Structure Determination of a Flexible Cyclic Peptide Based on NMR and MD Simulation 3J‐Coupling

Molecular dynamics (MD) simulations, in which experimental values such as nuclear Overhauser effects (NOEs), dipolar couplings, ³J‐coupling constants or crystallographic structure factors are used to bias the values of specific molecular properties towards experimental ones, are often carried out to study the structure refinement of peptides and proteins. However, ³J‐coupling constants are usually not employed because of the multiplicity of torsional angle values (φ) corresponding to each ³J‐coupling constant value. Here, we apply the method of adaptively enforced restraining using a local‐elevation (LE) biasing potential energy function in which a memory function penalizes conformations in case both the average <³J> and the current ³J‐values deviate from the experimental target value. Then, the molecule is forced to sample other parts of the conformational space, thereby being able to cross high energy barriers and to bring the simulated average <³J> close to the measured <³J> value. Herein, we show the applicability of this method in structure refinement of a cyclo‐β‐tetrapeptide by enforcing the ³J‐value restraining with LE on twelve backbone torsional angles. The resulting structural ensemble satisfies the experimental ³J‐coupling data better than the NMR model structure derived using conventional single‐structure refinement based on these data. Thus, application of local‐elevation search MD simulation in combination with biasing towards ³J‐coupling makes it possible to use ³J‐couplings quantitatively in structure determination of peptides.     

The adsorption and reaction of 2-butanol on clean and oxygen-covered Pd(100)

The surface chemistry of 2-butanol is explored on clean Pd(100), c(2 × 2)-O/Pd(100) and p(2 × 2)-O/Pd(100) surfaces by means of temperature-programmed desorption, reflection–absorption infrared and X-ray photoelectron spectroscopies. 2-Butanol adsorbs molecularly on clean and oxygen-covered Pd(100) below ～ 190 K, but then appears to react to form 2-butoxide species at ～ 200 K. Both 2-butanone and 2-butanol desorb from the clean surface at ～ 226 K, by β-hydride elimination from the 2-butoxide species and rehydrogenation of the 2-butoxide, respectively. In contrast, almost exclusively 2-butanone is formed on oxygen-covered surfaces. Butanone desorbs at ～ 195 K and ～ 260 K from c(2 × 2)-O/Pd(100) with the 195 K peak being the most intense. However, on p(2 × 2)-O/Pd(100), 2-butanone desorbs at ～ 195 K and ～ 295 K, and the latter peak is the most intense. The ～ 195 K, 2-butanone state is proposed to occur due to abstraction by adsorbed atomic oxygen and the change in relative intensity of these features is ascribed to the lower ability of surface hydroxyl groups to facilitate β-hydride elimination on oxygen-covered surfaces. Further heating results in the formation of hydrogen and carbon monoxide and leaves a small amount of carbon deposited on the surface.     

A Method to Explore Protein Side Chain Conformational Variability Using Experimental Data

Experimentally measured values of molecular properties or observables of biomolecules such as proteins are generally averages over time and space, which do not contain su?cient information to determine the underlying conformational distribution of the molecules in solution. The relationship between experimentally measured NMR ³J‐coupling values and the corresponding dihedral angle values is a particularly complicated case due to its nonlinear, multiple‐valued nature. Molecular dynamics (MD) simulations at constant temperature can generate Boltzmann ensembles of molecular structures that are free from a priori assumptions about the nature of the underlying conformational distribution. They suffer, however, from limited sampling with respect to time and conformational space. Moreover, the quality of the obtained structures is dependent on the choice of force ?eld and solvation model. A recently proposed method that uses time‐averaging with local‐elevation (LE) biasing of the conformational search provides an elegant means of overcoming these three problems. Using a set of side chain ³J‐coupling values for the FK506 binding protein (FKBP), we ?rst investigate the uncertainty in the angle values predicted theoretically. We then propose a simple MD‐based technique to detect inconsistencies within an experimental data set and identify degrees of freedom for which conformational averaging takes place or for which force ?eld parameters may be de?cient. Finally, we show that LE MD is the best method for producing ensembles of structures that, on average, ?t the experimental data.     

Multigraining: an algorithm for simultaneous fine-grained and coarse-grained simulation of molecular systems

A method to combine fine-grained and coarse-grained simulations is presented. The coarse-grained particles are described as virtual particles defined by the underlying fine-grained particles are described as virtual particles defined by the underlying fine-grained particles. The contribution of the two grain levels to the interaction between particles is specified by a grain-level parameter lambda. Setting lambda = 0 results in a completely fine-grained simulation, whereas lambda = 1 yields a simulation governed by the coarse-grained potential energy surface with small contributions to keep the fine-grained covalently bound particles together. Simulations at different lambda values may be coupled using the replica-exchange molecular dynamics method to achieve enhanced sampling at the fine-grained level.     

Configurational entropies of lipids in pure and mixed bilayers from atomic-level and coarse-grained molecular dynamics simulations

Single-chain and single-fragment configurational entropies of lipid tails in hydrated lipid bilayers are evaluated from molecular dynamics simulations using the quasi-harmonic approximation. The entropy distribution along individual acyl tails is obtained and compared to that of corresponding hydrocarbon chains in the liquid phase. We consider pure dipalmitoylphosphatidylcholine and mixed dioleoylphosphatidylcholine/dioleoylphosphatidylethanolamine bilayers. The systems are modeled at different levels of spatial resolution: In an atomic-level (AL) model all (heavy) atoms are explicitly simulated; in a coarse-grained (CG) model particles (beads) representing groups of covalently bound atoms are used, which map approximately four non-hydrogen atoms to one interaction site. Single-chain and single-fragment entropies and correlations between the motions of (single) acyl chains are compared. A good correspondence is found between the flexibility of the AL and CG models. The loss in configurational entropy due to the reduction in the number of degrees of freedom upon coarse-graining of the model is estimated. The CG model shows about 4 times faster convergence of the chain entropies than the more detailed AL model. Corrections to the quasi-harmonic entropy estimates were found to be small for the CG model. For the AL model, the correction due to mode anharmonicities is small, but the correction due to pairwise (supralinear) mode correlations is sizable.     

Combined phase-sensitive acoustic microscopy and confocal laser scanning microscopy

Combined phase-sensitive acoustic microscopy (PSAM) at 1.2 GHz and confocal laser scanning microscopy (CLSM) in reflection and fluorescence has been implemented and applied to polymer blend films and fluorescently labeled fibroblasts and neuronal cells in order to explore the prospects and the various contrast mechanisms of this powerful technique. Topographic contrast is available for appropriate samples from CLSM in reflection and, with significantly higher precision, from the acoustic phase images. Material contrast can be gained from acoustic amplitude V(z) graphs. In the case of the biological cells investigated, the optical and acoustic images are very different and exhibit different features of the samples.     

Using one‐step perturbation to predict the effect of changing force‐field parameters on the simulated folding equilibrium of a β‐peptide in solution

Computer simulation using molecular dynamics is increasingly used to simulate the folding equilibria of peptides and small proteins. Yet, the quality of the obtained results depends largely on the quality of the force field used. This comprises the solute as well as the solvent model and their energetic and entropic compatibility. It is, however, computational very expensive to perform test simulations for each combination of force‐field parameters. Here, we use the one‐step perturbation technique to predict the change of the free enthalpy of folding of a β‐peptide in methanol solution due to changing a variety of force‐field parameters. The results show that changing the solute backbone partial charges affects the folding equilibrium, whereas this is relatively insensitive to changes in the force constants of the torsional energy terms of the force field. Extending the cut‐off distance for nonbonded interactions beyond 1.4 nm does not affect the folding equilibrium. The same result is found for a change of the reaction‐field permittivity for methanol from 17.7 to 30. The results are not sensitive to the criterion, e.g., atom‐positional RMSD or number of hydrogen bonds, that is used to distinguish folded and unfolded conformations. Control simulations with perturbed Hamiltonians followed by backward one‐step perturbation indicated that quite large perturbations still yield reliable results. Yet, perturbing all solvent molecules showed where the limitations of the one‐step perturbation technique are met. The evaluated methodology constitutes an efficient tool in force‐field development for molecular simulation by reducing the number of required separate simulations by orders of magnitude. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

A GPU solvent–solvent interaction calculation accelerator for biomolecular simulations using the GROMOS software

During the past few years, graphics processing units (GPUs) have become extremely popular in the high performance computing community. In this study, we present an implementation of an acceleration engine for the solvent–solvent interaction evaluation of molecular dynamics simulations. By careful optimization of the algorithm speed‐ups up to a factor of 54 (single‐precision GPU vs. double‐precision CPU) could be achieved. The accuracy of the single‐precision GPU implementation is carefully investigated and does not influence structural, thermodynamic, and dynamic quantities. Therefore, the implementation enables users of the GROMOS software for biomolecular simulation to run the solvent–solvent interaction evaluation on a GPU, and thus, to speed‐up their simulations by a factor 6–9. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Synthesis, determination of absolute configuration, and biological evaluation of spiro-fused thiadiazoline inhibitors of kinesin spindle protein (KSP)

A facile and highly convergent synthesis of biologically active spiro-fused thiadiazoline KSP inhibitors is reported. The highlights of the synthesis include the Michael reaction and cyclization of thiosemicarbazone to 1,3,4-thiadiazoline. This chemistry lends itself to the preparation of (+)-2, a potent and orally bioavailable anti-cancer agent, and to the development of a structure-activity relationship program.     

Oligosaccharide-peptide ligation of glycosyl thiolates with dehydropeptides: synthesis of S-linked mucin-related glycopeptide conjugates

A chemoselective strategy for oligosaccharide-peptide ligation is described in which alpha-thio analogues of mucin-related glycoconjugates can be readily accessed through site-selective conjugate addition of complex oligosaccharide thiolates to dehydroalanine-containing peptides. The efficiency of the ligation is highlighted by the rapid convergent assembly of thio-isosteres of the four tumor-associated carbohydrate antigens, T(N), T, ST(N), and 2,6-ST, as a pair of diastereoisomers at the newly formed cysteine stereocenter. The process proceeds in high yield and with complete retention of the alpha-anomeric configuration.