Constraint structural

S Sun, PD Thomas, KA Dill. A simple protein folding algorithm using a binary code and secondary structure constraints. Protein Eng 8 769-778, 1995. 

Y Cm, RS Chen, WEI Wong. Protein folding simulation with genetic algorithm and supersecondary structure constraints. Proteins 31 247-257, 1998. 

Westlake developed a geometric model which is fairly successful in predicting site occupation in ABs and AB2 hydride phases [9], It involves two structural constraints ... 

Approaches of de novo predictions, which try to calculate how the structural elements are folded into the 3D-stmcture (tertiary structure) of complete proteins are nowadays far away from reliable large-scale applications. On the other, hand this topic is under strong development indicated by recent successful results at the contest for structural prediction methods CASP4. With the fast growing number of experimentally solved 3D-stmctures of protein and new promising approaches like threading tools combined with experimental structural constraints, one can expect more reliable de novo predictions for 3D-protein structures in the future. 

To summarize under favorable conditions the acidity of a-hydrogens facilitates the generation of a-sulfoxy and a-sulfonyl carbanions in thiirane and thiirene oxides and dioxides as in acyclic sulfoxides and sulfones. However, the particular structural constraints of three-membered ring systems may lead not only to different chemical consequences following the formation of the carbanions, but may also provide alternative pathways not available in the case of the acyclic counterparts for hydrogen abstraction in the reaction of bases. 

The solution structure determination of iron-sulfur proteins is feasible in most cases. To achieve this result, it is necessary to have enough structural constraints to make it possible to obtain a family of conformers with similar folding from many randomly generated structures (95). 

In addition to the standard constraints introduced previously, structural constraints obtainable from the effects of the paramagnetic center(s) on the NMR properties of the nuclei of the protein can be used (24, 103). In iron-sulfur proteins, both nuclear relaxation rates and hyperfine shifts can be employed for this purpose. The paramagnetic enhancement of nuclear relaxation rates [Eqs. (1) and (2)] depends on the sixth power of the nucleus-metal distance (note that this is analogous to the case of NOEs, where there is a dependence on the sixth power of the nucleus-nucleus distance). It is thus possible to estimate such distances from nuclear relaxation rate measurements, which can be converted into upper (and lower) distance limits. When there is more than one metal ion, the individual contributions of all metal ions must be summed up (101, 104-108). If all the metal ions are equivalent (as in reduced HiPIPs), the global paramagnetic contribution to the 7th nuclear relaxation rate is given by... 

NMR Assignments, Structural Constraints, and Structural Parameters for the Available NMR Solution Structures of Iron-Sulfur Proteins"- ... 

In contrast to this, there are no such structural constraints on a-adrenergic agonists or antagonists. Some of the most active a-sympathomimetic agents in fact contain an imidazoline moiety as part of the pharmacophore. The appropriate ring system can be... 

A core assumption of ultra-Darwinism is that if not all, then most observed characters must be adaptive, so as to provide the phenotypic material upon which natural selection can act. However, what constitutes a character - and what constitutes an adaptation - is as much in the eye of the beholder as in the organism that is beheld, as Gould and Lewontin pointed out in their famous paper on spandrels (Gould and Lewontin, 1979). Natural selection s continual scrutiny does not give it an a la carte freedom to accept or reject genotypic or phenotypic variation. Structural constraints insist that evolutionary, genetic mechanisms are not infinitely flexible but must work within the limits of what is physically or chemically possible (for instance, the limits to the size of a single cell occasioned by the physics of diffusion processes, the size of a crustacean like a lobster or crab by the constraints... 

The physical properties of probe molecules adsorbed in the confined space of porous materials are known to vary in dependence of structural constraints on molecular motion. Detailed investigations of adsorption geometries are possible, when well-defined sites and loadings exist. This was the case for the adsorption of strongly interacting probe molecules, such as pyridine, on SiOH groups in the... 

In this chapter, it will be described how we have utilized endogenous and engineered Zn2+ binding sites to explore the structure and molecular function of Na+/Cl -depen-dent neurotransmitter transporters. The work has not only allowed the definition of the first structural constraints in the tertiary structure of this class of transporters, but also provided new insight into both conformational changes accompanying substrate translocation and mechanisms governing conformational isomerization in the translocation cycle. In the chapter, we will also review the theoretical and practical basis for... 

The crystal structures of Zn2+ binding proteins not only revealed well-defined tertiary structure constraints to accommodate Zn2+ binding, but also well-defined con-... 

Altogether, the identification of the coordinating residues in the endogenous hDAT Zn2+ binding site followed by the engineering artificial sites have defined an important series of structural constraints in this transporter. This includes not only a series of proximity relationships in the tertiary structure, but also secondary structure relationships. The data also provided information about the orientation of TM7 relative to TM8. A model of the TM7/8 microdomain that incorporates all these structural constraints is shown in Fig. 4 (36). The model is an important example of how structural inferences derived from a series of Zn2+ binding sites can provide sufficient information for at least an initial structural mapping of a selected protein domain. 

Antzutkin, O. N., Leapman, R. D., Balbach, J. J., and Tycko, R. (2002). Supramolecular structural constraints on Alzheimer s beta-amyloid fibrils from electron microscopy and solid-state nuclear magnetic resonance. Biochemistry 41, 15436-15450. 

The structural constraints imposed by the fused cyclic structure of the catenates and the ability to cleanly separate product mixtures greatly facilitates crystallization, and single crystal X-ray structures have been obtained for a number of ladder polysilanes.3 8 For the all-anti molecules, the non-planarity of the SI rings induces a unidirectional helical twist to the ladder structure, as is evident in Figure 63. 

This sub-problem considers the structural constraints that result in generation of feasible molecular structures. Odele Machietto structural feasibility constraints are used. The sub-problem is a function of the binary variables alone. 

As in sub-problem 1 structural constraints are considered in sub-problem 1M. All the feasible molecular structures are passed to sub-problem 2M. 

---