Biophysical characterization

In the following, we will focus on biophysical characterization of material surfaces, especially on quantifying their interaction with proteins and cells, and on biological evaluation of biomaterials and medical devices by in vitro tests as a first step towards ensuring their biocompatibility. 

Biophysics in general studies life at every level, from atoms and molecules to cells, organisms, and environments. It aims to find out how biological systems work by looking for pattern in life and analyzing them with mathematics and physics. 

This chapter concentrates on biophysical characterization of material surfaces in biological environments and just highlights some examples. Especially, the quantification of protein adsorption and/or cell adhesion is important in order to evaluate the potential of a biomaterial for a given application. 

It is well described that materials in contact with biofluids are irmnediately coated with proteins. Protein adsorption is influenced by the underlying substrate surface properties including surface chemistry, charge, and free energy. After cell adhesion on top of this primary protein layer, the formation of secondary protein layers can take place due to nonspecific adsorption of ceU-secreted proteins (Fig. 4.27). 

A large spectrum of methods is utilized to characterize adsorbed proteins (Table 4.4), regarding the adsorption dynamics, the adsorbed amount and the composition of the protein layer, the lateral (or 3D) distribution, orientation 

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Fig. 14A-C. Guanosine-nucleotides for biophysical characterizations of Ras proteins A gua-nosinediphosphate with a methylanthraniloylester (in grey) at the 3 -position of the ribose B guanosine-5 -[/3,y-imido]-triphosphate (GppNHp) C guanosine-5 -0-(3-thiotriphosphate)...

Rasmussen, S. G Carroll, F. I., Maresch, M. J., Jensen, A. D Tate, C. G and Gether, U. (2001) Biophysical characterization of the cocaine binding pocket in the serotonin transporter using a fluorescent cocaine analogue as a molecular reporter. J. Biol. Chem. 276, 4717 1723. 

Matsuura, J.E., A.E. Morris, R.R. Ketchem, E.H. Braswell, R. Klinke, W.R. Gom-botz, and R.L. Remmele, Jr. 2001. Biophysical characterization of a soluble CD40 ligand (CD154) coiled-coil trimer evidence of a reversible acid-denatured molten globule. Arch Biochem Biophys 392 208-218. 

Eastman SJ, Siegel C, Tousignant J, Smith AE, Cheng SH, Scheule RK. Biophysical characterization of cationic lipid DNA complexes. Biochim Biophys Acta 1997 1325(l) 41-62. 

Jung Y-S, Gao-Sheridan HS, Christiansen J, et al. 1999. Purification and biophysical characterization of a new [2Ee-2S] ferredoxin from Azotobactervinelandii, a pnta-tive [Fe-S] cluster assembly/repair protein. J Biol Chem 274 32402-10. 

Aminoglycosides remain clinically important antibiotics. NMR provided the initial breakthrough in structural understanding of aminoglycoside action on the ribosome, and it remains a powerful tool for the biophysical characterization of drug-RNA interaction. The combined use of NMR, X-ray crystallography, thermodynamic and functional assays, and computational methods is needed to drive forward the development of new aminoglycosides with improved clinical properties. The rich data described above, combined with the application of new synthetic methods, bode well for the future. 

McLean, K. J. Warman, A. J. Seward, H. F. Marshall, K. R. Cirvan, H. M. Cheesman, M. R. Waterman, M. R. Munro, A. W. Biophysical Characterization of the Sterol Demethylase P450 from Mycobacterium tuberculosis, Its Cognate Ferredoxin, and Their Interactions. Biochemistry 2006, 45, 8427-8443. 

AMnc A, Lynn DM, Anderson DG, Langer R (2003) Parallel synthesis and biophysical characterization of a degradable polymer library for gene delivery. J Am Chem Soc 125 5316-5323... 

Gontrolled nanostructural morphology, in this case nanofibers with controlled length, was achieved by varying the ratio of the central repeating number of (Gin-Leu) and the flanking lysine residues. A variety of biophysical characterization methods indicated that the short, dispersed nanofibers formed by K2(QL)gK2 reached... 

G. Gairola. Biochemical and biophysical characterization of pulmonary surfactant in rats exposed chronically to cigarette smoke. Fundam Appl Toxicol 1995 27(1) 63-69. 

Pallela, R., Bojja, S., and Janapala, V. R. (2011). Biochemical and biophysical characterization of collagens of marine sponge, Ircinia fusca (Porifera Demospongiae Irciniidae). Int. J. Biol. Macromol. 49, 85-92. 

Wyss, M. Schlegel, J. James, P. Eppenberger, H.M. Wallimann, T. Mitochondrial creatine kinase from chicken brain. Purification, biophysical characterization, and generation of heterodimeric and heterooctameric molecules with subunits of other creatine kinase isoenzymes. J. Biol. Chem., 265, 15900-15908 (1990)... 

Biophysical characterization showed that a single HRP II protein bound 17 molecules of heme [35]. In an in vitro heme polymerization assay, HRP II promoted the synthesis of hemozoin, while controls, such as the proteins bovine serum albumin and lysozyme or the homopeptides polyhistidine, polylysine, and polyasparagine, did not. FT-IR analysis of the reaction product showed the characteristic vibrations of hemozoin. The polymerization activity had a pH maximum near 4.0, which dropped off precipitously near the pKa of histidine. The heme polymerization... 

Kreiter R, Kleij AW, Klein Gebbink RJM, van Koten G (2001) Dendritic Catalysts. 217 163-199 Kuhlmann J, Herrmann C (2000) Biophysical Characterization of the Ras Protein. 211 61-116... 

Vogel T, Leukert N, Barczyk, K. Strupat K, Roth J. Biophysical characterization of S100A8 and S100A9 in the absence and presence of bivalent cations. Biochim. Biophys. Acta - Molecular Cell Research 2006, in press. 

Patil SD, Rhodes DG, Burgess DJ (2005) Biophysical characterization of anionic lipoplexes. Biochim Biophys Acta 1711(1) 1—11... 

S. Mukund, Biochemical and Biophysical Characterization of Novel Tungsten-Containing Enzymes from Hyperthermophilic Archaea (Pyrococcusfuriosus, Thermococcus litoralis). Ph.D. Thesis, University of Georgia, Athens (1996). 

Satoh, K. (1996). Introduction to photosystem II reaction center Isolation and biochemical and biophysical characterization. In D.R. Qrt and C.F. Yocum, eds., Oxygenic Photosynthesis. Boston Kluwer, pp. 193-212. 

Chen F, Kuziemko GM, Stevens RC (1998a) Biophysical characterization of the stability of the 150-kilodalton botulinum toxin, the nontoxic component, and the 900-kilodalton botulinum toxin complex species. Infect Immun 66 2420-5... 

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