Conformation in aqueous solution

The conformation of bovine myelin basic protein (MBP) in AOT/isooctane/water reversed micellar systems was studied by Waks et al. 67). This MBP is an extrinsic water soluble protein which attains an extended conformation in aqueous solution 68 but is more density packed at the membrane surface. The solubilization of MBP in the AOT reversed micelles depends on the water/AOT-ratio w0 68). The maximum of solubilization was observed at a w0-value as low as 5.56. The same value was obtained for another major protein component of myelin, the Folch-Pi proteolipid 69). According to fluorescence emission spectra of MBP, accessibility of the single tryptophane residue seems to be decreased in AOT reversed micelles. From CD-spectra one can conclude that there is a higher conformational rigidity in reversed micelles and a more ordered aqueous environment. 

It is important to note that most molecules are not rigid but may prefer a distrinct structure and the conformation of a molecule strongly depends on its specific environment. Hence, the crystal structure of a drug does not have to correspond to the receptor bound conformation. Also, a conformation in solution depends on the nature of the solvent and measuring conditions, and may change when the molecule is bound to the receptor [4]. In addition, different receptors or receptor subtypes can bind the same drug in different conformations. It is a general assumption and observation, but by far not a strict condition, that the conformation in aqueous solution is similar to the bound conformation and is a better representation of the bioactive conformation than an X-ray structure of the isolated molecule in the crystalline state. 

Fig. 3. Backscattered Raman (/R + /L) and ROA (/R — /L) spectra of poly-L-lysine in o -helical (top pair) and disordered (second pair) conformations, and of poly-L-glutamic acid in a-helical (third pair) and disordered (bottom pair) conformations in aqueous solution. Reprinted from Barron et al., 2000, Prog. Biophys. Mol. Biol. 73, 1-49, with permission from Elsevier Science.

Kallenbach and co-workers have recently demonstrated via CD spec-tropolarimetry and NMR spectrometry that a seven-residue alanine peptide adopts predominantly the PPII helical conformation in aqueous solution (Shi et al., 2002). Since alanine is nothing but backbone, such a finding indicates that the polypeptide backbone possesses an intrinsic... 

A coirplete understanding of the role of carbohydrates in biological systems requires knowledge of the distribution at equilibrium of the various conformers in aqueous solution. The conformational behavior of carbohydrates in solution can be examined from different vantage points (1,), but the most relevant approach is, no doubt, study of dilute solutions themselves. At present, high resolution NMR spectroscopy is the primary tool for determination of three-dimensional structure of oligosaccharides in solution. Optical rotation is also very sensitive to conformation (2) and there is a new, semi-enqpirical theory of optical rotation of oligosaccharides ( ). 

Diastereomeric distributions (A A) in several tris-ligand Fe + complexes of chiral catecholamide and terephthalamide ligands have been established in solution by CD and NMR spectroscopies. The complex of (253), whose structure in the solid state was determined, exists wholly in the A conformation in aqueous solution. Weak polar interactions determine conformational preferences here. ... 

Figure 3. Structures of (7 ,7 )-tartaric acid diamide (a) lowest-energy conformer for isolated molecule (b) lowest-energ conformer in aqueous solution (c) crystal structure Figs (a), (c) adapted from ref. 22. ...

Within five years of the verification of VCD in solutions, first attempts were made to apply the technique to study biomolecular solution conformation in aqueous solution. The first samples studied as solutions in D.O were simple amino acids and di-and tripeptides [26]. However, due to instrumental limitations, VCD was collected only in the C-H and N-H stretching region (2.5 to 3.5 fim). Although these early studies were necessary for the development of the experimental technique, it was not until experimental advances allowed the detection of VCD in the 6 fxm region that the full potential of VCD was realized for peptide structural investigations. 

Intramolecular hydrogen bonding in sucrose may be retained in aqueous solution. Empirical force field calculations suggest that the molecule of sucrose retains its crystal structure conformation in aqueous solution with the loss of one of the... 

Chen, Y.Y. and Bleam, W.F., Two-dimensional NOESY nuclear magnetic resonance study of pH-dependent changes in humic acid conformation in aqueous solution,... 

The search for an enzymatic activity that would catalyze prolyl peptide bond isomerization began soon after the proposal of the proline hypothesis. The success came in 1984, when Fischer and co-workers discovered a peptidylprolyl m—tram-isomerase activity in porcine kidney and other tissues by an assay that is based on the conformational specificity of chymotrypsin. This protease cleaves the 4-nitroanilide moiety from the peptide glutaryl-Ala-Ala-Pro-Phe-4-nitroanilide only when the Ala-Pro peptide bond is in the trans conformation. In aqueous solution 90% of the molecules are trans in the assay peptide and only 10% are cis. Therefore, in the presence of a high concentration of chymotrypsin, 90% of the hydrolysis reaction occurs within the dead time of manual mixing. Hydrolysis of the remaining 10% is slow, limited in rate by the cis — ... 

We used diphenylmethanol to examine this point and found that in this compound also additivity does not hold. A definitive answer cannot therefore be given as to whether there is any hydrophobic driving force which causes Benadryl to exist in a folded conformation in aqueous solution. Moreover, with such strong interaction between the two aromatic rings, one cannot expect ir values for any substituents in the ortho ring positions to bear any relation to ir values in a simple benzene derivative. 

The tautomers of cytosine have also been examined with continuum solvation methods. Both Miertus-Scrocco-Tomasi (MST) and PCM computations predict that 13a is the lowest energy conformer in aqueous solution. This is consistent with the explicit water computations. Aqueous solvation, therefore, substantially alters the relative energies of the tautomers of cytosine. The canonical representation of cytosine 13a, the tautomer invoked in Watson-Crick base pairing, is in fact the most favorable tautomer in solution, but not in the gas phase. 

Nonetheless, this raises the question of what is an appropriate definition of the NAC. Mulholland suggests a definition that is much less arbitrary the NAC is the conformation of the substrate bound to the enzyme, and what is critical then is the free energy needed to form this conformation in aqueous solution. MulhoUand estimates this energy as 4-5 kcal mol through a free energy perturbation calculation and MD using AMI and CHARMM. This is half the estimate of Bruice and suggests that formation of the NAC is only partly responsible for the catalytic effect afforded by CM. 

Fig. 5. Schematic representations of a protein molecule in several possible conformational states (A) its native conformation in aqueous solution (B) an unfolded conformation retaining the net helical content of the native form but with hydro-phobic regions disrupted and (C) an extensively helical conformation.

Pyranose derivatives adopt chair conformations unless an unusual combination of destabilizing interactions is present. Angyal developed a set of destabilizing interactions that can be used to estimate the relative stabilities of the two chair conformers in aqueous solution [125,126]. These values were determined before many of the A-values discussed above for cyclohexane and tetrahydropyran derivatives were measured and are formulated in terms of 1,3-diaxial... 

The flounder protein has been shown from circular dichroism measurements to possess a large proportion (—85%) of the a-helical conformation in aqueous solution (pH 8.0) at — 1°C (Ananthanarayanan and Hew, 1977a). The helical content decreases as the temperature is raised (Fig. 32). Viscosity data at — 1°C indicate an asymmetric shape for the protein molecule compatible with its high helical content. Thus, the secondary and tertiary structure of this protein, as well as its primary structure, are found to be different from its counterpart glycoproteins isolated from other fish. No data are available concerning the assumption that this highly helical structure at — 1°C is related to its function. 

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