Structure folding and

Lilley, D. 2005. Structure, folding and mechanisms of ribozymes. Current Opinion in Structural Biology 15(3), 313-323. 

Cathepsin K (Cat K) is a member of the CA1 family of lysosomal cysteine proteases. This family is comprised of 11 human members (cathepsins B, C, F, H, K, L, O, S, V, W, Z) which share a common papain-like structural fold and a conserved active site Cys-Asn-His triad of residues [1-3]. These enzymes are synthesized as pre-pro-enzymes and are converted from the catalytically inactive zymogen into the active form in acidic lysosomal environment. In some cases, cathepsins are also secreted in the active form from cells. The sequence identity of... 

A collection of excellent articles on many topics, including protein structure, folding, and function. 

Deoxyribozymes (also called DNA enzymes or DNAzymes) are specific sequences of DNA that have catalytic activity. All currently known deoxyribozymes have been identified by in vitro selection from large random-sequence DNA pools (Joyce, 2004 Silverman, 2009). The catalytic range of DNA encompasses both oligonucleotide and nonoligonucleotide substrates (Baum and Silverman, 2008 Silverman, 2008). This report focuses on deoxyribozymes that are useful for reactions of RNA substrates, especially to assist studies of RNA structure, folding, and catalysis. 

Hydrophobic forces The hydrophobic effect is the name given to those forces that cause nonpolar molecules to minimize their contact with water. This is clearly seen with amphipathic molecules such as lipids and detergents which form micelles in aqueous solution (see Topic El). Proteins, too, find a conformation in which their nonpolar side chains are largely out of contact with the aqueous solvent, and thus hydrophobic forces are an important determinant of protein structure, folding and stability. In proteins, the effects of hydrophobic forces are often termed hydrophobic bonding, to indicate the specific nature of protein folding under the influence of the hydrophobic effect. 

Forrer, P., Jung, S., and Pluckthun, A. (1999). Beyond binding using phage display to select for structure, folding and enzymatic activity in proteins. Gun. Opin. Biotechnol. 9, 514-520. 

Maleknia, S.D. and Downard, K. (2001) Radical approaches to probe protein structure, folding, and interactions by mass spectrometry. Mass Spectrom. Rev., 20, 388—401. 

Arolas JL, et al. Secondary binding site of the potato carboxypepti-dase inhibitor. Contribution to its structure, folding, and biological properties. Biochemistry 2004 43 7973-7982. 

Whisstock JC, Bottomley SP. Molecular gymnastics serpin structure, folding and misfolding. Curr. Opin. Struct. Biol. 2006 16 761-768. 

The redox sensitivity of hemopexin-encapsulated heme to electrolyte composition and pH illustrate the importance of first coordination shell (bis-histidine ligation and heme structure) and second coordination shell (protein structure/folding and environment) effects in these heme proteins. These observations also suggest a possible role for Fe " /Fe redox in hemopexin-mediated heme transport/recycling, as high chloride anion concentration and low pH are known conditions for the endosome where the heme is released. 

Creighton, T.E. In Protein Structure, Folding, and Design 1986, AlanR. Liss, Inc., 249-257. 

Comparative studies on homologous proteins show a high conservation of the structural fold and constellation of amino acid side chains at the active site. The best example is that of the serine proteinase family of trypsin, chymotrypsin, elastase and protease A from Streptomyces griseus (see, for example, reference 97) (Fig. 10). 

Arrhenius, T., Lemer, R.A. and Satterthwait, A.C. (1987) The chemical synthesis of structured peptides using covalent hydrogen-bond mimics. In Oxender, D.L. (ed.). Protein Structure, Folding, and Design, vol. 2, pp. 453-465. Alan R. Liss, Inc. 

Cupredoxins refer to a group of copper proteins that share the same overall structural fold and perform biological electron transfer (ET) through their redox reactivity. The term cupredoxin comes from ferredoxin, the Fe-containing redox proteins. Cupredoxins comprise one of the three classes of metalloproteins known to carry out biological electron transfer, after cytochromes (see Chapter 8.2) and ferredoxins (see Chapter 8.3). 

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. 

D.W. Urry and C.-H. Luan, Proteins Structure, Folding and Function. In Bioelectrochemistry Principles and Practice, G. Lenaz, Ed., Birkhauser Verlag AG, Basel, Switzerland, 1995, pp. 105-182. 

Ahern TJ, KlibanovAM (1986) Why do enzymes irreversibly inactivate at high temperature In OxenderDL (ed) Protein structure folding and design. Liss, New York, p 283... 

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