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__FORCETOC__
=References =  
=References =  


Below is a list of all of the papers that we referenced during the course of our project.
Below is a list of all of the papers that we referenced during the course of our project.
__TOC__


==General==
==General==
Line 10: Line 11:
* Ha JH, Loh SN. 2012. "Protein Conformational Switches: From Nature to Design." ''Chemistry - A European Journal''  18 (26): 7984–7999.
* Ha JH, Loh SN. 2012. "Protein Conformational Switches: From Nature to Design." ''Chemistry - A European Journal''  18 (26): 7984–7999.


* Meister GE, Joshi NS. 2013. "An Engineered Calmodulin-Based ALlosteric Switch for Peptide Biosensing." ''ChemBioChem''  14 (_): __ - __.  
* Meister GE, Joshi NS. 2013. "An Engineered Calmodulin-Based Allosteric Switch for Peptide Biosensing." ''ChemBioChem''  14 : 1460 - 1467.  


* Mohanty SP, Kougianos E. 2006. "Biosensors: A Tutorial Review." ''Potentials, IEEE''  25 (2): 35-40.
* Mohanty SP, Kougianos E. 2006. "Biosensors: A Tutorial Review." ''Potentials, IEEE''  25 (2): 35-40.
Line 16: Line 17:
==Input Domain==
==Input Domain==


* Bloom JD, Arnold FH. 2009. "In the Light of Directed Evolution: Pathways of Adaptive Protein Evolution." ''Proceeding of the National Academy of Science of the United States of America''  106 (Supplement 1): 9995-10000.  
* Bloom JD, Arnold FH. 2009. "In the Light of Directed Evolution: Pathways of Adaptive Protein Evolution." ''Proceedings of the National Academy of Science of the United States of America''  106 (Supplement 1): 9995-10000.  


* Daugherty PS. 2007. "Protein Engineering with Bacterial Display." ''Current Opinions in Structural Biology'' 17 (4): 474–480.  
* Daugherty PS. 2007. "Protein Engineering with Bacterial Display." ''Current Opinions in Structural Biology'' 17 (4): 474–480.  


* Fernandez-Gacio A, Uguen M, Fastrez J. 2003. "Phage Display as a Tool for the Directed Evolution of Enzymes." ''Trends in Biotechnology''  21 (9): 408-414.  
* Fernandez-Gacio A, Uguen M, Fastrez J. 2003. "Phage Display as a Tool for the Directed Evolution of Enzymes." ''Trends in Biotechnology''  21 (9): 408-414.  
* Konieczny MPJ, Suhr M, Noll A, Autenreith IB, Schmidt MA. 2000. "Cell Surface Presentation of Recombinant (poly-) Peptides Including Functional T-cell Epitopes by the AIDA Autotransporter System." ''FEMS Immunology and Medical Microbiology'' 27 (2000): 321-332.
* Lattemann CT, Maurer J, Gerland E, Meyer TF. 2000. "Autodisplay: Functional Display of Active β-Lactamase on the Surface of ''Escherichia coli'' by the AIDA-I Autotransporter." ''Journal of Bacteriology'' 182 (13): 3726-3733.


* Leemhuis H, Kelly RM, Dijkhuizen L. 2009. "Directed Evolution of Enzymes: Library Screening Strategies." ''IUBMB Life''  61 (3): 222-228.
* Leemhuis H, Kelly RM, Dijkhuizen L. 2009. "Directed Evolution of Enzymes: Library Screening Strategies." ''IUBMB Life''  61 (3): 222-228.
* Rasila TS, Pajunena MI, Savilahtia H. 2009. "Critical Evaluation of Random Mutagenesis by Error-prone Polymerase Chain Reaction Protocols, ''Escherichia coli'' Mutator Strain, and Hydroxylamine Treatment." ''Analytical Biochemistry'' 388 (1): 71-80.
* Samuni A. 1975. "A Direct Spectrophotometric Assay and Determination of Michaelis Constants for the  β-Lactamase Reaction." ''Analytical Biochemistry'' 63 (1): 17-26.


==Output Domain==
==Output Domain==


* Inouye S, Sahara Y. 2008. " Identification of Two Catalytic Domains in a Luciferase Secreted by the Copepod ''Gaussia princeps''." '' Biochemical and Biophysical Research Communications''  365 (1): 96-101.  
* Inouye S, Sahara Y. 2008. " Identification of Two Catalytic Domains in a Luciferase Secreted by the Copepod ''Gaussia princeps''." '' Biochemical and Biophysical Research Communications''  365 (1): 96-101.  
* Karginov A.V., et al. 2010.  "Engineered allosteric activation of kinases in living cells." ''Nature Biotechnology'' Vol 28. (7): 743-748.


* Kim SB, Sato M, Tao H. 2009. "Split Gaussia Luciferase-Based Bioluminescence Template for Tracing Protein Dynamics in Living Cells." ''Analytical Chemistry''  81 (1): 67–74.
* Kim SB, Sato M, Tao H. 2009. "Split Gaussia Luciferase-Based Bioluminescence Template for Tracing Protein Dynamics in Living Cells." ''Analytical Chemistry''  81 (1): 67–74.


* Rathnayaka T, Tawa M, Nakamura T, Sohya S, Kuwajima K, Yohda M, Kuroda Y. 2011. "Solubilization and Folding of a Fully Active Recombinant Gaussia Luciferae with Native Disulfide Bonds By Using a SEP-Tag." ''Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics''  1814 (12): 1775-1778.
* Rathnayaka T, Tawa M, Nakamura T, Sohya S, Kuwajima K, Yohda M, Kuroda Y. 2011. "Solubilization and Folding of a Fully Active Recombinant Gaussia Luciferae with Native Disulfide Bonds By Using a SEP-Tag." ''Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics''  1814 (12): 1775-1778.
* Rathnayaka T, et al. 2010. "Biophysical characterization of highly active recombinant Gaussia luciferase expressed in Escherichia coli."  Biochimica et Biophysica Acta 1804: 1902–1907.
* Shierle CF, Berkmen M, Huber D, Kumamoto C, Boyd D, Beckwith J. 2003. "The DsbA Signal Sequence Directs Efficient, Cotranslational Export of Passenger Proteins to the ''Escherichia coli'' Periplasm via the Signal Recognition Particle Pathway." ''Journal of Bacteriology'' 185 (16): 5706-5713.
* Remy I. & Stephen M.W. 2006. "A highly sensitive protein- protein interaction assay based on Gaussia luciferase." ''Nature Methods'' Vol. 3 (12): 977-979.
* X. Chen, et al. 2013. "Fusion protein linkers: Property, design and functionality," Adv. Drug Deliv. Rev. Vol. 65 (10): 1357–1369.

Latest revision as of 13:16, 26 October 2013

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References

Below is a list of all of the papers that we referenced during the course of our project.

General

  • Ha JH, Loh SN. 2012. "Protein Conformational Switches: From Nature to Design." Chemistry - A European Journal 18 (26): 7984–7999.
  • Meister GE, Joshi NS. 2013. "An Engineered Calmodulin-Based Allosteric Switch for Peptide Biosensing." ChemBioChem 14 : 1460 - 1467.
  • Mohanty SP, Kougianos E. 2006. "Biosensors: A Tutorial Review." Potentials, IEEE 25 (2): 35-40.

Input Domain

  • Bloom JD, Arnold FH. 2009. "In the Light of Directed Evolution: Pathways of Adaptive Protein Evolution." Proceedings of the National Academy of Science of the United States of America 106 (Supplement 1): 9995-10000.
  • Daugherty PS. 2007. "Protein Engineering with Bacterial Display." Current Opinions in Structural Biology 17 (4): 474–480.
  • Fernandez-Gacio A, Uguen M, Fastrez J. 2003. "Phage Display as a Tool for the Directed Evolution of Enzymes." Trends in Biotechnology 21 (9): 408-414.
  • Konieczny MPJ, Suhr M, Noll A, Autenreith IB, Schmidt MA. 2000. "Cell Surface Presentation of Recombinant (poly-) Peptides Including Functional T-cell Epitopes by the AIDA Autotransporter System." FEMS Immunology and Medical Microbiology 27 (2000): 321-332.
  • Lattemann CT, Maurer J, Gerland E, Meyer TF. 2000. "Autodisplay: Functional Display of Active β-Lactamase on the Surface of Escherichia coli by the AIDA-I Autotransporter." Journal of Bacteriology 182 (13): 3726-3733.
  • Leemhuis H, Kelly RM, Dijkhuizen L. 2009. "Directed Evolution of Enzymes: Library Screening Strategies." IUBMB Life 61 (3): 222-228.
  • Rasila TS, Pajunena MI, Savilahtia H. 2009. "Critical Evaluation of Random Mutagenesis by Error-prone Polymerase Chain Reaction Protocols, Escherichia coli Mutator Strain, and Hydroxylamine Treatment." Analytical Biochemistry 388 (1): 71-80.
  • Samuni A. 1975. "A Direct Spectrophotometric Assay and Determination of Michaelis Constants for the β-Lactamase Reaction." Analytical Biochemistry 63 (1): 17-26.

Output Domain

  • Inouye S, Sahara Y. 2008. " Identification of Two Catalytic Domains in a Luciferase Secreted by the Copepod Gaussia princeps." Biochemical and Biophysical Research Communications 365 (1): 96-101.
  • Karginov A.V., et al. 2010. "Engineered allosteric activation of kinases in living cells." Nature Biotechnology Vol 28. (7): 743-748.
  • Kim SB, Sato M, Tao H. 2009. "Split Gaussia Luciferase-Based Bioluminescence Template for Tracing Protein Dynamics in Living Cells." Analytical Chemistry 81 (1): 67–74.
  • Rathnayaka T, Tawa M, Nakamura T, Sohya S, Kuwajima K, Yohda M, Kuroda Y. 2011. "Solubilization and Folding of a Fully Active Recombinant Gaussia Luciferae with Native Disulfide Bonds By Using a SEP-Tag." Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics 1814 (12): 1775-1778.
  • Rathnayaka T, et al. 2010. "Biophysical characterization of highly active recombinant Gaussia luciferase expressed in Escherichia coli." Biochimica et Biophysica Acta 1804: 1902–1907.
  • Shierle CF, Berkmen M, Huber D, Kumamoto C, Boyd D, Beckwith J. 2003. "The DsbA Signal Sequence Directs Efficient, Cotranslational Export of Passenger Proteins to the Escherichia coli Periplasm via the Signal Recognition Particle Pathway." Journal of Bacteriology 185 (16): 5706-5713.
  • Remy I. & Stephen M.W. 2006. "A highly sensitive protein- protein interaction assay based on Gaussia luciferase." Nature Methods Vol. 3 (12): 977-979.
  • X. Chen, et al. 2013. "Fusion protein linkers: Property, design and functionality," Adv. Drug Deliv. Rev. Vol. 65 (10): 1357–1369.
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