Biology's wires and motors : single-molecule mechanics of M13 bacteriophage and kinesin

Nature serves as an inspiration for engineering design, and, conversely, engineering principles have helped to usher in a quantitative frontier of biology. This intricate interdependency between engineering and biology is strongly evident in the single-molecule regime, where high-resolution tools are addressing previously intractable biological problems, while nanotechnology is being accelerated by advances in molecular biology. This thesis explores both sides of the dichotomy in an effort to reveal the mechanics of two biological systems - M13 filamentous bacteriophage and kinesin motor protein - and the properties of their underlying parts. M13 is a filamentous virus that has elicited the interest of the engineering community for its use in phage display of combinatorial peptide libraries and more recently as a 1D template for organizing and growing inorganic materials. Both applications rely on the direct link between genotype and phenotype, whereby each phage particle displays fusion molecules on its proteinaceous capsid and simultaneously carries the encoding DNA. A better understanding of its polymer mechanics is critical to the further development of future M13-based technologies. As a result, combined efforts in genetic engineering, optical trapping, and modeling were employed in the first characterization of the biopolymer's single-molecule elasticity, revealing a persistence length (1265 nm) that places it squarely in the semiflexible polymer regime. Single-molecule stretching also revealed a mechanically robust and genetically versatile tether that could serve as a general "molecular handle" for single-molecule biophysics. As such, M13 was further engineered to incorporate variants of the zinc finger, DNA-binding domain of transcription factor Zif268 as minor coat fusions.

Department dc:contributor.department

Massachusetts Institute of Technology. Dept. of Mechanical Engineering.

Grantor dc:publisher

Massachusetts Institute of Technology

Year dc:date.issued

2009

Author dc:creator

• Khalil, Ahmad S. (Ahmad Samir), 1980-

Advisor dc:contributor.advisor

• Angela M. Belcher and Matthew J. Lang.

• Mechanical Engineering.

Statement dc:rights

• M.I.T. theses are protected by copyright. They may be viewed from this source for any purpose, but reproduction or distribution in any format is prohibited without written permission. See provided URL for inquiries about permission.

Licence dc:rights.uri

• http://dspace.mit.edu/handle/1721.1/7582

Language dc:language.iso

eng

Handle dc:identifier.uri

http://hdl.handle.net/1721.1/46619

OAI identifier oai:identifier

oai:dspace.mit.edu:1721.1/46619