Studies on Proteins

Taketomi H, Ueda Y and Go N 1975 Studies on protein folding, unfolding, and fluctuations by computer simulation Int. J. Pept. Protein Res. 7 445-59... 

H Taketomi, Y Ueda, N Go. Studies on protein folding, unfolding and fluctuations by computer simulation. 1. The effect of specific ammo acid sequence represented by specific mter-umt interactions. Int J Peptide Protein Res 7 445-459, 1975. 

With a knowledge of the methodology in hand, let s review the results of amino acid composition and sequence studies on proteins. Table 5.8 lists the relative frequencies of the amino acids in various proteins. It is very unusual for a globular protein to have an amino acid composition that deviates substantially from these values. Apparently, these abundances reflect a distribution of amino acid polarities that is optimal for protein stability in an aqueous milieu. Membrane proteins have relatively more hydrophobic and fewer ionic amino acids, a condition consistent with their location. Fibrous proteins may show compositions that are atypical with respect to these norms, indicating an underlying relationship between the composition and the structure of these proteins. 

Marsh MM. Spectropolarimetric studies on proteins. Bovine plasma albumin and insulin. J Am Chem Soc 1962 84 1896-900. 

Eftink, M.R. and Chiron, C.A. (1984) Indole fluorescence quenching studies on proteins and model systems use of the efficient quencher succinimide. Biochemistry 23, 3891-3899. 

Radioiodination is the process of chemically modifying a molecule to contain one or more atoms of radioactive iodine. Early studies on protein modification determined that iodine in... 

Tadayoni, B.M., Friden, P.M., Walus, L.R., and Musso, G.F. (1993) Synthesis in vitro kinetics, and in vivo studies on protein conjugates of AZT Evaluation as a transport system to increase brain delivery. Bioconjugate Chem. 4, 139-145. 

All steps of the Ras pathway from ligand binding to receptor tyrosine kinases, down to activation of effectors like Raf kinase, occur at the plasma membrane. However, most biophysical studies on protein/protein interactions involved in this scenario have been carried out with bacterially synthesized proteins lacking... 

In fluorescence studies on proteins, apart from spectral, temporal, and polarization measurements, it appears of importance to investigate the... 

Calorimetric studies have been made on proteins S4, S7, S8, S15, S16, S18, Lll, and L7 (Khechinashvili et al., 1978 Gudkov and Behike, 1978). Most of these proteins displayed a cooperative tertiary structure in solution. Proteins S4, S7, SI5, and SI8 were extracted from the ribosome by a urea-LiCl technique followed by renaturation, whereas proteins S8, S16, and Lll were prepared by the mild isolation method. A calorimetric study on protein SI showed a noncooperative transition around 70-80 C, suggesting a flexible tertiary structure (L. Giri, unpublished). 

The Use of Immunochemical Methods in Studies on Proteins Pierre Grabar... 

Peck then became interested in sulfate-reducing bacteria, which he had got to know in Gest s laboratory. To study the reduction of sulfate. Peck worked in Fritz Lipmann s laboratory in Massachussetts General Hospital (1956) and with Lipmann at Rockefeller University (1957). Lipmann started work on active sulfate in 1954 with Helmut Hilz as a postdoctoral fellow and studied the activation of sulfate to APS and PAPS. Lipmann had left the active sulfate projects by 1957 and started, at Rockefeller University, the studies on protein synthesis. Peck published one paper on the reduction of sulfate with hydrogen in extracts of Desulfovibrio desul-furicans (1959) and one on APS as an intermediate on the oxidation of thiosulfate by Thiobacillus thioparus (1960). 

Mass spectrometry studies on proteins can determine the purity of the sample, verify amino acid substitutions in mutants, detect post-translational modihcations, or calculate the number of disulfide bridges. Amino acid... 

Gazia, N. and Agergoard, N. 1980. Electrophoretic studies on protein and enzyme systems in Egyptian water buffaloes. Arsheret-K Vet. Landhohoejsk Inst. Sterileletsf-orsk 23, 35-41 (Danish). 

New techniques for data analysis and improvements in instrumentation have now made it possible to carry out stmctural and conformational studies of biopolymers including proteins, polysaccharides, and nucleic acids. NMR, which may be done on noncrystalline materials in solution, provides a technique complementary to X-ray diffraction, which requires crystals for analysis. One-dimensional NMR, as described to this point, can offer structural data for smaller molecules. But proteins and other biopolymers with large numbers of protons will yield a very crowded spectrum with many overlapping lines. In multidimensional NMR (2-D, 3-D, 4-D), peaks are spread out through two or more axes to improve resolution. The techniques of correlation spectroscopy (COSY), nuclear Overhausser effect spectroscopy (NOESY), and transverse relaxation-optimized spectroscopy (TROSY) depend on the observation that nonequivalent protons interact with each other. By using multiple-pulse techniques, it is possible to perturb one nucleus and observe the effect on the spin states of other nuclei. The availability of powerful computers and Fourier transform (FT) calculations makes it possible to elucidate structures of proteins up to 40,000 daltons in molecular mass and there is future promise for studies on proteins over 100,000... 

Historically, coiled coils were identified with long fibrous molecules, from which their structural properties had been determined. Fiber diffraction studies on proteins of the k-m-e-f class were highly successful, initially on dried specimens but later also on native samples (Cohen and Holmes, 1963). However, these proteins turned out to be very difficult to analyze by high-resolution X-ray crystallography for the same reasons that made them so amenable to fiber diffraction—their tendency to aggregate into fibers rather than crystals and the extreme dimensions of their asymmetric units. It took decades to obtain a working structure for tropomyosin [at 15 A resolution (Phillips et al., 1986) at 9 A (Whitby et al.,... 

Homopolypeptides provide useful secondary structural models for spectroscopic studies on proteins and the ROA spectra of poly(L-lysine) in the three most important conformers are shown in Fig. 7.4. Poly(L-lysine) at alkaline pH... 

M. Mormann, B. Macek, A. Gonzalez de Peredo, J. Hofsteenge, and J. Peter-Katalinic, Structural studies on protein O-fucosylation by electron capture dissociation, Int. J. Mass Spectrom., 234 (2004) 11-21. 

As defined in Eqs. (6)—(13), the formulation is entirely general. What is required to evaluate structural stability of a protein are values for the fundamental parameters ACp ap, ACp>poi, Af/t, ASt, ASconf, T, and Tl with reference to some measurable structural property of the protein. In the next sections we will see that the values of these fundamental parameters can be estimated from studies on protein denaturation and on the dissolution of model compounds. 

There is a wealth of theory on the process of evolution that is largely overlooked in the experimental literature. Part of the difficulty is the abundance of jargon that is specific to relatively small clusters of theoretical literature. Theoretical studies on protein evolution, RNA evolution, DNA evolution, and algorithms in computer science often have interchangeable results. For instance, motifs that have important implications for experiments with proteins emerge from RNA secondary structure studies. However, using the information requires a substantial translation of the language. 

From a structural viewpoint, a polypeptide is composed of planar peptide units as shown in Figure 2.8. The usefulness of considering the peptide unit as opposed to the amino acid is that the peptide unit is almost planar as opposed to the amino acid, which has atoms that are in more than one plane. To illustrate this point, the coordinates of atoms in the peptide unit are given in Table 2.2 and nonbonded atoms cannot be closer than the sum of the minimum atomic distances (Table 2.3). Note that all the atoms from the first alpha carbon (Ca) to the second alpha carbon do not have a z-coordinate. These coordinates come from X-ray diffraction studies on proteins and represent the average coordinates found among many pro-... 

Photochemical methods offer a convenient tool to study intra- and interprotein ET because of their time resolution and selectivity. Various mechanistic and design approaches based on photochemistry of metal complexes have been undertaken. Most of the studies on protein electron transfer processes have been done for hae-moproteins using among others ruthenium complex as a photosensitizer, modified haemoproteins in which haem iron is substituted by another metal (mainly Zn), and CO-bonded haem proteins [6,7],... 

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