Conformation and location of membrane-bound salinomycin-sodium complex deduced from NMR in isotropic bicelles

An ionophore antibiotic salinomycin was studied in a membrane environment consisting of isotropic bicelles, a better model for biological membranes than micelles, and its conformation and topological orientation in bicelles was determined. 2D NMR measurements and restrained conformational search revealed that salinomycin-sodium salt in bicelles adopts an open conformation in which the orientation of the E-ring is significantly different from that in crystal and solution structures. This conformational alteration breaks an intramolecular hydrogen bond between 28-OH and 1-O, dislocates the ether oxygen of the E-ring from a coordinated position to the sodium ion observed in the crystal, and consequently weakens the complexation between salinomycin and the sodium ion. Paramagnetic relaxation experiments using doxyl-phospholipids reveal that salinomycin is embedded shallowly in bicelles, with both terminals being closer to the water interface and the olefin portion facing the bicelle interior. Measurements of intermolecular NOEs between salinomycin and phospholipids further supported this orientation. Weaker complexation with sodium ion and positional preference in the membrane polar region may facilitate the catch-and-release of metal ions at the polar/nonpolar interface of bilayers. On the basis of these findings, a model for salinomycin-assisted transport of metal ions across biological membranes is proposed.     

Solid-state 2H NMR studies of the effects of cholesterol on the acyl chain dynamics of magnetically aligned phospholipid bilayers

We report the utilization of magnetically aligned phospholipid bilayers (bicelles) to study the effects of cholesterol in phospholipid bilayers for both chain perdeuterated DMPC and partially deuterated alpha-[2,2,3,4,4,6-d(6)]-cholesterol using (2)H solid-state NMR spectroscopy. The quadrupolar splittings at 40 degrees C were 25.5 and 37.7 kHz, respectively, for the 2,4-(2)H(eq) and 2,4-(2)H(ax) deuterons when the bilayer normal of the discs was aligned perpendicular to the static magnetic field. The quadrupolar splittings were doubled when Yb(3+) ions were added to flip the bicelles 90 degrees such that the bilayer normal was colinear with the magnetic field. The results suggest that cholesterol is incorporated into the bicelle discs. For chain perdeuterated DMPC-d(54), incorporated into DMPC-DHPC bicelle discs, the individual quadrupolar splittings of the methylene and methyl groups doubled on going from the perpendicular to the parallel alignment. Also, the presence of cholesterol increased the overall ordering of the acyl chains of the phospholipids. S(CD) (i) calculations were extracted directly from the (2)H quadrupolar splittings of the chain perdeuterated DMPC. The order parameter, S(CD) (i), calculations clearly indicated an overall degree of ordering of the acyl chains in the presence of cholesterol. We also noted a disordering effect at higher temperatures. This study demonstrates the ease with which (2)H order parameters can be calculated utilizing magnetically aligned phospholipid bilayers when compared with randomly dispersed membrane samples.     

Evidence for effect of GM1 on opioid peptide conformation: NMR study on leucine enkephalin in ganglioside-containing isotropic phospholipid bicelles

Enkephalins are endogenous neuropeptides that have opioid-like activities and compete with morphines for the receptor binding. The binding of these neuropeptides to membrane appears crucial since enkephalins interact with the nerve cell membranes to achieve bioactive conformations that fit onto multiple receptor sites (micro, delta, and kappa). Using NMR spectroscopy, we have determined the solution structure of the small opiate pentapeptide leucine enkephalin in the presence of isotropic phospholipid bicelles: phosphocholine bicelles (DMPC:CHAPS 1:4) and phosphocholine bicelles doped with ganglioside GM1 (DMPC:CHAPS:GM1 1:4:0.3). Bicelles containing GM1 were found to interact strongly with leucine enkephalin, whereas a somewhat weaker interaction was observed in the case of bicelles without GM1. Structure calculation from torsion angles, chemical shifts, and NOE-based distance constraints explored that the peptide could flexibly switch between several mu- and delta-selective conformations in both the bicelles though micro-selective conformations turned out to be geometrically preferred in each bicellar system. A detailed analysis of the structures presented supports the variance over the singly associated conformation of enkephalin in nerve cell membranes.     

Structural properties of an artificial protein that regulates the nucleation of inorganic and organic crystals

Technological advances have facilitated the generation of artificial proteins that possess the capabilities of recognizing and binding to inorganic solids and/or controlling nucleation processes that form inorganic solids. However, very little is known regarding the structure of these interesting polypeptides and how their structure contributes to functionality. To address this deficiency, we report structural investigations of an artificial protein, p288, that self-assembles and controls the nucleation of simple salts and organic compounds into dendrite-like crystals. Under aqueous conditions at low pH and in the presence of high salt, p288 is conformationally labile and exists primarily as a random coil conformer in equilibrium with other undefined secondary structures, including polyproline type II and beta turn. We note that p288 can fold into either a partial beta strand (at neutral pH) or a predominantly alpha helical (in the presence of TFE) conformation. Solid-state 13C-15N NMR experiments also reveal that p288 in the lyophilized, hydrated state possesses some degree of nonrandom coil structure. These results indicate that p288 is conformationally labile but can undergo conformational transitions to a more stable structure when water solvent loss/displacement occurs and protein concentrations increase. We believe that conformational instability and the ability to adopt different structures as a function of different environmental conditions represent important molecular features that impact p288 supramolecular assembly and crystal nucleation processes.     

Effect of pH on the interaction of baicalein with lysozyme by spectroscopic approaches

The interaction mechanism of baicalein and lysozyme (Lys) has been characterized by fluorescence, synchronous fluorescence, ultraviolet-vis absorbance, and three-dimensional (3D) fluorescence. The structural characteristics of baicalein and Lys were probed, and their binding affinities were determined under different pH conditions (pH 7.4, 4.5, and 2.5). The results showed that the binding abilities of the drug to Lys increased under lower pH conditions (pH 4.5 and 2.5) due to the alterations of the protein secondary and tertiary structures or the structural change of baicalein. The effect of baicalein on the conformation of Lys was analyzed using UV, synchronous fluorescence and three-dimensional (3D) fluorescence under different pH conditions. These results indicate that the binding of baicalein to Lys causes apparent change in the secondary and tertiary structure of Lys. In the presence of Cu(2+), the decrease of the binding constant in buffer solution of pH 2.5 may result from the competition of the metal ion and baicalein binding to Lys. In addition, the presence of Cu(2+) increased the binding constants of baicalein-Lys complex under higher pH conditions (pH 7.4 and 4.5). The possible site of binding of baicalein to Lys has been proposed to explain these observations.     

Glycopeptides related to beta-endorphin adopt helical amphipathic conformations in the presence of lipid bilayers

A series of glycosylated endorphin analogues designed to penetrate the blood-brain barrier (BBB) have been studied by circular dichroism and by 2D-NMR in the presence of water; TFE/water; SDS micelles; and in the presence of both neutral and anionic bicelles. In water, the glycopeptides showed only nascent helix behavior and random coil conformations. Chemical shift indices and nuclear Overhauser effects (NOE) confirmed helices in the presence of membrane mimics. NOE volumes provided distance constraints for molecular dynamics calculations used to provide detailed backbone conformations. In all cases, the glycopeptides were largely helical in the presence of membrane bilayer models (micelles or bicelles). Plasmon waveguide resonance (PWR) studies showed hen egg phosphatidyl choline (PC) bilayers produce amphipathic helices laying parallel to the membrane surface, with dissociation constants (K(D)) in the low nanomolar to micromolar concentration range. Two low-energy states are suggested for the glycosylated endorphin analogues, a flexible aqueous state and a restricted membrane bound state. Strong interactions between the glycopeptide amphipaths and membranes are crucial for penetration of the BBB via an endocytotic mechanism (transcytosis).     

Bilayer in small bicelles revealed by lipid-protein interactions using NMR spectroscopy

Intermolecular nuclear Overhauser effects (NOEs) between the integral outer membrane protein OmpX from Escherichia coli and small bicelles of dihexanoyl phosphatidylcholine (DHPC) and dimyristoyl phosphatidylcholine (DMPC) give insights into protein-lipid interactions. Intermolecular NOEs between hydrophobic tails of lipid and protein in the bicelles cover the surface area of OmpX forming a continuous cylindric jacket of approximately 2.7 nm in height. These NOEs originate only from DMPC molecules, and no NOEs from DHPC are observed. Further, these NOEs are mainly from methylene groups of the hydrophobic tails of DMPC, and only a handful of NOEs arise from methyl groups of the hydrophobic tails. The observed contacts indicate that the hydrophobic tails of DMPC are oriented parallel to the surface of OmpX and thus DMPC molecules form a bilayer in the vicinity of the protein. Thus, a bilayer exists in the small bicelles not only in the absence of but also in the presence of a membrane protein. In addition, the number of NOEs between the polar head groups of lipid molecules and protein is increased in the bicelles compared with those in micelles. This observation may be due to the closely packed head groups of the bilayer. Moreover, irregularity of hydrophobic interactions in the middle of the bilayer environment was observed. This observation together with the interactions between polar head groups and proteins gives a possible rationale for structural and functional differences of membrane proteins solubilized in micelles and in bilayer systems and hints at structural differences between protein-free and protein-loaded bilayers.     

Molecular dynamics simulations of the helical antimicrobial peptide ovispirin-1 in a zwitterionic dodecylphosphocholine micelle: insights into host-cell toxicity

We have carried out a 40-ns all-atom molecular dynamics simulation of the helical antimicrobial peptide ovispirin-1 (OVIS) in a zwitterionic diphosphocholine (DPC) micelle. The DPC micelle serves as an economical and effective model for a cellular membrane owing to the presence of a choline headgroup, which resembles those of membrane phospholipids. OVIS, which was initially placed along a micelle diameter, diffuses out to the water-DPC interface, and the simulation stabilizes to an interface-bound steady state in 40 ns. The helical content of the peptide marginally increases in the process. The final conformation, orientation, and the structure of OVIS are in excellent agreement with the experimentally observed properties of the peptide in the presence of lipid bilayers composed of 75% zwitterionic lipids. The amphipathic peptide binds to the micelle with its hydrophobic face buried in the micellar core and the polar side chains protruding into the aqueous phase. There is overwhelming evidence that points to the significant and indispensable participation of hydrophobic residues in binding to the zwitterionic interface. The simulation starts with a conformation that is unbiased toward the final experimentally known binding state of the peptide. The ability of the model to reproduce experimental binding states despite this starting conformation is encouraging.     

Structure determination of a membrane protein with two trans-membrane helices in aligned phospholipid bicelles by solid-state NMR spectroscopy

The structure of the membrane protein MerFt was determined in magnetically aligned phospholipid bicelles by solid-state NMR spectroscopy. With two trans-membrane helices and a 10-residue inter-helical loop, this truncated construct of the mercury transport membrane protein MerF has sufficient structural complexity to demonstrate the feasibility of determining the structures of polytopic membrane proteins in their native phospholipid bilayer environment under physiological conditions. PISEMA, SAMMY, and other double-resonance experiments were applied to uniformly and selectively (15)N-labeled samples to resolve and assign the backbone amide resonances and to measure the associated (15)N chemical shift and (1)H-(15)N heteronuclear dipolar coupling frequencies as orientation constraints for structure calculations. (1)H/(13)C/(15)N triple-resonance experiments were applied to selectively (13)C'- and (15)N-labeled samples to complete the resonance assignments, especially for residues in the nonhelical regions of the protein. A single resonance is observed for each labeled site in one- and two-dimensional spectra. Therefore, each residue has a unique conformation, and all protein molecules in the sample have the same three-dimensional structure and are oriented identically in planar phospholipid bilayers. Combined with the absence of significant intensity near the isotropic resonance frequency, this demonstrates that the entire protein, including the loop and terminal regions, has a well-defined, stable structure in phospholipid bilayers.     

Unprecedented observation of days-long remnant orientation of phospholipid bicelles: a small-angle X-ray scattering and theoretical study

Nanometric bilayer-based self-assembled micelles commonly named as bicelles, formed with a mixture of long and short chains phosphatidylcholine lipids (PC), are known to orient spontaneously in a magnetic field. This field-induced orientational order strongly depends on the molecular structure of the phospholipids. Using small-angle X-ray scattering (SAXS), we performed detailed structural studies of bicelles and investigated the orientation/relaxation kinetics in three different systems: saturated-chain lipid bicelles made of DMPC (dimyristoyl PC)/DCPC (1,2-dicaproyl PC) with and without the added paramagnetic lanthanide ions Eu(3+), as well as bicelles of TBBPC (1-tetradecanoyl-2-(4-(4-biphenyl)butanoyl)-sn-glycero-3-PC)/DCPC. The structural study confirmed the previous NMR studies, which showed that DMPC bicelles orient with the membrane normal perpendicular (defined here as "nematic" orientation) to the magnetic field, whereas they orient parallel (defined here as "smectic" orientation) to the magnetic field in the presence of Eu(3+). The TBBPC bicelles also show smectic orientation. Surprisingly, the orientational order induced in the magnetic field remains even after the magnetic field is removed, which allowed us to investigate the orientation and relaxation kinetics of different bicelle structures. We demonstrate that this kinetics is very different for all three types of bicelles at the same lipid concentration; DMPC bicelles (~40 nm diameter) with and without Eu(3+) orient faster than TBBPC bicelles (~80 nm diameter). However, for the relaxation, DMPC bicelles (nematic) lose their macroscopic orientation only after one hour, whereas both DMPC bicelles with Eu(3+) and TBBPC bicelles (smectic) remarkably stay oriented for up to several days! These results indicate that the orientation mechanism of these nanometric disks in the magnetic field is governed by their size, with smaller bicelles orienting faster than the larger bicelles. Their relaxation mechanism outside the magnetic field, however, is governed by the degree of ordering. Indeed, the angular distribution of oriented bicelles is much narrower for the bicelles with smectic orientation, and, consequently, they keep aligned for much longer time (days) than those with nematic ordering (hours) outside the magnetic field. The understanding of the orientation/relaxation kinetics, as well as the morphologies of these "molecular goniometers" at molecular and supramolecular levels, allows controlling such an unprecedented long-range and long-lived smectic ordering of nanodisks and opens a wide field of applications for structural biology or material sciences.     

Electron paramagnetic resonance studies of magnetically aligned phospholipid bilayers utilizing a phospholipid spin label

X-band electron paramagnetic resonance (EPR) spectroscopy was used to study the structural and dynamic properties of magnetically aligned phospholipid bilayers utilizing a variety of phosphocholine spin labels (PCSL) as a function oftemperature. 1-Palmitoyl-2-[n-(4,4-dimethyloxazolidine-N-oxyl)stearoyl]-sn-glycero-3-phosphocholine (n-PCSL) in which a nitroxide group was attached to the different acyl chain positions of the phospholipid (n = 5, 7, 12, and 14) were used as an EPR spin probe to investigate magnetically aligned phospholipid bilayers from the plateau (near to the headgroup) region to the end of the acyl chain (center of the bilayers). The addition of certain types of paramagnetic lanthanide ions changes the overall magnetic susceptibility anisotropy tensor of the bicelles, such that the bicelles flip with their bilayer normal either parallel or perpendicular to the magnetic field. The present study reveals for the first time that, in the case of the n-PCSL, the bilayer normal is aligned parallel and perpendicular to the magnetic field in the presence of lanthanide ions having positive delta(chi) (e.g., Tm3+) and negative delta(chi) (e.g., Dy3+), respectively. The magnetic alignment of the bilayers and the corresponding segmental molecular order parameter, S(mol), were investigated as a function of the temperature. The S(mol) values decrease in the following order, 5-PCSL > 7-PCSL > 12-PCSL > 14-PCSL, for the magnetically aligned phospholipid bilayers. Also, the variable temperature study indicates that, by increasing the temperature, the order parameters S(mol) decreased for all the n-PCSLs. The results indicate that magnetically aligned phospholipid bilayers represent an excellent model membrane system for X-band EPR studies.     

A model of interdomain mobility in a multidomain protein

Domain mobility plays an essential role in the biological function of multidomain systems. The characteristic times of domain motions fall into the interval from nano- to milliseconds, amenable to NMR studies. Proper analysis of NMR relaxation data for these systems in solution has to account for interdomain motions, in addition to the overall tumbling and local intradomain dynamics. Here we propose a model of interdomain mobility in a multidomain protein, which considers domain reorientations as exchange/interconversion between two distinct conformational states of the molecule, combined with fully anisotropic overall tumbling. Analysis of 15N-relaxation data for Lys48-linked diubiquitin at pH 4.5 and 6.8 showed that this model adequately fits the experimental data and allows characterization of both structural and motional properties of diubiquitin, thus providing information about the relative orientation of ubiquitin domains in both interconverting states. The analysis revealed that the two domains reorient on a time scale of 9-30 ns, with the amplitudes sufficient for allowing a protein ligand access to the binding sites sequestered at the interface in the closed conformation. The analysis of a possible mechanism controlling the equilibrium between the interconverting states in diubiquitin points toward protonation of His68, which results in three different charged states of the molecule, with zero, +e, and +2e net charge. Only two of the three states are noticeably populated at pH 4.5 or 6.8, which assures applicability of the two-state model to diubiquitin at these conditions. We also compare our model with the "extended model-free" approach and discuss possible future developments of the model.     

Vesicles from docosahexaenoic acid

In dilute aqueous solution and at room temperature, cis-4,7,10,13,16,19-docosahexaenoic acid (DHA) self-assembles into vesicles (self-closed bilayers), if the molar ratio of the neutral form of DHA to anionic DHA is kept between 1:1 and 1:3 (corresponding to a bulk pH between 8.5 and 9.2 for a system with 10 mM DHA). By using polycarbonate membrane extrusion, stable unilamellar DHA vesicles with an average diameter of 80 nm can be prepared at pH 8.8. Cryo-transmission electron microscopy indicates that the width of the DHA bilayers in the vesicles is clearly below twice the length of an extended DHA molecule, indicating a high conformational flexibility of DHA within the vesicle bilayer. These DHA bilayers have a similar thickness like bilayers of vesicles prepared at pH 8.5 from oleic acid (cis-9-octadecenoic acid). Using calcein as fluorescent reference compound, it is shown that water-soluble molecules can be encapsulated inside DHA vesicles which may make them interesting for medical or food applications.     

Probing the conformational features of a phage display polypeptide sequence directed against single-walled carbon nanohorn surfaces

Single-walled carbon nanohorns (SWNHs) are interesting carbon nanostructures that have applications to science and technology. Using M13 phage display technology, polypeptides directed again SWNHs surfaces have been created for a number of nanotechnology and pharmaceutical purposes, yet the molecular mechanism of polypeptide sequence interaction and binding to SWNHs surfaces is not known. Recently, we identified a linear 12-AA M13 phage pIII sequence, NH-12-5-2 (DYFSSPYYEQLF), that binds with high affinity to SWNHs surfaces. To probe the structure of this pIII tail polypeptide further, we investigated the conformation of a model peptide representing the 12 AA NH-12-5-2 sequence. At neutral pH, the NH-12-5-2 model polypeptide is conformationally labile and exhibits two-state conformational exchange involving the D1-S5 N-terminal segment. Simultaneous with this conformational exchange process is the observation that the P6 residue exhibits imido ring conformational variation. In the presence of the structure-stabilizing solvent, TFE, or at pH 2.5, both the exchange process and Pro ring motion phenomena disappear, indicating that the structure of this peptide sequence can be stabilized by extrinsic factors. Interestingly, we observe NMR parameters (ROEs, (3)J coupling constants) for NH-12-5-2 in 90% v/v TFE that are consistent with the presence of a partial helical structure, similar to what was observed at low pH in our earlier CD experiments. We conclude that the NH-12-5-2 model polypeptide sequence possesses an inherent conformational instability that involves the D1-S5 sequence segment and the P6 residue but that this instability can be offset by extrinsic factors (e.g., charge neutralization, imido ring interconversion, and hydrophobic-hydrophobic interactions). These nonbonding interactions may play a role in the recognition and binding of this phage sequence region to SWNHs surfaces.     

Structure of membrane-bound amphidinol 3 in isotropic small bicelles

Amphidinol 3 (AM3) exhibits a potent membrane permeabilizing activity by forming pores in biological membranes. We examined the conformation and location of AM3 using isotropic bicelles, a more natural membrane model than micelles. The results show that AM3 takes turn structures at the two tetrahydropyran rings. Most of the hydrophilic region of the molecule is predominantly present in the surface, while the hydrophobic polyolefin penetrates in the bicelle interior.     

α‐Aminoxy Oligopeptides: Synthesis,Secondary Structure,and Cytotoxicity of a New Class of Anticancer Foldamers

α‐Aminoxy peptides are peptidomimetic foldamers with high proteolytic and conformational stability. To gain an improved synthetic access to α‐aminoxy oligopeptides we used a straightforward combination of solution‐ and solid‐phase‐supported methods and obtained oligomers that showed a remarkable anticancer activity against a panel of cancer cell lines. We solved the first X‐ray crystal structure of an α‐aminoxy peptide with multiple turns around the helical axis. The crystal structure revealed a right‐handed 2₈‐helical conformation with precisely two residues per turn and a helical pitch of 5.8 Å. By 2D ROESY experiments, molecular dynamics simulations, and CD spectroscopy we were able to identify the 2₈‐helix as the predominant conformation in organic solvents. In aqueous solution, the α‐aminoxy peptides exist in the 2₈‐helical conformation at acidic pH, but exhibit remarkable changes in the secondary structure with increasing pH. The most cytotoxic α‐aminoxy peptides have an increased propensity to take up a 2₈‐helical conformation in the presence of a model membrane. This indicates a correlation between the 2₈‐helical conformation and the membranolytic activity observed in mode of action studies, thereby providing novel insights in the folding properties and the biological activity of α‐aminoxy peptides.     

Investigation of folding in protamine by FTIR

The secondary structure of purified protamine, a non-specific DNA binding protein, was studied in solution at pH 4, 7 and 8 by FTIR. This permitted analysis of the folded form of the protein (acidic pH) as well as the folded conformers (neutral and basic pH). Hg(2+) was utilized to probe the accessibility of the free thiol groups (cysteine residues). The SH groups form when disulfides, which play the major role in stabilizing the conformation of this protein, are broken. It was possible to observe different conformational states in protamine as a function of pH and the presence of Hg(2+) via spectral changes primarily in the amide region. The results lead to the conclusion that protamine is not completely folded under conditions similar to those found in vivo (37 degrees , neutral pH, phosphate buffer and high protein concentration).     

Ultrafast solvation dynamics of human serum albumin: correlations with conformational transitions and site-selected recognition

Human serum albumin, the most abundant protein found in blood plasma, transports a great variety of ligands in the circulatory system and undergoes reversible conformational transitions over a wide range of pH values. We report here our systematic studies of solvation dynamics and local rigidity in these conformations using a single intrinsic tryptophan (W214) residue as a local molecular probe. With femtosecond resolution, we observed a robust bimodal distribution of time scales for all conformational isomers. The initial solvation occurs in several picoseconds, representing the local librational/rotational motions, followed by the dynamics, in the tens to hundreds of picoseconds, which result from the more bonded water in the tryptophan crevice. Under the physiological condition of neutral pH, we measured approximately 100 ps for the decay of the solvation correlation function and observed a large wobbling motion at the binding site that is deeply buried in a crevice, revealing the softness of the binding pocket and the large plasticity of the native structure. At acidic pH, the albumin molecule transforms to an extended conformation with a large charge distribution at the surface, and a similar temporal behavior was observed. However, at the basic pH, the protein opens the crevice and tightens its globular structure, and we observed significantly faster dynamics, 25-45 ps. These changes in the solvation dynamics are correlated with the conformational transitions and related to their structural integrity.     

Multiple protonation equilibria in electrostatics of protein-protein binding

All proteins contain groups capable of exchanging protons with their environment. We present here an approach, based on a rigorous thermodynamic cycle and the partition functions for energy levels characterizing protonation states of the associating proteins and their complex, to compute the electrostatic pH-dependent contribution to the free energy of protein-protein binding. The computed electrostatic binding free energies include the pH of the solution as the variable of state, mutual "polarization" of associating proteins reflected as changes in the distribution of their protonation states upon binding and fluctuations between available protonation states. The only fixed property of both proteins is the conformation; the structure of the monomers is kept in the same conformation as they have in the complex structure. As a reference, we use the electrostatic binding free energies obtained from the traditional Poisson-Boltzmann model, computed for a single macromolecular conformation fixed in a given protonation state, appropriate for given solution conditions. The new approach was tested for 12 protein-protein complexes. It is shown that explicit inclusion of protonation degrees of freedom might lead to a substantially different estimation of the electrostatic contribution to the binding free energy than that based on the traditional Poisson-Boltzmann model. This has important implications for the balancing of different contributions to the energetics of protein-protein binding and other related problems, for example, the choice of protein models for Brownian dynamics simulations of their association. Our procedure can be generalized to include conformational degrees of freedom by combining it with molecular dynamics simulations at constant pH. Unfortunately, in practice, a prohibitive factor is an enormous requirement for computer time and power. However, there may be some hope for solving this problem by combining existing constant pH molecular dynamics algorithms with so-called accelerated molecular dynamics algorithms.