抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

Combined quantum-mechanics/molecular-mechanics (QM/MM) approaches have become the method of choice for modeling reactions in biomolecular systems. Quantum-mechanical (QM) methods are required for describing chemical reactions and other electronic processes, such as charge transfer or electronic excitation. However, QM methods are restricted to systems of up to a few hundred atoms. However, the size and conformational complexity of biopolymers calls for methods capable of treating up to several 100,000 atoms and allowing for simulations over time scales of tens of nanoseconds. This is achieved by highly efficient, force-field-based molecular mechanics (MM) methods. Thus to model large biomolecules the logical approach is to combine the two techniques and to use a QM method for the chemically active region (e.g., substrates and co-factors in an enzymatic reaction) and an MM treatment for the surroundings (e.g., protein and solvent). The resulting schemes are commonly referred to as combined or hybrid QM/MM methods. They enable the modeling of reactive biomolecular systems at a reasonable computational effort while providing the necessary accuracy.

QM/MM Methods for Biomolecular Systems

https://www.cell.com/biophysj/pdf/S0006-3495(01)76183-8.pdf

Mechanisms of Tryptophan Fluorescence Shifts in Proteins

THE timescale of the response of solvent molecules to electronic rearrangement of solute molecules has a critical influence on the rates of chemical reactions in liquids1–10. In particular, if the solvent cannot adapt quickly enough to this rearrangement as the reactants pass through the transition state, the evolving products may recross the free-energy barrier, reducing the reaction rate. Computer simulations have shown11–18 that the response of a solvent to a change in solute charge distribution is strongly bimodal: there is an initial ultrafast response owing to inertial (mainly libra-tional) motions of the solvent molecules, followed by a slow component owing to diffusive motions. Water seems to be by far the 'fastest' solvent studied so far: simulations predict that well over half of the solvation response for atomic solutes is inertial, happening on a timescale of about 20 femtoseconds12,13. The presence of this ultrafast component implies that solvent friction plays an important role in many aqueous charge-transfer processes9,10,19–21. Experimental verification of this prediction has been lacking, however, in part because of the difficulty of obtaining sufficient time resolution. Here we present experimental measurements of the ultrafast solvation dynamics of a coumarin salt in water. When considered in conjunction with computer simulations, our results demonstrate that a solvent response on a timescale faster than 50 fs can dominate aqueous solvation dynamics.

Femtosecond solvation dynamics of water

Wave propagation and group velocity

Solute–solvent interactions and dynamics are simulated with a fully molecular hybrid method consisting of a semiempirical quantum mechanical method with singly excited configurations for the solute and classical molecular dynamics (MD) for the solvent (H2O). The interactions are purely electrostatic, with the solute being polarizable and sharing its charge information with the MD at 5 fs intervals. The solvent charges are fixed and the results are not sensitive to the point charges used. For the solute, the results depend on the dipole moment much more than on the point charge magnitudes leading to a given dipole. This method is applied to the spectral shifts, dynamics, linewidths, and free energies of indole and 3‐methylindole (3MI) in water at 300 K, including the effect of geometry changes and clarifications concerning vertical vs 0–0 transition predictions. Large fluorescence Stokes shifts are predicted, in fair agreement with observed values. The 1La excited state dipole is calculated to be about 12 ...

Hybrid simulations of solvation effects on electronic spectra: Indoles in water

Hybrid quantum mechanical/molecular mechanics (QM-MM) calculations [Callis and Liu, J. Phys. Chem. B 2004, 108, 4248-4259] make a strong case that the large variation in tryptophan (Trp) fluorescence yields in proteins is explained by ring-to-backbone amide electron transfer, as predicted decades ago. Quenching occurs in systems when the charge transfer (CT) state is brought below the fluorescing state (1L(a)) as a result of strong local electric fields. To further test this hypothesis, we have measured the fluorescence quantum yield in solvents of different polarity for the following systems: N-acetyl-L-tryptophanamide (NATA), an analogue for Trp in a protein; N-acetyl-L-tryptophan ethyl ester (NATE), wherein the Trp amide is replaced by an ester group, lowering the CT state energy; and 3-methylindole (3MI), a control wherein this quenching mechanism cannot take place. Experimental yields in water are 0.31, 0.13, and 0.057 for 3MI, NATA, and NATE, respectively, whereas, in the nonpolar aprotic solvent dioxane, all three have quantum yields near 0.35, indicating the absence of electron transfer. In alkyl alcohols the quantum yield for NATA and NATE is between that found for water and that found for dioxane, and it is surprisingly independent of chain length (varying from methanol to decanol), revealing that microscopic H-bonding, and not the bulk dielectric constant, dictates the electron transfer rate. QM-MM calculations indicate that, when averaged over the six rotamers, the greatly increased quenching found in water relative to dioxane can be attributed mainly to the larger fluctuations of the energy gap in water. These experiments and calculations are in complete accord with quenching by a solvent stabilized charge transfer from ring to amide state in proteins.

Solvent Effects on the Fluorescence Quenching of Tryptophan by Amides via Electron Transfer. Experimental and Computational Studies

Tryptophan (Trp) fluorescence is potentially a powerful probe for studying the conformational ensembles of proteins in solution, as it is highly sensitive to the local electrostatic environment of the indole side chain. However, interpretation of the wavelength-dependent complex fluorescence decays of proteins has been stymied by controversy about two plausible origins of the typical multiple fluorescence lifetimes: multiple ground-state populations or excited-state relaxation. The latter naturally predicts the commonly observed wavelength−lifetime correlation between decay components, which associates short lifetimes with blue-shifted emission spectra and long lifetimes with red-shifted spectra. Here we show how multiple conformational populations also lead to the same strong wavelength−lifetime correlation in cyclic hexapeptides containing a single Trp residue. Fluorescence quenching in these peptides is due to electron transfer. Quantum mechanics−molecular mechanics simulations with 150-ps trajectories...

Correlation of tryptophan fluorescence spectral shifts and lifetimes arising directly from heterogeneous environment.

We report quantum mechanical-molecular mechanical (QM-MM) predictions of fluorescence quantum yields for 20 tryptophans in 17 proteins, whose yields span the range from 0.01 to 0.3, using ab initio computed coupling matrix elements for photoinduced electron transfer from the 1La excited indole ring to a local backbone amide. The average coupling elements span the range 140-1000 cm-1, depending on tryptophan rotamer conformation. The matrix elements were from the singles configuration interaction matrix, and were largely insensitive to which of the three basis sets was used. Large fluctuations were seen on the time scale of tens of femtoseconds, caused primarily by side chain and backbone torsional variations for 150 ps of dynamics at 300 K. The largest coupling occurs for the chi1 = -60 degrees rotamer and is purely through-bond. There is no apparent correlation between the coupling magnitude and quantum yield, which is still dominated by energy gap and reorganization energy. The source of error bars for predicted quenching rates using the weak coupling golden rule may be due to inaccurate averaged Franck-Condon weighted densities because of inadequate simulation times and parameters and/or to failure of the weak coupled golden rule used in these predictions because of the broad distribution of Landau-Zener probabilities arising from the large variable coupling.

Pedro L. Muíño

Papers

Hybrid simulations of solvation effects on electronic spectra: Indoles in water

Solvent Effects on the Fluorescence Quenching of Tryptophan by Amides via Electron Transfer. Experimental and Computational Studies

Correlation of tryptophan fluorescence spectral shifts and lifetimes arising directly from heterogeneous environment.

Ab initio prediction of tryptophan fluorescence quenching by protein electric field enabled electron transfer.

Fluorescence excitation spectrum of indole—D2O in supersonic jet