| Onset of Anthrax Toxin Pore Formation Biophysical Journal, Volume 90, Issue 9, 1 May 2006, Pages 3267-3279 Mu Gao and Klaus Schulten Abstract Protective antigen (PA) is the anthrax toxin protein recognized by capillary morphogenesis gene 2 (CMG2), a transmembrane cellular receptor. Upon activation, seven ligand-receptor units self-assemble into a heptameric ring-like complex that becomes endocytozed by the host cell. A critical step in the subsequent intoxication process is the formation and insertion of a pore into the endosome membrane by PA. The pore conversion requires a change in binding between PA and its receptor in the acidified endosome environment. Molecular dynamics simulations totaling ∼136ns on systems of over 92,000 atoms were performed. The simulations revealed how the PA-CMG2 complex, stable at neutral conditions, becomes transformed at low pH upon protonation of His-121 and Glu-122, two conserved amino acids of the receptor. The protonation disrupts a salt bridge important for the binding stability and leads to the detachment of PA domain II, which weakens the stability of the PA-CMG2 complex significantly, and subsequently releases a PA segment needed for pore formation. The simulations also explain the great strength of the PA-CMG2 complex achieves through extraordinary coordination of a divalent cation. Abstract | Full Text | PDF (1512 kb) |
| Electrostatic Influence of PsaC Protein Binding to the PsaA/PsaB Heterodimer in Photosystem I Biophysical Journal, Volume 90, Issue 3, 1 February 2006, Pages 1081-1089 Hiroshi Ishikita, Dietmar Stehlik, John H. Golbeck and Ernst-Walter Knapp Abstract The absence of the PsaC subunit in the photosystem I (PSI) complex (native PSI complex) by mutagenesis or chemical manipulation yields a PSI core (P700-F core) that also lacks subunits PsaD and PsaE and the two iron-sulfur clusters F and F, which constitute an integral part of PsaC. In this P700-F core, the redox potentials () of the two quinones A and the iron-sulfur cluster F as well as the corresponding protonation patterns are investigated by evaluating the electrostatic energies from the solution of the linearized Poisson-Boltzmann equation. The B-side specific Asp-B558 changes its protonation state significantly upon isolating the P700-F core, being mainly protonated in the native PSI complex but ionized in the P700-F core. In the P700-F core, (A) remains practically unchanged, whereas (F) is upshifted by 42mV. With these calculated values, the electron transfer rate from A to F in the P700-F core is estimated to be slightly faster on the A side than that of the wild type, which is consistent with kinetic measurements. Abstract | Full Text | PDF (316 kb) |
| Protonation Studies and Multivariate Curve Resolution on Oligodeoxynucleotides Carrying the Mutagenic Base 2-Aminopurine Biophysical Journal, Volume 81, Issue 5, 1 November 2001, Pages 2886-2896 R. Gargallo, M. Vives, R. Tauler and R. Eritja Abstract 2-Aminopurine (P) is a mutagen causing A·T to G·C transitions in prokaryotic systems. To study the base-pairing schemes between P and cytosine (C) or thymine (T), two self-complementary dodecamers containing P paired with either C or T were synthesized, and their protonation equilibria were studied by acid-base titrations and melting experiments. The mismatches were incorporated into the self-complementary sequence d(CGCPCCGGXGCG), where X was C or T. Spectroscopic data obtained from molecular absorption, circular dichroism (CD), and molecular fluorescence spectroscopy were analyzed by a factor-analysis-based method, multivariate curve resolution based on the alternating least squares optimization procedure (MCR-ALS). This procedure allows determination of the number of acid-base species or conformations present in an acid-base or melting experiment and the resolution of the concentration profiles and pure spectra for each of them. Acid-base experiments have shown that at pH 7, 150mM ionic strength, and 37°C, both C and P are deprotonated. At pH near 4, the majority of species shows C protonated and P deprotonated. Finally, at pH values near 3, the majority of species shows both protonated C and P. These results are in agreement with NMR studies showing a wobble geometry for the P·C base pair and a Watson-Crick geometry for the P·T base pair at neutral pH. Melting experiments were carried out to confirm the proposed acid-base distribution profile. For the sequence including the P·T mismatch, only one transition was observed at neutral pH. However, for the sequence including the P·C mismatch, two transitions were detected by CD but only one by molecular absorption. This behavior agrees with that observed by other authors for oligonucleotides of similar sequence and suggests the following sequence of conformational changes during melting: duplex→hairpin→random coil. Abstract | Full Text | PDF (179 kb) |
Copyright © 1996 The Biophysical Society. All rights reserved.
Biophysical Journal, Volume 70, Issue 1, 473-481, 1 January 1996
doi:10.1016/S0006-3495(96)79591-7
Research Article
S.P. Balashov, E.S. Imasheva, R. Govindjee and T.G. Ebrey
Titration of Asp-85, the proton acceptor and part of the counterion in bacteriorhodopsin, over a wide pH range (2–11) leads us to the following conclusions: 1) Asp-85 has a complex titration curve with two values of pKa; in addition to a main transition with pKa = 2.6 it shows a second inflection point at high pH (pKa = 9.7 in 150-mM KCl). This complex titration behavior of Asp-85 is explained by interaction of Asp-85 with an ionizable residue X'. As follows from the fit of the titration curve of Asp-85, deprotonation of X' increases the proton affinity of Asp-85 by shifting its pKa from 2.6 to 7.5. Conversely, protonation of Asp-85 decreases the pKa of X' by 4.9 units, from 9.7 to 4.8. The interaction between Asp-85 and X' has important implications for the mechanism of proton transfer. In the photocycle after the formation of M intermediate (and protonation of Asp-85) the group X' should release a proton. This deprotonated state of X' would stabilize the protonated state of Asp-85.2) Thermal isomerization of the chromophore (dark adaptation) occurs on transient protonation of Asp-85 and formation of the blue membrane. The latter conclusion is based on the observation that the rate constant of dark adaptation is directly proportional to the fraction of blue membrane (in which Asp-85 is protonated) between pH 2 and 11. The rate constant of isomerization is at least 10(4) times faster in the blue membrane than in the purple membrane. The protonated state of Asp-85 probably is important for the catalysis not only of all-trans <=> 13-cis thermal isomerization during dark adaptation but also of the reisomerization of the chromophore from 13-cis to all-trans configuration during N-->O-->bR transition in the photocycle. This would explain why Asp-85 stays protonated in the N and O intermediates.