Multiple conformations

Many approaches and methods for the generation of multiple conformations have been developed and published since the early 1980s. Below we describe briefly some of the basic concepts and methods of automatic conformer generation. However, interested readers are referred to Chapter 11, Section 7.2 in the Handbook, where the approaches to automatic generation of ensembles of conformations and the program systems that have been developed are described in detail. 

Figure 2-103. General work flow scheme for the generation of multiple conformations.

Other methods which are applied to conformational analysis and to generating multiple conformations and which can be regarded as random or stochastic techniques, since they explore the conformational space in a non-deterministic fashion, arc genetic algorithms (GA) [137, 1381 simulation methods, such as molecular dynamics (MD) and Monte Carlo (MC) simulations 1139], as well as simulated annealing [140], All of those approaches and their application to generate ensembles of conformations arc discussed in Chapter II, Section 7.2 in the Handbook. 

In all of the 3D search methods the conformational flexibility creates considerable difficulties. Large databases of multiple conformations for each structure have been developed which make the solution of this problem possible. 

Chain growth algorithms that build up the chain one unit at a time with some randomness in the way units are added. This process can be repeated to yield multiple conformations. 

Fiber, R. Karplus, M. Multiple conformational states of proteins a molecular dynamics analysis of myoglobin. Science 235 318-321, 1987. 

The hst which follows gives an outline of the properties of a Monte Carlo simulation used in the context of molecular modeling studies for sampling either multiple conformations of smaller, flexible stmctures or multiple local minima of larger macromolecules or polymers ... 

As has been demonstrated for tenofovir, when incorporated at the 3 -end of reverse transcriptase (RT)-driven DNA chain allows the PMPA residue to adopt multiple conformations [in contrast with the more rigid conformation of the 2, 3 -dideoxynucleosides (see infra) (Tuske et al. 2004). This greater flexibility in conformation may impede development of resistance to tenofovir. 

B. Stabilization of Multiple Conformers of Higher Order Complexes ... 

A totally different situation is encountered for dihedral or torsional angles, which describe the twisting of a fragment of four atoms cormected by a sequence of bonds. As the steric energy may have multiple minima around a rotatable bond with similar energy content, this leads to more than one possibility for constructing a 3D model for such molecules, or in other terms, to multiple conformations. 

In the case of being successful in calculating multiple conformations by using time- or ensemble-averaged MD restraints the solved molecular structures are presented as 3D models and can be deposited in an electronic structure database (17). Finally, it is recommended to provide an accurate explanation of the procedures used for the structure elucidation because the application of different methods (NMR, DG, MD, SA, Monte-Carlo calculations. X-ray crystallography) may result in varying conformational models which do not implicitly display the real state of a molecule. This aspect should be always kept in mind when dealing with structure determination methods. 

Lee B, Sharron M, Blanpain C, et al. Epitope mapping of CCR5 reveals multiple conformational states and distinct but overlapping structures involved in chemokine and coreceptor function. J Biol Chem 1999 274(14) 9617-9626. 

The multiple conformational restriction of dermorphin-related tet-rapeptide analogues that was performed represents a rational design of opioid peptidomimetics characterized by a high degree of structural rigid-ification. This is indicated by the fact that the p-selective agonist H-Hat-D-Orn-Aic-Glu-NH2 contains only two freely rotatable bonds, whereas there are 14 freely rotatable bonds in [Leu5]enkephalin. 

Wilkes BC, Schiller PW. Molecular dynamics simulations of opioid peptide analogs containing multiple conformational restrictions. Int J Peptide Protein Res 1992 40 249-254. 

Several remedies have been suggested for improving the PB based pKa prediction methods. Most of them are based on strategies that combine conformational flexibility with the PB calculation. You and Bashford included multiple conformers by systematically scanning the side chain torsion angles [107], Alexov and Gunner used Monte-Carlo protocol to sample positions of hydroxyl and other polar protons [1], This method, referred to as the multi-conformation continuum electrostatic (MCCE), was later extended to include rotamers for residues that have strong electrostatic... 

The method is likely to be useful for the numerical calculation of other correlation functions of importance to complex molecules. An example is the orientation correlation functions of interest in NMR-derived dynamical estimates for proteins and nucleic acids [134], Such correlations are difficult to converge numerically when multiple conformations separated by large free energy barriers contribute to their measurement. 

Compared to this system, the histamine flexible side-chain introduces the complication of multiple conformers. The histamine base and monocation have been studied by Worth et al,14 22 and by Nagy et al.23 The latter study... 

To achieve receptor desensitization and activation by ligand, multiple conformational states of the receptor are required. The binding steps represented in horizontal equilibria are rapid vertical steps reflect the slow, unimolecular isomerizations involved in desensitization (scheme 2). Rapid isomerization to the open channel state (scheme 1) should be added. To accommodate the additional complexities of the observed fast and slow steps of desensitization, additional states have to be included. 

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