Structural Motifs as Functional

Visiers, I., Ebersole, B. J., Dracheva, S Ballesteros, J., Sealfon, S. C., and Weinstein, H. (2002) Structural motifs as functional microdomains in GPCRs energetic considerations in the mechanism of activation of the serotonin 5-HT2A receptor by dismption of the ionic lock of the arginine cage. Inti. J. Quant. Chem. 88,65-75. 

Type 1 copper proteins are the class of proteins for which cupredoxins were originally named. Type 1 copper proteins include both proteins with known electron transfer function (e.g., plastocyanin and rusticyanin), and proteins whose biological functions have not been determined conclusively (e.g., stellacyanin and plantacyanin). Although these proteins with unknown function cannot be called cupredoxins by the strict functional definition, they have been classified as cupredoxins because they share the same overall structural fold and metal-binding sites as cupredoxins. In addition, many multidomain proteins, such as laccase, ascorbate oxidase, and ceruloplasmin, contain multiple metal centers, one of which is a type 1 copper. Those cupredoxin centers are also included here. Finally, both the Cua center in cytochrome c oxidase (CcO) and nitrous oxide reductase (N2OR), and the red copper center in nitrocyanin will be discussed in this chapter because their metal centers are structurally related to the type 1 copper center and the protein domain that contains both centers share the same overall structural motif as those of cupredoxins. The Cua center also functions as an electron transfer agent. Like ferredoxins, which contain either dinuclear or tetranuclear iron-sulfur centers, cupredoxins may include either the mononuclear or the dinuclear copper center in their metal-binding sites. 

The other structural feature that improves potential charge mobility is the 2-D expansion of the heteroarenes. This has been accomplished in many different structural motifs, as representatively shown in Figure 12.7 (9-11). Compound 9 was first synthesized by Matano etal. in 2009 and showed potential applications as an electron-transport material, with electron-drift mobUity of 8X10 cm V s [16]. Like the phosphole compounds discussed thus far, this molecule also had low-lying frontier molecular orbitals as well as a reduced energy gap between the frontier molecular orbitals. As an extension, in 2012, functionalization via the a positions resulted in a series of molecules with potential application in OPVs [17]. In addition to the expected red shift, these materials were incorporated into devices with power conversion efficiencies of up to 4.2%. Compound 10 also showed favorable electron carrier mobilities of 2.4 X 10 cm s from vacuum-deposited films measured... 

Structural keys describe the chemical composition and structural motifs of molecules represented as a Boolean array. If a certain structural feature is present in a molecule or a substructure, a particular bit is set to 1 (true), otherwise to 0 (false). A bit in this array may encode a particular functional group (such as a carboxylic acid or an amidelinkage), a structural element (e.g., a substituted cyclohexane), or at least n occurrences of a particular element (e.g., a carbon atom). Alternatively, the structural key can be defined as an array of integers where the elements of this array contain the frequency of a specific feature in the molecule. 

Polypeptide chains are folded into one or several discrete units, domains, which are the fundamental functional and three-dimensional structural units. The cores of domains are built up from combinations of small motifs of secondary structure, such as a-loop-a, P-loop-p, or p-a-p motifs. Domains are classified into three main structural groups a structures, where the core is built up exclusively from a helices p structures, which comprise antiparallel p sheets and a/p structures, where combinations of p-a-P motifs form a predominantly parallel p sheet surrounded by a helices. 

Simultaneous to the understanding of some basics of hydrothermal carbonization using pure carbohydrate models, the synthesis of hydrothermal carbon materials using raw biomass was continued. It has been analyzed whether complex biomass - hy-drothermally carbonized - can also be directed to complex structural motifs with distinct surface polarities. Ideally, for this purpose one can use the structures and functionalization components already included in the biomass. We specifically selected waste biomass for material synthesis, starting products which are known to be hard to use otherwise, rich in ternary components, and applied different HTC conditions [29]. That way, one can avoid the food-raw materials competition, a prerequisite we regard as crucial for the development of a fully sustainable chemistry. 

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