Temperature Replica Exchange Molecular Dynamics Research Articles

Conformational Sampling of Peptides in the Presence of Protein Crowders from AA/CG-Multiscale Simulations

Macromolecular crowding is recognized as an important factor influencing folding and conformational dynamics of proteins and nucleic acids. Previous views of crowding have focused on the mostly entropic volume exclusion effect of crowding, but recent studies are indicating the importance of enthalpic effects, in particular, changes in electrostatic interactions due to crowding. Here, temperature replica exchange molecular dynamics simulations of trp-cage and melittin in the presence of explicit protein crowders are presented to further examine the effect of protein crowders on peptide dynamics. The simulations involve a three-component multiscale modeling scheme where the peptides are represented at an atomistic level, the crowder proteins at a coarse-grained level, and the surrounding aqueous solvent as implicit solvent. This scheme optimally balances a physically realistic description for the peptide with computational efficiency. The multiscale simulations were compared with simulations of the same peptides in different dielectric environments with dielectric constants ranging from 5 to 80. It is found that the sampling in the presence of the crowders resembles sampling with reduced dielectric constants between 10 and 40. Furthermore, diverse conformational ensembles are generated in the presence of crowders including partially unfolded states for trp-cage. These findings emphasize the importance of enthalpic interactions over volume exclusion effects in describing the effects of cellular crowding.

Why the OPLS-AA Force Field Cannot Produce the β-Hairpin Structure of H1 Peptide in Solution When Comparing with the GROMOS 43A1 Force Field?

The optimal combination of force field and water model is an essential problem that is able to increase molecular dynamics simulation quality for different types of proteins and peptides. In this work, an attempt has been made to explore the problem by studying H1 peptide using four different models based on different force fields, water models and electrostatic schemes. The driving force for H1 peptide conformation transition and the reason why the OPLS-AA force field cannot produce the β-hairpin structure of H1 peptide in solution while the GROMOS 43A1 force field can do were investigated by temperature replica exchange molecular dynamics simulation (T-REMD). The simulation using the GROMOS 43A1 force field preferred to adopt a β-hairpin structure, which was in good agreement with the several other simulations and the experimental evidences. However, the simulation using the OPLS-AA force field has a significant difference from the simulations with the GROMOS 43A1 force field simulation. The results show that the driving force in H1 peptide conformation transition is solvent exposure of its hydrophobic residues. However, the subtle balances between residue-residue interactions and residue-solvent interaction are disrupted by using the OPLS-AA force field, which induced the reduction in the number of residue-residue contact. Similar solvent exposure of the hydrophobic residues is observed for all the conformations sampled using the OPLS-AA force field. For H1 peptide which exhibits large solvent exposure of the hydrophobic residues, the GROMOS 43A1 force field with the SPC water model can provide more accurate results.

Effects of Different Force Fields and Temperatures on the Structural Character of Abeta (12–28) Peptide in Aqueous Solution

The aim of this work is to investigate the effects of different force fields and temperatures on the structural character of Aβ (12–28) peptide in aqueous solution. Moreover, the structural character of Aβ (12–28) peptide is compared with other amyloid peptides (such as H1 and α-syn12 peptide). The two independent temperature replica exchange molecular dynamics (T-REMD) simulations were completed by using two different models (OPLS-AA/TIP4P and GROMOS 43A1/SPC). We compared the models by analyzing the distributions of backbone dihedral angles, the secondary structure propensity, the free energy surface and the formation of β-hairpin. The results show that the mostly populated conformation state is random coil for both models. The population of β-hairpin is below 8 percent for both models. However, the peptide modeled by GROMOS 43A1 form β-hairpin with turn located at residues F19-E22, while the peptide modeled by OPLS-AA form β-hairpin with turn located at residues L17-F20.

Structural and thermodynamics characters of isolated α-syn12 peptide: long-time temperature replica-exchange molecular dynamics in aqueous solution

The structural and thermodynamics characters of α-syn12 (residues 1-12 of the human α-synuclein protein) peptide in aqueous solution were investigated through temperature replica-exchange molecular dynamics (T-REMD) simulations with the GROMOS 43A1 force field. The two independent T-REMD simulations were completed starting from an initial conformational α-helix and an irregular structure, respectively. Each replica was run for 300 ns. The structural and thermodynamics characters were studied based on parameters such as distributions of backbone dihedral angles, free energy surface, stability of folded β-hairpin structure, and favorite conformations. The results showed that the isolated α-syn12 peptide in water adopted four different conformational states: the first state was a β-hairpin ensemble with Turn(9-6) and four hydrogen bonds, the second state was a β-hairpin ensemble with two turns (Turn(9-6) and Turn(5-2)) and three hydrogen bonds, the third state was a disordered structure with both Turn(8-5) and Turn(5-2), and the last state was a π-helix ensemble. Meanwhile, we studied the free energy change of α-syn12 peptide from the unfolded state to the β-hairpin state, which was in good agreement with the experiments and molecular dynamics simulations for some other peptides. We also analyzed the driving force of the peptide transition. The results indicated that the driving forces were high solvent exposure of hydrophobic Leu8 and hydrophobic residues in secondary structure. To our knowledge, this was the first report to study the isolated α-syn12 peptide in water by T-REMD.

Effects of pH and Temperature on the Structural and Thermodynamic Character of a-syn12 Peptide in Aqueous Solution

The structural and thermodynamic characters of α-syn12 peptide in aqueous solution at different pH and temperatures have been investigated through temperature replica exchange molecular dynamics (T-REMD) simulations with GROMOS 43A1 force field. The two independent T-REMD simulations were completed at pH = 7.0 and 10.0, respectively. Each replica was run for 300 ns. The structural and thermodynamic characters of α-syn12 peptide were studied based on the distributions of backbone dihedral angles, the free energy surface, and the stability of different type structure and the favorite conformations of the peptide. The results showed that the simulation at pH = 10.0 produced more sampling in α region than the simulation at pH = 7.0. The temperature changes from 283 K to 308 K result in negligible effects on the distributions of backbone dihedral angle. The β hairpin conformation with Turn9-6 and four hydrogen bonds (HB4-11, HB6-9, HB9-6 and HB11-4) is the lowest free energy state in the simulation at pH = 7.0. However, for the simulation at pH = 10.0, the lowest free energy state corresponds to a structure with Turn9-6 and two hydrogen bonds (HB6-10 and HB10-6) induced by an overly strong residue-residue interaction effect between lysine residues. For the simulation at pH = 7.0, the free energy change of the α-syn12 peptide from the unfolded state to the β hairpin state was in good agreement with the experiments and molecular dynamics simulation results for the other β-peptides, the β hairpin state of the α-syn12 peptide included the conformations that not only the Turn9-6 is formed, but also the terminus are closed together in space. However, the subtle balances between lysine-lysine interactions and lysine-solvent interaction are disrupted in the simulation at pH = 10.0, which induced the assembly of lysine residues, the β hairpin conformation is destabilized by the deprotonation of the Lys side chain. This study can help us to understand the conformation changes and the thermodynamic character of α-syn12 peptide at atomic level induced by changing pH and temperature, which is propitious to reveal the nosogenesis of Parkinson disease. In our knowledge, this is the first report to study the influence of pH and temperature on isolated α-syn12 peptide in water by T-REMD.

A classical molecular dynamics investigation of the free energy and structure of short polyproline conformers

Folded polyproline peptides can exist as either left-(PPII) or right-handed (PPI) helices, depending on their environment. In this work, we have characterized the conformations and the free energy landscapes of Ace-(Pro)(n)-Nme, n=2,3, ... ,9, and 13 peptides both in vacuo and in an implicit solvent environment. In order to enhance the sampling provided by regular molecular dynamics simulations, we have used the recently developed adaptively biased molecular dynamics method--which provides an accurate description of the free energy landscapes in terms of a set of relevant collective variables--combined with Hamiltonian and temperature replica exchange molecular dynamics methods. The collective variables, which are chosen so as to reflect the stable structures and the "slow modes" of the polyproline system, were based primarily on properties of length and of the cis/trans isomerization associated with the prolyl bonds. Results indicate that the space of peptide structures is characterized not just by pure PPII and PPI structures, but rather by a broad distribution of stable minima with similar free energies. These results are in agreement with recent experimental work. In addition, we have used steered molecular dynamics methods in order to quantitatively estimate the free energy difference of PPI and PPII for peptides of the length n=2, ... ,5 in vacuo and implicit water and qualitatively investigate transition pathways and mechanisms for the PPII to PPI transitions. A zipper-like mechanism, starting from either the center of the peptide or the amidated end, appear to be the most likely mechanisms for the PPII→PPI transition for the longer peptides.

Model Amyloid Peptide B18 Monomer and Dimer Studied by Replica Exchange Molecular Dynamics Simulations

Peptide misfolding and aggregation are the early steps during the formation of amyloid fibrils. Understanding these processes in detail is crucial for the development of therapeutic strategies against amyloid diseases. Here I present temperature replica exchange molecular dynamics (TREMD) simulations of the model amyloid peptide B18 in the mono- and dimeric states in explicit aqueous solution. Both the monomer and the dimer involve β-sheets consisting of different residues in different registers with comparable statistical weight. The dimer forms intra- as well as intermolecular β-sheets. The average β-sheet content is in agreement with previous estimates from circular dichroism (CD) spectra for monomers and is lower for dimers. The tendency of B18 to form β-sheets likely contributes to its fibrillogenic property. For both the monomer and the dimer, individual peptides form U-shaped or other partially collapsed conformations. Combined with data from electron microscopy, this suggests that for higher aggregates during fibrillization B18 undergoes a transition from U-shaped to outstretched conformations. The tendency of B18 to form U-shaped conformations, intramolecular β-sheets, and intermolecular β-sheets with different register will contribute to the lag phase for fibril formation.

Effect of the Disulfide Bond on the Monomeric Structure of Human Amylin Studied by Combined Hamiltonian and Temperature Replica Exchange Molecular Dynamics Simulations

The human Islet amyloid polypeptide (hIAPP or amylin) is a 37-residue peptide hormone that is normally cosecreted with insulin by the pancreatic beta-cells. In patients with type 2 diabetes, hIAPP deposits as amyloid fibrils in the extracellular spaces of the pancreatic islets. Recent experimental studies show that the intramolecular disulfide bond between Cys2 and Cys7 plays a central role in the process of fibril formation. However, the effect of the disulfide bond on the intrinsic structural properties of monomeric hIAPP is yet to be determined. In this study, we characterize the atomic structure and the thermodynamics of full-length hIAPP in the presence and absence of a disulfide bond using extensive combined Hamiltonian and temperature replica exchange molecular dynamics simulations (HT-REMD) with a coarse grained protein force field. Our simulations show that HT-REMD is more efficient in sampling than temperature REMD. On the basis of a total simulation time of 28 mus, we find that, although native hIAPP (in the presence of a disulfide bond) essentially adopts a disordered conformation in solution, consistent with the signal measured by ultraviolet-circular dichroism (UV-CD) spectroscopy, it also transiently samples alpha-helical structure for residues 5-16. In comparison with the N-terminal region, the C-terminal region is highly disordered and populates a much lesser content of isolated beta-strand conformation for residues 22-26 and 30-35. Moreover, the absence of the disulfide bond greatly decreases the extent of helix formed throughout residues 5-9 in favor of random coil and beta-sheet structure. Implications of the stabilization of N-terminal helical structure by disulfide bond on the initialization of hIAPP amyloid formation are discussed.

Spontaneous formation of polyglutamine nanotubes with molecular dynamics simulations

Expansion of polyglutamine (polyQ) beyond the pathogenic threshold (35-40 Gln) is associated with several neurodegenerative diseases including Huntington's disease, several forms of spinocerebellar ataxias and spinobulbar muscular atrophy. To determine the structure of polyglutamine aggregates we perform replica-exchange molecular dynamics simulations coupled with the optimized potential for effective peptide forcefield. Using a range of temperatures from 250 to 700 K, we study the aggregation kinetics of the polyglutamine monomer and dimer with chain lengths from 30 to 50 residues. All monomers show a similar structural change at the same temperature from alpha-helical structure to random coil, without indication of any significant beta-strand. For dimers, by contrast, starting from random structures, we observe spontaneous formation of antiparallel beta-sheets and triangular and circular beta-helical structures for polyglutamine with 40 residues in a 400 ns 50 temperature replica-exchange molecular dynamics simulation (total integrated time 20 micros). This approximately 32 A diameter structure reorganizes further into a tight antiparallel double-stranded approximately 22 A nanotube with 22 residues per turn close to Perutz' model for amyloid fibers as water-filled nanotubes. This diversity of structures suggests the existence of polymorphism for polyglutamine with possibly different pathways leading to the formation of toxic oligomers and to fibrils.

Replica exchange simulation method using temperature and solvent viscosity

We propose an efficient and simple method for fast conformational sampling by introducing the solvent viscosity as a parameter to the conventional temperature replica exchange molecular dynamics (T-REMD) simulation method. The method, named V-REMD (V stands for viscosity), uses both low solvent viscosity and high temperature to enhance sampling for each replica; therefore it requires fewer replicas than the T-REMD method. To reduce the solvent viscosity by a factor of lambda in a molecular dynamics simulation, one can simply reduce the mass of solvent molecules by a factor of lambda(2). This makes the method as simple as the conventional method. Moreover, thermodynamic and conformational properties of structures in replicas are still useful as long as one has sufficiently sampled the Boltzmann ensemble. The advantage of the present method has been demonstrated with the simulations of the trialanine, deca-alanine, and a 16-residue beta-hairpin peptides. It shows that the method could reduce the number of replicas by a factor of 1.5 to 2 as compared with the T-REMD method.

A Comparative Study of Two Different Force Fields on Structural and Thermodynamics Character of H1 Peptide via Molecular Dynamics Simulations

The dynamics and thermodynamics character of H1 peptide in aqueous solution has been investigated through temperature replica exchange molecular dynamics (T-REMD) simulations using two different force fields (OPLS-AA and GROMOS 43A1). The two independent T-REMD simulations were completed starting from initial conformations a-helix and β-sheet, respectively. Each replica was run for 300 ns. The performance of each force field was assessed from the parameters such as the distributions of backbone dihedral angles, the number of native hydrogen bond, root mean square deviations (RMSD) of Ca atoms and all heavy atoms, formation of β-turn, the stability of folded β-hairpin structure and the favorite conformations of different force fields. The simulation using GROMOS 43A1 force field starting from a-helix structure sampled the conformation cluster which Ca RMSD was 0.05 nm from β-sheet structure and the cluster contains 39% of all conformations. The simulation using OPLS-AA force field produced more sampling in PII region than in GROMOS 43A1 force field. The both force field simulations produced some sampling in the a region, but the probabilities of the conformations including any helical content were only 1–2%. Under the both force fields, the β-turn structures exhibited higher stability than a-helix structures and the folded β-hairpin structures. In the GROMOS 43A1 force field, the free energy change from the unfolded state to the hairpin state was in good agreement with the results of several experiments about some β-peptides (not the H1 peptide) and the other molecular dynamics simulations of H1 peptide. However, the folded β-hairpin structure was more destabilized in the OPLS-AA force field than in the GROMOS 43A1 force field and experiments.

Reordering Hydrogen Bonds Using Hamiltonian Replica Exchange Enhances Sampling of Conformational Changes in Biomolecular Systems

Hydrogen bonds play an important role in stabilizing (meta-)stable states in protein folding. Hence, they can potentially be used as a way to bias these states in molecular simulation methods. Previously, Wolf et al. showed that applying repulsive and attractive hydrogen bond biasing potentials in an alternating way significantly accelerates the folding process (Wolf, M. G.; de Leeuw, S. W. Biophys. J. 2008, 94, 3742). As the biasing potentials are only active during a fixed time interval, this alternating scheme does not represent a thermodynamic equilibrium. In this work, we present a Hamiltonian replica exchange molecular dynamics (REMD) scheme that aims to shuffle and reorder hydrogen bonds in the protein backbone. We therefore apply adapted hydrogen bond potentials in a Hamiltonian REMD scheme, which we call hydrogen bond switching (HS). To compare the performance of the HS to a standard REMD method, we performed HS and temperature REMD simulations of a beta-heptapeptide in methanol. Both methods sample the conformational space to a similar extent. As the HS simulation required only five replicas, while the REMD simulation required 20 replicas, the HS method is significantly more efficient. We tested the HS method also on a larger system, 16-residue polyalanine in water. Both of the simulations starting from a completely unfolded and a folded conformation resulted in an ensemble with, apart from the starting structure, similar conformational minima. We can conclude that the HS method provides an efficient way to sample the conformational space of a protein, without requiring knowledge of the folded states beforehand. In addition, these simulations revealed that convergence was hampered by replicas having a preference for specific biasing potentials. As this sorting effect is inherent to any Hamiltonian REMD method, finding a solution will result in an additional increase in the efficiency of Hamiltonian REMD methods in general.

Folding of Trp-cage mini protein using temperature and biasing potential replica-exchange molecular dynamics simulations.

The folding process of the 20 residue Trp-cage mini-protein was investigated using standard temperature replica exchange molecular dynamics (T-RexMD) simulation and a biasing potential RexMD (BP-RexMD) method. In contrast to several conventional molecular dynamics simulations, both RexMD methods sampled conformations close to the native structure after 10–20 ns simulation time as the dominant conformational states. In contrast, to T-RexMD involving 16 replicas the BP-RexMD method achieved very similar sampling results with only five replicas. The result indicates that the BP-RexMD method is well suited to study folding processes of proteins at a significantly smaller computational cost, compared to T-RexMD. Both RexMD methods sampled not only similar final states but also agreed on the sampling of intermediate conformations during Trp-cage folding. The analysis of the sampled potential energy contributions indicated that Trp-cage folding is favored by both van der Waals and to a lesser degree electrostatic contributions. Folding does not introduce any significant sterical strain as reflected by similar energy distributions of bonded energy terms (bond length, bond angle and dihedral angle) of folded and unfolded Trp-cage structures.

Reordering Hydrogen Bonds In The Protein Backbone In Hamiltonian Exchange MD Enhances Sampling Of Conformational Changes

Molecular simulation enables detailed insight into the mechanisms underlying protein conformational changes and is complementary to experiments. Studying a protein folding reaction at atomistic resolution with conventional Molecular Dynamics (MD) is unpractical due to the long time scales involved. These long time scales originate from the presence of local free energy minima from which it is not trivial to escape.The replica exchange MD (REMD) method allows for the escape of such local minima by letting multiple replicas diffuse through temperature space while maintaining the canonical distribution at the temperature of interest. Instead of switching temperatures, the replicas can also exchange (part of) their Hamiltonians. A smooth interpolation between the regular Hamiltonian and one that enables swift conformational changes of the protein (e.g. by lowering barriers) enhances sampling of the conformational space.As hydrogen bonds play an important role in conformational changes of proteins, including folding, it seems natural to bias these bonds specifically. We have developed biasing potentials that allow the breaking and formation of bonds between arbitrary hydrogen bond donors and acceptors in the protein backbone. Employing these potentials in a Hamiltonian REMD scheme we aim to reorder hydrogen bonds in the protein backbone, and thus speed up the conformational sampling.For a simple beta-heptapeptide test system, we show that our hydrogen bond switching scheme is four times more efficient in sampling the conformational space of the peptide as conventional temperature REMD, while it also has the advantage of not having to know the stable states in advance.Finally, we discuss the slow convergence for larger systems, which is often observed in REMD or Hamiltonian exchange. This is caused by replicas having a preference for specific biasing potentials.

Molecular dynamics study of chemically engineered green fluorescent protein mutants: Comparison of intramolecular fluorescence resonance energy transfer rate

Because of its unusual spectroscopic properties, green fluorescent protein (GFP) has become a useful tool in molecular genetics, biochemistry and cell biology. Here, we computationally characterize the behavior of two GFP constructs, designed as bioprobes for enzymatic triggering using intramolecular fluorescence resonance energy transfer (FRET). These constructs differ in the location of an intramolecular FRET partner, an attached chemical chromophore (either near an N-terminal or C-terminal site). We apply the temperature replica exchange molecular dynamics method to the two flexible constructs in conjunction with a generalized Born implicit solvent model. The calculated rate of FRET was derived from the interchromophore distance, R, and orientational factor, kappa(2). In agreement with experiment, the construct with the C-terminally attached dye was predicted to have higher energy transfer rate than observed for the N-terminal construct. The molecular basis for this observation is discussed. In addition, we find that the orientational factor, kappa(2), deviates from the commonly assumed value, the implications of which are also considered.

Prediction of Protein Loop Conformations Using the AGBNP Implicit Solvent Model and Torsion Angle Sampling

The OPLS-AA all-atom force field and the Analytical Generalized Born plus Non-Polar (AGBNP) implicit solvent model, in conjunction with torsion angle conformational search protocols based on the Protein Local Optimization Program (PLOP), are shown to be effective in predicting the native conformations of 57 9-residue and 35 13-residue loops of a diverse series of proteins with low sequence identity. The novel nonpolar solvation free energy estimator implemented in AGBNP augmented by correction terms aimed at reducing the occurrence of ion pairing are important to achieve the best prediction accuracy. Extended versions of the previously developed PLOP-based conformational search schemes based on calculations in the crystal environment are reported that are suitable for application to loop homology modeling without the crystal environment. Our results suggest that in general the loop backbone conformation is not strongly influenced by crystal packing. The application of the temperature Replica Exchange Molecular Dynamics (T-REMD) sampling method for a few examples where PLOP sampling is insufficient are also reported. The results reported indicate that the OPLS-AA/AGBNP effective potential is suitable for high-resolution modeling of proteins in the final stages of homology modeling and/or protein crystallographic refinement.

Convergence and sampling efficiency in replica exchange simulations of peptide folding in explicit solvent

Replica exchange methods (REMs) are increasingly used to improve sampling in molecular dynamics (MD) simulations of biomolecular systems. However, despite having been shown to be very effective on model systems, the application of REM in complex systems such as for the simulation of protein and peptide folding in explicit solvent has not been objectively tested in detail. Here we present a comparison of conventional MD and temperature replica exchange MD (T-REMD) simulations of a beta-heptapeptide in explicit solvent. This system has previously been shown to undergo reversible folding on the time scales accessible to MD simulation and thus allows a direct one-to-one comparison of efficiency. The primary properties compared are the free energy of folding and the relative populations of different conformers as a function of temperature. It is found that to achieve a similar degree of precision T-REMD simulations starting from a random set of initial configurations were approximately an order of magnitude more computationally efficient than a single 800 ns conventional MD simulation for this system at the lowest temperature investigated (275 K). However, whereas it was found that T-REMD simulations are more than four times more efficient than multiple independent MD simulations at one temperature (300 K) the actual increase in conformation sampling was only twofold. The overall gain in efficiency using REMD resulted primarily from the ordering of different conformational states over temperature, as opposed to a large increase of conformational sampling. It is also shown that in this system exchanges are accepted primarily based on (random) fluctuations within the solvent and are not strongly correlated with the instantaneous peptide conformation raising questions in regard to the efficiency of T-REMD in larger systems.

Replica exchange molecular dynamics simulations of reversible folding

The replica exchange molecular dynamics (REMD) approach is applied to a 20-residue three-stranded antiparallel β-sheet peptide. At physiologically relevant temperature REMD samples conformational space much more efficiently than constant temperature molecular dynamics (MD) and allows reversible folding (312 folding events during a total simulation time of 32 μs). The energetic and structural properties during the folding process are similar in REMD and conventional MD at the temperature values where there is enough statistics for the latter. The simulation results indicate that the unfolded state contains a significant amount of non-native interactions especially at low temperature. The folding events consist of a gradual replacement of non-native contacts with native ones which is coupled with an almost monotonic decrease of the REMD temperature.