Tim Whitehead.

Post-Doctorate Researcher
University of California, Berkeley

Ph.D. Chemical Engineering, 2008
University of California, BerkeleyB.E. Chemical Engineering, 2001
Vanderbilt University

taw(AT)berkeley.edu

Office Location: 497A Tan Hall
Office Telephone: 510-643-8340
Office Fax: 510-643-1228



Tunable filament dimensions from an engineered hyperthermophilic protein

Self-assembled biomaterials exhibit tremendous promise in creating a wide variety of tunable smart materials and inorganic/organic functional devices. I am interested in programming proteins that assemble from the nanoscale into large, regular complexes. These protein complexes could be scaffolds in applications that range from bio-templating of inorganic material to create metallic and semiconductor nanowires to construction of precisely spaced immobilized enzyme arrays for biomedical devices.

Much work has been done on creating DNA sequences to self-assemble into precise 1D, 2D, and 3D architecture. However, disadvantages of DNA-templated assembly include the short persistence length of dsDNA (50 nm) and the lack of chemical functionality along the DNA sequence. Proteins have the potential to be a much more general design framework for use in these biotemplated ideas. Many attempts have been made to exhibit multiple length-scale control for proteins. At this point many of these solutions are ad hoc, and many of these rationally engineered proteins cannot readily be modified to assemble in differing geometries. There is a need to develop a protein framework that could enable control over protein assembly in disparate geometries over multiple length scales. A good toolbox would include a protein sequence that can be designed modularly to assemble in specific geometries that also allows large peptide insertions for added functionality.

Recently I have discovered and characterized a unique protein filament, g Pfd, from the hyperthermophile Methanoccocus jannaschii. The filament lengths are polydisperse and exceed 1 mM, and are assembled by a proposed single repeating beta strand scaffold, flanked by a series of protruding coiled-coils (fig1A-B). However, the distinct architecture of the g PFD filament in which the coiled-coil is modular and separable from the interface is intriguing, as well as the extraordinary stability of the protein assembly at temperatures in excess of 97oC. My previous work has also established that the filament can tolerate large peptide insertions (ca. 25 a.a.) at both the N- and C- termini of the protein, and that inorganic materials such as gold can be nucleated off of the filament chain to form inorganic nanowires.

My current research focuses on the different parameters governing filament formation such as stability, kinetic rates of filament assembly, and structural integrity. I have also demonstrated tunability of the filament width and overall length through rational design of a capping protein. We would like to use this filament as a starting point towards designing more complicated geometrical patterns such as T-junctions or cubic arrays, enabling creation of more complicated devices built from the bottom-up.

Fig1: TEM of g PFD filaments, dimensions of the functional dimer, and possible filament assembly. Scale bar, 200 nm.



Publications

7. Slocik JM, Kim SN, Whitehead TA, Clark DS, Naik RR, “Biotemplated metal nanowires using hyperthermophilic protein filaments”, submitted

6. Whitehead TA, Je E, Clark DS, “Rational shape engineering of a filamentous protein for preferential surface deposition”,submitted

5. Bergeron LM, Gomez L, Whitehead TA, Clark DS, “Self-renaturing enzymes: Design of an enzyme-chaperone chimera as a new approach to enzyme stability”, submitted

4. Whitehead TA, Meadows AL, Clark DS (2008), “Controlling the self-assembly of a filamentous hyperthermophilic chaperone by an engineered capping protein,” Small, 4(7): 956-960

3. Whitehead TA, Boonyaratanakornkit BB, Hoellrigl V, Clark DS (2007), “A filamentous molecular chaperone of the prefoldin family from the deep-sea hyperthermophile Methanocaldococcus jannaschii”, Protein Science 16 (4): 626-634

2. Boonyaratanakornkit BB, Simpson AJ, Whitehead TA, Fraser CM, El-Sayed NMA, Clark DS (2005), “Transcriptional profiling of the hyperthermophilic methanarchaeon Methanococcus jannaschii in response to lethal heat and non-lethal cold shock”, Environmental Microbiology 7 (6): 789-797

1. Laksanalamai P, Whitehead TA, Robb FT (2004), “Minimal protein-folding systems in hyperthermophilic archaea”, Nature Reviews Microbiology 2 (4): 315-324