Proteins patterning

Fig. 11.5 Differential phase contrast detection of patterned protein in a 10 mm by 30 mm region, (a) Protein height signal showing ridges of protein in a checker board pattern, (b) Side band demodulated signal image in which the carrier frequency of the ridges is removed to show only the protein envelope. Reprinted from Ref. 21. with permission. 2008 Optical Society of America...

Whitesides and coworkers describe the use of an elastomeric membrane to pattern proteins and cells on bacteriological polystyrene (PS), glass, and poly(dimethyl-siloxane) (PDMS) substrates [92], A patterned PDMS membrane was casted from lithographically structured photoresists and brought into close contact with the substrates (Fig. 6). When incubated with a solution of fibronectin (FN), adsorption of the cell-adhesion-mediating protein to the surface was restricted to the exposed areas. The membrane was peeled off and cells were seeded from a serum-free medium. Passivation to cell attachment of the untreated portions of the surface was achieved by adding 1% bovine serum albumin (BSA) to the cell-seeding medium, which... 

Microcontact printing (pCP, see Fig. 10 for an example) has been used for the spatially resolved modification of gold, silver, or titanium surfaces with SAMs of methyl-terminated alkanethiolates, which favor protein adsorption [99-101], Backfilling around the patterned protein-attractive islands was performed by a subsequent self-assembly of an ethylene-glycol-terminated alkanethiol. In a next step, the hydrophobic methyl-terminated SAMs were covered by adsorbed FN or other cell-adhesion-mediating proteins. 

The Sequence Retrieval System (Etzold et ah, 1996) is a network browser for databases at EBI. The system allows users to retrieve, link, and access entries from all the interconnected resources such as nucleic acid, EST, protein sequence, protein pattern, protein structure, specialist/boutique, and/or bibliographic databases. The SRS is also a database browser of DDBJ, ExPASy, and a number of servers as the query system. The SRS can be accessed from EBI Tools server at http // www2.ebi.ac.uk/Tools/index.html or directly at http //srs6.ebi.ac.uk/. The SRS permits users to formulate queries across a range of different database types via a single interface in three different methods (Figure 3.4) ... 

Considering the affinity between metal ions (i.e., Zn2+, Cu2+, Ni2+, and Co2+) and proteins another method to pattern proteins on gold surfaces by DPN was developed.130 This method utilizes Zn2+ ions (Zn(N03)2 6H20) that can be coordinated with MHDA, which can be patterned on gold by an AFM tip after passivation of the remaining gold areas with PEG-SH. The Zn-modified features can be subsequently reacted with the desired antibody. Biorecognition properties can be further studied by interaction with other proteins. 

Primary Results Morphology Population Distribution Chemical Patterns Elemental Composition Macromolecular Composition Lipid pattern Protein Pattern Small Key Metabolites Enzyme Activities Stress Markers... 

Kane, R., et ah. Patterning proteins and cells using soft lithography. Biomaterials 1999, 20 (23/24), 2363-2376. 

Britland S, Perez-Amaud E, Clark P, McGinn B, Connolly P, Moores G. Micro-patterning proteins and synthetic peptides on solid supports A novel application for microelectronics fabrication technology. Biotechnol Prog 1992 8 155-60. 

Kane RS, Takayama S, Ostuni E, Ingber DE, Whitesides GM. Patterning proteins and cells using soft hthography. Biomaterials 1999 20 2363-76. 

Pattern Protein Concentration (mg/dL) Pattern Protein Concentration Pattern (mg/dL) Protein Concentration (mg/dL)... 

Protein Concentration Pattern Protein Concentration Pattern Protein Concentration... 

Multiple inking is possible using microfluidic networks over the PDMS stamps.Papra, A. Bernard, A. Juncker, D. Larsen, N. B. Michel, B. Delamarche, E. Microfluidic Networks Made of Poly(Dimethylsiloxane), Si, and Au Coated With Polyethylene Glycol for Patterning Proteins Onto Surfaces. Langmuir 2001, 17, 4090-4095... 

Lahann, J. Balcells, M. Rodon, T. Lee, J. Choi, I.S. Jensen, K.F. Langer, R. Reactive polymer coatings a platform for patterning proteins and mammalian cells onto a broad range of materials. Langmuir 2002, 18, 3632-3638. 

Key Words Motif discovery sequence motif sequence pattern protein domain multiple alignment position-specific scoring matrix PSSM position-specific weight matrix PWM transcription factor-binding site transcription factor promoter protein features. 

Sequence patterns Protein sequence is not well conserved, because protein function is often attributed to only a small set of residues, such as the catalytic triad Serine-Histidine-Aspartate in serine protease enzymes. Special algorithms have been developed to find these patterns or motifs, of which the constituting parts are most often discontinuous parts of a protein sequence. 

Genetic diversity within a popnlation adds statistical noise to stndies of diet in hitmans. Variations in response to diet are cansed by differences in gene expression patterns, protein, and enzyme activities. Natnrally occurring dietary chemicals may interact with the same classes of proteins in each individual, but because individuals have different variants of these proteins, the responses among individuals differ. 

Stachowiak, T. B., Svec, F., and Frdchet, J. M. J., Patternable Protein resistant surfaces for multifunctional microfluidic devices via surface hydrophihzation of porous polymer monoliths using photografting, Chem. Mater., 18, 5950, 2006. 

Hie ability to culture cells on a surface with control over size, shape, and position is a powerful tool for examining and controlling the cell microenvironment. A common approach has been to pattern protein on a 2D surface and then seed cells on the patterned regions. This has been accomplished by using metal templates, SAMs, stamped proteins and peptides, biopolymers, miaofluidic channels, and cross-linked PEG. Noncontact methods have also been used to generate protein patterns by photolithography that selectively promote or exclude cell adhesion. Nonspecific biological molecules such as short chains of PEG have been assembled on surfaces to form a bmsh-like layer that resists protein adsorption and as a consequence cell attachment. 

Belisle, J. M., Correia, J. P., Wiseman, P. W., Kennedy, T. E., Costantino, S. (2008). Patterning protein concentration using laser-assisted adsorption by photobleaching, LAPAP. Lab on a Chip, 8 2), 2164. 

Papra A, Bernard A, Juncker D, Larsen NB, Michel B, Delamarche E (2001) Microfluidic networks made of poly(dimethylsiloxane), Si, and Au coated with polyethylene glycol for patterning proteins onto surfaces. Langmuir 17 4090-4095... 

Lahann J, Balcells M, Rodon T, Lee J, Choi IS, Jensen KF, Danger R (2002) Reactive Polymer Coatings A Platform for Patterning Proteins and MammaUan Cells onto a Broad Range of Materials. Langmuir 18(9) 3632—3638... 

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