Protein potential surfaces

Protein dipoles-Langevin dipoles model (PDLD), 123-125,124 Protein potential surfaces, see Enzyme potential surfaces... 

Protems can be physisorbed or covalently attached to mica. Another method is to innnobilise and orient them by specific binding to receptor-fiinctionalized planar lipid bilayers supported on the mica sheets [15]. These surfaces are then brought into contact in an aqueous electrolyte solution, while the pH and the ionic strength are varied. Corresponding variations in the force-versus-distance curve allow conclusions about protein confomiation and interaction to be drawn [99]. The local electrostatic potential of protein-covered surfaces can hence be detemiined with an accuracy of 5 mV. 

In light of tire tlieory presented above one can understand tliat tire rate of energy delivery to an acceptor site will be modified tlirough tire influence of nuclear motions on tire mutual orientations and distances between donors and acceptors. One aspect is tire fact tliat ultrafast excitation of tire donor pool can lead to collective motion in tire excited donor wavepacket on tire potential surface of tire excited electronic state. Anotlier type of collective nuclear motion, which can also contribute to such observations, relates to tire low-frequency vibrations of tire matrix stmcture in which tire chromophores are embedded, as for example a protein backbone. In tire latter case tire matrix vibration effectively causes a collective motion of tire chromophores togetlier, witliout direct involvement on tire wavepacket motions of individual cliromophores. For all such reasons, nuclear motions cannot in general be neglected. In tliis connection it is notable tliat observations in protein complexes of low-frequency modes in tlie... 

Keywords, protein folding, tertiary structure, potential energy surface, global optimization, empirical potential, residue potential, surface potential, parameter estimation, density estimation, cluster analysis, quadratic programming... 

KD Ball, RS Beii y, RE Kunz, E-Y Li, A Proykova, DJ Wales. Erom topographies to dynamics of multidimensional potential energy surfaces of atomic clusters. Science 271 963-966, 1996. RS Berry, N Elmaci, JP Rose, B Vekhter. Linking topography of its potential surface with the dynamics of folding of a protein model. Proc Natl Acad Sci USA 94 9520-9524, 1997. Z Guo, D Thii-umalai. J Mol Biol 263 323-343, 1996. 

Energy minimization methods that exploit information about the second derivative of the potential are quite effective in the structural refinement of proteins. That is, in the process of X-ray structural determination one sometimes obtains bad steric interactions that can easily be relaxed by a small number of energy minimization cycles. The type of relaxation that can be obtained by energy minimization procedures is illustrated in Fig. 4.4. In fact, one can combine the potential U r) with the function which is usually optimized in X-ray structure determination (the R factor ) and minimize the sum of these functions (Ref. 4) by a conjugated gradient method, thus satisfying both the X-ray electron density constraints and steric constraint dictated by the molecular potential surface. 

The simplest way to consider the energetics of this reaction is to use the EVB model for the reacting region and PDLD model for the protein. The EVB potential surface is formally identical to that used in Chapter 2, where the reaction is described in terms of two resonance structures,... 

After learning to estimate AG7" and AS, we might ask how AASf is affected by the steric restriction of the protein environment. As is clear from eq. (9.7), we need the differences between the entropic contributions to A G rather than the individual AS. This requires the examination of the difference between the potential surfaces of the protein and solution reaction. Here we exploit the fact that the electrostatic potential changes rather slowly and use the approximation... 

As well as predicting protein structure, it is also of interest to try to predict solvent accessibility from the protein s primary sequence of amino acid residues. Solvent accessibility concerns the area of a protein s surface that is exposed to the surrounding solvent. The importance of this concept is that these accessible regions have the potential to interact with other entities, including endogenous proteins and drugs. Similarly, if the protein of interest is an enzyme, only residues with solvent accessibility could be part of the enzyme s active site. This means that an interaction site of interest, one involved in signal transduction (see Krauss, 2003), requires spatial accessibility to the solvent (Ofiran and Rost, 2005). 

In the following, we proceed to several new aspects regarding molecular resolution of adsorbed metalloproteins. In Section 5.3, we first show that close to molecular resolution of the interfacial ET patterns of some two-centre proteins is within reach. The number of intermetallic interactions and resulting microscopic reduction potentials and rate constants in metalloproteins with more than two centres is, however, prohibitively large for such resolution. In Section 5.4 we address molecular and supramolecu-lar adsorption. We show here that in situ STM and AFM, indeed do hold exciting new perspectives for this important and central structural aspect of proteins at surfaces. 

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