Proteins, conformational analysis

Dryden, K. A., Wang, G., Yeager, M., Nibert, M. L., Coombs, K. M., Furlong, D. B., Fields, B. N., and Baker, T. S. (1993). Early steps in reovirus infection are associated with dramatic changes in supramolecular structure and protein conformation Analysis of virions and subviral particles by cryoelectron microscopy and image reconstruction./. Cell Biol. 122, 1023-1041. 

G. M. Crippen and P, K. Ponnuswamy,/. Comput. Chem., 8, 972 (1987). Determination of an Empirical Energy Function for Protein Conformational Analysis by Energy Embedding. 

Figure 19.1). The amide I region is more often used for protein conformational analysis because its Raman spectrum is stronger. 

M. Oobatake and G.M. Crippen, Residue-residue potential function for conformational analysis of proteins, J.Phys. Chem. 85 (1981), 1187-1197. 

Gilson M K and B Honig 1988. Calculation of the Total Electrostatic Energy of a Macromoleculai System Solvation Energies, Binding Energies and Conformational Analysis. Proteins Structure Function and Genetics 4 7-18. 

CS Ring, DG Kneller, R Langndge, FE Cohen. Taxonomy and conformational analysis of loops m proteins. I Mol Biol 224 685-699, 1992. 

Analysis and prediction of side-chain conformation have long been predicated on statistical analysis of data from protein structures. Early rotamer libraries [91-93] ignored backbone conformation and instead gave the proportions of side-chain rotamers for each of the 18 amino acids with side-chain dihedral degrees of freedom. In recent years, it has become possible to take account of the effect of the backbone conformation on the distribution of side-chain rotamers [28,94-96]. McGregor et al. [94] and Schrauber et al. [97] produced rotamer libraries based on secondary structure. Dunbrack and Karplus [95] instead examined the variation in rotamer distributions as a function of the backbone dihedrals ( ) and V /, later providing conformational analysis to justify this choice [96]. Dunbrack and Cohen [28] extended the analysis of protein side-chain conformation by using Bayesian statistics to derive the full backbone-dependent rotamer libraries at all... 

RL Dunbrack Jr, M Karplus. Conformational analysis of the backbone-dependent rotamer preferences of protein sidechams. Nature Struct Biol 1 334-340, 1994. 

MK Gilson, B Homg. Calculation of the total electrostatic energy of a macromolecular system Solution energies, binding energies, and conformational analysis. Proteins 4 7-18, 1988. 

This chapter summarizes the computational methodologies used for conformational analysis. Specifically, Section 8.1 gives a theoretical outUne of the problem and presents details of various implementations of computer codes to perform conformational analysis. Section 8.2 describes calculations illustrative of the current accuracy in generating the conformation of a ligand when bound to proteins (the bioactive conformer) by comparisons to crystaUographically observed data. Finally, Section 8.3 concludes by presenting some practical... 

Perola, E., Charifson, P. S. Conformational analysis of drug-like molecules bound to proteins an extensive study of ligand reorganization upon binding. /. Med. Chem. 2004, 47, 2499-2510. 

D. P. Goldenberg, Analysis of protein conformation by gel electrophoresis, in Protein Structure—A Practical Approach (T.E. Creighton, ed.), IRL Press, Oxford, 1989, pp. 225-250. 

However, 2D NOE studies are invaluable in structure determination, in particular of peptides and proteins here the NOEs give invaluable information for conformational analysis and the determination of the tertiary structures of proteins. 

Ultrafast ESPT from the neutral form readily explains why excitation into the A and B bands of AvGFP leads to a similar green anionic fluorescence emission [84], Simplistic thermodynamic analysis, by way of the Forster cycle, indicates that the excited state protonation pK.J of the chromophore is lowered by about 9 units as compared to its ground state. However, because the green anionic emission is slightly different when it arises from excitation into band A or band B (Fig. 5) and because these differences are even more pronounced at low temperatures [81, 118], fluorescence after excitation of the neutral A state must occur from an intermediate anionic form I not exactly equivalent to B. State I is usually viewed as an excited anionic chromophore surrounded by an unrelaxed, neutral-like protein conformation. The kinetic and thermodynamic system formed by the respective ground and excited states of A, B, and I is sometimes called the three state model (Fig. 7). 

Peters, D., and J. Peters. 1982c. Quantum Theory of the Structure and Bonding in Proteins Part 12. Conformational analysis of side chains and the ethyl group as a model side chain. J. Mol. Struct. (Theochem) 88, 137-156. 

---