Temperature Replica Exchange Research Articles

Mechanism Underlying Conformational Effects of a Disease-Associated Hydrophobic-to-Hydrophobic Substitution on an Intrinsically Disordered Region

Disease-associated Single Nucleotide Polymorphisms (SNPs) are common in the disordered regions of proteins (21.7 % of SNPs are found in the disordered region). Most mutational studies of IDP's consider loss or gain of a charged residue. In this study, we explore the local and global effect of a charge-neutral mutation between two hydrophobic residues, with known effects on function: the Val66Met SNP in the 100-residue disordered prodomain of Brain Derived Neurotropic Factor (BDNF). Val66Met is the most frequently found SNP in the BDNF disordered domain, and is associated with various neurological and psychiatric disorders such as bipolar disorder and Alzheimer's disease. Previously, NMR studies demonstrated that the prodomain is disordered with different secondary structure preferences for Val and Met at 275K (Anastasia et al 2013). We attempt to elucidate this phenomenon at the microscopic level using large-scale, fully atomistic temperature replica exchange calculations of both the Val and Met forms of the BDNF prodomain. MD simulations indicate high propensity of secondary structure in regions similar to those identified in NMR studies. Interestingly, we observe reversed temperature dependence of the secondary structure around the SNP between Val and Met from 300K to 420K. With increasing temperature, Val66 is less likely to assume helical secondary structure, while Met66 is more likely, which is consistent with previous observations that entropy of the valine side-chain is significantly reduced upon helix formation. This cost likely offsets the entropic gain of nearby water molecules upon helix formation, associated with the hydrophobic effect and common to Val66 and Met66 helices. At room temperature, we also observe an increase in the radius of gyration of the Met66 prodomain relative to the Val66 prodomain, which can be reliably attributed to differential hydrogen bonding preferences of residues near in sequence to the SNP, affecting their likelihood of forming beta-bridges with distant residues. This is consistent with an experimentally observed higher hydrodynamic radius for the Met66 proregion than for Val66 proregion. These results indicate the seemingly subtle substitution may exert its effects by critically adjusting entropic cost of local secondary-structure elements, which, in turn, affects the conformational ensemble via differential long-range beta bridging patterns. Furthermore, although the SNP is neutral, it alters the exposure of charged residues around the SNP, which can potentially affect the binding characteristics of the prodomain to its highly charged receptor, SORCS2.

Fibrillation-prone conformations of the amyloid-β-42 peptide at the gold/water interface

Proteins in the proximity of inorganic surfaces and nanoparticles may undergo profound adjustments that trigger biomedically relevant processes, such as protein fibrillation. The mechanisms that govern protein-surface interactions at the molecular level are still poorly understood. In this work, we investigate the adsorption onto a gold surface, in water, of an amyloid-β (Aβ) peptide, which is the amyloidogenic peptide involved in Alzheimer's disease. The entire adsorption process, from the peptide in bulk water to its conformational relaxation on the surface, is explored by large-scale atomistic molecular dynamics (MD) simulations. We start by providing a description of the conformational ensemble of Aβ in solution by a 22 μs temperature replica exchange MD simulation, which is consistent with previous results. Then, we obtain a statistical description of how the peptide approaches the gold surface by multiple MD simulations, identifying the preferential gold-binding sites and giving a kinetic picture of the association process. Finally, relaxation of the Aβ conformations at the gold/water interface is performed by a 19 μs Hamiltonian-temperature replica exchange MD simulation. We find that the conformational ensemble of Aβ is strongly perturbed by the presence of the surface. In particular, at the gold/water interface the population of the conformers akin to amyloid fibrils is significantly enriched, suggesting that this extended contact geometry may promote fibrillation.

Sampling conformational space of intrinsically disordered proteins in explicit solvent: Comparison between well-tempered ensemble approach and solute tempering method

Intrinsically disordered proteins (IDPs) are a class of proteins that expected to be largely unstructured under physiological conditions. Due to their heterogeneous nature, experimental characterization of IDP is challenging. Temperature replica exchange molecular dynamics (T-REMD) is a widely used enhanced sampling method to probe structural characteristics of these proteins. However, its application has been hindered due to its tremendous computational cost, especially when simulating large systems in explicit solvent. Two methods, parallel tempering well-tempered ensemble (PT-WTE) and replica exchange with solute tempering (REST), have been proposed to alleviate the computational expense of T-REMD. In this work, we select three different IDP systems to compare the sampling characteristics and efficiencies of the two methods Both the two methods could efficiently sample the conformational space of IDP and yield highly consistent results for all the three IDPs. The efficiencies of the two methods: are compatible, with about 5–6 times better than the plain T-REMD. Besides, the advantages and disadvantages of each method are also discussed. Specially, the PT-WTE method could provide temperature dependent data of the system which could not be achieved by REST, while the REST method could readily be used to a part of the system, which is quite efficient to simulate some biological processes.

Comparing generalized ensemble methods for sampling of systems with many degrees of freedom.

We compare two standard replica exchange methods using temperature and dielectric constant as the scaling variables for independent replicas against two new corresponding enhanced sampling methods based on non-equilibrium statistical cooling (temperature) or descreening (dielectric). We test the four methods on a rough 1D potential as well as for alanine dipeptide in water, for which their relatively small phase space allows for the ability to define quantitative convergence metrics. We show that both dielectric methods are inferior to the temperature enhanced sampling methods, and in turn show that temperature cool walking (TCW) systematically outperforms the standard temperature replica exchange (TREx) method. We extend our comparisons of the TCW and TREx methods to the 5 residue met-enkephalin peptide, in which we evaluate the Kullback-Leibler divergence metric to show that the rate of convergence between two independent trajectories is faster for TCW compared to TREx. Finally we apply the temperature methods to the 42 residue amyloid-β peptide in which we find non-negligible differences in the disordered ensemble using TCW compared to the standard TREx. All four methods have been made available as software through the OpenMM Omnia software consortium (http://www.omnia.md/).

Computer Folding of RNA Tetraloops: Identification of Key Force Field Deficiencies.

The computer-aided folding of biomolecules, particularly RNAs, is one of the most difficult challenges in computational structural biology. RNA tetraloops are fundamental RNA motifs playing key roles in RNA folding and RNA-RNA and RNA-protein interactions. Although state-of-the-art Molecular Dynamics (MD) force fields correctly describe the native state of these tetraloops as a stable free-energy basin on the microsecond time scale, enhanced sampling techniques reveal that the native state is not the global free energy minimum, suggesting yet unidentified significant imbalances in the force fields. Here, we tested our ability to fold the RNA tetraloops in various force fields and simulation settings. We employed three different enhanced sampling techniques, namely, temperature replica exchange MD (T-REMD), replica exchange with solute tempering (REST2), and well-tempered metadynamics (WT-MetaD). We aimed to separate problems caused by limited sampling from those due to force-field inaccuracies. We found that none of the contemporary force fields is able to correctly describe folding of the 5'-GAGA-3' tetraloop over a range of simulation conditions. We thus aimed to identify which terms of the force field are responsible for this poor description of TL folding. We showed that at least two different imbalances contribute to this behavior, namely, overstabilization of base-phosphate and/or sugar-phosphate interactions and underestimated stability of the hydrogen bonding interaction in base pairing. The first artifact stabilizes the unfolded ensemble, while the second one destabilizes the folded state. The former problem might be partially alleviated by reparametrization of the van der Waals parameters of the phosphate oxygens suggested by Case et al., while in order to overcome the latter effect we suggest local potentials to better capture hydrogen bonding interactions.

Free-energy landscape of a hyperstable RNA tetraloop

We report the characterization of the energy landscape and the folding/unfolding thermodynamics of a hyperstable RNA tetraloop obtained through high-performance molecular dynamics simulations at microsecond timescales. Sampling of the configurational landscape is conducted using temperature replica exchange molecular dynamics over three isochores at high, ambient, and negative pressures to determine the thermodynamic stability and the free-energy landscape of the tetraloop. The simulations reveal reversible folding/unfolding transitions of the tetraloop into the canonical A-RNA conformation and the presence of two alternative configurations, including a left-handed Z-RNA conformation and a compact purine Triplet. Increasing hydrostatic pressure shows a stabilizing effect on the A-RNA conformation and a destabilization of the left-handed Z-RNA. Our results provide a comprehensive description of the folded free-energy landscape of a hyperstable RNA tetraloop and highlight the significant advances of all-atom molecular dynamics in describing the unbiased folding of a simple RNA secondary structure motif.

Peptide Bond Isomerization in High-Temperature Simulations.

Force fields for molecular simulation are generally optimized to model macromolecules such as proteins at ambient temperature and pressure. Nevertheless, elevated temperatures are frequently used to enhance conformational sampling, either during system setup or as a component of an advanced sampling technique such as temperature replica exchange. Because macromolecular force fields are now put upon to simulate temperatures and time scales that greatly exceed their original design specifications, it is appropriate to re-evaluate whether these force fields are up to the task. Here, we quantify the rates of peptide bond isomerization in high-temperature simulations of three octameric peptides and a small fast-folding protein. We show that peptide octamers with and without proline residues undergo cis/trans isomerization every 1-5 ns at 800 K with three classical atomistic force fields (AMBER99SB-ILDN, CHARMM22/CMAP, and OPLS-AA/L). On the low microsecond time scale, these force fields permit isomerization of nonprolyl peptide bonds at temperatures ≥500 K, and the CHARMM22/CMAP force field permits isomerization of prolyl peptide bonds ≥400 K. Moreover, the OPLS-AA/L force field allows chiral inversion about the Cα atom at 800 K. Finally, we show that temperature replica exchange permits cis peptide bonds developed at 540 K to subsequently migrate back to the 300 K ensemble, where cis peptide bonds are present in 2 ± 1% of the population of Trp-cage TC5b, including up to 4% of its folded state. Further work is required to assess the accuracy of cis/trans isomerization in the current generation of protein force fields.

Overcoming potential energy distortions in constrained internal coordinate molecular dynamics simulations.

The Internal Coordinate Molecular Dynamics (ICMD) method is an attractive molecular dynamics (MD) method for studying the dynamics of bonded systems such as proteins and polymers. It offers a simple venue for coarsening the dynamics model of a system at multiple hierarchical levels. For example, large scale protein dynamics can be studied using torsional dynamics, where large domains or helical structures can be treated as rigid bodies and the loops connecting them as flexible torsions. ICMD with such a dynamic model of the protein, combined with enhanced conformational sampling method such as temperature replica exchange, allows the sampling of large scale domain motion involving high energy barrier transitions. Once these large scale conformational transitions are sampled, all-torsion, or even all-atom, MD simulations can be carried out for the low energy conformations sampled via coarse grained ICMD to calculate the energetics of distinct conformations. Such hierarchical MD simulations can be carried out with standard all-atom forcefields without the need for compromising on the accuracy of the forces. Using constraints to treat bond lengths and bond angles as rigid can, however, distort the potential energy landscape of the system and reduce the number of dihedral transitions as well as conformational sampling. We present here a two-part solution to overcome such distortions of the potential energy landscape with ICMD models. To alleviate the intrinsic distortion that stems from the reduced phase space in torsional MD, we use the Fixman compensating potential. To additionally alleviate the extrinsic distortion that arises from the coupling between the dihedral angles and bond angles within a force field, we propose a hybrid ICMD method that allows the selective relaxing of bond angles. This hybrid ICMD method bridges the gap between all-atom MD and torsional MD. We demonstrate with examples that these methods together offer a solution to eliminate the potential energy distortions encountered in constrained ICMD simulations of peptide molecules.

Recovering Protein Thermal Stability Using All-Atom Hamiltonian Replica-Exchange Simulations in Explicit Solvent

The REST2 method is successfully applied to investigate the thermal stability of chignolin CLN025 and of Trp-cage. As opposed to temperature replica exchange, REST2 relies on the rescaling of the protein potential energy, which allows a smaller number of replicas. The shape of the stability curve reconstructed on the basis of the corresponding-state principle is in very good agreement with experimental data; for chignolin, the effect of mutations is also recovered.

Aggregation process of Aβ1-40 with non-Aβ amyloid component of α-synuclein

Many neurodegenerative diseases, such as Alzheimer's and Parkinson's diseases, are characterized by the presence of amyloid fibers. Recently, attention has turned from the fibers to the early stages of oligomerization where toxicity could be highest. Here, we focus on the interactions between non-Aβ amyloid component of a-synuclein (NAC) and Aβ1-40, two proteins found in amyloid fibrils associated with Alzheimer's disease. We combine the coarse-grained OPEP potential with a Hamiltonian and temperature replica exchange molecular dynamics simulation (HT-REMD) to identify mechanisms leading to the formation of secondary structures promoting fibrillation. We observe that the propensity to form beta-sheet remains the same for Aβ1-40 whereas is decreases significantly for NAC. In particular, the 25-35 region of Aβ1-40 is a significant area of secondary structure stabilization with NAC. The ionic interactions between salt-bridge D23 and K28 in Aβ1-40 and K20 and E23 in NAC of the heterogeneous dimer are consistent with the salt-bridges found in NAC and Aβ1-40 homogenous dimers and allow us to see that these interactions don't necessarily dominate the interchain stabilizations. Our numerical simulation also show the formation of interaction between the early oligomer of NAC and Aβ1-40.

Effect of pH on the Aggregation of α-syn12 Dimer in Explicit Water by Replica-Exchange Molecular Dynamics Simulation.

The dimeric structure of the N-terminal 12 residues drives the interaction of α-synuclein protein with membranes. Moreover, experimental studies indicated that the aggregation of α-synuclein is faster at low pH than neutral pH. Nevertheless, the effects of different pH on the structural characteristics of the α-syn12 dimer remain poorly understood. We performed 500 ns temperature replica exchange molecular dynamics (T-REMD) simulations of two α-syn12 peptides in explicit solvent. The free energy surfaces contain ten highly populated regions at physiological pH, while there are only three highly populated regions contained at acidic pH. The anti-parallel β-sheet conformations were found as the lowest free energy state. Additionally, these states are nearly flat with a very small barrier which indicates that these states can easily transit between themselves. The dimer undergoes a disorder to order transition from physiological pH to acidic pH and the α-syn12 dimer at acidic pH involves a faster dimerization process. Further, the Lys6–Asp2 contact may prevent the dimerization.

Application of Enhanced Sampling Monte Carlo Methods for High-Resolution Protein-Protein Docking in Rosetta.

The high-resolution refinement of docked protein-protein complexes can provide valuable structural and mechanistic insight into protein complex formation complementing experiment. Monte Carlo (MC) based approaches are frequently applied to sample putative interaction geometries of proteins including also possible conformational changes of the binding partners. In order to explore efficiency improvements of the MC sampling, several enhanced sampling techniques, including temperature or Hamiltonian replica exchange and well-tempered ensemble approaches, have been combined with the MC method and were evaluated on 20 protein complexes using unbound partner structures. The well-tempered ensemble method combined with a 2-dimensional temperature and Hamiltonian replica exchange scheme (WTE-H-REMC) was identified as the most efficient search strategy. Comparison with prolonged MC searches indicates that the WTE-H-REMC approach requires approximately 5 times fewer MC steps to identify near native docking geometries compared to conventional MC searches.

Free energy surface of an intrinsically disordered protein: comparison between temperature replica exchange molecular dynamics and bias-exchange metadynamics.

Intrinsically disordered proteins (IDPs), which are expected to be largely unstructured under physiological conditions, make up a large fraction of eukaryotic proteins. Molecular dynamics simulations have been utilized to probe structural characteristics of these proteins, which are not always easily accessible to experiments. However, exploration of the conformational space by brute force molecular dynamics simulations is often limited by short time scales. Present literature provides a number of enhanced sampling methods to explore protein conformational space in molecular simulations more efficiently. In this work, we present a comparison of two enhanced sampling methods: temperature replica exchange molecular dynamics and bias exchange metadynamics. By investigating both the free energy landscape as a function of pertinent order parameters and the per-residue secondary structures of an IDP, namely, human islet amyloid polypeptide, we found that the two methods yield similar results as expected. We also highlight the practical difference between the two methods by describing the path that we followed to obtain both sets of data.

Constant pH Simulations with the Double Reservoir pH Replica Exchange

We present the double reservoir pH replica exchange (DR-pH-Rex) method, which can improve convergence of constant pH simulations in situations where proper sampling is difficult. This method separates the sampling of protonation states from much of the sampling of protein conformations. The DR-pH-Rex method was inspired by the single reservoir temperature replica exchange method. The DR-pH-Rex method relies on pre-generation of two Boltzmann-weighted structural reservoirs of conformations that correspond to two end states at pH values where titratable groups are fully protonated and fully deprotonated. The end state conformations are coupled to simulations at intermediate pH values through the pH replica exchange (pH-Rex) methodology. We tested this method on three different systems: amino acid model compounds Lys and Glu, a small peptide, and a challenging case of V66K variant of Staphylococcal nuclease (SNase) which exhibits two distinctly different conformations of Lys-66 with slow transitions between the two conformations. We benchmarked the performance of the method through comparison with results of the pH-Rex method, which already provides better sampling than regular constant pH simulations. For the model compounds pH-Rex and DR-pH-Rex methods yield identical results. For the peptide, the pKa values are comparable between the two methods, but the DR-pH-Rex method exhibits faster convergence and less noise. For the V66K variant the pH-Rex method fails to properly sample conformational transitions of Lys-66 and results in two different pKa values when different conformations are used as starting structure. The DR-pH-Rex method, however, results in convergence of pKa values. Additionally we construct a four state model with two protonation states and only two conformations of Lys-66 and show that the pKa values calculated from DR-pH-Rex simulations are in excellent agreement with the pKa values determined from the four state model.

A Computational Study of Mono- and Poly-Ubiquitin Recognition by the Proteasome Subunit Rpn10

Accurate and timely protein degradation is a vital cellular process. Protein degradation is performed by the 26S proteasome complex, a large multi-subunit molecular machine that recognizes, binds, and degrades protein substrates covalently bound to poly-ubiquitin tags. The 26S proteasome, which recognizes ubiquitin tags through its subunit Rpn10, has a preference for binding K48-linked tetra-ubiquitin chains. However, Rpn10 and its homologs usually have only one or two ubiquitin binding sites, located on their long and flexible C-terminal arms. Here, to examine the role of Rpn10 in the 26S proteasome preference for tetra-ubiquitin tags, we perform molecular dynamics simulations of Rpn10 bound to mono-ubiquitin and poly-ubiquitin chains. To overcome timescale and sampling limitations, we use a combination of a hybrid model force field (PACE) and temperature replica exchange molecular dynamics (T-REMD) simulations. The performed simulations characterize in detail Rpn10 binding to its ubiquitin partners and identify transient contacts that could stabilize Rpn10 (and 26S proteasome) binding to poly-ubiquitin chains. Our results demonstrate at atomic resolution how the flexible Rpn10 subunit contributes to the recognition of poly-ubiquitin tags.

A LAMMPS implementation of volume–temperature replica exchange molecular dynamics

A driver module for executing volume–temperature replica exchange molecular dynamics (VTREMD) was developed for the LAMMPS package. As a patch code, the VTREMD module performs classical molecular dynamics (MD) with Monte Carlo (MC) decisions between MD runs. The goal of inserting the MC step was to increase the breadth of sampled configurational space. In this method, states receive better sampling by making temperature or density swaps with their neighboring states. As an accelerated sampling method, VTREMD is particularly useful to explore states at low temperatures, where systems are easily trapped in local potential wells. As functional examples, TIP4P/Ew and TIP4P/2005 water models were analyzed using VTREMD. The phase diagram in this study covered the deeply supercooled regime, and this test served as a suitable demonstration of the usefulness of VTREMD in overcoming the slow dynamics problem. To facilitate using the current code, attention was also paid on how to optimize the exchange efficiency by using grid allocation. VTREMD was useful for studying systems with rough energy landscapes, such as those with numerous local minima or multiple characteristic time scales. Program summaryProgram title: vttemperCatalogue identifier: AEVB_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEVB_v1_0.htmlProgram obtainable from: CPC Program Library, Queen’s University, Belfast, N. IrelandLicensing provisions: GNU General Public License, version 3No. of lines in distributed program, including test data, etc.: 49706No. of bytes in distributed program, including test data, etc.: 1249424Distribution format: tar.gzProgramming language: C++/MPI.Computer: Tested on Intel X86 and AMD64 architectures. Should be operational on any computer with a C++ compiler.Operating system: Tested on Linux. Should run on any platform with C++ and MPI library.Has the code been vectorized or parallelized?: Yes. 1 to N processors may be used.RAM: Depends on the system size and how the program is partitioned.Classification: 16.13.External routines: LAMMPS (http://lammps.sandia.gov)Nature of problem: The code implements volume–temperature replica exchange molecular dynamics for LAMMPS. Each replica has its own temperature and density. A two-dimensional temperature–density grid is constructed.Solution method: Extending the ability of the existing temper command in LAMMPS to handle replicas of two state variables.Restrictions: The code is based on LAMMPS. A well-designed grid on temperature and density is required.Running time: Running time depends on the system size and the complexity of the problem. Using 8 processors the test run takes approximately 1 minute.

Early oligomerization stages for the non-amyloid component of α-synuclein amyloid.

In recent years, much effort has focused on the early stages of aggregation and the formation of amyloid oligomers. Aggregation processes for these proteins are complex and their non-equilibrium nature makes any experimental study very difficult. Under these conditions, simulations provide a useful alternative for understanding the dynamics of the early stages of oligomerization. Here, we focus on the non-Aβ amyloid component (NAC) of the monomer, dimer, and trimer of α-synuclein, an important 35-residue sequence involved in the aggregation and fibrillation of this protein associated with Parkinson's disease. Using Hamiltonian and temperature replica exchange molecular dynamics simulations combined with the coarse grained Optimized Potential for Efficient peptide structure Prediction potential, we identify the role of the various regions and the secondary structures for the onset of oligomerization. For this sequence, we clearly observe the passage from α-helix to β-sheet, a characteristic transition of amyloid proteins. More precisely, we find that the NAC monomer is highly structured with two α-helical regions, between residues 2-13 and 19-25. As the dimer and trimer form, β-sheet structures between residues 2-14 and 26-34 appear and rapidly structure the system. The resulting conformations are much more structured than similar dimers and trimers of β-amyloid and amylin proteins and yet display a strong polymorphism at these early stages of aggregation. In addition to its inherent experimental interest, comparison with other sequences shows that NAC could be a very useful numerical model for understanding the onset of aggregation.

Acceleration of Lateral Equilibration in Mixed Lipid Bilayers Using Replica Exchange with Solute Tempering.

The lateral heterogeneity of cellular membranes plays an important role in many biological functions such as signaling and regulating membrane proteins. This heterogeneity can result from preferential interactions between membrane components or interactions with membrane proteins. One major difficulty in molecular dynamics simulations aimed at studying the membrane heterogeneity is that lipids diffuse slowly and collectively in bilayers, and therefore, it is difficult to reach equilibrium in lateral organization in bilayer mixtures. Here, we propose the use of the replica exchange with solute tempering (REST) approach to accelerate lateral relaxation in heterogeneous bilayers. REST is based on the replica exchange method but tempers only the solute, leaving the temperature of the solvent fixed. Since the number of replicas in REST scales approximately only with the degrees of freedom in the solute, REST enables us to enhance the configuration sampling of lipid bilayers with fewer replicas, in comparison with the temperature replica exchange molecular dynamics simulation (T-REMD) where the number of replicas scales with the degrees of freedom of the entire system. We apply the REST method to a cholesterol and 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) bilayer mixture and find that the lateral distribution functions of all molecular pair types converge much faster than in the standard MD simulation. The relative diffusion rate between molecules in REST is, on average, an order of magnitude faster than in the standard MD simulation. Although REST was initially proposed to study protein folding and its efficiency in protein folding is still under debate, we find a unique application of REST to accelerate lateral equilibration in mixed lipid membranes and suggest a promising way to probe membrane lateral heterogeneity through molecular dynamics simulation.

Thermodynamics of Coupled Protein Adsorption and Stability Using Hybrid Monte Carlo Simulations

A better understanding of changes in protein stability upon adsorption can improve the design of protein separation processes. In this study, we examine the coupling of the folding and the adsorption of a model protein, the B1 domain of streptococcal protein G, as a function of surface attraction using a hybrid Monte Carlo (HMC) approach with temperature replica exchange and umbrella sampling. In our HMC implementation, we are able to use a molecular dynamics (MD) time step that is an order of magnitude larger than in a traditional MD simulation protocol and observe a factor of 2 enhancement in the folding and unfolding rate. To demonstrate the convergence of our systems, we measure the travel of our order parameter the fraction of native contacts between folded and unfolded states throughout the length of our simulations. Thermodynamic quantities are extracted with minimum statistical variance using multistate reweighting between simulations at different temperatures and harmonic distance restraints from the surface. The resultant free energies, enthalpies, and entropies of the coupled unfolding and absorption processes are in qualitative agreement with previous experimental and computational observations, including entropic stabilization of the adsorbed, folded state relative to the bulk on surfaces with low attraction.

Simulation study of the effects of surface chemistry and temperature on the conformations of ssDNA oligomers near hydrophilic and hydrophobic surfaces

We study the effects of the presence of a hydrophilic and a hydrophobic surface on the conformations and interactions of a single-stranded DNA (ssDNA) oligomer using atomistic molecular dynamics, umbrella sampling, and temperature-replica exchange. Our simulations capture the expected interactions between the ssDNA and the two surfaces (e.g., hydrogen bonds, hydrophobic interactions), but we find that the surface chemistry does not strongly affect the exposure of the relatively hydrophobic nucleobases or the hydrophilic phosphate backbone in a 16-base ssDNA. Likewise, the surfaces do not strongly affect the preferred size of the ssDNA compared to bulk solution, although the hydrophilic surface does favor slightly more compact ssDNA conformations than the hydrophobic surface. In more compact conformations, the negative charge of the ssDNA is more concentrated, and the energetic interactions of the DNA and DNA-bound counterions with the hydrophilic surface are more favorable, which consequently favors smaller ssDNA sizes. Increasing temperature, regardless of the presence or chemistry of a surface, makes it less unfavorable for the ssDNA to assume both compact and extended conformations. With increasing temperature the free energy cost of assuming a compact conformation is reduced to a greater extent than the cost of assuming an extended conformation. The reason for this difference is the entropically favorable release of DNA-bound water molecules upon assuming a compact conformation. Increasing temperature decreases water-DNA interactions while surprisingly increasing counterion-DNA interactions, changes which are attributed to the relative balance of entropic and energetic contributions for water molecules and counterions bound to the ssDNA.