Torsion angle preference and energetics of small-molecule ligands bound to proteins

Small organic molecules can assume conformations in the protein-bound state that are significantly different from those in solution. We have analyzed the conformations of 21 common torsion motifs of small molecules extracted from crystal structures of protein-ligand complexes and compared them with their torsion potentials calculated by an ab initio DFT method. We find a good correlation between the potential energy of the torsion motifs and their conformational distribution in the protein-bound state: The most probable conformations of the torsion motifs agree well with the calculated global energy minima, and the lowest torsion-energy state becomes increasingly dominant as the torsion barrier height increases. The torsion motifs can be divided into 3 groups based on torsion barrier heights: high (>4 kcal/mol), medium (2-4 kcal/mol), and low (<2 kcal/mol). The calculated torsion energy profiles are predictive for the most preferred bound conformation for the high and medium barrier groups, the latter group common in druglike molecules. In the high-barrier group of druglike ligands, >95% of conformational torsions occur in the energy region <4 kcal/mol. The conformations of the torsion motifs in the protein-bound state can be modeled by a Boltzmann distribution with a temperature factor much higher than room temperature. This high-temperature factor, derived by fitting the theoretical model to the experimentally observed conformation occurrence of torsions, can be interpreted as the perturbation that proteins inflict on the conformation of the bound ligand. Using this model, it is calculated that the average strain energy of a torsion motif in ligands bound to proteins is approximately 0.6 kcal/mol, a result which can be related to the lower binding efficiency of larger ligands with more rotatable bonds. The above results indicate that torsion potentials play an important role in dictating ligand conformations in both the free and the bound states.     

EXCITATION-ENERGY TRANSFER BETWEEN TYROSINE AND TRYPTOPHAN IN PROTEINS EVALUATED BY THE SIMULTANEOUS MEASUREMENT OF FLUORESCENCE AND ABSORBANCE

Abstract— The efficiencies of the excitation–energy transfer from tyrosine to tryptophan residues in eight globular proteins in the native and denatured states are obtained by studying the wavelength dependence of the fluorescence quantum yield. The measurements are made over a wide wavelength range using a computer-controlled spectrophotometer which can measure the fluorescence and absorbance simultaneously in one sample solution (Wada et al. , 1980). The values of the energy transfer efficiencies ranged from 0.17 ± 0.12 to 0.69 ± 0.06 in the native state and from -0.04 ± 0.09 to 0.12 ± 0.06 in the denatured state. These values are considerably lower than the values reported by Kronman and Holmes (1971); in particular, an almost complete absence of energy transfer for the denatured state is shown.     

Photodissociation reaction of 1,2-diiodoethane in solution: a theoretical and X-ray diffraction study

Various molecular species are known to form during the photoreaction of C2H4I2 in the gas phase and in solution. We have studied all species involved in this reaction by ab initio and density functional theory (DFT) calculations: Geometries, energies, and vibrational frequencies of C2H4I2, bridged C2H4I*, anti C2H4I*, C4H4, I2, I3-, and the isomer C2H4I-I were calculated. The absorption peaks and oscillator strengths of selected species along the potential energy surface (PES) were calculated using time-dependent DFT and were compared with available experimental results. The calculated PES satisfactorily describes the observed reactions of the photoexcited C2H4I2 molecule. In the gas phase, there is only one reaction pathway: the first C-I bond ruptures followed by a secondary C-I breakage in the haloethyl radical C2H4I*. In solution, by contrast, another reaction channel, which is energetically more favored over the secondary dissociation, is switched on due to a solvation effect: the bridged C2H4I* can bind to the free iodine atom to form a C2H4I-I isomer without any energy barrier. The isomer can then break into C2H4 and I2. The rotational barriers in the gas phase and in solution were also calculated and compared. To provide experimental data on the structure of C2H4I2 in solution, the ground state structure of C2H4I2 in methanol was determined from static X-ray diffraction data using 88 keV (lambda = 0.14 A) X-rays. The structural parameters are compared with those from the theoretical results.     

sDFIRE: Sequence‐specific statistical energy function for protein structure prediction by decoy selections

An important unsolved problem in molecular and structural biology is the protein folding and structure prediction problem. One major bottleneck for solving this is the lack of an accurate energy to discriminate near‐native conformations against other possible conformations. Here we have developed sDFIRE energy function, which is an optimized linear combination of DFIRE (the Distance‐scaled Finite Ideal gas Reference state based Energy), the orientation dependent (polar‐polar and polar‐nonpolar) statistical potentials, and the matching scores between predicted and model structural properties including predicted main‐chain torsion angles and solvent accessible surface area. The weights for these scoring terms are optimized by three widely used decoy sets consisting of a total of 134 proteins. Independent tests on CASP8 and CASP9 decoy sets indicate that sDFIRE outperforms other state‐of‐the‐art energy functions in selecting near native structures and in the Pearson's correlation coefficient between the energy score and structural accuracy of the model (measured by TM‐score). © 2016 Wiley Periodicals, Inc.     

Hybrid QM/MM simulation of the hydration phenomena of dipalmitoylphosphatidylcholine headgroup

The polar headgroup of dipalmitoylphosphatidylcholine (DPPC) molecule both in gas phase and aqueous solution is investigated by the hybrid quantum mechanical/molecular mechanical (QM/MM) method, in which the polar head of DPPC molecule and the bound water molecules are treated with density functional theory (DFT), while the apolar hydrocarbon chain of DPPC molecule is treated with MM method. It is demonstrated that the hybrid QM/MM method is both accurate and efficient to describe the conformations of DPPC headgroup. Folded structures of headgroup are found in gas phase calculations. In this work, both monohydration and polyhydration phenomena are investigated. In monohydration, different water association sites are studied. Both the hydration energy and the quantum properties of DPPC and water molecules are calculated at the DFT level of theory after geometry optimization. The binding force of monohydration is estimated by using the scan method. In polyhydration, more extended conformations are found and hydration energies in different polyhydration styles are estimated.     

The dynamics of conformational isomerization in flexible biomolecules. I. Hole-filling spectroscopy of N-acetyl tryptophan methyl amide and N-acetyl tryptophan amide

The conformational isomerization dynamics of N-acetyl tryptophan methyl amide (NATMA) and N-acetyl tryptophan amide (NATA) have been studied using the methods of IR-UV hole-filling spectroscopy (HFS) and IR-induced population transfer spectroscopy (IR-PTS), which were developed for this purpose. Single conformations of these molecules were selectively excited in well-defined NH stretch fundamentals. This excess energy was used to drive conformational isomerization. By carrying out the infrared excitation early in a supersonic expansion, the excited molecules were recooled into their zero-point levels, partially refilling the hole created in the ground state population of one of the conformers, and creating gains in population in other conformers. These changes in population were detected using laser-induced fluorescence downstream in the expansion. In HFS, the IR wavelength is fixed and the UV laser tuned in order to determine where the population went following selective infrared excitation. In IR-PTS, the UV is fixed to monitor the population of a given conformation, and the IR is tuned to record the IR-induced changes in the population of the monitored conformer. Besides demonstrating the capability of the experiment to change the downstream conformational population distribution, the IR-PTS scans were used to extract two quantitative results: (i) The fractional populations of the conformers in the absence of the infrared, and (ii) the isomerization quantum yields for each of the six unique amide NH stretch fundamentals (three conformers each with two amide groups). The method for obtaining quantum yields is described in detail. In both NATMA and NATA, the quantum yields show modest conformational specificity, but only a hint of vibrational mode specificity. The prospects for the hole-filling technique for providing insight into energy flow in large molecules are discussed, leaving a more detailed theoretical modeling to the adjoining paper [Evans et al. J. Chem. Phys. 120, 148 (2004)].     

Density functional theory study of triphenyl phosphite: molecular flexibility and weak intermolecular hydrogen bonding

The high conformational flexibility of triphenyl phosphite (TPP) is investigated by density functional theory (DFT) calculations. First, through a scan of the molecular potential energy surface, we bring to light a new stable conformation of an isolated molecule, not yet encountered in the crystal states of TPP. Different relevant conformations of the TPP monomer in the gas state are further presented and discussed in terms of molecular structure, relative energy, and dipole moments. Second, we considered dimer and trimer of TPP starting from their structural topology within the hexagonal crystal, which is characterized by the existence of molecular rods. It is shown that weak C-H...O intermolecular hydrogen bonds in TPP cannot definitely be excluded, and finally this point is discussed in the scope of the glacial state problem.     

气相中W+活化CO2分解的自旋禁阻反应机理

用密度泛函理论中的UB3LYP方法, 对W采用相对论校正赝势基组(SDD), 对C、O采用6-311+G(3d)基组, 研究了气相中不同自旋态W+活化CO2分解的反应机理. 计算结果表明, W+活化CO2分解反应以六重态进入反应通道, 经过六重态势能面到四重态势能面的系间窜越(ISC),最后产物WO+和CO以四重态离开反应通道. 运用Harvey方法优化出最低能量交叉点(MECP), 并计算了MECP处的自旋-轨道耦合(SOC)常数(494.95 cm-1), 势能面的交叉和在MECP处较强的自旋-轨道耦合作用降低了自旋禁阻反应能垒, 为反应提供了一条低能反应路径, 反应总放热量为122.33 kJ·mol-1.     

Comparison between self-guided Langevin dynamics and molecular dynamics simulations for structure refinement of protein loop conformations

This article presents a comparative analysis of two replica‐exchange simulation methods for the structure refinement of protein loop conformations, starting from low‐resolution predictions. The methods are self‐guided Langevin dynamics (SGLD) and molecular dynamics (MD) with a Nosé–Hoover thermostat. We investigated a small dataset of 8‐ and 12‐residue loops, with the shorter loops placed initially from a coarse‐grained lattice model and the longer loops from an enumeration assembly method (the Loopy program). The CHARMM22 + CMAP force field with a generalized Born implicit solvent model (molecular‐surface parameterized GBSW2) was used to explore conformational space. We also assessed two empirical scoring methods to detect nativelike conformations from decoys: the all‐atom distance‐scaled ideal‐gas reference state (DFIRE‐AA) statistical potential and the Rosetta energy function. Among the eight‐residue loop targets, SGLD out performed MD in all cases, with a median of 0.48 Å reduction in global root‐mean‐square deviation (RMSD) of the loop backbone coordinates from the native structure. Among the more challenging 12‐residue loop targets, SGLD improved the prediction accuracy over MD by a median of 1.31 Å, representing a substantial improvement. The overall median RMSD for SGLD simulations of 12‐residue loops was 0.91 Å, yielding refinement of a median 2.70 Å from initial loop placement. Results from DFIRE‐AA and the Rosetta model applied to rescoring conformations failed to improve the overall detection calculated from the CHARMM force field. We illustrate the advantage of SGLD over the MD simulation model by presenting potential‐energy landscapes for several loop predictions. Our results demonstrate that SGLD significantly outperforms traditional MD in the generation and populating of nativelike loop conformations and that the CHARMM force field performs comparably to other empirical force fields in identifying these conformations from the resulting ensembles. Published 2011 Wiley Periodicals, Inc. J Comput Chem, 2011     

Analyzing slowly exchanging protein conformations by ion mobility mass spectrometry: study of the dynamic equilibrium of prolyl oligopeptidase

Ion mobility mass spectrometry (IMMS) is a biophysical technique that allows the separation of isobaric species on the basis of their size and shape. The high separation capacity, sensitivity and relatively fast time scale measurements confer IMMS great potential for the study of proteins in slow (µs–ms) conformational equilibrium in solution. However, the use of this technique for examining dynamic proteins is still not generalized. One of the major limitations is the instability of protein ions in the gas phase, which raises the question as to what extent the structures detected reflect those in solution. Here, we addressed this issue by analyzing the conformational landscape of prolyl oligopeptidase (POP) – a model of a large dynamic enzyme in the µs–ms range – by native IMMS and compared the results obtained in the gas phase with those obtained in solution. In order to interpret the experimental results, we used theoretical simulations. In addition, the stability of POP gaseous ions was explored by charge reduction and collision‐induced unfolding experiments. Our experiments disclosed two species of POP in the gas phase, which correlated well with the open and closed conformations in equilibrium in solution; moreover, a gas‐phase collapsed form of POP was also detected. Therefore, our findings not only support the potential of IMMS for the study of multiple co‐existing conformations of large proteins in slow dynamic equilibrium in solution but also stress the need for careful data analysis to avoid artifacts. Copyright © 2016 John Wiley & Sons, Ltd.     

An Assessment of Computational Methods for Obtaining Structural Information of Moderately Flexible Biomolecules from Ion Mobility Spectrometry

When utilized in conjunction with modeling, the collision cross section (Ω) from ion mobility spectrometry can be used to deduce the gas phase structures of analyte ions. Gas phase conformations are determined computationally, and their Ω calculated using an approximate method, the results of which are compared with experimental data. Though prior work has focused upon rigid small molecules or large biomolecules, correlation of computational and experimental Ω has not been thoroughly examined for analytes with intermediate conformational flexibility, which constitute a large fraction of the molecules studied in the field. Here, the computational paradigm for calculating Ω has been tested for the tripeptides WGY, YGW, and YWG (Y = tyrosine, W = tryptophan, G = glycine). Experimental data indicate that Ω_exp (YWG) > Ω_exp (WGY) ≈ Ω_exp (YGW). The energy distributions of conformations obtained from tiers of simulated annealing molecular dynamics (SAMD) were analyzed using a wide array of density functionals. These quantum mechanical energy distributions do not agree with the MD data, which leads to structural differences between the SAMD and DFT conformations. The latter structures are obtained by reoptimization of the SAMD geometries, and are the only suite of structures that reproduce the experimental trend in analyte separability. In the absence of fitting Lennard Jones potentials that reproduce experimental results for the Trajectory Method, the Exact Hard Sphere Scattering method produced numerical values that are in best agreement with the experimental cross sections obtained in He drift gas.     

Inherent structure versus geometric metric for state space discretization

Inherent structure (IS) and geometry‐based clustering methods are commonly used for analyzing molecular dynamics trajectories. ISs are obtained by minimizing the sampled conformations into local minima on potential/effective energy surface. The conformations that are minimized into the same energy basin belong to one cluster. We investigate the influence of the applications of these two methods of trajectory decomposition on our understanding of the thermodynamics and kinetics of alanine tetrapeptide. We find that at the microcluster level, the IS approach and root‐mean‐square deviation (RMSD)‐based clustering method give totally different results. Depending on the local features of energy landscape, the conformations with close RMSDs can be minimized into different minima, while the conformations with large RMSDs could be minimized into the same basin. However, the relaxation timescales calculated based on the transition matrices built from the microclusters are similar. The discrepancy at the microcluster level leads to different macroclusters. Although the dynamic models established through both clustering methods are validated approximately Markovian, the IS approach seems to give a meaningful state space discretization at the macrocluster level in terms of conformational features and kinetics. © 2016 Wiley Periodicals, Inc.     

Application of DFT and MP2 calculations on structural and water-assisted proton transfer in 3-amino-4-nitrofurazan

Density functional theory (DFT) and MP2 calculations have been employed to study of 3-amino-4-nitrofurazan molecule using the standard 6-311++G(d,p) basis set. The chemical properties of the 3-amino-4-nitrofurazan have been extensively studied. The geometries of molecules in the gas phase were optimized and compared with the crystallography of this substance. The results suggest that A form is the most stable form in the gas phase and it is the predominant tautomer in solution according to the DFT and MP2 calculations, respectively. In addition, variation of dipole moments in the gas phase, the specific solvent effects with addition of one molecule of water near the electrophilic centers of tautomers, the transition state of proton transfer assisted by a water molecule, the NBO charges of atoms and the potential energy surface were investigated. The calculated highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) are presented.     

Folding of small proteins using a single continuous potential

Extensive Monte Carlo folding simulations for four proteins of various structural classes are carried out, using a single continuous potential (united-residue force field). In all cases, collapse occurs at a very early stage, and proteins fold into their nativelike conformations at appropriate temperatures. We also observe that glassy transitions occur at low temperatures. The simulation results demonstrate that the folding mechanism is controlled not only by thermodynamic factors but also by kinetic factors: The way a protein folds into its native structure is also determined by the convergence point of early folding trajectories, which cannot be obtained by the free energy surface.     

Six-dimensional potential energy surface of the dissociative chemisorption of HCl on Au(111) using neural networks

We constructed a six-dimensional potential energy surface(PES)for the dissociative chemisorption of HCl on Au(111)using the neural networks method based on roughly 70000 energies obtained from extensive density functional theory(DFT)calculations.The resulting PES is accurate and smooth,based on the small fitting errors and good agreement between the fitted PES and the direct DFT calculations.Time-dependent wave packet calculations show that the potential energy surface is very well converged with respect to the number of DFT data points,as well as to the fitting process.The dissociation probabilities of HCl initially in the ground rovibrational state from six-dimensional quantum dynamical calculations are quite diferent from the four-dimensional fixed-site calculations,indicating it is essential to perform full-dimensional quantum dynamical studies for the title molecule-surface interaction system.     

A molecular dynamics study of Lys-Trp-Lys: structure and dynamics in solution following photoexcitation

We report studies of the structure and dynamics of a tripeptide Lys-Trp-Lys (KWK) in aqueous solution following photoexcitation by molecular dynamics simulations. For ground-state KWK, we observe three stable conformations with free energy differences of less than 5.2 kJ/mol. Each conformer is stabilized by a pi-cation interaction between one of three protonated amino groups and the indole moiety. For the excited state of tryptophan in KWK, the simulated molecular dynamics of the three isomers are similar, all in good agreement with recent femtosecond experiments (J. Phys. Chem. B 2005, 109, 16901). Specifically, we observe: (1) the fluorescence anisotropy is dominated by a single-exponential component and decays in approximately 130 ps, (2) the total dynamic Stokes shift reaches approximately 2700 cm(-1), and (3) the excited state relaxation dynamics occurs on several time scales ranging from femtoseconds to tens of picoseconds. The relaxation dynamics involve rapid initial response of neighboring water, followed by local motions of flexible peptide chains. These processes drive global restructuring of the tripeptide on a rather flat energy surface, inducing slower dynamics evident in both the water and protein contributions to the stabilization energy of the photoexcited chromophore. The water and protein dynamics are strongly correlated. On a still longer time scale, we observe isomerization of two excited state conformers to the other most stable one, an analogue for evolution of trajectories along the funnel on the rugged free energy landscape to the final "native" state. Our studies suggest new experiments to detect this unique dynamics.