Functional protein-functionalized

There are at least two ways by which lipids can affect protein structure and function and thereby cell function. Protein function is influenced by specific protein-lipid interactions that depend on the chemical and structural anatomy of lipids (head group, backbone, alkyl chain length, degree of unsaturation, chirality, ionization, and chelating properties). However, protein function is also influenced by the unique self-association properties of lipids that result from the collective properties (fluidity, bilayer thickness, shape, and packing properties) of the lipids organized into membrane structures. 

Membrane proteins comprise another important class of protein crystallized in 2D. These proteins perform important functions as membrane channels and recognition sites for cells. Unlike the streptavidin crystals, membrane proteins... 

A large number of studies concerned witli tliiol-tenninated molecules has been directed at tire preparation of tailored organic surfaces, since tlieir importance has been steadily increasing in various applications. Films of o> functionalized alkanetliiols have facilitated fundamental studies of interfacial phenomena, such as adhesion [190, 191], corrosion protection [192], electrochemistry [193], wetting [194], protein adsorjDtion [195, 196] or molecular recognition [197, 198, 199, 200 and 201] to mention only a few. 

The sequence space of proteins is extremely dense. The number of possible protein sequences is 20. It is clear that even by the fastest combinatorial procedure only a very small fraction of such sequences could have been synthesized. Of course, not all of these sequences will encode protein stmctures which for functional purjDoses are constrained to have certain characteristics. A natural question that arises is how do viable protein stmctures emerge from the vast sea of sequence space The two physical features of folded stmctures are (l)in general native proteins are compact but not maximally so. (2) The dense interior of proteins is largely made up of hydrophobic residues and the hydrophilic residues are better accommodated on the surface. These characteristics give the folded stmctures a lower free energy in comparison to all other confonnations. 

Figure C2.5.4. Schematic illustration of the stages in the drastic reduction of sequence space in tire process of evolution to functionally competent protein stmctures.

A salient feature of natural surfaces is tliat tliey are overwhelmingly electron donors [133]. This is tlie basis for tlie ubiquitous hydrophilic repulsion which ensures tliat a cell can function, since massive protein-protein aggregation and protein-membrane adsorjition is tliereby prevented. In fact, for biomolecule interactions under typical physiological conditions, i.e. aqueous solutions of moderately high ionic strengtli, tlie donor-acceptor energy dominates. 

Bdhm H-J 1994 The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure J. Comp.-Aided Mol. Design 8 243-56... 

The pathway model makes a number of key predictions, including (a) a substantial role for hydrogen bond mediation of tunnelling, (b) a difference in mediation characteristics as a function of secondary and tertiary stmcture, (c) an intrinsically nonexponential decay of rate witlr distance, and (d) patlrway specific Trot and cold spots for electron transfer. These predictions have been tested extensively. The most systematic and critical tests are provided witlr mtlrenium-modified proteins, where a syntlretic ET active group cair be attached to the protein aird tire rate of ET via a specific medium stmcture cair be probed (figure C3.2.5). 

The cross relation has proven valuable to estimate ET rates of interest from data tliat might be more readily available for individual reaction partners. Simple application of tire cross-relation is, of course, limited if tire electronic coupling interactions associated with tire self exchange processes are drastically different from tliose for tire cross reaction. This is a particular concern in protein/protein ET reactions where tire coupling may vary drastically as a function of docking geometry. 

In special cases (as in colloidal solutions) some particles can be considered as essential and other particles as irrelevant , but in most cases the essential space will itself consist of collective degrees of freedom. A reaction coordinate for a chemical reaction is an example where not a particle, but some function of the distance between atoms is considered. In a simulation of the permeability of a lipid bilayer membrane for water [132] the reaction coordinate was taken as the distance, in the direction perpendicular to the bilayer, between the center of mass of a water molecule and the center of mass of the rest of the system. In proteins (see below) a few collective degrees of freedom involving all atoms of the molecule, describe almost all the... 

Interestingly, there are many proteins with two domains that show a very clear hinge-bending motion with an obvious functional significance. Such domains have often been reported in the literature, but were never detected on an automated basis. 

Proteins are biopolymers formed by one or more continuous chains of covalently linked amino acids. Hydrogen bonds between non-adjacent amino acids stabilize the so-called elements of secondary structure, a-helices and / —sheets. A number of secondary structure elements then assemble to form a compact unit with a specific fold, a so-called domain. Experience has shown that a number of folds seem to be preferred, maybe because they are especially suited to perform biological protein function. A complete protein may consist of one or more domains. 

Grubmiiller described a method to induce conformational transitions in proteins and derived rate constants for these ([Grubmiiller 1994]). The method employs subsequent modifications of the original potential function based on a principal component analysis of a short MD simulation. It is discussed in more detail in the chapter of Eichinger et al. in this volume. 

By applying a pulling force at a portion of the solute molecule in a specific direction (see chapters of Eichinger et al. and Schulten in this volume), conformational transitions can be induced in specific directions. In order to reconstruct information about the underlying potential function governing protein motion, the irreversible work performed on the system by these forces must be discounted ([Balsera et al. 1997]). 

Amadei et al. 1993] Amadei, A., Linssen, A.B.M., Berendsen, H.J.C. Essential Dynamics of Proteins. Proteins 17 (1993) 412-425 [Balsera et al. 1997] Balsera, M., Stepaniants, S., Izrailev, S., Oono, Y., Schiilten, K. Reconstructing Potential Energy Functions from Simulated Force-Induced Unbinding Processes. Biophys. J. 73 (1997) 1281-1287 [Case 1996] Case, D.A. Normal mode analysis of protein dynamics. Curr. Op. Struct. Biol. 4 (1994) 285-290... 

As an example for an efficient yet quite accurate approximation, in the first part of our contribution we describe a combination of a structure adapted multipole method with a multiple time step scheme (FAMUSAMM — fast multistep structure adapted multipole method) and evaluate its performance. In the second part we present, as a recent application of this method, an MD study of a ligand-receptor unbinding process enforced by single molecule atomic force microscopy. Through comparison of computed unbinding forces with experimental data we evaluate the quality of the simulations. The third part sketches, as a perspective, one way to drastically extend accessible time scales if one restricts oneself to the study of conformational transitions, which arc ubiquitous in proteins and are the elementary steps of many functional conformational motions. 

The previous application — in accord with most MD studies — illustrates the urgent need to further push the limits of MD simulations set by todays computer technology in order to bridge time scale gaps between theory and either experiments or biochemical processes. The latter often involve conformational motions of proteins, which typically occur at the microsecond to millisecond range. Prominent examples for functionally relevant conformatiotial motions... 

Zhang, Z.-Y., Dixon, J. E. Active site labeling of the yersinia protein tyrosine phosphatase The determination of the pKa of active site cysteine and the function of the conserved histidine 402. Biochem. 32 (1993) 9340-9345. 

Abstract. A smooth empirical potential is constructed for use in off-lattice protein folding studies. Our potential is a function of the amino acid labels and of the distances between the Ca atoms of a protein. The potential is a sum of smooth surface potential terms that model solvent interactions and of pair potentials that are functions of a distance, with a smooth cutoff at 12 Angstrom. Techniques include the use of a fully automatic and reliable estimator for smooth densities, of cluster analysis to group together amino acid pairs with similar distance distributions, and of quadratic progrmnming to find appropriate weights with which the various terms enter the total potential. For nine small test proteins, the new potential has local minima within 1.3-4.7A of the PDB geometry, with one exception that has an error of S.SA. 

While this is disappointing, the nonuniqueness theorem also shows that if some empirical potential is able to predict correct protein folds then many other empirical potentials will do so, too. Thus, the construction of empirical potentials for fold prediction is much less constrained than one might think initially, and one is justified in using additional qualitative theoretical assumptions in the derivation of an appropriate empirical potential function. 

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