Peptide Conformation from Coupling Constants: Scalar Couplings as Restraints in MD Simulations

The question of how far one can go in the determination of conformation with the sole use of coupling constants as restraints in MD simulations was addressed. Couplings are being used ever more frequently as constraints as measuring heteronuclear long-range coupling constants becomes easier. For this investigation, cyclosporin A, which has previously been extensively examined with NOE-restrained simulations, is used as a model system. Many additional one-and three-bond coupling constants have been measured. The MD simulations were carried out with the addition of a potential-energy penalty function based directly on the Karplus curve. It is shown that, for dihedral angles with more than one coupling, the restraints are very efficient, in agreement with the structure observed from NOEs. However, it turned out that the structure of CsA is not adequately described, when only J couplings are used.     

Structure determination of a key intermediate of the enantioselective Pd complex catalyzed allylic substitution reaction

The structure of a catalytic intermediate with important implications for the interpretation of the stereochemical outcome of the palladium complex catalyzed allylic substitution with phosphino-oxazoline (PHOX) ligands is determined by liquid state NMR. The complex displays a novel structure that is highly distorted compared with other palladium eta2-olefin complexes known so far. The structure has been determined from nuclear overhauser data (NOE), scalar coupling constants, and long range projection angle restraints derived from dipole dipole cross-correlated relaxation of multiple quantum coherence. The latter restraints have been implemented into a distance geometry protocol. The projection angle restraints yield a higher precision in the determination of the relative orientation of the two molecular moieties and are essential to provide an exact structural definition of the olefinic part of the catalytic intermediate with respect to the ligand.     

Structure and dynamics of the Abeta(21-30) peptide from the interplay of NMR experiments and molecular simulations

We combine molecular dynamics simulations and new high-field NMR experiments to describe the solution structure of the Abeta(21-30) peptide fragment that may be relevant for understanding structural mechanisms related to Alzheimer's disease. By using two different empirical force-field combinations, we provide predictions of the three-bond scalar coupling constants ((3)J(H(N)H(alpha))), chemical-shift values, (13)C relaxation parameters, and rotating-frame nuclear Overhauser effect spectroscopy (ROESY) crosspeaks that can then be compared directly to the same observables measured in the corresponding NMR experiment of Abeta(21-30). We find robust prediction of the (13)C relaxation parameters and medium-range ROESY crosspeaks by using new generation TIP4P-Ew water and Amber ff99SB protein force fields, in which the NMR validates that the simulation yields both a structurally and dynamically correct ensemble over the entire Abeta(21-30) peptide. Analysis of the simulated ensemble shows that all medium-range ROE restraints are not satisfied simultaneously and demonstrates the structural diversity of the Abeta(21-30) conformations more completely than when determined from the experimental medium-range ROE restraints alone. We find that the structural ensemble of the Abeta(21-30) peptide involves a majority population (approximately 60%) of unstructured conformers, lacking any secondary structure or persistent hydrogen-bonding networks. However, the remaining minority population contains a substantial percentage of conformers with a beta-turn centered at Val24 and Gly25, as well as evidence of the Asp23 to Lys28 salt bridge important to the fibril structure. This study sets the stage for robust theoretical work on Abeta(1-40) and Abeta(1-42), for which collection of detailed NMR data on the monomer will be more challenging because of aggregation and fibril formation on experimental timescales at physiological conditions. In addition, we believe that the interplay of modern molecular simulation and high-quality NMR experiments has reached a fruitful stage for characterizing structural ensembles of disordered peptides and proteins in general.     

Conformational Ensemble of Disordered Proteins Probed by Solvent Paramagnetic Relaxation Enhancement (sPRE)

Characterization of the conformational ensemble of disordered proteins is highly important for understanding protein folding and aggregation mechanisms, but remains a computational and experimental challenge owing to the dynamic nature of these proteins. New observables that can provide unique insights into transient residual structures in disordered proteins are needed. Here using denatured ubiquitin as a model system, NMR solvent paramagnetic relaxation enhancement (sPRE) measurements provide an accurate and highly sensitive probe for detecting low populations of residual structure in a disordered protein. Furthermore, a new ensemble calculation approach based on sPRE restraints in conjunction with residual dipolar couplings (RDCs) and small‐angle X‐ray scattering (SAXS) is used to define the conformational ensemble of disordered proteins at atomic resolution. The approach presented should be applicable to a wide range of dynamic macromolecules.     

Exchange coupling in transition-metal complexes via density-functional theory: comparison and reliability of different basis set approaches

Theoretical methods based on density-functional theory with Gaussian, plane waves, and numerical basis sets were employed to evaluate the exchange coupling constants in transition-metal complexes. In the case of the numerical basis set, the effect of different computational parameters was tested. We analyzed whether and how the use of pseudopotentials affects the calculation of the exchange coupling constants. For the three different basis sets, a comparison of the exchange coupling constants and spin distributions shows that both the plane-wave and the numerical basis set approaches are accurate and reliable alternatives to the more established Gaussian basis functions.     

ALMOST: An all atom molecular simulation toolkit for protein structure determination

Almost ( al l atom mo lecular s imulation t oolkit) is an open source computational package for structure determination and analysis of complex molecular systems including proteins, and nucleic acids. Almost has been designed with two primary goals: to provide tools for molecular structure determination using various types of experimental measurements as conformational restraints, and to provide methods for the analysis and assessment of structural and dynamical properties of complex molecular systems. The methods incorporated in Almost include the determination of structural and dynamical features of proteins using distance restraints derived from nuclear Overhauser effect measurements, orientational restraints obtained from residual dipolar couplings and the structural restraints from chemical shifts. Here, we present the first public release of Almost , highlight the key aspects of its computational design and discuss the main features currently implemented. Almost is available for the most common Unix‐based operating systems, including Linux and Mac OS X. Almost is distributed free of charge under the GNU Public License, and is available both as a source code and as a binary executable from the project web site at http://www.open‐almost.org . Interested users can follow and contribute to the further development of Almost on http://sourceforge.net/projects/almost . © 2014 Wiley Periodicals, Inc.     

Simulated Isotope Exchange Patterns Enable Protein Structure Determination

Understanding the myriad protein–protein interactions required for cell function requires efficient leveraging of biophysical data to drive computational docking. The detailed insight into protein interfaces provided by isotope exchange endows this experimental technique with a unique importance for docking approaches. However, progress in coupling these methods is hindered by the inability to interpret the complex exchange patterns in relation to protein structure. A method to simulate protein isotope exchange patterns from docking outputs is described and its utility to guide the selection of native assemblies demonstrated. Unique signatures are generated for each docking pose, allowing high‐throughput ranking of whole docking simulations by pairwise comparison to experimental outputs. Native assemblies are obtained using nothing but their simulated profiles as restraints and experimental difference data for individual proteins are sufficient to drive structure determination for the whole complex.     

Scalar Coupling Constants—Their Analysis and Their Application for the Elucidation of Structures

Since their discovery in the early fifties, scalar/coupling constants have been of great interest to the NMR spectroscopist. Their impact on structure determination by NMR spectroscopy is founded on the fact that the size of the coupling constant is directly related to molecular conformation. Today, for most chemical substances the parameters for the Karplus relationship, which relates the vicinial (3-bond) coupling constant to the dihedral angle, have been determined. In addition to proton–proton distances, the application of coupling constants in modern conformational analysis is indispensable. In the study of larger molecules which are of current interest, more and more involved experiments are necessary in order to overcome signal overlap and increasing line widths. A large number of experimental techniques for the determination of coupling constants has been developed; however, for this reason the choice of the most appropriate experiment to use has become more difficult. This decision must be made carefully to maximize instrument usage and obtain the largest number of couplings with the greatest accuracy possible. Many of the computer programs used in structure calculations can directly apply coupling constant restraints, similar to proton–proton distances developed from NOEs. Therefore, not only is the quality of the structure improved, but the molecular motions (internal dynamics) are better described. In this article, we review the techniques that exist today with particular attention paid to helping the non-expert to choose the appropriate experiment for the problem at hand. In addition, the use of coupling constants in computer simulations are discussed.     

Calculations of 13C NMR chemical shifts and F–C coupling constants of ciprofloxacin

Ciprofloxacin is a widely used fluoroquinolone antibiotic. In this work, a comprehensive evaluation of MP2 and DFT with different functionals and basis sets was carried out to select the most suitable level of theory for the study of the NMR properties of ciprofloxacin. Their relative predictive capabilities were evaluated comparing the theoretically predicted and experimental spectral data. Our computational results indicated that in contrast to the solid state, the molecule of ciprofloxacin does not exist as a zwitterion in gaseous state. The results of the calculations of the chemical shifts most close to the experimental were obtained with B3LYP/aug-cc-pVDZ. The F–C coupling constants were calculated systematically with different DFT methods and several basis sets. In general, the calculations of the coupling constants with the BHandH computational method including the applied in this work 6-311++G**, EPRII, and EPRIII basis sets showed a good reproducibility of the experimental values of the coupling constants.     

Toward ab initio refinement of protein X-ray crystal structures: interpreting and correlating structural fluctuations

The refinement of protein crystal structures currently involves the use of empirical restraints and force fields that are known to work well in many situations but nevertheless yield structural models with some features that are inconsistent with detailed chemical analysis and therefore warrant further improvement. Ab initio electronic structure computational methods have now advanced to the point at which they can deliver reliable results for macromolecules in realistic times using linear-scaling algorithms. The replacement of empirical force fields with ab initio methods in a final refinement stage could allow new structural features to be identified in complex structures, reduce errors and remove computational bias from structural models. In contrast to empirical approaches, ab initio refinements can only be performed on models that obey basic qualitative chemical rules, imposing constraints on the parameter space of existing refinements, and this in turn inhibits the inclusion of unlikely structural features. Here, we focus on methods for determining an appropriate ensemble of initial structural models for an ab initio X-ray refinement, modeling as an example the high-resolution single-crystal X-ray diffraction data reported for the structure of lysozyme (PDB entry “2VB1”). The AMBER force field is used in a Monte Carlo calculation to determine an ensemble of 8 structures that together embody all of the partial atomic occupancies noted in the original refinement, correlating these variations into a set of feasible chemical structures while simultaneously retaining consistency with the X-ray diffraction data. Subsequent analysis of these results strongly suggests that the occupancies in the empirically refined model are inconsistent with protein energetic considerations, thus depicting the 2VB1 structure as a deep-lying minimum in its optimized parameter space that actually embodies chemically unreasonable features. Indeed, density-functional theory calculations for one specific nitrate ion with an occupancy of 62% indicate that water replaces this ion 38% of the time, a result confirmed by subsequent crystallographic analysis. It is foreseeable that any subsequent ab initio refinement of the whole structure would need to locate a globally improved structure involving significant changes to 2VB1 which correct these identified local structural inconsistencies.     

Determination of 29Si-1H spin-spin coupling constants in organoalkoxysilanes with nontrivial scalar coupling patterns

Application of polarization transfer techniques such as DEPT and INEPT in (29)Si NMR investigation of bridged silane polymerization requires knowledge of indirect (29)Si-(1)H scalar coupling constants in the silane system. However, the fully coupled (29)Si NMR spectra of these molecules, specifically those containing ethylene bridging groups, are too complicated to measure the coupling constants directly by visual inspection. This is because unlike hydrocarbon systems where one-bond proton-carbon coupling constants exceed other coupling constants by an order of magnitude, in silanes the closest proton-silicon pairs are separated by two bonds and all coupling coefficients (both homonuclear and heteronuclear) are of similar magnitude. In these systems, theoretical tools are required to interpret the spectra of even simple molecules. Here, we determine density functional theory estimates of (29)Si-(1)H scalar coupling constants and use these along with homonuclear coupling constant estimates to resolve the nontrivial nature of these spectra. We also report a Karplus equation consistent with the dihedral angle dependence of the three-bond homo- and heteronuclear coupling in the ethylene bridge. By thermal averaging of DFT coupling constants, a good initial guess of the coupled (29)Si spectral pattern is made, which is easily refined by curve fitting to determine estimates of all coupling constants in the system.     

Refinement of local and long-range structural order in theophylline-binding RNA using (13)C-(1)H residual dipolar couplings and restrained molecular dynamics.

13C-(1)H residual dipolar couplings (RDC) have been measured for the bases and sugars in the theophylline-binding RNA aptamer, dissolved in filamentous phage medium, and used to investigate the long-range structural and dynamic behavior of the molecule in the solution state. The orientation dependent RDC provide additional restraints to further refine the overall structure of the RNA-theophylline complex, whose long-range order was poorly defined in the NOE-based structural ensemble. Structure refinement using RDC normally assumes that molecular alignment can be characterized by a single tensor and that the molecule is essentially rigid. To address the validity of this assumption for the complex of interest, we have analyzed distinct domains of the RNA molecule separately, so that local structure and alignment tensors experienced by each region are independently determined. Alignment tensors for the stem regions of the molecule were allowed to float freely during a restrained molecular dynamics structure refinement protocol and found to converge to similar magnitudes. During the second stage of the calculation, a single alignment tensor was thus applied for the whole molecule and an average molecular conformation satisfying all experimental data was determined. Semirigid-body molecular dynamics calculations were used to reorient the refined helical regions to a relative orientation consistent with this alignment tensor, allowing determination of the global conformation of the molecule. Simultaneously, the local structure of the theophylline-binding core of the molecule was refined under the influence of this common tensor. The final ensemble has an average pairwise root mean square deviation of 1.50 +/- 0.19 A taken over all heavy atoms, compared to 3.5 +/- 1.1 A for the ensemble determined without residual dipolar coupling. This study illustrates the importance of considering both the local and long-range nature of RDC when applying these restraints to structure refinements of nucleic acids.     

Determination of an ensemble of structures representing the denatured state of the bovine acyl-coenzyme a binding protein

The denatured state of a protein contains important information about the determinants of the folding process. By combining site-directed spin-labeling NMR experiments and restrained computer simulations, we have determined ensembles of conformations that represent the denatured state of the bovine acyl-coenzyme A binding protein (ACBP) at three different concentrations of guanidine hydrochloride. As the experimentally determined distance information corresponds to weighted averages over a broad ensemble of structures, we applied the experimental restraints to a system of noninteracting replicas of the protein by using a Monte Carlo sampling scheme. This procedure permits us to sample ensembles of conformations that are compatible with the experimental data and thus to obtain information regarding the distribution of structures in the denatured state. Our results show that the denatured state of ACBP is highly heterogeneous. The high sensitivity of the computational method that we present, however, enabled us to identify long-range interactions between two regions, located near the N- and C-termini, that include both native and non-native elements. The preferential formation of these contacts suggests that the sequence-dependent patterns of helical propensity and hydrophobicity are important determinants of the structure in the denatured state of ACBP.     

Theoretical investigation of the mechanism and dynamics of intramolecular coherent resonance energy transfer in soft molecules: a case study of dithia-anthracenophane

A computational study is conducted on dithia-anthracenophane (DTA), for which there is experimental evidence for coherent resonance energy transfer dynamics, and on dimethylanthracene (DMA), a molecule representing the energy donor and the acceptor in DTA. Electronic excitation energies are calculated by configuration interaction singles (CIS) and time-dependent density functional theory (TD-DFT) methods and are compared to experimental ones. Electronic coupling constants are calculated between two DMAs embedded into the ground-state structure of DTA employing methods based on transition densities. The resulting values of electronic coupling provide a more consistent interpretation of experiments than those based on one-half the level spacing of DTA excitation energies. Solvation effects are studied based on the polarizable continuum model (PCM). Solvent-induced polarization and screening effects are shown to make opposite contributions, and the net electronic coupling is little different from the value in a vacuum. The likelihood of coherent population transfer is assessed on the basis of a recently developed theory of coherent resonance energy transfer. The time scale of bath is shown to have an important role in sustaining the quantum coherence. The combination of quantum chemical and dynamical data suggests that the electronic coupling in DTA is in the range of 50-100 cm(-1). The presence of oscillatory excitation population dynamics can be understood from the picture of polaronic excitation moderately dressed with dispersive vibrational modes. The effect of torsional modulation on the excitation energies of DTA and electronic coupling is examined on the basis of optimized structures with the torsional angle constrained. The result suggests that inelastic effect due to torsional motion cannot be disregarded in DTA.     

An ab initio study of the hyperfine structure in the X2 Pi electronic state of CCCH

The results of an ab initio study of the magnetic hyperfine structure in the X (2)Pi electronic state of CCCH are reported. The potential surfaces for two components of the X (2)Pi electronic state were computed by means of an extensive configuration interaction approach. The electronically averaged hyperfine coupling constants of H and (13)C for (12)C (12)C (12)CH, (13)C (12)C (12)CH, (12)C (13)C (12)CH, and (12)C (12)C (13)CH are obtained as functions of two bending vibrational modes by the density functional theory method. The vibronic wave functions are calculated with the help of a variational approach which takes into account the Renner-Teller effect and spin-orbit coupling. The model Hamiltonian is expressed in terms of the normal bending coordinates. It is found that, due to the generally strong geometry dependence of the hyperfine coupling constants, it is necessary to carry out the vibronic averaging of the corresponding functions in order to obtain the values which can be compared to the results of the measurements. The results of the present study help to reliably interpret the experimental data previously published. They also predict the yet unobserved hyperfine structure in excited vibronic states.     

Direct measurement of single and ensemble average particle-surface potential energy profiles

This work involves the development of a novel technique that integrates total internal reflection and video microscopy methods to simultaneously measure single particle and ensemble average particle-surface interactions. For the 2 mum silica colloids and glass coverslip used in this study, particle size polydispersity is found to be a dominant factor in determining the distribution of single particle profiles about ensemble average profiles. In conjunction with this observation, chemical and physical nonuniformity are not evident in any of our measurements even with sensitivity to interactions on the order of kT. One advantage of using ensemble averaging in conjunction with time averaging is the ability to dramatically decrease the time required to measure average particle-wall interactions which scales inversely with interfacial particle concentration. A number of experimental issues are addressed in the development of this technique including (1) combining single particle distribution functions, (2) statistical sampling of distribution functions using both time and ensemble averaging, and (3) correcting overlapping scattering signals between adjacent particles. The capabilities of the ensemble averaging technique are also demonstrated to provide unique measurements of particle-surface interactions in metastable systems by selecting only height excursions of levitated particles when calculating potentials. Ultimately, this new technique provides several important advantages over single particle measurements, which provides a foundation for measuring interactions in increasingly complex interfacial systems.     

Automated protein structure determination from NMR spectra

Fully automated structure determination of proteins in solution (FLYA) yields, without human intervention, three-dimensional protein structures starting from a set of multidimensional NMR spectra. Integrating existing and new software, automated peak picking over all spectra is followed by peak list filtering, the generation of an ensemble of initial chemical shift assignments, the determination of consensus chemical shift assignments for all (1)H, (13)C, and (15)N nuclei, the assignment of NOESY cross-peaks, the generation of distance restraints, and the calculation of the three-dimensional structure by torsion angle dynamics. The resulting, preliminary structure serves as additional input to the second stage of the procedure, in which a new ensemble of chemical shift assignments and a refined structure are calculated. The three-dimensional structures of three 12-16 kDa proteins computed with the FLYA algorithm coincided closely with the conventionally determined structures. Deviations were below 0.95 A for the backbone atom positions, excluding the flexible chain termini. 96-97% of all backbone and side-chain chemical shifts in the structured regions were assigned to the correct residues. The purely computational FLYA method is suitable for substituting all manual spectra analysis and thus overcomes a main efficiency limitation of the NMR method for protein structure determination.