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You searched for +publisher:"University of North Carolina" +contributor:("Richardson, Jane"). Showing records 1 – 2 of 2 total matches.

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University of North Carolina

1. Jacobs, Tim. De Novo Proteins Designed From Evolutionary Principles.

Degree: 2015, University of North Carolina

URL: https://cdr.lib.unc.edu/record/uuid:e5c99a71-24d2-46bc-bbfe-4ff6c8607fa5 

Protein engineering has rapidly developed into a powerful method for the optimization, alteration, and creation of protein functions. Current protein engineering methods fall into the category of either high-throughput directed evolution techniques, or engineering through the use of computational models of protein structure. Despite significant innovation in both of these categories, neither is capable of handling the most difficult and desirable protein engineering goals. The combination of these two categories is an area of active research, and the development and testing of combination methods is the focus of this dissertation. Chapters 2 and 3 describe the development of a computational framework for de novo protein design called SEWING (Structural Extension WIth Native-fragment Graphs). In contrast to existing methods of de novo design, which attempt to design proteins that match a designer-supplied target topology, SEWING generates large numbers of diverse protein structures. We show that this strategy is highly effective at creating diverse helical backbones. Experimental characterization of SEWING designs shows that the experimental structures match the design models with sub-angstrom root mean square deviation (RMSD). Chapter 3 extends this methodology to the creation of protein interfaces. Using this method, several de novo designed proteins are created that bind their designated target. Chapter 4 describes the combination of directed evolution and computational modeling through the improvement of directed evolution techniques. In this chapter, a web tool called SwiftLib is developed, which allows rapid generation of degenerate codon libraries. SwiftLib allows protein engineers to determine optimal degenerate codon primers for the incorporation of desired sequences, such as sequence profiles generated from computational modeling and evolutionary data. Together, these chapters outline the creation of tools for the engineering of protein functions, and provide additional evidence that computational modeling and evolutionary principles can be combined for the improvement of protein engineering methods. Advisors/Committee Members: Jacobs, Tim, Kuhlman, Brian, Snoeyink, Jack, Tropsha, Alexander, Collins, Edward, Richardson, Jane.

Subjects/Keywords: Biochemistry; Bioinformatics; School of Medicine; Curriculum in Bioinformatics and Computational Biology

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6th Edition):

Jacobs, T. (2015). De Novo Proteins Designed From Evolutionary Principles. (Thesis). University of North Carolina. Retrieved from https://cdr.lib.unc.edu/record/uuid:e5c99a71-24d2-46bc-bbfe-4ff6c8607fa5

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16th Edition):

Jacobs, Tim. “De Novo Proteins Designed From Evolutionary Principles.” 2015. Thesis, University of North Carolina. Accessed January 19, 2021. https://cdr.lib.unc.edu/record/uuid:e5c99a71-24d2-46bc-bbfe-4ff6c8607fa5.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7th Edition):

Jacobs, Tim. “De Novo Proteins Designed From Evolutionary Principles.” 2015. Web. 19 Jan 2021.

Vancouver:

Jacobs T. De Novo Proteins Designed From Evolutionary Principles. [Internet] [Thesis]. University of North Carolina; 2015. [cited 2021 Jan 19]. Available from: https://cdr.lib.unc.edu/record/uuid:e5c99a71-24d2-46bc-bbfe-4ff6c8607fa5.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Jacobs T. De Novo Proteins Designed From Evolutionary Principles. [Thesis]. University of North Carolina; 2015. Available from: https://cdr.lib.unc.edu/record/uuid:e5c99a71-24d2-46bc-bbfe-4ff6c8607fa5

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation


University of North Carolina

2. Kim, Doo Nam. Computer-based Design of β-sheet Containing Proteins.

Degree: Biochemistry and Biophysics, 2016, University of North Carolina

URL: https://cdr.lib.unc.edu/record/uuid:076f3980-6637-481b-bece-d26ad5cdb96a 

Protein design is an excellent test of the minimal determinants of protein structure. Although 70% of naturally occurring proteins contain β-sheets, most previous design efforts have been limited to α-helix bundle proteins or the redesign of naturally occurring proteins. Here, we test and develop computer based methods for designing proteins rich in β-strands. The molecular modeling program Rosetta was used for three separate design tasks: (1) the design of α/β and α+β proteins with a new method called SEWING, which builds proteins from pieces of naturally occurring proteins, (2) the stabilization of β-sheet proteins via the redesign of surface-facing residues, and (3) the de novo design of β-sandwich proteins. This research showed that it is possible to extend the SEWING method to non-α-helix proteins, allowing the incorporation of structural features found in nature, and that it is possible to dramatically boost protein thermal stability (> 25 °C) with the redesign β-sheet surfaces. However, we also found that the de novo design of β-sandwich proteins still remains an elusive goal. Advisors/Committee Members: Kim, Doo Nam, Kuhlman, Brian, Zhang, Qi, Lee, Andrew, Erickson, Harold, Richardson, Jane.

Subjects/Keywords: School of Medicine; Department of Biochemistry and Biophysics

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6th Edition):

Kim, D. N. (2016). Computer-based Design of β-sheet Containing Proteins. (Thesis). University of North Carolina. Retrieved from https://cdr.lib.unc.edu/record/uuid:076f3980-6637-481b-bece-d26ad5cdb96a

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16th Edition):

Kim, Doo Nam. “Computer-based Design of β-sheet Containing Proteins.” 2016. Thesis, University of North Carolina. Accessed January 19, 2021. https://cdr.lib.unc.edu/record/uuid:076f3980-6637-481b-bece-d26ad5cdb96a.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7th Edition):

Kim, Doo Nam. “Computer-based Design of β-sheet Containing Proteins.” 2016. Web. 19 Jan 2021.

Vancouver:

Kim DN. Computer-based Design of β-sheet Containing Proteins. [Internet] [Thesis]. University of North Carolina; 2016. [cited 2021 Jan 19]. Available from: https://cdr.lib.unc.edu/record/uuid:076f3980-6637-481b-bece-d26ad5cdb96a.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Kim DN. Computer-based Design of β-sheet Containing Proteins. [Thesis]. University of North Carolina; 2016. Available from: https://cdr.lib.unc.edu/record/uuid:076f3980-6637-481b-bece-d26ad5cdb96a

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

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