate<br /> # Universal--does not require knowledge of computer commands specific to a program<br /> # 2D imaging is dependent on learners' spacial visualization ability<br /> # Appeals to tactile learners<br /> <br /> === Feasibility ===<br /> Rapid prototyping--the computer guided construction of 3 dimensional objects--allows autonomous assembly of complex structures. XYZ coordinate data from the popular molecular viewer, Rasmol, can be used to guide the production of these models. Our connection with the SMART Program through the Milwaukee School of Engineering gives us access to these technologies. The number of proteins we can reasonably expect Milwaukee to produce models of on budget may be limited to very few. The <br /> [http://www.3dmoleculardesigns.com/quote.asp cost of model production] ranges from about $600 for a simple, 5-inch, backbone model to quite possibly in excess of $1000 for larger, more complex models. The balance between cost and usefulness to the project is important to consider.<br /> <br /> === How can we use physical modeling in our research? ===<br /> Harris, et al (2009) (below) found that physical modeling in conjunction with computer-based imaging improved student understanding of complex protein concepts better than computer modeling alone. Students used physical models to assist them in answering application-, analysis-, and synthesis-type questions. '''Understanding and utilizing physical modeling could help us choose proper sites for adding or removing amino acids from a protein, and compare the wild type and modified protein.''' It would also allow us to understand substrate-enzyme interactions, and how changes to either would affect functionality. Additionally, one or more physical models would be a good addition to our display at iGEM in the fall.<br /> <br /> == References/Additional Reading ==<br /> # [http://www.lifescied.org/cgi/content/abstract/8/1/29 Study of Advantages of Using Physical Modeling in Educational Applications (web)]<br /> # [http://gcat.davidson.edu/GcatWiki/images/3/33/Molecular_Modeling_and_Student_Learning.pdf Study of Advantages of Using Physical Modeling in Educational Applications (PDF for download)]</div>

Eric.sawyer http://gcat.davidson.edu/GcatWiki/index.php?title=What_role_can_physical_modeling_of_proteins_play_in_our_project%3F_Eric_Sawyer&diff=8312 2009-06-08T16:52:40Z

<p>Eric.sawyer: /* Feasibility */</p> <hr /> <div>=== Advantages of Protein Modeling in General ===<br /> # An amino acid sequence alone does not describe the secondary, tertiary, and quaternary structures of a protein that provide functionality.<br /> # &quot;Seeing&quot; a protein increases understanding.<br /> <br /> === Advantages of Physical Modeling over 2D Computer Modeling ===<br /> # Comprehensive view and feel of protein secondary/tertiary/quaternary structure.<br /> # Demonstrate the interactions between enzyme and substrate<br /> # Universal--does not require knowledge of computer commands specific to a program<br /> # 2D imaging is dependent on learners' spacial visualization ability<br /> # Appeals to tactile learners<br /> <br /> === Feasibility ===<br /> Rapid prototyping--the computer guided construction of 3 dimensional objects--allows autonomous assembly of complex structures. XYZ coordinate data from the popular molecular viewer, Rasmol, can be used to guide the production of these models. Our connection with the SMART Program through the Milwaukee School of Engineering gives us access to these technologies. The number of proteins we can reasonably expect Milwaukee to produce models of on budget may be limited to a few. The <br /> [http://www.3dmoleculardesigns.com/quote.asp cost of model production] ranges from about $600 for a simple, 5-inch, backbone model to quite possibly in excess of $1000 for larger, more complex models. The balance between cost and usefulness to the project is important to consider.<br /> <br /> === How can we use physical modeling in our research? ===<br /> Harris, et al (2009) (below) found that physical modeling in conjunction with computer-based imaging improved student understanding of complex protein concepts better than computer modeling alone. Students used physical models to assist them in answering application-, analysis-, and synthesis-type questions. '''Understanding and utilizing physical modeling could help us choose proper sites for adding or removing amino acids from a protein, and compare the wild type and modified protein.''' It would also allow us to understand substrate-enzyme interactions, and how changes to either would affect functionality. Additionally, one or more physical models would be a good addition to our display at iGEM in the fall.<br /> <br /> == References/Additional Reading ==<br /> # [http://www.lifescied.org/cgi/content/abstract/8/1/29 Study of Advantages of Using Physical Modeling in Educational Applications (web)]<br /> # [http://gcat.davidson.edu/GcatWiki/images/3/33/Molecular_Modeling_and_Student_Learning.pdf Study of Advantages of Using Physical Modeling in Educational Applications (PDF for download)]</div>

Eric.sawyer http://gcat.davidson.edu/GcatWiki/index.php?title=What_role_can_physical_modeling_of_proteins_play_in_our_project%3F_Eric_Sawyer&diff=8089 2009-05-26T21:03:40Z

<p>Eric.sawyer: /* References/Additional Reading */</p> <hr /> <div>=== Advantages of Protein Modeling in General ===<br /> # An amino acid sequence alone does not describe the secondary, tertiary, and quaternary structures of a protein that provide functionality.<br /> # &quot;Seeing&quot; a protein increases understanding.<br /> <br /> === Advantages of Physical Modeling over 2D Computer Modeling ===<br /> # Comprehensive view and feel of protein secondary/tertiary/quaternary structure.<br /> # Demonstrate the interactions between enzyme and substrate<br /> # Universal--does not require knowledge of computer commands specific to a program<br /> # 2D imaging is dependent on learners' spacial visualization ability<br /> # Appeals to tactile learners<br /> <br /> === Feasibility ===<br /> Rapid prototyping--the computer guided construction of 3 dimensional objects--allows autonomous assembly of complex structures. XYZ coordinate data from the popular molecular viewer, Rasmol, can be used to guide the production of these models. Our connection with the SMART Program through the Milwaukee School of Engineering gives us access to these technologies. The number of proteins we can reasonably expect Milwaukee to produce models of may be limited to a few.<br /> <br /> === How can we use physical modeling in our research? ===<br /> Harris, et al (2009) (below) found that physical modeling in conjunction with computer-based imaging improved student understanding of complex protein concepts better than computer modeling alone. Students used physical models to assist them in answering application-, analysis-, and synthesis-type questions. '''Understanding and utilizing physical modeling could help us choose proper sites for adding or removing amino acids from a protein, and compare the wild type and modified protein.''' It would also allow us to understand substrate-enzyme interactions, and how changes to either would affect functionality. Additionally, one or more physical models would be a good addition to our display at iGEM in the fall.<br /> <br /> == References/Additional Reading ==<br /> # [http://www.lifescied.org/cgi/content/abstract/8/1/29 Study of Advantages of Using Physical Modeling in Educational Applications (web)]<br /> # [http://gcat.davidson.edu/GcatWiki/images/3/33/Molecular_Modeling_and_Student_Learning.pdf Study of Advantages of Using Physical Modeling in Educational Applications (PDF for download)]</div>

Eric.sawyer http://gcat.davidson.edu/GcatWiki/index.php?title=What_role_can_physical_modeling_of_proteins_play_in_our_project%3F_Eric_Sawyer&diff=8088 2009-05-26T21:03:26Z

<p>Eric.sawyer: /* References/Additional Reading */</p> <hr /> <div>=== Advantages of Protein Modeling in General ===<br /> # An amino acid sequence alone does not describe the secondary, tertiary, and quaternary structures of a protein that provide functionality.<br /> # &quot;Seeing&quot; a protein increases understanding.<br /> <br /> === Advantages of Physical Modeling over 2D Computer Modeling ===<br /> # Comprehensive view and feel of protein secondary/tertiary/quaternary structure.<br /> # Demonstrate the interactions between enzyme and substrate<br /> # Universal--does not require knowledge of computer commands specific to a program<br /> # 2D imaging is dependent on learners' spacial visualization ability<br /> # Appeals to tactile learners<br /> <br /> === Feasibility ===<br /> Rapid prototyping--the computer guided construction of 3 dimensional objects--allows autonomous assembly of complex structures. XYZ coordinate data from the popular molecular viewer, Rasmol, can be used to guide the production of these models. Our connection with the SMART Program through the Milwaukee School of Engineering gives us access to these technologies. The number of proteins we can reasonably expect Milwaukee to produce models of may be limited to a few.<br /> <br /> === How can we use physical modeling in our research? ===<br /> Harris, et al (2009) (below) found that physical modeling in conjunction with computer-based imaging improved student understanding of complex protein concepts better than computer modeling alone. Students used physical models to assist them in answering application-, analysis-, and synthesis-type questions. '''Understanding and utilizing physical modeling could help us choose proper sites for adding or removing amino acids from a protein, and compare the wild type and modified protein.''' It would also allow us to understand substrate-enzyme interactions, and how changes to either would affect functionality. Additionally, one or more physical models would be a good addition to our display at iGEM in the fall.<br /> <br /> == References/Additional Reading ==<br /> # [http://www.lifescied.org/cgi/content/abstract/8/1/29 Study of Advantages of Using Physical Modeling in Educational Applications (WEB)]<br /> # [http://gcat.davidson.edu/GcatWiki/images/3/33/Molecular_Modeling_and_Student_Learning.pdf Study of Advantages of Using Physical Modeling in Educational Applications (PDF for download)]</div>

Eric.sawyer http://gcat.davidson.edu/GcatWiki/index.php?title=File:Molecular_Modeling_and_Student_Learning.pdf&diff=8087 2009-05-26T21:00:32Z

<p>Eric.sawyer: A study on the effect of using physical and virtual protein modeling on student class performance.</p> <hr /> <div>A study on the effect of using physical and virtual protein modeling on student class performance.</div>

Eric.sawyer http://gcat.davidson.edu/GcatWiki/index.php?title=What_role_can_physical_modeling_of_proteins_play_in_our_project%3F_Eric_Sawyer&diff=8042 2009-05-25T19:32:10Z

<p>Eric.sawyer: </p> <hr /> <div>=== Advantages of Protein Modeling in General ===<br /> # An amino acid sequence alone does not describe the secondary, tertiary, and quaternary structures of a protein that provide functionality.<br /> # &quot;Seeing&quot; a protein increases understanding.<br /> <br /> === Advantages of Physical Modeling over 2D Computer Modeling ===<br /> # Comprehensive view and feel of protein secondary/tertiary/quaternary structure.<br /> # Demonstrate the interactions between enzyme and substrate<br /> # Universal--does not require knowledge of computer commands specific to a program<br /> # 2D imaging is dependent on learners' spacial visualization ability<br /> # Appeals to tactile learners<br /> <br /> === Feasibility ===<br /> Rapid prototyping--the computer guided construction of 3 dimensional objects--allows autonomous assembly of complex structures. XYZ coordinate data from the popular molecular viewer, Rasmol, can be used to guide the production of these models. Our connection with the SMART Program through the Milwaukee School of Engineering gives us access to these technologies. The number of proteins we can reasonably expect Milwaukee to produce models of may be limited to a few.<br /> <br /> === How can we use physical modeling in our research? ===<br /> Harris, et al (2009) (below) found that physical modeling in conjunction with computer-based imaging improved student understanding of complex protein concepts better than computer modeling alone. Students used physical models to assist them in answering application-, analysis-, and synthesis-type questions. '''Understanding and utilizing physical modeling could help us choose proper sites for adding or removing amino acids from a protein, and compare the wild type and modified protein.''' It would also allow us to understand substrate-enzyme interactions, and how changes to either would affect functionality. Additionally, one or more physical models would be a good addition to our display at iGEM in the fall.<br /> <br /> == References/Additional Reading ==<br /> [http://www.lifescied.org/cgi/content/abstract/8/1/29 Study of Advantages of Using Physical Modeling in Educational Applications]</div>

Eric.sawyer http://gcat.davidson.edu/GcatWiki/index.php?title=What_role_can_physical_modeling_of_proteins_play_in_our_project%3F_Eric_Sawyer&diff=8041 2009-05-25T15:24:02Z

<p>Eric.sawyer: /* How can we use physical modeling in our research? */</p> <hr /> <div>=== Advantages of Protein Modeling in General ===<br /> # An amino acid sequence alone does not describe the secondary, tertiary, and quaternary structures of a protein that provide functionality.<br /> # &quot;Seeing&quot; a protein increases understanding.<br /> <br /> === Advantages of Physical Modeling over 2D Computer Modeling ===<br /> # Demonstrate the interactions between enzyme and substrate<br /> # Universal--does not require knowledge of computer commands specific to a program<br /> # 2D imaging is dependent on learners' spacial visualization ability<br /> # Appeals to tactile learners<br /> <br /> === Feasibility ===<br /> Rapid prototyping--the computer guided construction of 3 dimensional objects--allows autonomous assembly of complex structures. XYZ coordinate data from the popular molecular viewer, Rasmol, can be used to guide the production of these models. Our connection with the SMART Program through the Milwaukee School of Engineering gives us access to these technologies.<br /> <br /> === How can we use physical modeling in our research? ===<br /> Harris, et al (2009) (below) found that physical modeling in conjunction with computer-based imaging improved student understanding of complex protein concepts better than computer modeling alone. Students used physical models to assist them in answering application-, analysis-, and synthesis-type questions. **Understanding and utilizing physical modeling could help us choose proper sites for adding or removing amino acids from a protein, and compare the wild type and modified protein.** It would also allow us to understand substrate-enzyme interactions, and how changes to either would affect functionality. Additionally, one or more physical models would be a good addition to our display at iGEM in the fall.<br /> <br /> == References/Additional Reading ==<br /> [http://www.lifescied.org/cgi/content/abstract/8/1/29 Study of Advantages of Using Physical Modeling in Educational Applications]</div>

Eric.sawyer http://gcat.davidson.edu/GcatWiki/index.php?title=What_role_can_physical_modeling_of_proteins_play_in_our_project%3F_Eric_Sawyer&diff=7816 2009-05-01T15:28:41Z

<p>Eric.sawyer: /* How can we use physical modeling in our research? */</p> <hr /> <div>=== Advantages of Protein Modeling in General ===<br /> # An amino acid sequence alone does not describe the secondary, tertiary, and quaternary structures of a protein that provide functionality.<br /> # &quot;Seeing&quot; a protein increases understanding.<br /> <br /> === Advantages of Physical Modeling over 2D Computer Modeling ===<br /> # Demonstrate the interactions between enzyme and substrate<br /> # Universal--does not require knowledge of computer commands specific to a program<br /> # 2D imaging is dependent on learners' spacial visualization ability<br /> # Appeals to tactile learners<br /> <br /> === Feasibility ===<br /> Rapid prototyping--the computer guided construction of 3 dimensional objects--allows autonomous assembly of complex structures. XYZ coordinate data from the popular molecular viewer, Rasmol, can be used to guide the production of these models. Our connection with the SMART Program through the Milwaukee School of Engineering gives us access to these technologies.<br /> <br /> === How can we use physical modeling in our research? ===<br /> Harris, et al (2009) (below) found that physical modeling in conjunction with computer-based imaging improved student understanding of complex protein concepts better than computer modeling alone. Students used physical models to assist them in answering application-, analysis-, and synthesis-type questions. Understanding and utilizing physical modeling could help us choose proper sites for adding or removing amino acids from a protein. It would also allow us to understand substrate-enzyme interactions, and how changes to either would affect functionality. Additionally, one or more physical models would be a good addition to our display at iGEM in the fall.<br /> <br /> == References/Additional Reading ==<br /> [http://www.lifescied.org/cgi/content/abstract/8/1/29 Study of Advantages of Using Physical Modeling in Educational Applications]</div>

Eric.sawyer http://gcat.davidson.edu/GcatWiki/index.php?title=What_role_can_physical_modeling_of_proteins_play_in_our_project%3F_Eric_Sawyer&diff=7815 2009-04-30T23:51:17Z

<p>Eric.sawyer: </p> <hr /> <div>=== Advantages of Protein Modeling in General ===<br /> # An amino acid sequence alone does not describe the secondary, tertiary, and quaternary structures of a protein that provide functionality.<br /> # &quot;Seeing&quot; a protein increases understanding.<br /> <br /> === Advantages of Physical Modeling over 2D Computer Modeling ===<br /> # Demonstrate the interactions between enzyme and substrate<br /> # Universal--does not require knowledge of computer commands specific to a program<br /> # 2D imaging is dependent on learners' spacial visualization ability<br /> # Appeals to tactile learners<br /> <br /> === Feasibility ===<br /> Rapid prototyping--the computer guided construction of 3 dimensional objects--allows autonomous assembly of complex structures. XYZ coordinate data from the popular molecular viewer, Rasmol, can be used to guide the production of these models. Our connection with the SMART Program through the Milwaukee School of Engineering gives us access to these technologies.<br /> <br /> === How can we use physical modeling in our research? ===<br /> Harris, et al (2009) (below) found that physical modeling in conjunction with computer-based imaging improved student understanding of complex protein concepts better than computer modeling alone. Understanding and utilizing physical modeling could help us choose proper sites for adding or removing amino acids from a protein. It would also allow us to understand substrate-enzyme interactions, and how changes to either would affect functionality. Additionally, one or more physical models would be a good addition to our display at iGEM in the fall.<br /> <br /> == References/Additional Reading ==<br /> [http://www.lifescied.org/cgi/content/abstract/8/1/29 Study of Advantages of Using Physical Modeling in Educational Applications]</div>

Eric.sawyer