The relative helix and hydrogen bond stability in the B domain of protein A as revealed by integrated tempering sampling molecular dynamics simulation

The B domain of protein A retains residual structures in 6 M guanidinium chloride as revealed by hydrogen/deuterium-exchange NMR spectroscopy

The characterization of residual structures persistent in unfolded proteins is an important issue in studies of protein folding, because the residual structures present, if any, may form a folding initiation site and guide the subsequent folding reactions. Here, we studied the residual structures of the isolated B domain (BDPA) of staphylococcal protein A in 6 M guanidinium chloride. BDPA is a small three-helix-bundle protein, and until recently its folding/unfolding reaction has been treated as a simple two-state process between the native and the fully unfolded states. We employed a dimethylsulfoxide (DMSO)-quenched hydrogen/deuterium (H/D)-exchange 2D NMR techniques with the use of spin desalting columns, which allowed us to investigate the H/D-exchange behavior of individually identified peptide amide (NH) protons. We obtained H/D-exchange protection factors of the 21 NH protons that form an α-helical hydrogen bond in the native structure, and the majority of these NH protons were significantly protected with a protection factor of 2.0-5.2 in 6 M guanidinium chloride, strongly suggesting that these weakly protected NH protons form much stronger hydrogen bonds under native folding conditions. The results can be used to deduce the structure of an early folding intermediate, when such an intermediate is shown by other methods. Among three native helical regions, the third helix in the C-terminal side was highly protected and stabilized by side-chain salt bridges, probably acting as the folding initiation site of BDPA. The present results are discussed in relation to previous experimental and computational findings on the folding mechanisms of BDPA.

Enhanced sampling in molecular dynamics

Although molecular dynamics simulations have become a useful tool in essentially all fields of chemistry, condensed matter physics, materials science, and biology, there is still a large gap between the time scale which can be reached in molecular dynamics simulations and that observed in experiments. To address the problem, many enhanced sampling methods were introduced, which effectively extend the time scale being approached in simulations. In this perspective, we review a variety of enhanced sampling methods. We first discuss collective-variables-based methods including metadynamics and variationally enhanced sampling. Then, collective variable free methods such as parallel tempering and integrated tempering methods are presented. At last, we conclude with a brief introduction of some newly developed combinatory methods. We summarize in this perspective not only the theoretical background and numerical implementation of these methods but also the new challenges and prospects in the field of the enhanced sampling.

Enhanced QM/MM sampling for free energy calculation of chemical reactions: A case study of double proton transfer

Free energy calculations for chemical reactions with a steep energy barrier require well defined reaction coordinates (RCs). However, when multiple parallel channels exist along selected RC, the application of conventional enhanced samplings is difficult to generate correct sampling within limited simulation time and thus cannot give correct prediction about the favorable pathways, the relative stability of multiple products or intermediates. Here, we implement the selective integrated tempering sampling (SITS) method with quantum mechanical and molecular mechanical (QM/MM) potential to investigate the chemical reactions in solution. The combined SITS-QM/MM scheme is used to identify possible reaction paths, intermediate and product states, and the free energy profiles for the different reaction paths. Two double proton transfer reactions were studied to validate the implemented method and simulation protocol, from which the independent and correlated proton transfer processes are identified in two representative systems, respectively. This protocol can be generalized to various kinds of chemical reactions for both academic studies and industry applications, such as in exploration and optimization of potential reactions in DNA encoded compound library and halogen or deuterium substitution of the hit discovery and lead optimization stages of drug design via providing a better understanding of the reaction mechanism along the designed chemical reaction pathways.

Nonnative contact effects in protein folding

The folding simulations of three ββα-motifs and β-barrel structured proteins (NTL9, NuG2b, and CspA) were performed to determine the important roles of native and nonnative contacts in protein folding.

Assessing AMBER force fields for protein folding in an implicit solvent

Molecular dynamics (MD) simulation implemented with a state-of-the-art protein force field and implicit solvent model is an attractive approach to investigate protein folding, one of the most perplexing problems in molecular biology. But how well can force fields developed independently of implicit solvent models work together in reproducing diverse protein native structures and measuring the corresponding folding thermodynamics is not always clear. In this work, we performed enhanced sampling MD simulations to assess the ability of six AMBER force fields (FF99SBildn, FF99SBnmr, FF12SB, FF14ipq, FF14SB, and FF14SBonlysc) as coupled with a recently improved pair-wise GB-Neck2 model in modeling the folding of two helical and two β-sheet peptides. Whilst most of the tested force fields can yield roughly similar features for equilibrium conformational ensembles and detailed folding free-energy profiles for short α-helical TC10b in an implicit solvent, the measured counterparts are significantly discrepant in the cases of larger or β-structured peptides (HP35, 1E0Q, and GTT). Additionally, the calculated folding/unfolding thermodynamic quantities can only partially match the experimental data. Although a combination of the force fields and GB-Neck2 implicit model able to describe all aspects of the folding transitions towards the native structures of all the considered peptides was not identified, we found that FF14SBonlysc coupled with the GB-Neck2 model seems to be a reasonably balanced combination to predict peptide folding preferences.

The effects of implicit modeling of nonpolar solvation on protein folding simulations

Implicit solvent models, in which the polar and nonpolar solvation free-energies of solute molecules are treated separately, have been widely adopted for molecular dynamics simulation of protein folding. While the development of the implicit models is mainly focused on the methodological improvement and key parameter optimization for polar solvation, nonpolar solvation has been either ignored or described by a simplistic surface area (SA) model. In this work, we performed the folding simulations of multiple β-hairpin and α-helical proteins with varied surface tension coefficients embedded in the SA model to clearly demonstrate the effects of nonpolar solvation treated by a popular SA model on protein folding. The results indicate that the change in the surface tension coefficient does not alter the ability of implicit solvent simulations to reproduce a protein native structure but indeed controls the components of the equilibrium conformational ensemble and modifies the energetic characterization of the folding transition pathway. The suitably set surface tension coefficient can yield explicit solvent simulations and/or experimentally suggested folding mechanism of protein. In addition, the implicit treatment of both polar and nonpolar components of solvation free-energy contributes to the overestimation of the secondary structure in implicit solvent simulations.

Efficient sampling over rough energy landscapes with high barriers: A combination of metadynamics with integrated tempering sampling

In order to efficiently overcome high free energy barriers embedded in a complex energy landscape and calculate overall thermodynamics properties using molecular dynamics simulations, we developed and implemented a sampling strategy by combining the metadynamics with (selective) integrated tempering sampling (ITS/SITS) method. The dominant local minima on the potential energy surface (PES) are partially exalted by accumulating history-dependent potentials as in metadynamics, and the sampling over the entire PES is further enhanced by ITS/SITS. With this hybrid method, the simulated system can be rapidly driven across the dominant barrier along selected collective coordinates. Then, ITS/SITS ensures a fast convergence of the sampling over the entire PES and an efficient calculation of the overall thermodynamic properties of the simulation system. To test the accuracy and efficiency of this method, we first benchmarked this method in the calculation of ϕ - ψ distribution of alanine dipeptide in explicit solvent. We further applied it to examine the design of template molecules for aromatic meta-C-H activation in solutions and investigate solution conformations of the nonapeptide Bradykinin involving slow cis-trans isomerizations of three proline residues.

Combine umbrella sampling with integrated tempering method for efficient and accurate calculation of free energy changes of complex energy surface

Umbrella sampling is an efficient method for the calculation of free energy changes of a system along well-defined reaction coordinates. However, when there exist multiple parallel channels along the reaction coordinate or hidden barriers in directions perpendicular to the reaction coordinate, it is difficult for conventional umbrella sampling to reach convergent sampling within limited simulation time. Here, we propose an approach to combine umbrella sampling with the integrated tempering sampling method. The umbrella sampling method is applied to chemically more relevant degrees of freedom that possess significant barriers. The integrated tempering sampling method is used to facilitate the sampling of other degrees of freedom which may possess statistically non-negligible barriers. The combined method is applied to two model systems, butane and ACE-NME molecules, and shows significantly improved sampling efficiencies as compared to standalone conventional umbrella sampling or integrated tempering sampling approaches. Further analyses suggest that the enhanced performance of the new method come from the complemented advantages of umbrella sampling with a well-defined reaction coordinate and integrated tempering sampling in orthogonal space. Therefore, the combined approach could be useful in the simulation of biomolecular processes, which often involves sampling of complex rugged energy landscapes.

From thermodynamics to kinetics: enhanced sampling of rare events

Despite great advances in molecular dynamics simulations, there remain large gaps between the simulations and experimental observations in terms of the time and length scales that can be approached. Developing fast and accurate algorithms and methods is of ultimate importance to bridge these gaps. In this Account, we briefly summarize recent efforts in such directions. In particular, we focus on integrated tempering sampling. The efficiency of this sampling method has been demonstrated by applications to a range of chemical and biological problems: protein folding, molecular cluster structure searches, and chemical reactions. The combination of integrated tempering sampling and a trajectory sampling method allows the calculation of rate constants and reaction pathways without predefined collective coordinates.

Fast helix formation in the B domain of protein A revealed by site-specific infrared probes

Comparison of experimental and computational protein folding studies can be difficult because of differences in structural resolution. Isotope-edited infrared spectroscopy offers a direct measure of structural changes involved in protein folding at the single-residue level. Here we demonstrate the increased resolution of site-specific infrared probes to the peptide backbone in the B domain of staphylococcal protein A (BdpA). (13)C═(18)O-labeled methionine was incorporated into each of the helices using recombinant protein expression. Laser-induced temperature jumps coupled with infrared spectroscopy were used to probe changes in the peptide backbone on the submillisecond time scale. The relaxation kinetics of the buried helices, solvated helices, and labeled positions were measured independently by probing the corresponding bands assigned in the amide I region. Using these wavelength-dependent measurements, we observe a fast nanosecond phase and slower microsecond phase at each position. We find at least partial formation of helices 1-3 in the fast intermediate state that precedes the transition state. These measurements provide direct, time-resolved experimental evidence of the early formation of partial helical structure in helices 1 and 3, supporting folding models proposed by computer simulations.

Important roles of hydrophobic interactions in folding and charge interactions in misfolding of α-helix bundle protein

An enhanced-sampling molecular dynamics simulation is presented to quantitatively demonstrate the important roles of hydrophobic and charge interactions in the folding and misfolding of α-helix bundle protein, respectively.

Improvement of alkali stability and thermostability of Paenibacillus campinasensis Family-11 xylanase by directed evolution and site-directed mutagenesis

The extreme process condition of high temperature and high alkali limits the applications of most of natural xylanases in pulp and paper industry. Recently, various methods of protein engineering have been used to improve the thermal and alkalic tolerance of xylanases. In this work, directed evolution and site-directed mutagenesis were performed to obtain a mutant xylanase improved both on alkali stability and thermostability from the native Paenibacillus campinasensis Family-11 xylanase (XynG1-1). Mutant XynG1-1B43 (V90R/P172H) with two units increased in the optimum pH (pH 7.0–pH 9.0) and significant improvement on alkali stability was selected from the second round of epPCR library. And the further thermoduric mutant XynG1-1B43cc16 (V90R/P172H/T84C-T182C/D16Y) with 10 °C increased in the optimum temperature (60–70 °C) was then obtained by introducing a disulfide bridge (T84C-T182C) and a single amino acid substitution (D16Y) to XynG1-1B43 using site-directed mutagenesis. XynG1-1B43cc16 also showed higher thermostability and catalytic efficiency (k  cat/K  m) than that of wild-type (XynG1-1) and XynG1-1B43. The attractive improved properties make XynG1-1B43cc16 more suitable for bioleaching of cotton stalk pulp under the extreme process condition of high temperature (70 °C) and high alkali (pH 9.0).