Biomolecular surface

Altelaar A, Klinkert I, Jalink K, et al. Gold-enhanced biomolecular surface imaging of cells and tissue by SIMS and MALDI mass spectrometry. Anal. Chem. 2006 78 734-742. 

McKarnin, M. A., Aris, R., and Schmidt, L. D. (1988). Autonomous bifurcations of a simple biomolecular surface-reaction model. Proc. R. Soc., A415, 363-87. 

NMR can be used to determine the presence and the movement of water molecules next to biomolecular surfaces (33). Sometimes it is particularly useful to detect the links to buried water and to water molecules that mediate between biomolecules. 

The quartz crystal microbalance (QCM) is an excellent tool for these investigations since the frequency change produced by the adsorption on the surface of a piezoelectric crystal can be used to assess the mass (to a few ng/cm ) of the adsorbent using the Sauerbrey equation. Since the adsorbed protein layers can have some degree of structural flexibility or viscoelasticity that is undetectable by the determination of the resonance frequency alone, the energy loss, or dissipation factor (D), due to the shear of the adsorbent on the crystal in aqueous solution must also be determined.The technique is termed QCM-D and as well as representing an improvement in the study of biomolecular-surface interactions, it presents an opportunity to observe the adsorption of AFP and PVP, on a model nucleator with a hydrophilic surface. 

The dynamic exchange model (illustrated in Figure 6.2) is based on the assumption that the water molecules at the surface of proteins can be categorized into distinct species as bound and free depending on the nature of their hydrogenbonding to the biomolecular surface (Figure 6.2). This equilibrium can be symbolically written as [4]... 

Reeent studies in different systems seem to reveal certain commonalities that have motivated the use of the term biological water to distinguish water in biologieal systems. First and foremost, the extended hydrogen-bond network present in bulk water is mostly lost near a biomolecular surface. Second, water can exist in different states. These molecules differ in their coordination with other water moleeules and with the surface of proteins or DNA or tissues. The term biological water serves to emphasize this difference between water in biology and the one we... 

MMS approach has been used to calculate both solvation energies and electrostatics [1,123], Potential-driven geometric flows, which admit non-curvature-driven terms, have also been proposed for biomolecular surface construction [124], While our approaches were employed by many others [125-128] for molecular surface analysis, our curvature-controlled PDEs and the geometric flow-based MMS model proposed in 2005 [120, 121, 123, 124] are, to our knowledge, the first of their kind for biomolecular surface and electrostatics/solvation modeling. 

S. Zhao. Pseudo-time-coupled nonlinear models for biomolecular surface representation and solvation analysis. Int J. Numerical Methods Biomed. Eng., 27 1964-1981, 2011. 

Altelaar, A.F.M., Klinkert, I., Jalink, K., De Lange, R.P.J., Adan, R.A.H., Heeren, R.M.A., Piersma, S.R., 2005. Gold-enhanced biomolecular surface imaging of cells and tissue by SIMS and MALDI mass spectrometry. Anal. Chem. 78, 734—742. 

Secondly, the water layer hypothesis proposes that the stabilization of proteins is achieved by the trapping of water molecules close to the biomolecular surface (Belton and Gill, 1994). The protein stabilization conferred by the excipients during dehydration is brought about primarily by these excipients substituting for water molecules on the surface of the protein. 

The soft elastomeric stamp can be used either as a vehicle for biomolecular surface patterning (an application called microcontact printing (p.CP)) or to create three dimensional reliefs, particularly on polymer materials, as in micromolding in capillaries (MIMIC), microtransfer molding (pTM) or solvent-assisted molding. These techniques have been successfully applied in the fabrication of polymer patterns with dimensions down to the sub-100 nm scale and will be described in this chapter. These patterns have found many relevant applications in the life sciences, where scientists often need to spatially control topographical and chemical properties of surfaces at small scales [1, 5, 6]. 

Below we show how the appearance of spanning water networks may be detected in computer simulations. In particular, a percolation transition of water upon hydration was studied by simulations in model lysozyme powders and on the surface of a single lysozyme molecule. In protein crystals, increase in hydration of a biomolecular surface may be achieved by applying pressure. In some hydration range, pressurization leads to the formation of spanning water networks enveloping the surface of each biomolecule. Finally, the formation of the spanning water network is shown for the DNA molecule at various conformations and for different forms of DNA. 

Effect of hydration on the properties of biosystems was extensively studied both experimentally and by computer simulations. We have already considered how biological activity and conformational dynamics of hydrated biomolecules (Section 6) as well as conductivity of biosystems (Section 7.1) develop upon hydration. Now we analyze some other physical properties of hydrated biosystems (first, their dynamical properties) in relation to the percolation transition of water. Typical biomolecular surface is characterized by heterogeneity (presence of strongly hydrophilic and strongly hydrophobic groups), roughness, and finite size (closed surface of a single biomolecule). These features determine several steps in the process of hydration of biomolecules. 

Figure 2 Illustration of a negatively charged biomolecular surface with charge density a in the presence of a mixed electrolyte. The surface may represent that of a colloidal or biophysical particle such as a membrane (plane), polynucleic acid (cylinder), or micelle (sphere) where the distance of closest approach of ions is designated x — a. n the solution of the Gouy-Chapman equation, and of the Poisson-Boltzmann equation in general, the charged surface is usually displaced from its actual position (relative to the solvent) to the plane of closest approach of nonadsorbed ions, also called the outer Helmholtz plane.

Having dissected the ways in which ions bind to biomolecular surfaces, we attempt for predict ion specific phenomena in protein solutions. In Hofmeister s original work, salts were ranked according to their ability to precipitate egg white proteins. Since then, many more experiments have been conducted with a rather general conclusion for protein-protein association" ... 

---