Maximized alignment

The other point of interest relates to the nature of the highest spin state observed, that decaying by the 971 keV transition. If the 971 and 1031 keV lines are stretched E2 transitions, as we suspect, this state is the 46+ one that is the maximally aligned state predicted by theory and analogous to... 

Fig. 3. (A.B). Alignment of immunoglobulin and T cell receptor V (panel A) and C (panel B) units. /3-strand sequences (from [6] and [205]) are boxed and indicated by letters A to G. , padding characters introduced to maximize alignments. Panel A CDR s (T cell receptor hypervariable regions...

Fig. 6. Structure of TcR y chain connecting peptides, as deduced from cDN A clones. Boxes with similar filling patterns (i.c. either cross-stripes or shaded) arc homologous in sequence. Blank spaces are introduced to maximize alignments. Fro 2.2, HPB-MLT and PEER are cell lines established from different individuals [74]. The lengths of the C unit (1 10 amino acids) and of the transmembrane and cytoplasmic segment (approximately 53 amino acids) is also shown as a reference. S, potential disulphide bridge N, potential N-linked glycosvlation site.

FIGURE 3 Comparison of the amino acid sequences of CPs from different species. The amino acid positions are numbered according to the chicken alpha (upper lane) and rat acidic (lower lane) sequences. Dots represent identical residues, horizontal bars indicate gaps introduced into the sequences for maximal alignment, and asterisks represent incomplete sequences. 

The relative descriptor C(R, 0) provides a criterion with which to obtain the optimum molecular alignment. Although the problem of achieving a maximized alignment is encountered routinely in computer-assisted drug design, a completely satisfactory solution is elusive. Improved solutions have been stud-ied232-239 and continue to be developed. 

Figure 1. Comparison of the sequences of venom phospholipases from bumble bee, Bombus pennsylvanicus (61), and gila monster, Heloderma suspectum (63). The double dots indicate identical residues and the single dots residues that differ by only a single base (conservative substitutions). Dashes indicate positions inserted to maximize alignment.

Figure 4. Comparison of the sequences of antigen 5 from Vespula flavopilosa (85), Dolichovespula arenaria (88), Vespa crabro (85) dindSolenopsis richteri (97). The asterisks indicate residues identical to those in Vespula flavopilosa antigen 5. Dashes indicate positions inserted to maximize alignment.

The deviation from planarity that is present in a structure such as 1 raises the question of how severely a conjugated system can be distorted from the ideal coplanar alignment of p orbitals and still retain aromaticity. This problem has been analyzed by determining the degree of rehybridization necessary to maximize p orbital overlap in 1. It is found that rehybridization to incorporate fractional amounts of s character can improve orbital alignment substantially. Orbitals with about 6% s character are suggested to be involved... 

Williams, G.T. Morimoto, R.I. (1990). Maximal stress-induced transcription from the human hsp70 promoter requires interactions with the basal promoter elements independent of rotational alignment. Mol. Cell. Biol. 10, 3125-3136. 

Today it is an alternative method for alignment of molecular structures that maximizes the steric and electrostatic overlap using randomly generated starting configurations and keeping only the best results based on the value of the alignment function. 

Kearsley, S.K. and Smith, G.M. (1990). An alternative method for the alignment of molecular structures Maximizing electrostatic and steric overlap. Tetrahedron Computer Methodology 3 615-633. 

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