Protein, analysis conformations

Hayward, S., Berendsen, H.J.C. Systematic analysis of domain motions in proteins from conformational change New results on citrate synthase and T4 lysozyme. Proteins 30 (1998) 144-154. 

In the following, the method itself is introduced, as are the various techniques used to perform normal mode analysis on large molecules. The method of normal mode refinement is described, as is the place of normal mode analysis in efforts to characterize the namre of a protein s conformational energy surface. 

The wavelengths of IR absorption bands are characteristic of specific types of chemical bonds. In the past infrared had little application in protein analysis due to instrumentation and interpretation limitations. The development of Fourier transform infrared spectroscopy (FUR) makes it possible to characterize proteins using IR techniques (Surewicz et al. 1993). Several IR absorption regions are important for protein analysis. The amide I groups in proteins have a vibration absorption frequency of 1630-1670 cm. Secondary structures of proteins such as alpha(a)-helix and beta(P)-sheet have amide absorptions of 1645-1660 cm-1 and 1665-1680 cm, respectively. Random coil has absorptions in the range of 1660-1670 cm These characterization criteria come from studies of model polypeptides with known secondary structures. Thus, FTIR is useful in conformational analysis of peptides and proteins (Arrondo et al. 1993). 

The physical environment within a crystal, of course, is not identical to that in solution or in a living cell. A crystal imposes a space and time average on the structure deduced from its analysis, and x-ray diffraction studies provide little information about molecular motion within the protein. The conformation of proteins in a crystal could in principle also be affected by nonphysiological factors such as incidental... 

E. Peggion, A. Bisello, M. Rosenblatt, M. Chorev, D. F. Mierke, Mono- and bicyclic analogs of parathyroid hormone-related protein. 2. Conformational analysis of antagonists by CD, NMR, and distance geometry calculations, Biochemistry 1997, 36, 3300-3307. 

Querol E, Perez-Pons JA, Mozo-Villarias A. Analysis of protein 41. conformational characteristics related to thermostability. Protein Eng. 1996 9 265-271. 

The X-ray crystal structure database led us to believe that peptide bonds adopt either the cis or trans conformation in native proteins [22,128]. However, NMR spectroscopy [143], and in a few cases, crystal structure analysis [144], provide encouraging experimental evidence of conformational peptide bond polymorphism of folded proteins. Furthermore, conformational changes in response to ligand binding, crystallization conditions and point mutations at remote sites are frequent. Consequently, the three-dimensional protein structure database contains homologous proteins that have different native conformations for a critical prolyl bond [12]. 

Once ions are included in water, it is crucial to employ the dielectrically consistent version of the RISM theory [11, 12]. The basic equations and the algorithm for numerically solving them are described in the Appendix. In the analysis, we choose acetylglycine ethyl ester (AGE) CH3CONHCH2COOCH2CH3 because the salting-out coefficients of this peptide in various salt solutions are experimentally available [53]. Besides, such a peptide serves as one of the basic models of proteins. The conformation is fixed at the all-trans form in our calculations. The SPC/E model is employed for water. The following two sets of salt solutions are considered to examine the effects of cations and anions on the solvation properties of AGE LiCl, NaCl, and KGl (set 1) for the cation effects, and NaCl, NaBr, and Nal (set 2) for the anion effects. The temperature and the salt concentration are fixed at 298K and IM, respectively. The number density and the dielectric constant of each salt solution, which are used as part of the input data in the dielectrically consistent version of the RISM theory, are taken from the experimental data. We adopt the Coulomb plus L-J potential functions for all the interactions between water-solute and ion-solute atomic pairs. That is, the site-site pair potential Uab r) is expressed as Eq.(3.17) (for the NaCl-solution, for example, 6=H,0,Na+,Cl ). The AMBER-type potential parameters are employed for the peptide. 

The primary structure of P. is elucidated by the standard methods of sequence analysis (see Proteins). The conformation of P. is an important determinant of their biological activity. It is stabilized by peptide and disulfide bonds In P. containing unusual bonds and/or constituents other factors also stabilize the conformation. Although X-ray crystallography (see) was used in the elucidation of the three-dimensional structures of insulin and gramicidin S, the conformational analysis of P. is now by preference carried out in solution, using the spectroscopic methods ORD, CD, IR, NMR and ESR. 

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