| Use of protein database for the computation of the dipole moments of normal and abnormal hemoglobins Biophysical Journal, Volume 64, Issue 5, 1 May 1993, Pages 1550-1558 S. Takashima Abstract Previously, we discussed the calculation of the dipole moments of small proteins using the three-dimensional protein data-base. Our results demonstrate that the calculated dipole moments are in acceptable agreement with measured values. We, however, noted the difficulty of the calculation with larger proteins, in particular those consisting of several subunits. Hemoglobin (Hb) is a protein having a molecular weight of 64,000 that consists of four subunits, a typical case where the computation was found to be difficult. To circumvent the difficulties, we calculated the dipole moment of each subunit separately. The dipole moment of the whole protein was calculated by the vectorial summation of subunit moments. With this method, the calculated net dipole moment is in good agreement with the experimental value. Our calculation shows that the dipole moment vectors of subunits are, by and large, antiparallel in tetramers causing partial cancellation of the net dipole moment. In addition to normal HbA, the dipole moment of abnormal HbS was calculated using an approximate computational technique. Because of the loss of two negative changes as a result of the replacement of glutamic acid with valine in beta-chains, the dipole moment of HbS was found, experimentally and theoretically, to be significantly smaller than that of HbA. Abstract | PDF (852 kb) |
| The electric dipole moment of rhodopsin solubilized in Triton X-100 Biophysical Journal, Volume 15, Issue 12, 1 December 1975, Pages 1181-1200 D.C. Petersen and R.A. Cone Abstract The electric dipole moment of solubilized rhodopsin was determined with dielectric dispersion measurements. Rhodopsin was extracted from disc membranes of cattle rod outer segments with the nonionic detergent Triton X-100. The dipole moment of rhodopsin at its isoionic point in the detergent micelle is 720 D (150 charge-A). This value is comparable to dipole moments of nonmembrane proteins, especially those which tend to aggregate or polymerize. Flash irradiation of the rhodopsin results in an increase in the dipole moment of about 25 D (5 charge-A). The light-induced increase in dipole moment appears to be composed of two parts--a faster component related to a change in the number of protons bound by rhodopsin and a slower component apparently independent of the change in proton binding. Abstract | PDF (1404 kb) |
| Effects of Phenylalanine Substitutions in Gramicidin A on the Kinetics of Channel Formation in Vesicles and Channel Structure in SDS Micelles Biophysical Journal, Volume 88, Issue 1, 1 January 2005, Pages 224-234 J.B. Jordan, P.L. Easton and J.F. Hinton Abstract The common occurrence of Trp residues at the aqueous-lipid interface region of transmembrane channels is thought to be indicative of its importance for insertion and stabilization of the channel in membranes. To further investigate the effects of Trp→Phe substitution on the structure and function of the gramicidin channel, four analogs of gramicidin A have been synthesized in which the tryptophan residues at positions 9, 11, 13, and 15 are sequentially replaced with phenylalanine. The three-dimensional structure of each viable analog has been determined using a combination of two-dimensional NMR techniques and distance geometry-simulated annealing structure calculations. These phenylalanine analogs adopt a homodimer motif, consisting of two helices joined by six hydrogen bonds at their NH-termini. The replacement of the tryptophan residues does not have a significant effect on the backbone structure of the channels when compared to native gramicidin A, and only small effects are seen on side-chain conformations. Single-channel conductance measurements have shown that the conductance and lifetime of the channels are significantly affected by the replacement of the tryptophan residues (Wallace, 2000; Becker et al., 1991). The variation in conductance appears to be caused by the sequential removal of a tryptophan dipole, thereby removing the ion-dipole interaction at the channel entrance and at the ion binding site. Channel lifetime variations appear to be related to changing side chain-lipid interactions. This is supported by data relating to transport and incorporation kinetics. Abstract | Full Text | PDF (568 kb) |
Copyright © 1975 The Biophysical Society. All rights reserved.
Biophysical Journal, Volume 15, Issue 3, 239-251, 1 March 1975
doi:10.1016/S0006-3495(75)85815-2
Research Article
E. Levitan and Y. Palti
Dipole moment, enthalpy, and entropy changes were calculated for hypothetical structural units which control the opening and closing of ionic channels in axon membranes. The changes of these thermodynamic functions were calculated both for activation (transition to intermediate complex) and for the structural transformation as a whole. The calculations are based on the experimentally determined Q10 values and the empirical formulae for the rate constants (alpha's and beta's) as functions of membrane potentials in Hodgkin-Huxley type models. From the calculated thermodynamic functions we suggest that the specific structural units of the axon membranes are probably of macromolecular (possible protein-like) dimensions with large dipole moments (hundreds of debyes). The calculated dipole moment changes of a single structural unit indicate that in many cases these dipole moments saturate at strong depolarizations or hyperpolarizations. The transitions in structural units show substantial activation enthalpies and entropies but the net enthalpy and entropy changes are practically negligible for the transition as a whole, i.e. the structural units presumably undergo displacements. While the calculated dipole moment changes associated with structural transformations in Loligo and Myxicola show similar potential dependencies, those for Rana usually show a different behavior. The relevance of the dipole moment changes to gating currents is discussed.