Unique conformation

After an initial starting geometry has been generated and optimized (e.g., in a force field), the new conformation is compared with all the previously generated conformations, which are usually stored as a list of unique conformations. If a substantially different geometry is detected it is added to the list otherwise, it is rejected. Then a new initial structure is generated for the next iteration. Finally, a preset stop criterion, e.g., that a given number of loops has been performed or that no new conformations can be found, terminates the procedure. 

If the sampling interval is too short, the total number of structures that belong to unique structural families is small compared to the total number available. If the sampling interval is too large, the total number of available structures is small, and you can miss unique conformations. 

The concept that different ligands play an active role in ER function is apparent at the biochemical level. In addition to competitive inhibition of estrogen binding, antiestrogens induce unique conformations/stiuctures of both ERa and ER 3. This provides a structural basis for the unique biological activities displayed by the different compounds [1]. 

Each intermediate form of the substrate along the reaction pathway is accompanied by a unique conformational state of the enzyme. 

We first examined ketone 48 and hydroxy ketone 56 because (1) no reduction of C5a-carbonyl in 48 occurred when using L-Selectride to reduce the C3-ketone and (2) NaBH4 did not touch the C5a-carbonyl group in hydroxy ketone 56. By using minimized Spartan model of vinylogous ester 48 and the X-ray structure of hydroxy ketone 56, we found unique conformational elements (Fig. 8.10) in addition to fully validating the aforementioned NMR analysis of possible positions for H8a when C8a is ip2-hybridzied and H7 when C8a is sp3-hybridized. In 48,... 

Global-MMX (GMMX) is a steric energy minimization program that uses the MMX force field and operates in batch mode. Its main purpose is to search conformational space and to fist the lowest-energy unique conformations found. It is available in desktop PC running Windows, Macintosh OS, and Unix-based workstation versions. 

Figure 1. A general scheme of idiotypes and anti-idiotypes. Depicted here are immunoglobulin proteins whose antigencombining site expresses unique conformations or epitopes, that are termed idiotopes. A collection of idiotopes constitute what is termed idiotype. Some idiotypes are shared by many immunoglobulins with the same antigenic specificity.

The very high diastereofacial differentiation in the dialkylation of 2 to 7 can be attributed to a unique conformation of 2 and its enolate 8. There is NMR evidence of 2, X-ray crystallographic analysis of (Z)-9 and molecular mechanics calculations on 2, all of which suggest that the trityl group is on the a-face of the enolate, as shown in 8, resulting in attack of the electrophile on the /3-face30. 

Rather more theoretical work has been done with respect to tris(ethylenediamine) complexes. By considering the two stable chiral (skew) conformations of the five-membered chelate rings (designated k and S as above), four unique conformers of M(en)"+ can be constructed for each absolute configuration (A or A) (12) kkk, kkS, kSS, and 886. In this representation, A(1U) is energetically equivalent to A(<5<5<5). 

Simulation of spectra for (R)-acacpnH2 and its trifluoro derivative indicates that the syn conformation, predominant in solution, is that having the pn methyl group anti to the N atom, as found in the solid state.101 A similar conformer distribution is expected also for acacenH2 in view of the similarity of absorption spectra. In conclusion, it appears that these compounds exist in solution essentially in a unique conformation, maintained by strong intramolecular hydrogen bonds. 

T he enormous structural diversity of proteins begins with the amino acid sequences of polypeptide chains. Each protein consists of one or more unique polypeptide chains, and each of these polypeptide chains is folded into a three-dimensional structure. The final folded arrangement of the polypeptide chain in the protein is referred to as its conformation. Most proteins exist in unique conformations exquisitely suited to their function. It is the availability of a wide variety of conformations that permits proteins as a group to perform a broader range of functions than any other class of biomolecules. 

As a result of the branched chain architecture, TASP molecules exhibit some unique conformational properties)5 12-14 47 75 76 148 For example, the folding to a compact state proceeds via two distinct steps the onset of secondary structure in the attached peptide blocks followed by their template-directed self-assembly to a three-dimensional packing topology. Due to its characteristic branched chain connectivity, the conformational space accessible in the unfolded state is considerably reduced compared to a linear chain of similar size (excluded volume effect), resulting in a smaller chain entropy. Thus, folded TASP molecules are expected to show higher thermodynamic stability compared to unbranched polypeptides of comparable size. 

F. Are Unique Conformational Changes in Receptors Elicited by Interactions with Ligands Resulting in Varied G Protein Interactions... 

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