Protem structure

Interactions between macromolecules (protems, lipids, DNA,.. . ) or biological structures (e.g. membranes) are considerably more complex than the interactions described m the two preceding paragraphs. The sum of all biological mteractions at the molecular level is the basis of the complex mechanisms of life. In addition to computer simulations, direct force measurements [98], especially the surface forces apparatus, represent an invaluable tool to help understand the molecular interactions in biological systems. 

Polarization Properties. One of Ae key attractions of XAS for biological systems is Ae ability to study unoriented samples such as protems in solution. If samples can be oriented, however, it is possible to greatly enhance Ae information content of XAS spectra. In particular, it is possible to obtain direct information about Ae relative orientation of specific structural features. These experiments are possible because the synchrotron X-ray beam is highly plane polarized. Several examples of polarized XAS of biologicA samples are Ascussed below. 

Quasicrystal structures have been known for a long time to occur in condensed matter and rejected as inexplicable curiosities. They may emerge naturally too in mathematical descriptions of surfaces. (The decagonal variant certainly arises, cf. [36]). It is not an entirely idle speculation to conjecture, e.g. that the principles exploited in construction of quasi-crystals may be precisely those used by nature to build protems that solve the problem... 

All proteins of the cell are synthesized on structures called ribosomes. The proteins of the cytoplasm are synthesized on ribosomes that float free in the cytoplasm, whereas those of the plasma membrane are sjmthesized on ribosomes that bind to the outside of the endoplasmic reticulum (ER), a network of interconnected tubules in the cytoplasm resembling a nest of hollow noodles. During polymerization of the amino acids, a nascent protein is driven into the ER. From there it is shimted into secretory vesicles, some of which insert protems into the PM, while others deliver different proteins to the outside of the cell (into the extracellular fluid). 

In proteomics and biomarker discovery, complex mass spectra from single protems, protein mixtures, or protein digests are obtained. Data systems exist that aid in characterization of spectral data to identify such properties as intact protein mass, amino acid subsequences, and post-translational modifications. Fragmentation information can also be compared with peptide databases to identify structural mutations that may be present. 

Another useful structure tool is RasMol (or RasMac). This will allow you to view the detailed structure of a protein and rotate it on coordinates so you can see it from all perspectives. A hyperlink to RasMol is present under the View Structure function )ust above Chime. You may need to study RasMol instructions provided under Help, or you may use a Ras Mol tutorial listed m Table El.2. Another useful protein viewer is the Swiss-Protem Pdv Viewer (Table E1.2). BLAST is an advanced sequeme similarity tool available at NCBI. To access this, go to the NCBI home page (www.ncbi.nlm.nih.gov) and click on BLAST. Then click on Basu BLAST search to obtain a dialogue box into which you may type the amino acid sequence of human a-lactalbumm. This process may be stream lined by downloading the amino acid sequence m PASTA format into a fiK and transferring the file into the BLAST dialogue box. BLAST will provide a list of proteins with sequences similar to the one entered. 

A complete understanding of the biochemical functions of DNA requires a clear picture of its structural and physical characteristics. DNA has significant absorption m the UV range because of the presence of the aromatic bases adenine, guanine, cytosine, and thymine. This provides a useful probe into DNA structure because structural changes such as helix unwinding affect the extent of absorption. In addition, absorption measurements are used as an indication of DNA purity. The major absorption band for purified DNA peaks at about 260 nm. Protein material, the primary contaminant m DNA, has a peak absorption at 280 nm. The ratio 260 280 often used as a relative measure of the nucleic acid/protem content of a DNA sample The typical 26o 2so isolated DNA is about 1.8. A smaller ratio indicates increased contamination by protein. 

Figures 4 and 5 illustrate the use of these shape descriptors. As a first example, we have considered two proteins with a similar number of amino acid residues but radically different folding patterns. Figure 4 contrasts the backbone of ribonudease inhibitor ( = 456) and yeast hexokinase ( = 457). These structures are found in the Brookhaven Protein Data Bank (PDB) with the codes IBNH and 2YHX, respectively. Ribonudease inhibitor is a very unusual horseshoe-shaped protein, the first known 3D structure of a protein with a highly repetitive amino acid sequence. Table 1 gives their size and entanglement characterization in terms of Rq, A, N, andN. Protem IBNH is less compact and less entangled than 2YHX (note the smaller N and N values).

Figure 3.37. Amino acid sequence and chroinophore structure in green fluoieiccDt protem. The dashed lines repfesent the protein backbone. Revised from Ref. 108.

Schematic model of the core-shell structure of soy protem/PS rnanoblends and synthesized process of the nanoblend [96],...

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