Dipole moments of proteins

The dipole moments of protein and other gas-phase macroions differ from those of solution or solid state precursors because of (i) the change of z and consequent rearrangement of partial charges over the molecule and (ii) unavoidable geometry distortion upon ionization, even with the softest sources.At still higher z... 

Felder, C.E., Prilusky, J., Silman, I., Sussman, J.L., A server and database for dipole moments of proteins. Nucleic Acids Res. 2007, 35, W512. The server is available at http //bioportal.weizmann.ac.il/dipol/index.html... 

Experimental dipole moments may be used to check the validity of electrostatic calculations. In the past, dipole moments of proteins were often characterized by measurements of dielectric relaxation. More information may be obtained by measurements of the electric dichroism because these measurements provide not only the magnitude of the dipole moment but also the optical anisotropy with respect to the dipole vector. Thus, measurements of the electric dichroism provide a more rigorous test for calculations of electrostatic parameters of proteins. Using the calculations described earlier for pK s of titratable groups, one can predict dipole moments of proteins and their axes given by the principal axes of the rotational diffusion tensor and compare them with electrooptical data. ° One important aspect of comparison of computed and experimental dipole moment is that computations of dipole moments, optical anisotropy, and rotational diffusion coefficients can be used in combination with experimental electrooptical procedures to determine the long-range structure of biomacromolecular assemblies, such as the complexes of DNA and proteins described by Pbrschke et al. so... 

Computed dipole moments of proteins presented here refer to a particular point within the structures of the proteins named center of diffusion (CD). As is known, a calculated dipole moment depends on the choice of coordinate system origin when the total charge on the molecule is not zero. Experimental values of dipole moments are derived from the orientational behavior of molecules under electric field pulses, which obviously is independent of any coordinate system but can be biased by other factors. For example, Wegener " showed that rotational velocity > driven by the external electric field, E at low Reynold s number can be expressed as... 

It should be borne in mind, however, that enzyme proteins, like other proteins, are dipolar ionic structures surrounded by an intense electrostatic field. Horse carboxyhemoglobin, for example, has a dipole moment of 480 Debye units (molecular weight, 67,000). Compared with amino acids, sugars have a rather low dipole moment, due mainly to a considerable measure of mutual cancellation of the constituent link moments resulting from their disposition in space (glycine = 15, a- and... 

Observation of reorientational dynamics of dipolar groups surrounding the fluorophore in response to changes in the dipole moment of the fluorophore occurring upon electronic excitation. Such dynamics result in the appearance of spectral shifts with time,(1 ) in changes of fluorescence lifetime across the fluorescence spectrum,(7,32) and in a decrease in the observable effects of selective red-edge excitation.(1,24 33 34) The studies of these processes yield a very important parameter which characterizes dynamics in proteins— the reorientational dipolar relaxation time, xR. 

B, C, and D are constants, the electrostatic term is expressed by A = Dfi/RT in which fl is the dipole moment of the protein, and the hydrophobic term is expressed by Q, = [N + 4.8N1 3V2/3(Ke -1)]/RT, where N is Avogadro s number, is the non-polar surface area of the protein, V the molar volume of the solvent, and <7 is the surface tension increment, i.e., the difference between the surface tensions with and without salt x6 is a correction factor for the surface tension to take account of the curvature of the protein surface at molecular dimensions. 

Amino acids, the building blocks of proteins, can exist in two principal tautomeric forms. In aqueous solution, the naturally occurring a-amino acids are found in their zwitterionic form 42Z, but in the gas phase, the neutral form 42N is the only structure observed. This substantial solvent effect is understood in terms of the dipole moments of the tautomers. The dipole moment of the zwitterion is very large and is favorably stabilized by electrostatic interactions with the polar water molecules. In the absence of the polar environment (the gas phase), the charge separation of the zwitterion is unsustainable and only the neutral form exists. 

This technique was employed to monitor the B —> A transition of DNA as a function of the relative humidity (Pilet and Brahms, 1973 Pohle et al., 1984). The investigated bands are those which reflect the vibrations of the phosphate groups. As shown by Fig. 4.7-3, which presents the polarized infrared spectra of a salmon sperm DNA hydrated film with 93% RH (top, B form) and 58% RH (bottom, A form), the dichroism of the two phosphate bands changes. The B form of the antisymmetric PO2 stretching vibration around 1230 cm is non-dichroic, while that of the A form is perpendicular. The B form of the symmetric PO2 stretching vibration around 1090 cm is perpendicular, while that of the A form is parallel. A simple computation, for instance for the latter band, shows that the value of the angle between the transition dipole moment of this vibration and the double helical axis varies between 68 ° (B form) and 49 ° (A form). This parameter is an extremely sensitive indicator of a B A transition and may also be employed to show the inhibition of a B —> A transition by various classes of molecules, such as proteins (Liquier et al., 1977 Taillandier et al., 1979) or drugs (Fritzsche and Rupprecht, 1990). 

Another, but to some extent similar mechanism has been proposed by Kirkwood and Shumaker with special regard to protein molecules. These authors pointed out that at appropriate pH values protons may fluctuate between the various acidic and basic groups of the amino-acid side-chains. This was shown to result in a non-vanishing mean square of the overall dipole moment of the molecule, namely... 

Numerical calculations were carried out for several proteins. They yielded dipole moments of about the same magnitude as actually measured. The Afi apparently becomes fi ly large when the pH is close to the pA" range of the frequently occurring carboxy and amino-groups, respectively. Therefore, sharp maximum values of the dipole must be expected at about pH 4 and 10. Experimental tests of this diaracteristic feature have failed, however. The discrqrancy between the theory and these measurements are so obvious that one must conclude that protons are not sufficiently mobile to contribute significantly to the dielectric polarization of protein solutions. 

The constant Rq is dependent on several parameters 1) the relative orientation of the transition dipole moments of the two molecules (these dipoles are the spectroscopic transition dipoles), 2) the extent that the fluorescence spectrum of the donor overlaps with the absorption spectrum of the acceptor, and 3) the surrounding index of refraction. We will deal with each of these below (see Equation 8). Because many proteins have diameters less than lOnm, this distance dependence explains the usefulness of ERET for determiiung distances inside proteins as well as between interacting proteins, which is the reason that the name spectroscopic ruler was coined for FRET (20). ERET is a convenient method for determining the distance between two locations on proteins, or for determining whether two proteins interact intimately with each other. Fluorescence instrumentation is available in many laboratories, and a plethora of dyes and a wide variety of fluorescent proteins are now readily available. Therefore, FRET is a viable option for most researchers. With care, FRET can yield valuable information concerning protein-protein interactions, interactions of proteins with other molecules, and protein conformational changes. 

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