Protein theoretical analysis

Many key protein ET processes have become accessible to theoretical analysis recently because of high-resolution x-ray stmctural data. These proteins include the bacterial photosynthetic reaction centre [18], nitrogenase (responsible for nitrogen fixation), and cytochrome c oxidase (the tenninal ET protein in mammals) [19, 20]. Although much is understood about ET in these molecular machines, considerable debate persists about details of the molecular transfonnations. 

Esteban-Martin S, Strandberg E, Fuertes G, Ulrich AS, Salgado J (2009) Influence of whole-body dynamics on 15N PISEMA NMR spectra of membrane proteins a theoretical analysis. Biophys J 96 3233-3241... 

The contributions to this volume demonstrate that structural studies of fibrous /1-proteins, as well as prion and amyloid fibrils, have advanced rapidly thanks in large part to improved experimental techniques and better theoretical analysis of the ever-increasing structural data. It is also possible to learn from studies of naturally occurring silks (Dicko et al., this volume) howvariations in the conditions of production of silk threads from the same protein can produce a variety of /1-structures with very distinct... 

Equations (1-3) are widely used for protein dynamics analysis from relaxation measurements. The primary goals here are (A) to measure the spectral densities J(co) and, most important, (B) to translate them into an adequate picture of protein dynamics. The latter goal requires adequate theoretical models of motion that could be obtained from comparison with molecular dynamics simulations (see for example Ref. [23]). However, accurate analysis of experimental data is an essential prerequisite for such a comparison. 

The a-helix is the classic element of protein structure. A single a-helix can order as many as 35 residues whereas the longest strands include only about 15 residues, and one helix can have more influence on the stability and organization of a protein than any other individual structure element. a-Helices have had an immense influence on our understanding of protein structure because their regularity makes them the only feature readily amenable to theoretical analysis. 

Torii H, Tasumi M. Theoretical analysis of the amide I infrared bands of globular proteins. In Mantsch HH, Chapman D, eds. Infrared Spectroscopy of Biomolecules. New York Wiley-Liss, Inc., 1996 1-18. 

Murzin, A. G., Lesk, A. M., and Chothia, C. (1994a). Principles determining the structure of /3-sheet barrels in proteins. I. A theoretical analysis./ Mol. Biol. 236, 1369-1381. 

D. Bashford, M. Karplus, and G. W. Canters, J. Mol. Biol., 203, 507 (1988). Electrostatic Effects of Charge Perturbations Introduced by Metal Oxidation in Proteins. A Theoretical Analysis. 

Also, Schellman s work is pertinent (1809). From studies on heats of dilution of urea in water he concludes that the N—H 0=C bond has an enthalpy of 1.5 kcal/mole in aqueous solution, and he carries this value over to proteins and polypeptides. Among these complicated materials he is forced to approximate—but he deduces relations which show the stability of helices and sheets in terms of H bond enthalpy and configurational entropy. From this he draws the important conclusion that H bonds, taken by themselves, give a marginal stability to ordered structures which may be enhanced or disrupted by the interactions of the side chains. Schellman ends his papers with a discussion of experimental tests needed to eliminate some of the assumptions in his theoretical analysis. 

An important reason for calculating the electrostatic potential distribution is to obtain experimentally measurable properties. In some cases the electrostatic potential or field itself is directly measurable. In these cases no further calculation is necessary to obtain the appropriate experimental quantity. Examples of applications like this include the measurement and calculation of a-helix potentials and fields (Lockhart and Kim 1993 Lockhart and Kim 1992 Sitkoff et al. 1994a), the measurment and calculation of potentials around DNA (Hecht and Honig 1995 Shin and Hubbell 1992) and at membrane surfaces (McDaniel et al. 1986). Another application is when the stabilization potential at a particular site in a protein is required. An example is the evaluation of the protein potential at the oxyanion hole in a serine protease (Soman et al. 1989). Most experimental parameters of interest, however, are obtained by combining the results of an electrostatic calculation with further theoretical analysis or calculations. 

Rather than resort to purely empirical selection of suitable values of ni and p(/Cint)< for equation 1 it is more usual to begin by fitting experimental data with values of m chosen to conform with the numbers of prototropic groups determined by several more direct and specific methods of examination of titration data. Even where the theoretical analysis of a titration curve is not attempted and exact values of p(Ki t), for each type of group are therefore lacking, the numbers of groups so determined may furnish valuable clues to the internal structure of the protein, especially when they are compared with the results of amino acid analyses. 

The hydrophobic interactions are known to control many aspects of self-assembly and stability of macromolecular and snpramolecular structures. This has obviously been useful in both theoretical analysis and technical development of chemical structures. Furthermore, the interaction between nonpolar parts of amphiphiles and water is an important factor in many physicochemical processes, such as surfactant micelle formation and adsorption or protein stability. To make the discussion short, this interaction will be discussed in terms of the measured data of the surface and interfacial tension of homologous series. Analyses have shown that there is no clear correlation therefore, different homologous series will be discussed separately. 

---