Solution conformation

The solvent can strongly influence the energies of different solute conformations or configurations of atoms. 

Analytical ultracentrifugation (AUC) Molecular weight M, molecular weight distribution, g(M) vs. M, polydispersity, sedimentation coefficient, s, and distribution, g(s) vs. s solution conformation and flexibility. Interaction complex formation phenomena. Molecular charge No columns or membranes required [2]... 

Static (multi-angle laser) light scattering (SLS or MALLs) Molecular weight, radius of gyration, Rg solution conformation and flexibility. Solutions need to be clear of supramolecular aggregates. Rg more sensitive to conformation than s. [3]... 

Size exclusion chromatography coupled to static light scattering (SEC-MALLs) Molecular weight, molecular weight distribution. Polydispersity. Radius of gyration and distribution solution conformation and flexibility. Method of choice for moleciflar weight work. [4]... 

Small angle X-ray scattering Rg, chain contour length, L solution conformation and flexibility If M is also known, can provide mass per unit length Ml [5]... 

If two different three-dimensional arrangements in space of the atoms in a molecule are interconvertible merely by free rotation about bonds, they are called conformationsIf they are not interconvertible, they are called configurations Configurations represent isomers that can be separated, as previously discussed in this chapter. Conformations represent conformers, which are rapidly interconvertible and are thus nonseparable. The terms conformational isomer and rotamer are sometimes used instead of conformer . A number of methods have been used to determine conformations. These include X-ray and electron diffraction, IR, Raman, UV, NMR, and microwave spectra, photoelectron spectroscopy, supersonic molecular jet spectroscopy, and optical rotatory dispersion (ORD) and CD measurements. Some of these methods are useful only for solids. It must be kept in mind that the conformation of a molecule in the solid state is not necessarily the same as in solution. Conformations can be calculated by a method called molecular mechanics (p. 178). 

Monkos, Karol 2000. Viscosity analysis of the temperature dependence of the solution conformation of ovalbumin. Biophysical Chemistry 85, 7-16. 

Monkos, Karol 2004. On the hydrodynamics and temperature dependence of the solution conformation of human serum albumin from viscometry approach. Biochimica et Biophysica Acta 1700, 27-34. 

Monkos, Karol 2005. A comparison of solution conformation and hydrodynamic properties of equine, porcine and rabbit serum albumin using viscometric measurements. Biochimica et Biophysica Acta 1748,100-109. 

Mierke, D. F., Cohen, F.F., Zuckermann, R. N., and Bradley, F. K. NMR determination of the major solution conformation of a peptoid pentamer with chiral... 

More recent studies on the folded toxin structure by Norton and colleagues have utilized h- and C-NMR techniques (19,20). By using 2D-FT-NMR, it was possible to localize a four stranded, antiparallel )5-pleated sheet "backbone structure in As II, Ax I, and Sh I (21,22), In addition, Wemmer et al. (23) have observed an identical )5-pleated structure in Hp II. No a-helix was observed in these four variants. In the near future, calculated solution conformations of these toxins, utilizing distance measurements from extracted Nuclear Overhauser Enhancement (NOE) effects should greatly stimulate structure-activity investigations. 

The activities of the various components 1,2,3. .. of an ideal solution are, according to the definition of an ideal solution, equal to their mole fractions Ni, N2,. . . . The activity, for present purposes, may be taken as the ratio of the partial pressure Pi of the constituent in the solution to the vapor pressure P of the pure constituent i in the liquid state at the same temperature. Although few solutions conform even approximately to ideal behavior at all concentrations, it may be shown that the activity of the solvent must converge to its mole fraction Ni as the concentration of the solute(s) is made sufficiently small. According to the most elementary considerations, at sufficiently high dilutions the activity 2 of the solute must become proportional to its mole fraction, provided merely that it does not dissociate in solution. In other words, the escaping tendency of the solute must be proportional to the number of solute particles present in the solution, if the solution is sufficiently dilute. This assertion is equally plausible for monomeric and polymeric solutes, although the... 

A simplified analysis of the effect of particle shape or molecular conformation on SEC calibration has led to the prediction that the more open structure of rigid rod shaped solutes gives a relatively flat SEC-MW calibration curve. As the solute conformation becomes more compact (random-coil to solid-sphere), the SEC-MW calibration curve becomes increasingly steep... 

Glass, G.E., Konnert, J.H., Miles, M.G., Britton, D. and Tobias, R.S. (1968) Crystal and molecular structure and the solution conformation of dimefhylgold(III) hydroxide, inorganic intermediate ring compound. Journal of the American Chemical Society, 90, 1131. 

Phan-Chan-Du, A., Hemmerlin, C., Krikorian, D., Sakarellos-Daitsiotis, M., Tsikaris, V., Sakarellos, C., Marinou, M., Thureau, A., Cung, M. T., Tzartos, S. J. Solution conformation of... 

Ralph, J. Landucci, L. L. Nicholson, B. K. Wilkins, A. L. Adducts of anthrahydro-quinone and anthranol with lignin model quinone methides. 4. Proton NMR hindered rotation studies. Correlation between solution conformations and X-ray crystal structure. J. Org. Chem. 1984, 49, 3337-3340. 

Figure 4 Proposed solution conformations of H-Tyr-c-[-D-Orn-2-Nal-D-Pro-Gly-] (left panel) and H-Tyr-c-[D-Orn-Phe-D-Pro-Gly-] (right panel).

Lee JP, Stimson ER, Ghilardi JR, Mantyh PW, Lu Y-A, Felix AM, Llanos W, Behbin A, Cummings M, Criekinge MV, Timms W, Maggio JE. 1H NMR of A(i amyloid peptide congeners in water solution. Conformational changes correlate with plaque competence. Biochemistry 1995 34 5191-5200. 

Figure 1-2. The two dominant conformers of prephenate in solution. Conformer (a) has both the OH and COO- groups solvated by the environment. Conformer (b) has a strong H-bond between the OH and the COO groups. Adapted from Ref. [18]...

Osterhout JJ Jr, Baldwin RL, York EJ, Stewart JM, Dyson HJ, Wright PE (1989) 11 NMR studies of the solution conformations of an analogue of the C-peptide of ribonuclease A. Biochemistry 28 7059-7064. 

A difference in the solid state and solution conformation of 5 -de-oxyadenosylcobinamide (cobinamide coenzyme) has been inferred from the NMR spectrum of cobinamide coenzyme 123) which indicates that the resonance due to the proton at carbon R-l of the ribose is shifted significantly upfield from its expected position. Such an upfield shift would probably have to arise from the ring current of the adenine ring. 

Raman optical activity is an excellent technique for studying polypeptide and protein structure in aqueous solution since, as mentioned above, their ROA spectra are often dominated by bands originating in the peptide backbone that directly reflect the solution conformation. Furthermore, the special sensitivity of ROA to dynamic aspects of structure makes it a new source of information on order-disorder transitions. 

Recently, aqueous solution conformational studies of three short peptides from 9 to 12 residues corresponding to sequences present in titin... 

The quantity of primary interest in our thermodynamic construction is the partial molar Gibbs free energy or chemical potential of the solute in solution. This chemical potential reflects the conformational degrees of freedom of the solute and the solution conditions (temperature, pressure, and solvent composition) and provides the driving force for solute conformational transitions in solution. For a simple solute with no internal structure (i.e., no intramolecular degrees of freedom), this chemical potential can be expressed as... 

We note that the calculation of At/ will depend primarily on local information about solute-solvent interactions i.c., the magnitude of A U is of molecular order. An accurate determination of this partition function is therefore possible based on the molecular details of the solution in the vicinity of the solute. The success of the test-particle method can be attributed to this property. A second feature of these relations, apparent in Eq. (4), is the evaluation of solute conformational stability in solution by separately calculating the equilibrium distribution of solute conformations for an isolated molecule and the solvent response to this distribution. This evaluation will likewise depend on primarily local interactions between the solute and solvent. For macromolecular solutes, simple physical approximations involving only partially hydrated solutes might be sufficient. 

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