Protein Structures and Assemblies

Proteins are large biological molecules made up of different combinations of amino acids, the basic protein building blocks. In eukaryotes, there are 20 different amino acids, and these small molecules are linked together into a long chain to form the protein. Most proteins consist of a large number of amino acids with total molecular weights in the tens or even 

FIGURE 6.9 Waxes are found widely in nature and provide plants with a protective waterproof coating. They are also flammable hydrocarbons and useful for burning. 

You may not have considered proteins to be a soft material before, but if we think about all of the different structures proteins can form (e.g., long polymer-like filaments, flexible sheets) or their behavior in solutions (as colloids and emulsifiers), then it is clear that they should naturally find a home in this field. 

Proteins form the functional building blocks of our cellular machinery and have a complex hierarchical structure. This structure cannot simply be described in terms of the amino acid sequence the way the amino acid chain folds is as important for function as the sequence. Protein molecules have specific shapes for their functions, including how they bind to other biological molecules. Protein structure is therefore described in terms of primary, secondary, and tertiary structures. 

The primary structure of a protein is the amino acid sequence. This is basically a list of the amino acids in the chain in the correct order. Each amino acid is commonly referred to by an abbreviated name (lysine is LYS, cysteine is CYS, etc.) Appendix E includes the structure of all of the amino acids with their three-letter abbreviations. Each amino acid has the same structural basis of a carbon attached to a carboxyl group and an amine group. They differ in the third attached group. Primary structure represents the smallest length scale of structure in a protein molecule, but an analysis of the amino acid sequence alone will not reveal complete information on the overall structure of the molecule because this chain must next be folded into a specific shape. 

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Most of the molecules introduced in this chapter are hydrophobic. Even those molecules that have been functionalized to improve water-solubility (for example, CCVJ and CCVJ triethyleneglycol ester 43, Fig. 14) contain large hydrophobic structures. In aqueous solutions that contain proteins or other macromolecules with hydrophobic regions, molecular rotors are attracted to these pockets and bind to the proteins. Noncovalent attraction to hydrophobic pockets is associated with restricted intramolecular rotation and consequently increased quantum yield. In this respect, molecular rotors are superior protein probes, because they do not only indicate the presence of proteins (similar to antibody-conjugated fluorescent markers), but they also report a constricted environment and can therefore be used to probe protein structure and assembly. 

Protein Aggregation and Fibril Formation Membrane Protein Structure and Assemblies... 

Translation—translation of the RNA-coded message, by the ribosomes, into the 20 amino acid alphabet of protein structure, and assembly of the latter ... 

Parise, G. and Bazzicalupo, P. (1997) Assembly of nematode cuticle role of hydro-phobic interactions in CUT-2 cross-linking. Biochimica et Biophysica Acta - Protein Structure and Molecular Enzymology 1337, 295-301. 

The structure and assembly of the photosystems are dependent on the availability of specific carotenoids that assist in the correct folding and maintain stability of the photosystem proteins. 

Histone acetyltransferases (HATs) are enzymes that acetylate specific lysine residues in histones through the transfer of an acetyl group from an acetyl-coenzymeA (AcCoA) molecule, causing profound effects on chromatin structure and assembly as well as gene transcription. HATs are found in most, if not all, eukaryotic organisms as multiprotein complexes, some HAT catalytic subunits even being shared between various complexes that display different substrate specificities based on their subunit composition [12]. Despite their name, HATs do not restrict themselves to the acetylation of histones, since these enzymes have also been shown to act on nonhistone proteins, broadening their scope of action [13]. 

AMINO ACIDS. The scores of proteins which make up about one-half of the dry weight of the human body and that are so vital to life functions are made up of a number of amino adds in various combinations and configurations. The manner in which the complex protein structures are assembled from amino acids is described in the entry on Ihotcin. For some useis of tills book, it may be helpful to scan that portion of the piotein entry that deals with the chemical nature of proteins prior to considering the details of this immediate entry on amino acids. 

Steven, A. C., Mack, J. W., Trus, B. L., Bisher, M. E., and Steinert, P. M. (1989). Structure and assembly of intermediate filaments Multi-faceted, myosin-like (but non-motile) cytoskeletal Polymers. In Cytoskeletal and Extracellular Proteins (U. Aebi andj. Engel, Eds.), pp. 15-26. Springer-Verlag, Berlin. 

First, a review of the properties and the structure of silk is given followed by a discussion on the relationship between molecular composition, assembled protein structure, and mechanical properties. Second, artificial spinning of silk proteins and their bioapplications are emphasized. Finally, the potential role of silk proteins in biomineralization is introduced and discussed. 

Standard molecular mechanics (MM) force fields have been developed that provide a good description of protein structure and dynamics,21 but they cannot be used to model chemical reactions. Molecular dynamics simulations are very important in simulations of protein folding and unfolding,22 an area in which they complement experiments and aid in interpretation of experimental data.23 Molecular dynamics simulations are also important in drug design applications,24 and particularly in studies of protein conformational changes,25,26 simulations of the structure and function of ion channels and other membrane proteins,27-29 and in studies of biological macromolecular assemblies such as F-l-ATPase.30... 

Tamm, L. K., Arora, A., and Kleinschmidt, J. H. (2001). Structure and assembly of beta-barrel membrane proteins./. Biol. Chem. 276, 32399-32402. 

The addition of one more component (a cosolvent) to aqueous solutions of proteins can dramatically change the properties of those solutions, such as the protein solubility, protein self-assembling, and protein stabihty. Indeed, the solubility of proteins can be essentiahy changed by the addition of a third component.It is well known for a long time that the addition of certain compounds (such as urea) can cause protein denaturation, and that other cosolvents, such as glycerol, sucrose, etc., can stabilize at high concentrations the protein structure and preserve its enzymatic. .. . 1-6 activity. 

Woolfson, D. N. (2005) The design of coiled coil structures and assemblies. Advances in Protein Chemistry, 70, 79-112. 

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