Amber ff99SB Force Field Research Articles

The inhibitory mechanism of echinacoside against Staphylococcus aureus Ser/Thr phosphatase Stp1 by virtual screening and molecular modeling.

Stp1 is a new potential target closely related to the pathogenicity of Staphylococcus aureus (S. aureus). In this study, effective Stp1 inhibitors were screened via virtual screening and enzyme activity experiments, and the inhibition mechanism was analyzed using molecular dynamics simulation. AutoDock Vina 4.0 software was used for virtual screening. The molecular structures of Stp1 and ligands were obtained from the RCSB Protein Data Bank and Zinc database, respectively. The molecular dynamics simulation used the Gromacs 4.5.5 software package with the Amberff99sb force field and TIP3P water model. AutoDock Tools was used to add polar hydrogen atoms to Stp1 and distribute part of the charge generated by Kollman's combined atoms. The binding free energies were calculated using the Amber 10 package. The theoretical calculation results are consistent with the experimental results. We found that echinacoside (ECH) substantially inhibits the hydrolytic activity of Stp1. ECH competes with the substrate by binding to the active center of Stp1, resulting in a decrease in Stp1 activity. In addition, Met39, Gly41, Asp120, Asn162, and Ile163 were identified to play key roles in the binding of Stp1 to ECH. The benzene ring of ECH also plays an important role in complex binding. These findings provide a robust foundation for the development of innovative anti-infection drugs.

A Hierarchical Approach to Predict Conformation-Dependent Histidine Protonation States in Stable and Flexible Proteins.

Solution acidity measured by pH is an important environmental factor that affects protein structure. It influences the protonation state of protein residues, which in turn may be coupled to protein conformational changes, unfolding, and ligand binding. It remains difficult to compute and measure the p Ka of individual residues, as well as to relate them to pH-dependent protein transitions. This paper presents a hierarchical approach to compute the p Ka of individual protonatable residues, specifically histidines, coupled with underlying structural changes of a protein. A fast and efficient free energy perturbation (FEP) algorithm has also been developed utilizing a fast implementation of standard molecular dynamics (MD) algorithms. Specifically, a CUDA version of the AMBER MD engine is used in this paper. Eight histidine p Ka's are computed in a diverse set of pH stable proteins to demonstrate the proposed approach's utility and assess the predictive quality of the AMBER FF99SB force field. A reference molecule is carefully selected and tested for convergence. A hierarchical approach is used to model p Ka's of the six histidine residues of the diphtheria toxin translocation domain (DTT), which exhibits a diverse ensemble of individual conformations and pH-dependent unfolding. The hierarchical approach consists of first sampling equilibrium conformational ensembles of a protein with protonated and neutral histidine residues via long equilibrium MD simulations (Flores-Canales, J. C.; et al. bioRxiv, 2019, 572040). A clustering method is then used to identify sampled protein conformations, and p Ka's of histidines in each protein conformation are computed. Finally, an ensemble averaging formalism is developed to compute weighted average histidine p Ka's. These can be compared with an apparent experimentally measured p Ka of the DTT protein and thus allows us to propose a mechanism of pH-dependent unfolding of the DTT protein.

Accurate PDZ/Peptide Binding Specificity with Additive and Polarizable Free Energy Simulations

PDZ domains contain 80–100 amino acids and bind short C-terminal sequences of target proteins. Their specificity is essential for cellular signaling pathways. We studied the binding of the Tiam1 PDZ domain to peptides derived from the C-termini of its Syndecan-1 and Caspr4 targets. We used free energy perturbation (FEP) to characterize the binding energetics of one wild-type and 17 mutant complexes by simulating 21 alchemical transformations between pairs of complexes. Thirteen complexes had known experimental affinities. FEP is a powerful tool to understand protein/ligand binding. It depends, however, on the accuracy of molecular dynamics force fields and conformational sampling. Both aspects require continued testing, especially for ionic mutations. For six mutations that did not modify the net charge, we obtained excellent agreement with experiment using the additive, AMBER ff99SB force field, with a root mean square deviation (RMSD) of 0.37 kcal/mol. For six ionic mutations that modified the net charge, agreement was also good, with one large error (3 kcal/mol) and an RMSD of 0.9 kcal/mol for the other five. The large error arose from the overstabilization of a protein/peptide salt bridge by the additive force field. Four of the ionic mutations were also simulated with the polarizable Drude force field, which represents the first test of this force field for protein/ligand binding free energy changes. The large error was eliminated and the RMS error for the four mutations was reduced from 1.8 to 1.2 kcal/mol. The overall accuracy of FEP indicates it can be used to understand PDZ/peptide binding. Importantly, our results show that for ionic mutations in buried regions, electronic polarization plays a significant role.

Ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB.

Molecular mechanics is powerful for its speed in atomistic simulations, but an accurate force field is required. The Amber ff99SB force field improved protein secondary structure balance and dynamics from earlier force fields like ff99, but weaknesses in side chain rotamer and backbone secondary structure preferences have been identified. Here, we performed a complete refit of all amino acid side chain dihedral parameters, which had been carried over from ff94. The training set of conformations included multidimensional dihedral scans designed to improve transferability of the parameters. Improvement in all amino acids was obtained as compared to ff99SB. Parameters were also generated for alternate protonation states of ionizable side chains. Average errors in relative energies of pairs of conformations were under 1.0 kcal/mol as compared to QM, reduced 35% from ff99SB. We also took the opportunity to make empirical adjustments to the protein backbone dihedral parameters as compared to ff99SB. Multiple small adjustments of φ and ψ parameters were tested against NMR scalar coupling data and secondary structure content for short peptides. The best results were obtained from a physically motivated adjustment to the φ rotational profile that compensates for lack of ff99SB QM training data in the β-ppII transition region. Together, these backbone and side chain modifications (hereafter called ff14SB) not only better reproduced their benchmarks, but also improved secondary structure content in small peptides and reproduction of NMR χ1 scalar coupling measurements for proteins in solution. We also discuss the Amber ff12SB parameter set, a preliminary version of ff14SB that includes most of its improvements.

Residue-Specific Force Field (RSFF2) Improves the Modeling of Conformational Behavior of Peptides and Proteins.

A recent report of (3)J(HNHα) scalar coupling constants for hundreds of two-residue peptides has provided an important opportunity to test simulation force fields for proteins. Here, we compare the abilities of three derivatives of the Amber ff99SB force field to reproduce these data. We report molecular dynamics (MD) simulations of 256 two-residue peptides and show that the recently developed residue-specific force field (RSFF2) produces a dramatic improvement in the agreement with experimental (3)J(HNHα) coupling constants. We further show that RSFF2 also appears to produce a modest improvement in reproducing the (3)J(HNHα) coupling constants of five model proteins. Perhaps surprisingly, an analysis of neighboring residue effects (NREs) on the (3)J(HNHα) coupling constants of the two-residue peptides indicates little difference between the force fields' abilities to reproduce experimental NREs. We speculate that this might indicate limitations in the force fields' descriptions of nonbonded interactions between adjacent side chains or with terminal capping groups.

QM/MM simulations of amyloid-β 42 degradation by IDE in the presence and absence of ATP.

The ability of the insulin-degrading enzyme (IDE) to degrade amyloid-β 42 (Aβ42), a process regulated by ATP, has been studied as an alternative path in the development of drugs against Alzheimer's disease. In this study, we calculated the potential of mean force for the degradation of Aβ42 by IDE in the presence and absence of ATP by umbrella sampling with hybrid quantum mechanics and molecular mechanics (QM/MM) calculations, using the SCC-DFTB QM Hamiltonian and Amber ff99SB force field. Results indicate that the reaction occurs in two steps: The first step is characterized by the formation of the intermediate. The second step is characterized by breaking the peptide bond of the substrate, the latter being the rate-determining step. In our simulations, the activation energy barrier in the absence of ATP is 15 ± 2 kcal mol(-1), which is 7 kcal mol(-1) lower than in the presence of ATP, indicating that the presence of the nucleotide decreases the reaction rate by about 10(5) times.

Residue-specific force field based on protein coil library. RSFF2: modification of AMBER ff99SB.

Recently, we developed a residue-specific force field (RSFF1) based on conformational free-energy distributions of the 20 amino acid residues from a protein coil library. Most parameters in RSFF1 were adopted from the OPLS-AA/L force field, but some van der Waals and torsional parameters that effectively affect local conformational preferences were introduced specifically for individual residues to fit the coil library distributions. Here a similar strategy has been applied to modify the Amber ff99SB force field, and a new force field named RSFF2 is developed. It can successfully fold α-helical structures such as polyalanine peptides, Trp-cage miniprotein, and villin headpiece subdomain and β-sheet structures such as Trpzip-2, GB1 β-hairpins, and the WW domain, simultaneously. The properties of various popular force fields in balancing between α-helix and β-sheet are analyzed based on their descriptions of local conformational features of various residues, and the analysis reveals the importance of accurate local free-energy distributions. Unlike the RSFF1, which overestimates the stability of both α-helix and β-sheet, RSFF2 gives melting curves of α-helical peptides and Trp-cage in good agreement with experimental data. Fitting to the two-state model, RSFF2 gives folding enthalpies and entropies in reasonably good agreement with available experimental results.

Assessing the influence of solvation models on structural characteristics of intrinsically disordered protein

Intrinsically disordered proteins are associated with functions of signaling and regulation as well as with a number of diseases such as cancer and neurodegenerative conditions. Molecular dynamics simulation is potentially a powerful tool to study those protein conformational disorders in full atomic details that would be difficult to gain from experimental measurements. However, the accuracy of the simulation critically relies on the quality of underlying potential energy functions or force fields. In particular, structural properties of intrinsically disordered proteins are expected to depend more sensitively on protein–water interactions because of their increased solvent exposure than folded globular proteins. Here, we investigate the impact of solvation models on structural characteristics of full-length amyloid-beta (Aβ) protein, an intrinsically disordered protein whose aggregation is linked to Alzheimer’s disease. For this purpose, we performed extensive molecular dynamics simulations by combining AMBER ff99SB force field for protein with differing solvent water models as well as solvation procedures with different solvent box sizes. We find that the structural characteristics of Aβ protein differ remarkably depending on the water model adopted as well as on the solvent box size. Our results demonstrate the significant sensitivity on the solvation procedure including the solvent force field in characterizing structural properties of intrinsically disordered proteins.

A Study of Intrinsically Disordered Proteins from Nuclear Pore Complex

Nuclear pore complex (NPC) is giant molecular assembly that acts as a highly selective gate. Its central channel is composed of FG repeat-containing nucleoporins (FG nups), which are natively disordered proteins that facilitate the passage of receptor-cargo complexes through the NPC. However, their mechanism to facilitate selective transport is still unknown. We carried out molecular dynamics simulations of single and multiple FG nups to unveil their dynamics and structures. As an important aspect of our studies of intrinsically disordered proteins (IDPs), we made extensive comparisons between two popular water models, TIP3P and TIP4P-Ew, in combination with Amber ff99sb force field to simulate different IDPs. We found that TIP4P-Ew combined with ff99sb gives better reproduction of experimental observations for FG nups. The reason is because of better solvation of water model to charged side chain of amino acid residues. However, we also identified a caveat of current force field by studying the mutated form of FG nups. We found that the shape of IDPs is much closer to a rod-like shape regardless of whether they are extended or collapsed, which could be a signature of IDPs. Then, we explored the interaction of multiple FG nups to show that the arrangement of the FG nups can be different depending on the inter-chain distances. We identified the influence from the types of FG nups and inter-molecular spacing. FG nups showed a strong dependence of inter-molecular interaction strength on molecular spacing. However, inter-molecular interaction for one type is weaker compared to that of another type. While most of the FG nups of the two types are mainly disordered despite inter- and intra- molecular interactions, we observed noticeable beta-sheet formation at certain inter-molecular spacings, indicating a significant role between inter-molecular interaction and secondary structure formation.

Extension of the AMBER force field to cyclic α,α dialkylated peptides

The popular biomolecular AMBER (ff99SB) force field (FF) has been extended with new parameters for the simulations of peptides containing α,α dialkylated residues with cyclic side chains. Together with the recent set of nitroxide parameters [E. Stendardo, A. Pedone, P. Cimino, M. C. Menziani, O. Crescenzi and V. Barone, Phys. Chem. Chem. Phys., 2010, 12, 11697] this extension allows treating the TOAC residue (TOAC, 2,2,6,6-tetramethylpiperidine-1-oxyl-4-amino-4-carboxylic acid) widely used as a spin label in protein studies. All the conformational minima of the Ac-Ac(6)C-NMe (Ac = acetyl, Ac(6)C = 1-aminocyclohexaneacetic acid, NMe = methylamino) and Ac-TOAC-NMe dipeptides have been examined in terms of geometry and relative energy stability by Quantum Mechanical (QM) computations employing an hybrid density functional (PBE0) for an extended training set of conformers with various folds. A very good agreement between QM and MM (molecular mechanics) data has been obtained in most of the investigated properties, including solvent effects. Finally, the new set of parameters has been validated by comparing the conformational and dynamical behavior of TOAC-labeled polypeptides investigated by means of classical molecular dynamics (MD) simulations with QM data and experimental evidence. The new FF accurately describes the tuning of conformational and dynamical behavior of the Ac-TOAC-NMe dipeptide and double spin-labeled heptapeptide Fmoc-(Aib-Aib-TOAC)(2)-Aib-OMe (Fmoc, fluorenyl-9-methoxycarbonyl; Aib, α-aminoisobutyric acid; OMe, methoxy) by solvents with different polarity. In particular, we found that the 3(10) helical structure of heptapeptide is the most stable one in vacuo, with a geometry very similar to the X-ray crystallographic structure, whereas a conformational equilibrium between the 3(10)- and α-helical structures is established in aqueous solution, in agreement with EPR data.

Iterative Optimization of Molecular Mechanics Force Fields from NMR Data of Full-Length Proteins.

High quality molecular mechanics force fields of proteins are key for the quantitative interpretation of experimental data and the predictive understanding of protein function based on computer simulations. A strategy is presented for the optimization of protein force fields based on full-length proteins in their native environment that is guided by experimental NMR chemical shifts and residual dipolar couplings (RDCs). An energy-based reweighting approach is applied to a long molecular dynamics trajectory, performed with a parent force field, to efficiently screen a large number of trial force fields. The force field that yields the best agreement with the experimental data is then used as the new parent force field, and the procedure is repeated until no further improvement is obtained. This method is demonstrated for the optimization of the backbone φ,ψ dihedral angle potential of the Amber ff99SB force field using six trial proteins and another 17 proteins for cross-validation using (13)C chemical shifts with and without backbone RDCs. The φ,ψ dihedral angle potential is systematically improved by the inclusion of correlation effects through the addition of up to 24 bivariate Gaussian functions of variable height, width, and tilt angle. The resulting force fields, termed ff99SB_φψ(g24;CS) and ff99SB_φψ(g8;CS,RDC), perform significantly better than their parent force field in terms of both NMR data reproduction and Cartesian coordinate root-mean-square deviations between the MD trajectories and the X-ray crystal structures. The strategy introduced here represents a powerful addition to force field optimization approaches by overcoming shortcomings of methods that are solely based on quantum-chemical calculations of small molecules and protein fragments in the gas phase.

Optimizing Protein-Solvent Force Fields to Reproduce Intrinsic Conformational Preferences of Model Peptides.

While most force field efforts in biomolecular simulation have focused on the parametrization of the protein, relatively little attention has been paid to the quality of the accompanying solvent model. These considerations are especially relevant for simulations of intrinsically disordered peptides and proteins, for which energy differences between conformations are small and interactions with water are enhanced. In this work, we investigate the accuracy of the AMBER ff99SB force field when combined with the standard TIP3P model or the more recent TIP4P-Ew water model, to generate conformational ensembles for disordered trialanine (Ala3), triglycine (Gly3), and trivaline (Val3) peptides. We find that the TIP4P-Ew water model yields significantly better agreement with experimentally measured scalar couplings-and therefore more accurate conformational ensembles-for both Ala3 and Gly3. For Val3, however, we find that the TIP3P and TIP4P-Ew ensembles are equivalent in their performance. To further improve the protein-water force field combination and obtain more accurate intrinsic conformational preferences, we derive a straightforward perturbation to the ϕ' backbone dihedral potential that shifts the β-PPII equilibrium. We find that the revised ϕ' backbone dihedral potential yields improved conformational ensembles for a variety of small peptides and maintains the stability of the globular ubiquitin protein in TIP4P-Ew water.

Evaluation and Improvement of the Amber ff99SB Force Field with an Advanced Water Model

A recurring concern when studying biomolecules with molecular dynamics (MD) simulations is the accuracy of the underlying force field and solvent model. These considerations are especially relevant for simulations of intrinsically disordered peptides and proteins, for which energy differences between conformations are small and interactions with water are enhanced. In this work, we investigate the accuracy of the AMBER ff99SB force field, combined with either the TIP3P or the TIP4P-Ew water model, using both conventional MD and replica exchange MD (REMD) simulations to generate conformational ensembles for (disordered) trialanine, triglycine, and trivaline peptides.We find that the TIP4P-Ew water model yields significantly better agreement with experimentally measured scalar couplings - and therefore more accurate conformational ensembles - for both trialanine and triglycine. For trivaline, however, we find that the TIP3P and TIP4P-Ew ensembles are equivalent in accuracy. To address this discrepancy and further improve the force field, we derive new van der Waals parameters for alkanes in TIP4P-Ew water and a straightforward perturbation to the f backbone dihedral potential that shifts the β-PPII equilibrium. Of the two, we find that the revised f backbone dihedral potential is more effective and yields significantly improved conformational ensembles for both the trialanine and trivaline peptides in TIP4P-Ew water.

A theoretical investigation of inositol 1,3,4,5-tetrakisphosphate

This paper describes the parameterization of inositol 1,3,4,5-tetrakisphosphate [Ins(1,3,4,5)P(4)] for use in molecular dynamics (MD) simulations. For this theoretical investigation, eleven isomers of Ins(1,3,4,5)P(4), with different levels and arrangements of protonation, have been considered. Herein we report accurate quantum mechanics (QM) calculations offering a detailed description of the energetic and structural properties of the Ins(1,3,4,5)P(4) isomers and subsequent development of parameters for these isomers for application in the AMBER force field. QM calculations were employed to geometry optimize the Ins(1,3,4,5)P(4) isomers, using the DFT-B3LYP level of theory in gas phase. In subsequent steps, charge parameters were generated for each isomer. These charge parameters, plus assigned atom-types from the AMBER ff99SB force field, were then applied to the optimized isomers for energy minimization in AMBER. The quality of the parameters was evaluated by comparing the structural, energetic and spectroscopic properties of the Ins(1,3,4,5)P(4) isomers between the QM geometry optimization stage, from which the parameters were generated, and the energy minimization stage, in which the parameters were applied. The results were shown to be in strong qualitative agreement between these stages, suggesting good quality parameters have been obtained. Additionally, adaptations to the gas phase protocol, investigating the use of the MP2 method for the geometry optimization stage and GAFF atom-types for the energy minimization stage, were tested. These results confirmed the initial protocol applied was the most appropriate. Calculations for the Ins(1,3,4,5)P(4) isomers were also carried out in the presence of implicit solvent, allowing comparison and validation of the theoretical calculations with experimental data. The computed energetic properties of the Ins(1,3,4,5)P(4) isomers were assessed against their experimental probabilities based on (31)P-NMR titration data. The computational and experimental results were shown to be in strong agreement, with the lower energy isomers corresponding to those more probable. This paper reports a clearly-defined algorithmic approach to generate parameters for the highly charged Ins(1,3,4,5)P(4) ligand, permitting their use in future MD studies.

Simulations of a Protein Crystal with a High Resolution X-ray Structure: Evaluation of Force Fields and Water Models

We use classical molecular dynamics and 16 combinations of force fields and water models to simulate a protein crystal observed by room-temperature X-ray diffraction. The high resolution of the diffraction data (0.96 Å) and the simplicity of the crystallization solution (nearly pure water) make it possible to attribute any inconsistencies between the crystal structure and our simulations to artifacts of the models rather than inadequate representation of the crystal environment or uncertainty in the experiment. All simulations were extended for 100 ns of production dynamics, permitting some long-time scale artifacts of each model to emerge. The most noticeable effect of these artifacts is a model-dependent drift in the unit cell dimensions, which can become as large as 5% in certain force fields; the underlying cause is the replacement of native crystallographic contacts with non-native ones, which can occur with heterogeneity (loss of crystallographic symmetry) in simulations with some force fields. We find that the AMBER FF99SB force field maintains a lattice structure nearest that seen in the X-ray data, and produces the most realistic atomic fluctuations (by comparison to crystallographic B-factors) of all the models tested. We find that the choice of water model has a minor effect in comparison to the choice of protein model. We also identify a number of artifacts that occur throughout all of the simulations: excessive formation of hydrogen bonds or salt bridges between polar groups and loss of hydrophobic interactions. This study is intended as a foundation for future work that will identify individual parameters in each molecular model that can be modified to improve their representations of protein structure and thermodynamics.

Abstract 2673: In silico design of E2F1 mimics as potential anticancer agents

Abstract Introduction. We report the construction of a homology model of the human E2F1-DP1 transcription factor complex with DNA to be used as a tool for design of drugs targeted to the promoter of this oncogene based on interference of transcription factor binding. Using shape-based docking and force field calculations, we investigate the development of novel penetratin-based (PED) peptides, obtained by phage display, (E2F1 mimics) as potential binders to the major groove of GC-rich regions of DNA. Computational Procedures. The homology model of E2F1-DP1 complex with DNA was built using the Modeller (9v5) program. We used the DNA binding domains of the E2F1 and DP1 sequences (NCBI accession #'s AAC50719 and NP009042 respectively), and the x-ray crystal structure of the E2F4-DP2 complex with DNA (1CF7.pdb) as the primary template. The DNA from the crystal structure was modeled in place using the default spatial constraints in Modeller. The PED based peptide models were built using the x-ray crystal structure of the antennapedia homeodomain-DNA complex (9ANT.pdb) as a template. The alignment is shown below (The penetratin portion is shown in bold and the variable portion is in italics.). _aln.pos 10 20 30 40 50 60 9antA RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKK—–EN brt1 ————————————–RQIKIWFQNRRMKWKKHHHRLSH _consrvd **************** The PatchDock program was used to dock the peptides to the DNA structure from 1CF7.pdb based on shape complementarity. The best shape scoring major-groove binding orientation was selected and refined via energy minimization using the Amber ff99SB force field. Interaction energy scores were computed from the non-bonded energy terms of the Amber force field (Eint = ∑ Evdw + ∑ Eelec). Data Summary. The HHHRLSH sequence is predicted to form a more stable complex compared to the GGGALSA sequence. The PED-HHHRLSH peptide was shown to have potent activity against several cancer cell lines (Xie, et al. AACR 2009). In the case of the HHHRLSH sequence, the model predicts enhanced stability in going from L-Arg (−646.0 kcal/mol) to D-Arg (−688.0 kcal/mol). Conclusions. The α3 helix of E2F1 composed of KRRIYDITNVLEGI binds to the major groove of GC-rich DNA. The PED-HHHRLSH peptide complex with DNA (−646.0 kcal/mol) has similar interaction energy to that of the E2F1-DNA complex (−653.0 kcal/mol), is a stable α-helical structure, and is a potential E2F1 mimic. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2673.

Improved side‐chain torsion potentials for the Amber ff99SB protein force field

Recent advances in hardware and software have enabled increasingly long molecular dynamics (MD) simulations of biomolecules, exposing certain limitations in the accuracy of the force fields used for such simulations and spurring efforts to refine these force fields. Recent modifications to the Amber and CHARMM protein force fields, for example, have improved the backbone torsion potentials, remedying deficiencies in earlier versions. Here, we further advance simulation accuracy by improving the amino acid side-chain torsion potentials of the Amber ff99SB force field. First, we used simulations of model alpha-helical systems to identify the four residue types whose rotamer distribution differed the most from expectations based on Protein Data Bank statistics. Second, we optimized the side-chain torsion potentials of these residues to match new, high-level quantum-mechanical calculations. Finally, we used microsecond-timescale MD simulations in explicit solvent to validate the resulting force field against a large set of experimental NMR measurements that directly probe side-chain conformations. The new force field, which we have termed Amber ff99SB-ILDN, exhibits considerably better agreement with the NMR data. Proteins 2010. © 2010 Wiley-Liss, Inc.

Microsecond simulations of the folding/unfolding thermodynamics of the Trp‐cage miniprotein

We study the unbiased folding/unfolding thermodynamics of the Trp-cage miniprotein using detailed molecular dynamics simulations of an all-atom model of the protein in explicit solvent using the Amberff99SB force field. Replica-exchange molecular dynamics simulations are used to sample the protein ensembles over a broad range of temperatures covering the folded and unfolded states at two densities. The obtained ensembles are shown to reach equilibrium in the 1 mus/replica timescale. The total simulation time used in the calculations exceeds 100 mus. Ensemble averages of the fraction folded, pressure, and energy differences between the folded and unfolded states as a function of temperature are used to model the free energy of the folding transition, DeltaG(P, T), over the whole region of temperatures and pressures sampled in the simulations. The DeltaG(P, T) diagram describes an ellipse over the range of temperatures and pressures sampled, predicting that the system can undergo pressure-induced unfolding and cold denaturation at low temperatures and high pressures, and unfolding at low pressures and high temperatures. The calculated free energy function exhibits remarkably good agreement with the experimental folding transition temperature (T(f) = 321 K), free energy, and specific heat changes. However, changes in enthalpy and entropy are significantly different than the experimental values. We speculate that these differences may be due to the simplicity of the semiempirical force field used in the simulations and that more elaborate force fields may be required to describe appropriately the thermodynamics of proteins.

Comparative Study of Electrostatic Models for the Amide-I and -II Modes: Linear and Two-Dimensional Infrared Spectra

We have carried out a comparative study of five ab initio electrostatic frequency maps and a semiempirical model for the amide-I and -II modes. Unrestrained molecular dynamics simulation of a 3(10)-helical peptide, Z-Aib-L-Leu-(Aib)(2)-Gly-OtBu, in CDCl(3) is performed using the AMBER ff99SB force field, and the linear and two-dimensional infrared (2D IR) spectra are simulated on the basis of a vibrational exciton Hamiltonian model. A new electrostatic potential-based amide-I and -II frequency map for N-methylacetamide is developed in this study. This map and other maps developed by different research groups are applied to calculate the local mode frequencies of the amide linkages in the hexapeptide. The simulated amide-I line shape from all models agrees well with the previous experimental results on the same system, except for an overall frequency shift. In contrast, the simulated amide-II bands are more sensitive to the frequency maps. Essential features obtained in the electrostatic models are captured by the semiempirical model that takes into account only the intramolecular hydrogen bonding effects and solvent shifts. Detailed comparisons between the models are also drawn through analysis of the local mode frequency shifts. Among all of the maps tested in this study, the new four-site potential map performs quite well in simulating the amide-II bands. It properly predicts the effects of hydrogen bonding on the amide-I and -II frequencies and reasonably simulates the isotope-dependent amide-I/II cross peaks upon (13)C=(18)O/(15)N substitutions.

Are Current Semiempirical Methods Better Than Force Fields? A Study from the Thermodynamics Perspective

The semiempirical Hamiltonians MNDO, AM1, PM3, RM1, PDDG/MNDO, PDDG/PM3, and SCC-DFTB, when used as part of a hybrid QM/MM scheme for the simulation of biological molecules, were compared on their abilities to reproduce experimental ensemble averages at or near room temperatures for the model system alanine dipeptide in water. Free energy surfaces in the (phi, psi) dihedral angle space, (3)J(H(N),H(alpha)) NMR dipolar coupling constants, basin populations, and peptide-water radial distribution functions (RDF) were calculated from replica exchange simulations and compared to both experiment and fully classical force field calculations using the Amber ff99SB force field. In contrast with the computational chemist's intuitive idea that the more expensive a method the better its accuracy, the ff99SB force field results were more accurate than most of the semiempirical methods, with the exception of RM1. None of the methods, however, was able to accurately reproduce the experimental data. Analysis of the results indicate that the specific QM/MM interactions have little influence on the sampling of free energy surfaces, and the differences are well explained simply by the intrinsic properties of the various QM methods.