Exploring the helix-coil transition via all-atom equilibrium ensemble simulations

Atomic-scale characterization of conformational changes in the preQ₁ riboswitch aptamer upon ligand binding

Riboswitches are mRNA structural elements that act as intracellular sensors of small-molecule metabolites. By undergoing conformational changes capable of modulating translation or terminating transcription, riboswitches are able to play a role in regulating the concentration of essential metabolites in the cell. Computer-guided fluorescence experiments were carried out to interrogate molecular dynamics and conformational changes in the minimal riboswitch aptamer that binds 7-aminomethyl-7-deazaguanine (preQ₁). Our combined experimental results and computational analysis suggest that the preQ₁ riboswitch apo form is structured but shows no evidence of a ligand-binding pocket. Simulations of the apo and bound forms indicate a large conformational change is triggered by the breaking of the Watson-Crick base pairing of nucleotides G11 and C31 upon preQ₁ removal, followed by collapse of the pocket due to interfering π-stacking. Computational predictions of local aptamer dynamics were validated by fluorescence experiments employing 2-aminopurine substitutions. In-line probing reactions confirmed that fluorophore-labeled riboswitches retain similar higher-order structural features as the unlabeled aptamer upon ligand binding, although their affinity for the ligand is reduced by the introduction of the fluorescent reporter.

Structural insights into the pre-amyloid tetramer of β-2-microglobulin from covalent labeling and mass spectrometry

The main pathogenic process underlying dialysis-related amyloidosis is the accumulation of β-2-microglobulin (β2m) as amyloid fibrils in the musculoskeletal system, and some evidence suggests that Cu(II) may play a role in β2m amyloid formation. Cu(II)-induced β2m fibril formation is preceded by the formation of discrete, oligomeric intermediates, including dimers, tetramers, and hexamers. In this work, we use selective covalent labeling reactions combined with mass spectrometry to investigate the amino acids responsible for mediating tetramer formation in wild-type β2m. By comparing the labeling patterns of the monomer, dimer, and tetramer, we find evidence that the tetramer interface is formed by the interaction of D strands from one dimer unit and G strands from another dimer unit. These covalent labeling data along with molecular dynamics calculations allow the construction of a tetramer model that indicates how the protein might proceed to form even higher-order oligomers.

Amyloid-associated nucleic acid hybridisation

Nucleic acids promote amyloid formation in diseases including Alzheimer's and Creutzfeldt-Jakob disease. However, it remains unclear whether the close interactions between amyloid and nucleic acid allow nucleic acid secondary structure to play a role in modulating amyloid structure and function. Here we have used a simplified system of short basic peptides with alternating hydrophobic and hydrophilic amino acid residues to study nucleic acid - amyloid interactions. Employing biophysical techniques including X-ray fibre diffraction, circular dichroism spectroscopy and electron microscopy we show that the polymerized charges of nucleic acids concentrate and enhance the formation of amyloid from short basic peptides, many of which would not otherwise form fibres. In turn, the amyloid component binds nucleic acids and promotes their hybridisation at concentrations below their solution K(d), as shown by time-resolved FRET studies. The self-reinforcing interactions between peptides and nucleic acids lead to the formation of amyloid nucleic acid (ANA) fibres whose properties are distinct from their component polymers. In addition to their importance in disease and potential in engineering, ANA fibres formed from prebiotically-produced peptides and nucleic acids may have played a role in early evolution, constituting the first entities subject to Darwinian evolution.

Staphylococcus lugdunensis strain with a modified PBP1A/1B expressing resistance to β-lactams

We describe for the first time the emergence of an mecA-negative Staphylococcus lugdunensis strain with a modified PBP1A/1B that expresses resistance to all β-lactams. A duplication of the tetrapeptide S(569)AYG, which is part of the transpeptidase domain of PBP1A/1B and closely located to the K(583)TG catalytic motif, was associated with this unusual phenotype.

Strength of hydrogen bond network takes crucial roles in the dissociation process of inhibitors from the HIV-1 protease binding pocket

To understand the underlying mechanisms of significant differences in dissociation rate constant among different inhibitors for HIV-1 protease, we performed steered molecular dynamics (SMD) simulations to analyze the entire dissociation processes of inhibitors from the binding pocket of protease at atomistic details. We found that the strength of hydrogen bond network between inhibitor and the protease takes crucial roles in the dissociation process. We showed that the hydrogen bond network in the cyclic urea inhibitors AHA001/XK263 is less stable than that of the approved inhibitor ABT538 because of their large differences in the structures of the networks. In the cyclic urea inhibitor bound complex, the hydrogen bonds often distribute at the flap tips and the active site. In contrast, there are additional accessorial hydrogen bonds formed at the lateral sides of the flaps and the active site in the ABT538 bound complex, which take crucial roles in stabilizing the hydrogen bond network. In addition, the water molecule W301 also plays important roles in stabilizing the hydrogen bond network through its flexible movement by acting as a collision buffer and helping the rebinding of hydrogen bonds at the flap tips. Because of its high stability, the hydrogen bond network of ABT538 complex can work together with the hydrophobic clusters to resist the dissociation, resulting in much lower dissociation rate constant than those of cyclic urea inhibitor complexes. This study may provide useful guidelines for design of novel potent inhibitors with optimized interactions.

What is the time scale for α-helix nucleation?

Helix formation is an elementary process in protein folding, influencing both the rate and mechanism of the global folding reaction. Yet, because helix formation is less cooperative than protein folding, the kinetics are often multiexponential, and the observed relaxation times are not straightforwardly related to the microscopic rates for helix nucleation and elongation. Recent ultrafast spectroscopic measurements on the peptide Ac-WAAAH(+)-NH(2) were best fit by two relaxation modes on the ∼0.1-1 ns time scale, (1) apparently much faster than had previously been experimentally inferred for helix nucleation. Here, we use replica-exchange molecular dynamics simulations with an optimized all-atom protein force field (Amber ff03w) and an accurate water model (TIP4P/2005) to study the kinetics of helix formation in this peptide. We calculate temperature-dependent microscopic rate coefficients from the simulations by treating the dynamics between helical states as a Markov process using a recently developed formalism. The fluorescence relaxation curves obtained from simulated temperature jumps are in excellent agreement with the experimentally determined results. We find that the kinetics are multiphasic but can be approximated well by a double-exponential function. The major processes contributing to the relaxation are the shrinking of helical states at the C-terminal end and a faster re-equilibration among coil states. Despite the fast observed relaxation, the helix nucleation time is estimated from our model to be 20-70 ns at 300 K, with a dependence on temperature well described by Arrhenius kinetics.

Accelerated convergence of molecular free energy via superposition approximation-based reference states

The free energy of a molecular system can, at least in principle, be computed by thermodynamic perturbation from a reference system whose free energy is known. The convergence of such a calculation depends critically on the conformational overlap between the reference and the physical systems. One approach to defining a suitable reference system is to construct it from the one-dimensional marginal probability distribution functions (PDFs) of internal coordinates observed in a molecular simulation. However, the conformational overlap of this reference system tends to decline steeply with increasing dimensionality, due to the neglect of correlations among the coordinates. Here, we test a reference system that can account for pairwise correlations among the internal coordinates, as captured by their two-dimensional marginal PDFs derived from a molecular simulation. Incorporating pairwise correlations in the reference system is found to dramatically improve the convergence of the free energy estimates relative to the first-order reference system, due to increased conformational overlap with the physical distribution.

Structural basis for the role of LYS220 as proton donor for nucleotidyl transfer in HIV-1 reverse transcriptase

Biochemical studies by Castro et al. have recently revealed a crucial role for a general acid in the catalysis of nucleic acid transfer in distinct classes of polymerases. For HIV-RT LYS220 was identified as proton donor. This was unanticipated from a structural point of view, since in all ternary crystal structures of HIV-RT LYS220 are too distant from the active site to fulfill this role. In this work molecular dynamics simulations were used to reveal the dynamics of HIV-RT and to provide structural evidence for the role of LYS220. During a 1μs molecular dynamics simulation LYS220 migrates toward the active site and occupies several positions enabling direct and water mediated proton transfer towards pyrophosphate. A combination of quantum mechanical and molecular mechanics methods was used to validate the different modes of interaction.

Optimization of parameters for molecular dynamics simulation using smooth particle-mesh Ewald in GROMACS 4.5

Based on our critique of requirements for performing an efficient molecular dynamics simulation with the particle-mesh Ewald (PME) implementation in GROMACS 4.5, we present a computational tool to enable the discovery of parameters that produce a given accuracy in the PME approximation of the full electrostatics. Calculations on two parallel computers with different processor and communication structures showed that a given accuracy can be attained over a range of parameter space, and that the attributes of the hardware and simulation system control which parameter sets are optimal. This information can be used to find the fastest available PME parameter sets that achieve a given accuracy. We hope that this tool will stimulate future work to assess the impact of the quality of the PME approximation on simulation outcomes, particularly with regard to the trade-off between cost and scientific reliability in biomolecular applications.

Comparison of models of thrombin-binding 15-mer DNA aptamer by molecular dynamics simulation

Two models of 15-mer thrombin-binding DNA aptamer (15TGT) were comparatively analyzed by molecular dynamics simulation using the GROMACS software package. The two original models of 15TGT were obtained by NMR and X-ray analyses. The models significantly differ in the topology of loops and the direction of oligodeoxyribonucleotide chain. The evolution of the two structures in parm99 force fields and parmbsc0 optimized for nucleic acids was analyzed in our adaptation of GROMACS architecture. It is shown that the best system for description of the 15TGT structure is the model obtained by X-ray analysis in the parmbsc0 force field.

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.

Nucleotide binding switches the information flow in ras GTPases

The Ras superfamily comprises many guanine nucleotide-binding proteins (G proteins) that are essential to intracellular signal transduction. The guanine nucleotide-dependent intrinsic flexibility patterns of five G proteins were investigated in atomic detail through Molecular Dynamics simulations of the GDP- and GTP-bound states (S^GDP and S^GTP, respectively). For all the considered systems, the intrinsic flexibility of S^GDP was higher than that of S^GTP, suggesting that Guanine Exchange Factor (GEF) recognition and nucleotide switch require higher amplitude motions than effector recognition or GTP hydrolysis. Functional mode, dynamic domain, and interaction energy correlation analyses highlighted significant differences in the dynamics of small G proteins and Gα proteins, especially in the inactive state. Indeed, S^GDP of Gα_t, is characterized by a more extensive energy coupling between nucleotide binding site and distal regions involved in GEF recognition compared to small G proteins, which attenuates in the active state. Moreover, mechanically distinct domains implicated in nucleotide switch could be detected in the presence of GDP but not in the presence of GTP. Finally, in small G proteins, functional modes are more detectable in the inactive state than in the active one and involve changes in solvent exposure of two highly conserved amino acids in switches I and II involved in GEF recognition. The average solvent exposure of these amino acids correlates in turn with the rate of GDP release, suggesting for them either direct or indirect roles in the process of nucleotide switch. Collectively, nucleotide binding changes the information flow through the conserved Ras-like domain, where GDP enhances the flexibility of mechanically distinct portions involved in nucleotide switch, and favors long distance allosteric communication (in Gα proteins), compared to GTP.

The Ras superfamily comprises many guanine nucleotide-binding proteins (G proteins) that are essential to intracellular signal transduction. These proteins act biologically as molecular switches cycling between ON and OFF states, thereby controlling a variety of processes ranging from cell growth and differentiation to vesicular and nuclear transport. In spite of the extremely high biological and medical relevance of the Ras GTPase superfamily, a comprehensive structural/dynamic view of the trans-family and family-specific functioning mechanisms is still lacking. In this study, we gained insights into the functional dynamics of Ras GTPases by deciphering the dynamic information encrypted in the topology of these proteins depending on the nucleotide-bound state, i.e. GDP- or GTP-bound (S^GDP and S^GTP, respectively). Collectively, nucleotide binding changes the information flow through the conserved Ras-like domain, where GDP enhances the flexibility of mechanically distinct portions involved in nucleotide switch, and favors long distance allosteric communication (in Gα proteins), compared to GTP. Functional dynamics is instrumental in GDP switch, which for the members of the Gα family, different from small G proteins, requires allosteric communication between nucleotide and Guanine Exchange Factor binding sites.

Molecular dynamics simulations of the folding of poly(alanine) peptides

The secondary structures and the shapes of long-chain polyalanine (PA) molecules were investigated by all-atom molecular dynamics simulations using a modified Amber force field. Homopolymers of polyaminoacids such as PA are convenient models to study the mechanism of protein folding. It was found that the conformational structures of PA peptides are highly sensitive to the chain length. In the absence of solvent, straight α-helices dominate in short (n ∼ 20) peptides at room temperature. A shape transition occurs at a chain length n of 40-45; the compact helix-turn-helix structure (the double-leg hairpin) becomes favored over a straight α-helix. For n=60, double-leg and the triple-leg hairpins are the only structures present in PA molecules. An exploration of a chain organization in a cubic cavity revealed a clear predisposition of PA molecules for additional breaks in α-helices and the formation of multifolded hairpins. Furthermore, under confinement the hairpin structure becomes much looser, the antiparallel positions of helical stems are disturbed, and a sizeable proportion of the helical stems are transformed from α-helices into 3(10)-helices.

Alchemical free energy methods for drug discovery: progress and challenges

Improved rational drug design methods are needed to lower the cost and increase the success rate of drug discovery and development. Alchemical binding free energy calculations, one potential tool for rational design, have progressed rapidly over the past decade, but still fall short of providing robust tools for pharmaceutical engineering. Recent studies, especially on model receptor systems, have clarified many of the challenges that must be overcome for robust predictions of binding affinity to be useful in rational design. In this review, inspired by a recent joint academic/industry meeting organized by the authors, we discuss these challenges and suggest a number of promising approaches for overcoming them.

The dynamics of Ca2+ ions within the solvation shell of calbindin D9k

The encounter of a Ca²⁺ ion with a protein and its subsequent binding to specific binding sites is an intricate process that cannot be fully elucidated from experimental observations. We have applied Molecular Dynamics to study this process with atomistic details, using Calbindin D9k (CaB) as a model protein. The simulations show that in most of the time the Ca²⁺ ion spends within the Debye radius of CaB, it is being detained at the 1st and 2nd solvation shells. While being detained near the protein, the diffusion coefficient of the ion is significantly reduced. However, due to the relatively long period of detainment, the ion can scan an appreciable surface of the protein. The enhanced propagation of the ion on the surface has a functional role: significantly increasing the ability of the ion to scan the protein's surface before being dispersed to the bulk. The contribution of this mechanism to Ca²⁺ binding becomes significant at low ion concentrations, where the intervals between successive encounters with the protein are getting longer. The efficiency of the surface diffusion is affected by the distribution of charges on the protein's surface. Comparison of the Ca²⁺ binding dynamics in CaB and its E60D mutant reveals that in the wild type (WT) protein the carboxylate of E60 function as a preferred landing-site for the Ca²⁺ arriving from the bulk, followed by delivering it to the final binding site. Replacement of the glutamate by aspartate significantly reduced the ability to transfer Ca²⁺ ions from D60 to the final binding site, explaining the observed decrement in the affinity of the mutated protein to Ca²⁺.

Towards a rational spacer design for bivalent inhibition of estrogen receptor

Estrogen receptors are known drug targets that have been linked to several kinds of cancer. The structure of the estrogen receptor ligand binding domain is available and reveals a homodimeric layout. In order to improve the binding affinity of known estrogen receptor inhibitors, bivalent compounds have been developed that consist of two individual ligands linked by flexible tethers serving as spacers. So far, binding affinities of the bivalent compounds do not surpass their monovalent counterparts. In this article, we focus our attention on the molecular spacers that are used to connect the individual ligands to form bivalent compounds, and describe their thermodynamic contribution during the ligand binding process. We use computational methods to predict structural and entropic parameters of different spacer structures. We find that flexible spacers introduce a number of effects that may interfere with ligand binding and possibly can be connected to the low binding affinities that have been reported in binding assays. Based on these findings, we try to provide guidelines for the design of novel molecular spacers.

Taming the complexity of protein folding

Protein folding is an important problem in structural biology with significant medical implications, particularly for misfolding disorders like Alzheimer's disease. Solving the folding problem will ultimately require a combination of theory and experiment, with theoretical models providing a comprehensive view of folding and experiments grounding these models in reality. Here we review progress towards this goal over the past decade, with an emphasis on recent theoretical advances that are empowering chemically detailed models of folding and the new results these technologies are providing. In particular, we discuss new insights made possible by Markov state models (MSMs), including the role of non-native contacts and the hub-like character of protein folded states.

Pseudouridylation of 23S rRNA helix 69 promotes peptide release by release factor RF2 but not by release factor RF1

Pseudouridine [Ψ] is a frequent base modification in the ribosomal RNA [rRNA] and may be involved in the modulation of the conformational flexibility of rRNA helix-loop structures during protein synthesis. Helix 69 of 23S rRNA contains pseudouridines at the positions 1911, 1915 and 1917 which are formed by the helix 69-specific synthase RluD. The growth defect caused by the lack of RluD can be rescued by mutations in class I release factor RF2, indicating a role for helix 69 pseudouridines in translation termination. We investigated the role of helix 69 pseudouridines in peptide release by release factors RF1 and RF2 in an in vitro system consisting of purified components of the Escherichia coli translation apparatus. Lack of all three pseudouridines in helix 69 compromised the activity of RF2 about 3-fold but did not significantly affect the activity of RF1. Reintroduction of pseudouridines into helix 69 by RluD-treatment restored the activity of RF2 in peptide release. A Ψ-to-C substitution at the 1917 position caused an increase in the dissociation rate of RF1 and RF2 from the postrelease ribosome. Our results indicate that the presence of all three pseudouridines in helix 69 stimulates peptide release by RF2 but has little effect on the activity of RF1. The interactions around the pseudouridine at the 1917 position appear to be most critical for a proper interaction of helix 69 with release factors.

Molecular dynamics of DNA: comparison of force fields and terminal nucleotide definitions

Despite DNA being a very important target for several proteins and drugs, molecular dynamics simulations with nucleic acids still encompass many challenges, such as the reliability of the chosen force field. In this paper, we carried out molecular dynamics simulations of the Dickerson-Drew dodecamer comparing GROMOS 53A6 and AMBER 03 force fields. While the AMBER force field presents specific topologies for the 5' and 3' terminal nucleotides, the GROMOS force field considers all nucleotides in the same way. To investigate the effects of the terminal nucleotide definitions, both force fields were modified to be applied in the two possible ways: with or without specific terminal nucleotide topologies. The analysis of global stability (rmsd, number of base pairs and hydrogen bonds) showed that both systems simulated with AMBER were stable, while the system simulated with the original GROMOS topologies was very unstable after 5 ns. When specific terminal topologies were included for GROMOS force field, DNA denaturation was delayed until 15 ns, but not avoided. The alpha/gamma transitions also displayed a strong dependence on the force field, but not on the terminal nucleotide definitions: AMBER simulations mainly explored configurations corresponding to the global minimum, while GROMOS simulations exhibited, very early in the simulations, an extensive sampling of local minima that may facilitate transitions to A-DNA isoform. The epsilon/zeta sampling was dependent both on the force field and on the terminal nucleotide definitions: while the AMBER simulations displayed well-defined B-I --> B-II transitions, the GROMOS force field clearly favored the B-I conformation. Also, the system simulated with the original GROMOS topologies displayed uncoupled epsilon/zeta transitions, leading to noncanonical conformations, but this was reverted when the new terminal nucleotide topologies were applied. Finally, the GROMOS force field leads to strong geometrical deformations on the DNA (overestimated groove widths and roll and strongly underestimated twist and slide), which restrict the use of GROMOS force field in long time scale DNA simulations unless a further reparametrization is made.

Serial tempering without exchange

Serial tempering is a computational method that turns the temperature T (or more generally any independent λ parameter) into a dynamical variable. It is shown that, under conditions for which this variable is fast, serial tempering is equivalent to the umbrella sampling method with a single effective potential. This equivalence is demonstrated using both a small one-dimensional system and a small solvated peptide. The suggestion is then made to replace the serial tempering protocol with the equivalent umbrella sampling calculation. This approach, serial tempering without exchange (STeWiE), has the same performance as serial tempering in the limit that exchanges are frequent, is simpler to implement, and has fewer adjustable parameters than conventional serial tempering. The equivalence of serial tempering and STeWiE also provides a convenient route for estimating and optimizing the performance of serial tempering simulations and other generalized-ensemble methods.

Experimental verification of force fields for molecular dynamics simulations using Gly-Pro-Gly-Gly

Experimental NMR verification of MD simulations using 12 different force fields (AMBER, CHARMM, GROMOS, and OPLS-AA) and 5 different water models has been undertaken to identify reliable MD protocols for structure and dynamics elucidations of small open chain peptides containing Gly and Pro. A conformationally flexible tetrapeptide Gly-Pro-Gly-Gly was selected for NMR (3)J-coupling, chemical shift, and internuclear distance measurements, followed by their calculations using 2 μs long MD simulations in water. In addition, Ramachandran population maps for Pro-2 and Gly-3 residues of GPGG obtained from MD simulations were used for detailed comparisons with similar maps from the protein data bank (PDB) for large number of Gly and Pro residues in proteins. The MD simulations revealed strong dependence of the populations and geometries of preferred backbone and side chain conformations, as well as the time scales of the peptide torsional transitions on the force field used. On the basis of the analysis of the measured and calculated data, AMBER99SB is identified as the most reliable force field for reproducing NMR measured parameters, which are dependent on the peptide backbone and the Pro side chain geometries and dynamics. Ramachandran maps showing the dependence of conformational populations as a function of backbone ϕ/ψ angles for Pro-2 and Gly-3 residues of GPGG from MD simulations using AMBER99SB, AMBER03, and CHARMM were found to resemble similar maps for Gly and Pro residues from the PDB survey. Three force fields (AMBER99, AMBER99ϕ, and AMBER94) showed the least satisfactory agreement with both the solution NMR and the PDB survey data. The poor performance of these force fields is attributed to their propensity to overstabilize helical peptide backbone conformations at the Pro-2 and Gly-3 residues. On the basis of the similarity of the MD and PDB Ramachandran plots, the following sequence of transitions is suggested for the Gly backbone conformation: α(L) ⇆ β(PR) ⇆ β(S) ⇆ β(P) ⇆ α, where backbone secondary structures α(L) and α are associated with helices and turns, β(P) and β(PR) correspond to the left- and right-handed polyproline II structures and β(S) denotes the fully stretched backbone conformation. Compared to the force field dependence, less significant, but noteworthy, variations in the populations of the peptide backbone conformations were observed. For different solvent models considered, a correlation was noted between the number of torsional transitions in GPGG and the water self-diffusion coefficient on using TIP3P, TIP4P, and TIP5P models. In addition to MD results, we also report DFT derived Karplus relationships for Gly and Pro residues using B972 and B3LYP functionals.

Crystal structures, dynamics and functional implications of molybdenum-cofactor biosynthesis protein MogA from two thermophilic organisms

Molybdenum-cofactor (Moco) biosynthesis is an evolutionarily conserved pathway in almost all kingdoms of life, including humans. Two proteins, MogA and MoeA, catalyze the last step of this pathway in bacteria, whereas a single two-domain protein carries out catalysis in eukaryotes. Here, three crystal structures of the Moco-biosynthesis protein MogA from the two thermophilic organisms Thermus thermophilus (TtMogA; 1.64 Å resolution, space group P2(1)) and Aquifex aeolicus (AaMogA; 1.70 Å resolution, space group P2(1) and 1.90 Å resolution, space group P1) have been determined. The functional roles and the residues involved in oligomerization of the protein molecules have been identified based on a comparative analysis of these structures with those of homologous proteins. Furthermore, functional roles have been proposed for the N- and C-terminal residues. In addition, a possible protein-protein complex of MogA and MoeA has been proposed and the residues involved in protein-protein interactions are discussed. Several invariant water molecules and those present at the subunit interfaces have been identified and their possible structural and/or functional roles are described in brief. In addition, molecular-dynamics and docking studies with several small molecules (including the substrate and the product) have been carried out in order to estimate their binding affinities towards AaMogA and TtMogA. The results obtained are further compared with those obtained for homologous eukaryotic proteins.

Ligand-induced conformational capture of a synthetic tetracycline riboswitch revealed by pulse EPR

RNA aptamers are in vitro-selected binding domains that recognize their respective ligand with high affinity and specificity. They are characterized by complex three-dimensional conformations providing preformed binding pockets that undergo conformational changes upon ligand binding. Small molecule-binding aptamers have been exploited as synthetic riboswitches for conditional gene expression in various organisms. In the present study, double electron-electron resonance (DEER) spectroscopy combined with site-directed spin labeling was used to elucidate the conformational transition of a tetracycline aptamer upon ligand binding. Different sites were selected for post-synthetic introduction of either the (1-oxyl-2,2,5,5-tetramethylpyrroline-3-methyl) methanethiosulfonate by reaction with a 4-thiouridine modified RNA or of 4-isocyanato-2,6-tetramethylpiperidyl-N-oxid spin label by reaction with 2'-aminouridine modified RNA. The results of the DEER experiments indicate the presence of a thermodynamic equilibrium between two aptamer conformations in the free state and capture of one conformation upon tetracycline binding.

Calculation of local water densities in biological systems: a comparison of molecular dynamics simulations and the 3D-RISM-KH molecular theory of solvation

Water plays a unique role in all living organisms. Not only is it nature's ubiquitous solvent, but it also actively takes part in many cellular processes. In particular, the structure and properties of interfacial water near biomolecules such as proteins are often related to the function of the respective molecule. It can therefore be highly instructive to study the local water density around solutes in cellular systems, particularly when solvent-mediated forces such as the hydrophobic effect are relevant. Computational methods such as molecular dynamics (MD) simulations seem well suited to study these systems at the atomic level. However, due to sampling requirements, it is not clear that MD simulations are, indeed, the method of choice to obtain converged densities at a given level of precision. We here compare the calculation of local water densities with two different methods: MD simulations and the three-dimensional reference interaction site model with the Kovalenko-Hirata closure (3D-RISM-KH). In particular, we investigate the convergence of the local water density to assess the required simulation times for different levels of resolution. Moreover, we provide a quantitative comparison of the densities calculated with MD and with 3D-RISM-KH and investigate the effect of the choice of the water model for both methods. Our results show that 3D-RISM-KH yields density distributions that are very similar to those from MD up to a 0.5 Å resolution, but for significantly reduced computational cost. The combined use of MD and 3D-RISM-KH emerges as an auspicious perspective for efficient solvent sampling in dynamical systems.

Practical considerations for building GROMOS-compatible small-molecule topologies

Molecular dynamics simulations are being applied to increasingly complex systems, including those involving small endogenous compounds and drug molecules. In order to obtain meaningful and accurate data from these simulations, high-quality topologies for small molecules must be generated in a manner that is consistent with the derivation of the force field applied to the system. Often, force fields are designed for use with macromolecules such as proteins, making their transferability to other species challenging. Investigators are increasingly attracted to automated topology generation programs, although the quality of the resulting topologies remains unknown. Here we assess the applicability of the popular PRODRG server that generates small-molecule topologies for use with the GROMOS family of force fields. We find that PRODRG does not reproduce topologies for even the most well-characterized species in the force field due to inconsistent charges and charge groups. We assessed the effects of PRODRG-derived charges on several systems: pure liquids, amino acids at a hydrophobic-hydrophilic interface, and an enzyme-cofactor complex. We found that partial atomic charges generated by PRODRG are largely incompatible with GROMOS force fields, and the behavior of these systems deviates substantially from that of simulations using GROMOS parameters. We conclude by proposing several points as "best practices" for parametrization of small molecules under the GROMOS force fields.

Computational approach to ensure the stability of the favorable ATP binding site in E. coli Hfq

Bacterial Hfq is a highly conserved thermostable protein of about 10 kDa. The Hfq protein was discovered in 1968 as an E. coli host factor that was essential for replication of the bacteriophage Qβ. It is now clear that Hfq has many important physiological roles. In E. coli, Hfq mutants show a multiple stress response related phenotypes. Hfq is now known to regulate the translation of two major stress transcription factors RpoS and RpoE in Enterobacteria and mediates its plieotrophic effects through several mechanisms. It interacts with regulatory sRNA and facilitates their antisense interaction with their targets. It also acts independently to modulate mRNA decay and in addition acts as a repressor of mRNA translation. Recent paper from Arluison et al. provided the first evidence indicating that Hfq is an ATP-binding protein. They determined a plausible ATP-binding site in Hfq and tested Hfq's ATP-binding affinity and stoichiometry. Experimental data suggest that the ATP-binding by the Hfq-RNA complex results in its significant destabilization of the protein and the result also proves important role of Tyr25 that flanks the cleft and stabilizes the adenine portion of ATP, possibly via aromatic stacking. In our study, the ATP molecule was docked into the predicted binding cleft using GOLD docking software. The binding nature of ATP and its effect on Hfq-RNA complex was studied using molecular dynamics simulations. Importance of Tyr25 residue was monitored and revealed using mutational study on the modeled systems. Our data and the corresponding results point to one of Hfq functional structural consequences due to ATP binding and Tyr25Ala mutation.

Nitrile bonds as infrared probes of electrostatics in ribonuclease S

Three different nitrile-containing amino acids, p-cyanophenylalanine, m-cyanophenylalanine, and S-cyanohomocysteine, have been introduced near the active site of the semisynthetic enzyme ribonuclease S (RNase S) to serve as probes of electrostatic fields. Vibrational Stark spectra, measured directly on the probe-modified proteins, confirm the predominance of the linear Stark tuning rate in describing the sensitivity of the nitrile stretch to external electric fields, a necessary property for interpreting observed frequency shifts as a quantitative measure of local electric fields that can be compared with simulations. The X-ray structures of these nitrile-modified RNase variants and enzymatic assays demonstrate minimal perturbation to the structure and function, respectively, by the probes and provide a context for understanding the influence of the environment on the nitrile stretching frequency. We examine the ability of simulation techniques to recapitulate the spectroscopic properties of these nitriles as a means to directly test a computational electrostatic model for proteins, specifically that in the ubiquitous Amber-99 force field. Although qualitative agreement between theory and experiment is observed for the largest shifts, substantial discrepancies are observed in some cases, highlighting the ongoing need for experimental metrics to inform the development of theoretical models of electrostatic fields in proteins.

Scrutinizing molecular mechanics force fields on the submicrosecond timescale with NMR data

Protein dynamics on the atomic level and on the microsecond timescale has recently become accessible from both computation and experiment. To validate molecular dynamics (MD) at the submicrosecond timescale against experiment we present microsecond MD simulations in 10 different force-field configurations for two globular proteins, ubiquitin and the gb3 domain of protein G, for which extensive NMR data is available. We find that the reproduction of the measured NMR data strongly depends on the chosen force field and electrostatics treatment. Generally, particle-mesh Ewald outperforms cut-off and reaction-field approaches. A comparison to measured J-couplings across hydrogen bonds suggests that there is room for improvement in the force-field description of hydrogen bonds in most modern force fields. Our results show that with current force fields, simulations beyond hundreds of nanoseconds run an increased risk of undergoing transitions to nonnative conformational states or will persist within states of high free energy for too long, thus skewing the obtained population frequencies. Only for the AMBER99sb force field have such transitions not been observed. Thus, our results have significance for the interpretation of data obtained with long MD simulations, for the selection of force fields for MD studies and for force-field development. We hope that this comprehensive benchmark based on NMR data applied to many popular MD force fields will serve as a useful resource to the MD community. Finally, we find that for gb3, the force-field AMBER99sb reaches comparable accuracy in back-calculated residual dipolar couplings and J-couplings across hydrogen bonds to ensembles obtained by refinement against NMR data.

Non-bulk-like solvent behavior in the ribosome exit tunnel

As nascent proteins are synthesized by the ribosome, they depart via an exit tunnel running through the center of the large subunit. The exit tunnel likely plays an important part in various aspects of translation. Although water plays a key role in many bio-molecular processes, the nature of water confined to the exit tunnel has remained unknown. Furthermore, solvent in biological cavities has traditionally been characterized as either a continuous dielectric fluid, or a discrete tightly bound molecule. Using atomistic molecular dynamics simulations, we predict that the thermodynamic and kinetic properties of water confined within the ribosome exit tunnel are quite different from this simple two-state model. We find that the tunnel creates a complex microenvironment for the solvent resulting in perturbed rotational dynamics and heterogenous dielectric behavior. This gives rise to a very rugged solvation landscape and significantly retarded solvent diffusion. We discuss how this non-bulk-like solvent is likely to affect important biophysical processes such as sequence dependent stalling, co-translational folding, and antibiotic binding. We conclude with a discussion of the general applicability of these results to other biological cavities.