Protein structure folding

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

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. 

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. 

Deivanayagam, C. C., Rich, R. L., Carson, M., Owens, R. T., Danthuluri, S., Bice, T., Hook, M., and Narayana, S. V. (2000). Novel fold and assembly of the repetitive B region of the Staphylococcus aureus collagen-binding surface protein. Structure Fold Des. 8, 67-78. 

Viral capsid proteins, in E. coli, 5 Viral genome organization, 219 Viral phylogeny, 185-186 Viral protein structural folds, 125-186 determination of, 125-126 four-helix bundle, 132 immunoglobulin fold, 131 jelly-roll /3 barrel, 128-131, 129 serine protease fold, 132 terminology, 125 virus families and, 125 Viral replication cycle, 8... 

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. 

Essen, L., Siegert, R., Lehmann, W.D., Oesterhelt, D. 1998. Lipid patches in membrane protein oligomers crystal structure of the bacteriorhodopsin-Iipid complex. Proc. Natl. Acad. Sci. USA 95 11673-11678. Ferguson, A.D., Welte, W., Hofmann, E., Lindner, B., Holst, O., Coulton, J.W., et al. 2000. A conserved structural motif for lipopolysaccharide recognition by procaryotic and eucaryotic proteins. Structure Fold. Des. 8 585-592. 

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. 

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. 

Fluorescence spectroscopy is an important tool for studying proteins [23]. It has sensitivity and time-scale features that can make it more attractive than absorbance spectroscopy [40], and it is one of the most common methods used to determine native protein structure, folding dynamics, and other conformational changes [33], Tryptophan is the most popular amino acid to study with fluorescence because it has the largest fluorescence quantum yield of the natural fluorescent amino acids, and its fluorescence is sensitive to its environment [5], The use of natural amino acid fluo-rophores is limited, however, because tryptophan is not very common, and phenylalanine has low fluorescence quantum yield. 

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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