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Sarikaya Research Group at the University of Washington
Professor Mehmet Sarikaya

Link to Sarikaya's CV

 

Molecular Biomimetics
 
is an emerging, key enabling paradigm in science and technology where we adapt and utilize the tools and approaches of molecular biology and genetics to engineer peptides, lipids, polysaccharides, and DNA, i.e., biological building blocks, for the purpose of using them in technology and medicine. This polydisciplinary field encompasses the common denominators from MSE (physics, chemistry and engineering), biological sciences (biochemistry/physics, molecular biology, genetics, microbiology), and computation/information fields.

Lessons from Biology:
Nature provides examples of inspiration for protein-controlled functional architectures and materials systems including examples of highly evolved hard tissues, from various organisms. (a) Magnetite particles in a magnetotatctic bacterium, Aquaspirillum magnetotacticum, forming a magnetic compass. (b) Spicules of the deep-sea sponge Rosella, which has optical characteristics comparable to synthetic optical fibers. (c) Mother-of-pearl of red abalone shell (Haliotis Rufescens) with segmented layered architecture of aragonitic CaCO3 platelets architectured in brick-mortar organization with a protein/polysaccharide in between resulting in highly desirable toughness/strength combination. (d) Hierarchical architecture of the mammalian enamel, the crown of the tooth. Enamel forms an integrated structure with the dentin underneath at the bulk scale. It has an architecture of woven enamel rods (3 mm diameter) at the micrometer-scale, each rod containing thousands of long HA crystallites on 10s of nm thick but mm long), all spatially and crystallographically well organized in the nanometer scale (all examples from Sarikaya et al., 1986-2008).

GEPI – Genetically Engineered Peptides for Inorganics:
Proteins are the workhorses of biology – all functional biological entities and systems are designed genetically. Following Mother Nature's molecular foot-steps, we select and tailor peptides with desired inorganic-binding and assembly properties that were never intended by nature for the purpose of using them as molecular building blocks in practical applications, from materialization, to molecular medicine, and energy systems. The central premise of peptide-based Molecular Biomimetics is that GEPI,1 either in isolation or when inserted within the structural framework of designer proteins with useful characteristics (such as enzymes), can be utilized as molecular erector sets to direct synthesis/fabrication and assembly/architecture of hybrid materials (such as nanoparticles and quantum dots) with programmed composition, phase, and topology, all at ambient and environmentally friendly conditions, towards designed and closely controlled, often molecular or nanoscale, functions, including photonics, electronics, magnetics, and mechanics. See. e.g., Sarikaya et al., Nature Materials, 2, 376 (2003).

Combinatorial Mutagenesis: Genetic Selection of Solid-Binding Peptides:
The In vivo approaches for the genetic selection of peptides include phage display and cell surface display which we have adapted to materials science and technology, as schematically illustrated here. Each approach has advantages and disadvantages as have been described in detail in recent reviews. See, e.g., Sarikaya et al., Ann. Rev. Mater. Sci., 34, (2004); Tamerler and Sarikaya, Acta Biomaterialia, 2, (2007).

Basic Research Approach:
The genetic selection (combinatorial mutagenesis) of solid binding peptides is but one step in selecting solid-binding peptides. In molecular biomimetics, the research approach involves five interrelated basic steps to achieve GEPI, i.e., well characterized inorganic binders that are utilized as molecular synthesizers, erectors, and assemblers in technology and medicine. See, e.g., Tamerler and Sarikaya, in: Bacterial Nanotechnology, 2006.

Molecular Binding, Structure, & Assembly:
The question "how does a peptide/protein recognize a solid," has been the hallmark of biomineralization, tissue engineering, and bioimplants for the last three decades. Our genetically engineered peptides bind specifically to solid materials of all kinds that require rigorous molecular characterization of GEPIs. The established steps for molecular characterization of a GEPI as a viable technological molecular tool. (a) The kinetics of solid binding and specificity of inorganic binding peptides for a given solid could be determined by SPR spectroscopy while whether a GEPI is specific for a solid surface compared to another solid is determined by QCM. (a) Spectroscopies, such as CD and NMR, could provide molecular architecture. (c) In the absence of (b), computational modeling, such as molecular dynamics, could provide molecular conformation and shed light on the mechanism of crystallographic surface recognition. Finally, supramolecular self-assembly of the peptide on the crystallographic surface of the inorganic could be visualized by AFM as demonstrated here for a gold binding peptide on Graphite(0001) and Au(111). See, e.g., M. Sarikaya and C. Tamerler, MRS May, 2008; C. So, et al., in preparation (2008).

Molecular Toolbox:
Selection (1), categorization/characterization (2) and molecular utility (3) of GEPI. The select GEPIs are utilized as building blocks, i.e., as synthesizers, erectors, and assemblers, in a wide range of practical applications from practical materialization to medicine and nanotechnology, including, specifically, directed assembly of quantum dots, targeted assembly of enzymes, molecular scaffolds for tissue regeneration, controlled materialization, bioassembled electronics, photonics, magnetic, and mechanics. See, e.g., M. Sarikaya and C. Tamerler, MRS Bulletin, Special Issue, May 2008.

International Collaboration – World Biomimetic Network:
The success of molecular biomimetics requires interdisciplinary approach where the solid-binding peptides are utilized as molecular building blocks for technology and medicine. Recognizing the fact that it is impossible to cover all aspects of potential use of GEPI in a single group, or even a center, our group collaborates with colleagues around the world, who are experts in their own fields for the purpose of using the concepts, tools and protocols developed collaboratively from fundamentals to practical applications.

Sarikaya Group News:

Molecular Biomimetics & Bionanotechnology- IV Workshop August 24-28, 2009 in Friday Harbor, WA.

Interview at ACS Nano: M Sarikaya & Z. Bao Episode 23 ACS Nano June 2009.
To listen online

Four GEMSEC students joined the 12th UG Research Symposium May 15, 2009 in Seattle, WA.

Sarikaya and Tamerler were interviewed by Bilgi, a monthly Science Journal in Turkey

ACS-09 GEMSEC supported Symposium: Genetically-Designed Molecular Materials, March 22-26, 2009 Salt Lake City, UT. Talks recorded online.

NUE-UNIQUE July 6-10, 2009, Seattle, WA.

Materials Camp July 6-11, 2009, Seattle, WA.

Radio Interview on NPR (KUOW): J. Benyus & M. Sarikaya, December 17, 2008. To listen online.

Molecular Biomimetics & Bionanotechnology- IV Workshop 7-11, 2009 in Friday Harbor, WA.

Student Research Discussions , E.O. Wednesday 12-1pm, 2009.

Journal Club, E.O. Wednesday 12-1pm, 2009.


Active Research Programs:

GEMSEC - Genetically Engineered Materials Science and Engineering Center:

DURINT - Defense-University Research Initiative on NanoTechnology: