Biophysical studies

Additional evidence for conformational changes in the transporter has come from measurement of the intrinsic fluorescence of the protein tryptophan residues, of which there are six, in the presence of substrates and inhibitors of transport. The fluorescence emission spectrum of the transporter has a maximum at about 336 nm, indicating the presence of tryptophan residues in both non-polar environments (which would emit maximally at about 330 nm) and in polar environments (which would emit at 340-350 nm) [154], The extent of quenching by the hydrophilic quencher KI indicates that more than 75% of the fluorescence is not available for quenching, and so probably stems from tryptophan residues buried within the hydrophobic interior of the protein or lipid bilayer [155]. Fluorescence is quenched 

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It is well known that the resources available on the Internet are in constant flux, with new sites appearing on a daily basis and established sites disappearing almost as frequently. This also holds true for the dedicated tools used in biochemical and biophysical studies. New tools are constantly becoming available, and established tools, obsolete. Such rapid change makes it difficult to stay current with the state-of-the-art technologies in the areas of bioinformatics and computational biochemistry and biophysics. 

Many biochemical and biophysical studies of CAP-DNA complexes in solution have demonstrated that CAP induces a sharp bend in DNA upon binding. This was confirmed when the group of Thomas Steitz at Yale University determined the crystal structure of cyclic AMP-DNA complex to 3 A resolution. The CAP molecule comprises two identical polypeptide chains of 209 amino acid residues (Figure 8.24). Each chain is folded into two domains that have separate functions (Figure 8.24b). The larger N-terminal domain binds the allosteric effector molecule, cyclic AMP, and provides all the subunit interactions that form the dimer. The C-terminal domain contains the helix-tum-helix motif that binds DNA. 

Fremont, D.H., Rees, W.A., Kozono, H. Biophysical studies of T-cell receptors and their ligands. Curr. Opin. Struct. Immunol. 8 93-100, 1996. 

M. Collagen-based structures containing the peptoid residue N-isobutylglycine (3t(leu) Synthesis and biophysical studies of Gly-Nleu-Pro sequences by circular di-chroism. Biochemistry 1997, 36, 8716-8724. 

Appropriately designed biophysical studies can elucidate the mode(s), the binding affinities and the nature of the ligand-nucleic acid interaction that give rise to the observed selectivity and specificities. Thus, it is worthwhile to describe briefly the various physical techniques used to study alkaloid-DNA/RNA interactions. 

Das S (2000) Biophysical studies on the interaction of benzophenanthridine alkaloids with polymorphic nucleic acid structures. PhD Thesis, Jadavpim University... 

Before the first indication of the existence of cannabinoid receptors, the prevailing theory on the mechanism of cannabinoid activity was that cannabinoids exert their effects by nonspecific interactions with cell membrane lipids (Makriyannis, 1990). Such interactions can increase the membrane fluidity, perturb the lipid bilayer and concomitantly alter the function of membrane-associated proteins (Loh, 1980). A plethora of experimental evidence suggests that cannabinoids interact with membrane lipids and modify the properties of membranes. However, the relevance of these phenomena to biological activities is still only, at best, correlative. An important conundrum associated with the membrane theories of cannabinoid activity is uncertainty over whether cannabinoids can achieve in vivo membrane concentrations comparable to the relatively high concentrations used in in vitro biophysical studies (Makriyannis, 1995). It may be possible that local high concentrations are attainable under certain physiological circumstances, and, if so, some of the cannabinoid activities may indeed be mediated through membrane perturbation. 

Wever R, Van Gelder BF, Der Vartanian DV. 1975. Biochemical and biophysical studies on cytochrome c oxidase XX. Reaction with sulphide. Biochem Biophys Acta 387 189-193. 

The significant enhancement in emission quantum yields and lifetimes suggests that 3 can be used as a noncovalent probe in immunochemical assay and biophysical studies. This dye is quite soluble in aqueous buffer and interacts with... 

Wolken, J. J. Euglena. An experimental organism for biochemical and biophysical studies. Rutgers Univ. Press (1967)... 

The aim of this series is to provide authoritative reviews in the rapidly expanding area of bioinorganic chemistry. The series will present state of the art reviews covering the whole field of bioinorganic chemistry. As the subject is, by its very nature, interdiciplinary, the editors feel that there is a need for articles covering the many different aspects of the subject from medicinal chemistry to biophysical studies. Suggestions from readers regarding topics to be covered in subsequent volumes will be welcomed. 

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... 

There has been enormous activity in the field of copper(I)-dioxygen chemistry in the last 25 years, with our information coming from both biochemical-biophysical studies and to a very important extent from coordination chemistry. This has resulted in the structural and spectroscopic characterization of a large number of copper dioxygen complexes, some of which are represented in Figure 14.2. The complex F, first characterized in a synthetic system was subsequently established to be present in oxy-haemocyanin, and is found in derivatives of tyrosinase and catechol oxidase, implying its involvement in aromatic hydroxylations in both enzymes and chemical systems. 

Van Buuren JH, Zuurendonk PF, Van Gelder BF, et al. 1972. Biochemical and biophysical studies on Cytochrome aa3 V. binding of cyanide to cytochrome aa3. Biochim Biophys Acta 256 (2) 243-257. 

Prylutskyy Yu. I, Yashchuk VM, Kushnir KM, Golub AA, Kudrenko VA, Prylutska SV, Grynyuk II, Buzaneva EV, ScharffP, Braun T, Matyshevska OP (2003) Biophysical studies of fulleiene-based composite for bio-nanotechnology. Mater. Sci. Eng. Sect C 23 109-111. 

Scheme 14 Structures of fluorescent lipidated peptides that were used for biophysical studies.

This review is a summary of our recent genetic, biochemical, and biophysical, studies of the Fe-S cluster assembly proteins of A. vinelandii, with particular emphasis on the role of the NifU and IscU proteins. The results reveal insight into the mechanism of both general and nitrogenase-specific Fe-S cluster biosynthesis in A. vinelandii and indicate a common mechanism for Fe-S cluster assembly that is used throughout nature. 

Phosphatidylcholines are the most prominent components of biological membranes and therefore often serve as model biomembrane systems in biophysical studies.Due to their amphiphathic character, phospholipids have a strong tendency to spontaneously form bilayer structures when... 

The basis of the preference of the A domain, relative to the B domain, of HMGBl for binding to distorted DNA structures has become apparent from numerous structural and biophysical studies. In contrast to the B domain, the A domain has only the secondary potentially intercalating residue, namely Phe at position Y (Table 1 and Fig. 2). This presumably accounts for the smaller bend angle in the A domain/cisplatin-modified DNA eomplex (61°) than in the B domain complex (80-95°) [34,43]. As yet, there is no strueture of a complex between the A domain and linear DNA. However, in the erystal structure of the A domain complexed with cisplatin-modified DNA the domain binds to one side of the cA-platinum adduet. 

It is interesting that a unique secondary structural element, designated the half-turn, was indentified in preliminary NMR studies of rabbit metallothionein-2 (Wagner etal., 1986). The half-turn element is defined as a type II turn with (f>3 rotated from 90° to -90° its occurrence in the metallothionein-2 structure arises from the constraints placed on the relatively short polypeptide chain by the metal clusters. Although these constraints are not well understood and are certainly difficult to predict, the continued biophysical study of metallothionein-2 will certainly improve our understanding of protein-metal cluster interactions. 

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