A vivid model illustrating chiral recognition induced by achiral structures

If diastereomeric complexes are adsorbed on a surface or if they include a molecule of solvent, two points of attractive interaction between the chiral species of the complex can be sufficient for mutual chiral recognition of these species. In special cases even one single point of interaction is sufficient. This extension of the three-point contact rule of Dalgliesh, first observed in chiral ligand-exchange chromatography, can be demonstrated by using hands.     

Exploring the effects of sparse restraints on protein structure prediction

One of the main barriers to accurate computational protein structure prediction is searching the vast space of protein conformations. Distance restraints or inter‐residue contacts have been used to reduce this search space, easing the discovery of the correct folded state. It has been suggested that about 1 contact for every 12 residues may be sufficient to predict structure at fold level accuracy. Here, we use coarse‐grained structure‐based models in conjunction with molecular dynamics simulations to examine this empirical prediction. We generate sparse contact maps for 15 proteins of varying sequence lengths and topologies and find that given perfect secondary‐structural information, a small fraction of the native contact map (5%‐10%) suffices to fold proteins to their correct native states. We also find that different sparse maps are not equivalent and we make several observations about the type of maps that are successful at such structure prediction. Long range contacts are found to encode more information than shorter range ones, especially for α and αβ‐proteins. However, this distinction reduces for β‐proteins. Choosing contacts that are a consensus from successful maps gives predictive sparse maps as does choosing contacts that are well spread out over the protein structure. Additionally, the folding of proteins can also be used to choose predictive sparse maps. Overall, we conclude that structure‐based models can be used to understand the efficacy of structure‐prediction restraints and could, in future, be tuned to include specific force‐field interactions, secondary structure errors and noise in the sparse maps.     

The role of atomic level steric effects and attractive forces in protein folding

Protein folding into tertiary structures is controlled by an interplay of attractive contact interactions and steric effects. We investigate the balance between these contributions using structure‐based models using an all‐atom representation of the structure combined with a coarse‐grained contact potential. Tertiary contact interactions between atoms are collected into a single broad attractive well between the C^β atoms between each residue pair in a native contact. Through the width of these contact potentials we control their tolerance for deviations from the ideal structure and the spatial range of attractive interactions. In the compact native state dominant packing constraints limit the effects of a coarse‐grained contact potential. During folding, however, the broad attractive potentials allow an early collapse that starts before the native local structure is completely adopted. As a consequence the folding transition is broadened and the free energy barrier is decreased. Eventually two‐state folding behavior is lost completely for systems with very broad attractive potentials. The stabilization of native‐like residue interactions in non‐perfect geometries early in the folding process frequently leads to structural traps. Global mirror images are a notable example. These traps are penalized by the details of the repulsive interactions only after further collapse. Successful folding to the native state requires simultaneous guidance from both attractive and repulsive interactions. Proteins 2012. © 2011 Wiley Periodicals, Inc.     

Molecular and supramolecular chirality: R2PI spectroscopy as a tool for the gas-phase recognition of chiral systems of biological interest

In life sciences, diastereomeric chiral molecule/chiral receptor complexes are held together by a different combination of intermolecular forces and are therefore endowed with different stability and reactivity. Determination of these forces, which are normally affected in the condensed phase by solvent and supramolecular interactions, can be accomplished through the generation of diastereomeric complexes in the isolated state and their spectroscopic investigation. This review presents a detailed discussion of the mass resolved Resonant Two Photon Ionization (R2PI-TOF) technique in supersonic beams and introduces an overview of various other technologies currently available for the spectroscopic study of gas phase chiral molecules and supramolecular systems. It reports case studies primarily from our recent work using R2PI-TOF methodology for chiral recognition in clusters containing molecules of biological interest. The measurement of absorption spectra, ionization and fragmentation thresholds of diastereomeric clusters by this technique allow the determination of the nature of the intrinsic interactions, which control their formation and which affect their stability and reactivity.     

Enantioselective complexation of 1‐phenylethanol with chiral compounds bearing urea moiety

A detailed study of diastereomeric complexes of chiral ureido‐1,1′‐binaphthalene derivatives with chiral 1‐phenylethanol showed that a derivative bearing only one urea unit makes five times more stable complex with (S)‐enantiomer than with (R)‐enantiomer of the alcohol. This phenomenon could be used in chiral discrimination processes. The influence of individual parts of the structure on the complexation properties is shown. The probable structure of diastereomeric complexes based on experimental results and computational methods is proposed.     

Comparison of molecular mechanisms mediating cell contact phenomena in model developmental systems: an exploration of universality

Are there universal molecular mechanisms associated with cell contact phenomena during metazoan ontogenesis? Comparison of adhesion systems in disparate model systems indicates the existence of unifying principles. Requirements for multicellularity are (a) the construction of three‐dimensional structures involving a crucial balance between adhesiveness and motility; and (b) the establishment of integration at molecular, cellular, tissue, and organismal levels of organization. Mechanisms for (i) cell–cell and cell–substrate adhesion, (if) cell movement, (Hi) cell‐cell communication, (iv) cellular responses, (v) regulation of these processes, and (vi) their integration with patterning, growth, and other developmental processes are all crucial to metazoan development, and must have been present for the emergence and radiation of Metazoa. The principal unifying themes of this review are the dynamics and regulation of cell contact phenomena. Our knowledge of the dynamic molecular mechanisms underlying cell contact phenomena remains fragmentary. Here we examine the molecular bases of cell contact phenomena using extant model developmental systems (representing a wide range of phyla) including the simplest i.e. sponges, and the eukaryotic protist Dictyostelium discoideum, the more complex Drosophila melanogaster, and vertebrate systems. We discuss cell contact phenomena in a broad developmental context. The molecular language of cell contact phenomena is complex; it involves a plethora of structurally and functionally diverse molecules, and diverse modes of intermolecular interactions mediated by protein and/or carbohydrate moieties. Reasons for this are presumably the necessity for a high degree of specificity of inter‐molecular interactions, the requirement for a multitude of different signals, and the apparent requirement for an increasingly large repertoire of cell contact molecules in more complex developmental systems, such as the developing vertebrate nervous system. However, comparison of molecular models for dynamic adhesion in sponges and in vertebrates indicates that, in spite of significant differences in the details of the way specific cell–cell adhesion is mediated, similar principles are involved in the mechanisms employed by members of disparate phyla. Universal requirements are likely to include (a) rapidly reversible intermolecular interactions; (b) low‐affinity intermolecular interactions with fast on–off rates; (c) the compounding of multiple intermolecular interactions; (d) associated regulatory signalling systems. The apparent widespread employment of molecular mechanisms involving cadherin‐like cell adhesion molecules suggests the fundamental importance of cadherin function during development, particularly in epithelial morphogenesis, cell sorting, and segregation of cells.     

A molecular dynamics investigation of chiral discrimination complexes as chiral stationary-phase models: Methyl N-(2-naphthyl)alaninate with N-(3,5-dinitrobenzoyl)leucine n-propylamide

Molecular dynamics simulations were performed on complexes of (S)-methyl N-(2-naphthyl)alaninate (NAP) with the enantiomers of N-(3,5-dinitrobenzoyl)leucine n-propylamide (DNB), which are used as models for chiral stationary-phase systems developed by Pirkle and co-workers. These studies were undertaken to qualitatively examine (pictorially) the role of entropic effects in these systems. The results of the dynamics calculations were used to refine the search for low-energy conformers. The structures were refined by the use of BioDesign's molecular mechanics method implemented in Biograf. The results of the structural refinements support our previous observation that the SR complex can achieve the same three primary interactions which are observed in the SS structure (i.e., two intermolecular hydrogen bonds and pi stacking) without a significant increase in energy. In addition, these primary interactions are conserved during molecular dynamics simulations with the occurrence of conformations which differ only in the rotational states of the alkyl side chains and ester group (which bears two potential hydrogen bond acceptors utilized in both the homo- and heterochiral complexes). The major difference in the two complexes is the relative position of the sec-butyl group and hydrogen atom on DNB's chiral center, both of which are outside the primary interaction region. All other local minima which have different relative pi orientations (“front–back,” “back–back,” and “back–front” as defined herein) are not sufficiently populated to make more than a negligible contribution to the statistical (time- or energy-averaged) analysis of the (SS)- and (SR)-NAP–DNB complexes. Thus the entropic effects observed in this study (e.g., alkyl side chain or ester group rotations) do not show evidence of qualitative differential effects on the maintenance of the same three primary interactions by both the homo- and heterochiral complexes. The reliability of the present study, which provides pictorial representations of the entropic effects, is not sufficient to determine whether the entropic effects observed herein are sufficient to achieve enantiomeric discrimination alone or in conjunction with other factors (e.g., conformational strain energy). Thus, all of the computational studies we have performed to date (i.e., our previous studies, which include strain energy and through-space field effects, and the present study, which includes entropic effects) show no evidence of any qualitative difference in the homo- and heterochiral complexes in terms of maintaining the same three “contact points”.     

PRODUCTIVITY AND DIVERSITY IN A CROSS‐FEEDING POPULATION OF ARTIFICIAL ORGANISMS

Cross‐feeding interactions are a common feature of many microbial systems, such as colonies of Escherichia coli grown on a single limiting resource, and microbial consortia cooperatively degrading complex compounds. We have studied this phenomenon from an abstract point of view by considering artificial organisms that metabolize binary strings from a shared environment. The organisms are represented as simple cellular automaton rules and the analog of energy in the system is an approximation of the Shannon entropy of the binary strings. Only organisms that increase the entropy of the transformed strings are allowed to replicate. This system exhibits a large degree of species diversity, which increases when the flow of binary strings into the system is reduced. Investigating the relation between ecosystem productivity and diversity we find that diversity is negatively correlated with biomass production and energy uptake, while it correlates positively with energy‐uptake efficiency. By performing invasion experiments, we show that the source of diversity is negative frequency‐dependent selection acting among the different species, and that some of these interactions are intransitive, another mechanism known to promote diversity.     

Dimensions,energetics, and denaturant effects of the protein unstructured state

Determining the energetics of the unfolded state of a protein is essential for understanding the folding mechanics of ordered proteins and the structure–function relation of intrinsically disordered proteins. Here, we adopt a coil‐globule transition theory to develop a general scheme to extract interaction and free energy information from single‐molecule fluorescence resonance energy transfer spectroscopy. By combining protein stability data, we have determined the free energy difference between the native state and the maximally collapsed denatured state in a number of systems, providing insight on the specific/nonspecific interactions in protein folding. Both the transfer and binding models of the denaturant effects are demonstrated to account for the revealed linear dependence of inter‐residue interactions on the denaturant concentration, and are thus compatible under the coil‐globule transition theory to further determine the dimension and free energy of the conformational ensemble of the unfolded state. The scaling behaviors and the effective θ‐state are also discussed.     

Three enhancements to the inference of statistical protein‐DNA potentials

The energetics of protein‐DNA interactions are often modeled using so‐called statistical potentials, that is, energy models derived from the atomic structures of protein‐DNA complexes. Many statistical protein‐DNA potentials based on differing theoretical assumptions have been investigated, but little attention has been paid to the types of data and the parameter estimation process used in deriving the statistical potentials. We describe three enhancements to statistical potential inference that significantly improve the accuracy of predicted protein‐DNA interactions: (i) incorporation of binding energy data of protein‐DNA complexes, in conjunction with their X‐ray crystal structures, (ii) use of spatially‐aware parameter fitting, and (iii) use of ensemble‐based parameter fitting. We apply these enhancements to three widely‐used statistical potentials and use the resulting enhanced potentials in a structure‐based prediction of the DNA binding sites of proteins. These enhancements are directly applicable to all statistical potentials used in protein‐DNA modeling, and we show that they can improve the accuracy of predicted DNA binding sites by up to 21%. Proteins 2013. © 2012 Wiley Periodicals, Inc.     

A versatile chiral selector for determination of enantiomeric composition of fluorescent and nonfluorescent chiral molecules using steady-state fluorescence spectroscopy

A fluorescent chiral molecular micelle (FCMM), poly (sodium N-undecanoyl-L-phenylalaninate) (poly-L-SUF), was developed as a chiral selector for enantiomeric recognition and determination of enantiomeric composition of four fluorescent and four nonfluorescent chiral molecules by use of steady-state fluorescence spectroscopy. The influence of FCMM concentration, buffer pH and complexation medium on FCMM-analyte host-guest complexation, and the emission spectral properties of the resulting complexes were investigated. The chiral interactions of the analytes,1,1'-binaphthyl-2,2'-diamine, 1-(9-anthryl)-2,2,2-trifluoroethanol, propranolol, naproxen, chloromethyl menthyl ether (CME), citramalic acid, tartaric acid, and limonene (LIM), in the presence of poly-L-SUF were based on diastereomeric complex formation. The figures of merit obtained from the partial-least-squares regression modeling of the calibration samples suggested good prediction ability for the validation of six of the eight chiral analytes. Better host-guest complexation of the more hydrophobic molecules, CME and LIM, were obtained in methanol/water mixtures, resulting in better predictability of the regression models. Prediction ability of the models was evaluated by use of the root-mean-square percent relative error (RMS%RE) and was found to range from 1.77 to 15.80% (buffer), 1.26 to 7.95% (25:75 methanol/water), and 1.21 to 4.28% (75:25 methanol/water).     

Multi‐scale characterization of the energy landscape of proteins with application to the C3D/Efb‐C complex

We present a novel multi‐level methodology to explore and characterize the low energy landscape and the thermodynamics of proteins. Traditional conformational search methods typically explore only a small portion of the conformational space of proteins and are hard to apply to large proteins due to the large amount of calculations required. In our multi‐scale approach, we first provide an initial characterization of the equilibrium state ensemble of a protein using an efficient computational conformational sampling method. We then enrich the obtained ensemble by performing short Molecular Dynamics (MD) simulations on selected conformations from the ensembles as starting points. To facilitate the analysis of the results, we project the resulting conformations on a low‐dimensional landscape to efficiently focus on important interactions and examine low energy regions. This methodology provides a more extensive sampling of the low energy landscape than an MD simulation starting from a single crystal structure as it explores multiple trajectories of the protein. This enables us to obtain a broader view of the dynamics of proteins and it can help in understanding complex binding, improving docking results and more. In this work, we apply the methodology to provide an extensive characterization of the bound complexes of the C3d fragment of human Complement component C3 and one of its powerful bacterial inhibitors, the inhibitory domain of Staphylococcus aureus extra‐cellular fibrinogen‐binding domain (Efb‐C) and two of its mutants. We characterize several important interactions along the binding interface and define low free energy regions in the three complexes. Proteins 2010. © 2009 Wiley‐Liss, Inc.     

Probing the effect of point mutations at protein-protein interfaces with free energy calculations

We have studied the effect of point mutations of the primary binding residue (P1) at the protein-protein interface in complexes of chymotrypsin and elastase with the third domain of the turkey ovomucoid inhibitor and in trypsin with the bovine pancreatic trypsin inhibitor, using molecular dynamics simulations combined with the linear interaction energy (LIE) approach. A total of 56 mutants have been constructed and docked into their host proteins. The free energy of binding could be reliably calculated for 52 of these mutants that could unambiguously be fitted into the binding sites. We find that the predicted binding free energies are in very good agreement with experimental data with mean unsigned errors between 0.50 and 1.03 kcal/mol. It is also evident that the standard LIE model used to study small drug-like ligand binding to proteins is not suitable for protein-protein interactions. Three different LIE models were therefore tested for each of the series of protein-protein complexes included, and the best models for each system turn out to be very similar. The difference in parameterization between small drug-like compounds and protein point mutations is attributed to the preorganization of the binding surface. Our results clearly demonstrate the potential of free energy calculations for probing the effect of point mutations at protein-protein interfaces and for exploring the principles of specificity of hot spots at the interface.     

A practical and efficient method for the resolution of 3‐phospholene 1‐oxides via coordination complex formation1

A simple, efficient, and economical method based on the combination of the exceptional behavior of o,o′‐dibenzoyl‐ or o,o′‐di‐p‐toluyl‐(2R,3R)‐tartaric acid in chiral recognition processes, and the coordination ability of calcium or magnesium ion was developed for the resolution of phospholene oxides 1 . The calcium or magnesium salt of (?)‐o,o′‐dibenzoyl‐(2R,3R)‐tartaric acid 2 , 4 ‐ 6 or calcium hydrogen (?)‐o,o′‐di‐p‐toluyl‐(2R,3R)‐tartrate 3 may form crystalline diastereomeric coordination complexes with the appropriate antipode of substituted 3‐phospholene oxides 1 that makes possible efficient resolutions. Optically active phospholene oxides 1 were prepared directly by simply crystallization and digestion of the corresponding diastereomeric complexes so formed. Thermal behavior of the crystalline diastereomeric complexes was studied by simultaneous TG/DTA. The novel method may be of more general value in respect of the resolution of tertiary phosphine oxides. Chirality, 2010. © 2010 Wiley‐Liss, Inc.     

Coarse‐ and fine‐grained models for proteins: Evaluation by decoy discrimination

Coarse‐grained models for protein structure are increasingly used in simulations and structural bioinformatics. In this study, we evaluated the effectiveness of three granularities of protein representation based on their ability to discriminate between correctly folded native structures and incorrectly folded decoy structures. The three levels of representation used one bead per amino acid (coarse), two beads per amino acid (medium), and all atoms (fine). Multiple structure features were compared at each representation level including two‐body interactions, three‐body interactions, solvent exposure, contact numbers, and angle bending. In most cases, the all‐atom level was most successful at discriminating decoys, but the two‐bead level provided a good compromise between the number of model parameters which must be estimated and the accuracy achieved. The most effective feature type appeared to be two‐body interactions. Considering three‐body interactions increased accuracy only marginally when all atoms were used and not at all in medium and coarse representations. Though two‐body interactions were most effective for the coarse representations, the accuracy loss for using only solvent exposure or contact number was proportionally less at these levels than in the all‐atom representation. We propose an optimization method capable of selecting bead types of different granularities to create a mixed representation of the protein. We illustrate its behavior on decoy discrimination and discuss implications for data‐driven protein model selection. Proteins 2013. © 2012 Wiley Periodicals, Inc.     

Combining genetic and biochemical approaches to identify functional molecular contact points

Protein-protein interactions are required for many viral and cellular functions and are potential targets for novel therapies. Here we detail a series of genetic and biochemical techniques used in combination to find an essential molecular contact point on the duck hepatitis B virus polymerase. These techniques include differential immunoprecipitation, mutagenesis and peptide competition. The strength of these techniques is their ability to identify contact points on intact proteins or protein complexes employing functional assays. This approach can be used to aid identification of putative binding sites on proteins and protein complexes which are resistant to characterization by other methods.     

Different combinations of atomic interactions predict protein‐small molecule and protein‐DNA/RNA affinities with similar accuracy

Interactions between proteins and other molecules play essential roles in all biological processes. Although it is widely held that a protein's ligand specificity is determined primarily by its three‐dimensional structure, the general principles by which structure determines ligand binding remain poorly understood. Here we use statistical analyses of a large number of protein?ligand complexes with associated binding‐affinity measurements to quantitatively characterize how combinations of atomic interactions contribute to ligand affinity. We find that there are significant differences in how atomic interactions determine ligand affinity for proteins that bind small chemical ligands, those that bind DNA/RNA and those that interact with other proteins. Although protein‐small molecule and protein‐DNA/RNA binding affinities can be accurately predicted from structural data, models predicting one type of interaction perform poorly on the others. Additionally, the particular combinations of atomic interactions required to predict binding affinity differed between small‐molecule and DNA/RNA data sets, consistent with the conclusion that the structural bases determining ligand affinity differ among interaction types. In contrast to what we observed for small‐molecule and DNA/RNA interactions, no statistical models were capable of predicting protein?protein affinity with >60% correlation. We demonstrate the potential usefulness of protein‐DNA/RNA binding prediction as a possible tool for high‐throughput virtual screening to guide laboratory investigations, suggesting that quantitative characterization of diverse molecular interactions may have practical applications as well as fundamentally advancing our understanding of how molecular structure translates into function. Proteins 2015; 83:2100–2114. © 2015 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.     

Elucidation of the chromatographic enantiomer elution order for praziquantel: An experimental and theoretical assessment

In this work, we have studied both experimentally and theoretically the praziquantel (PZQ) chiral discrimination. According to the main results, the enantioseparation of PZQ was efficiently optimized by HPLC on the reverse phase from the Chiralpak IB column, which has cellulose tris (3,5-dimethylphenylcarbamate) (CDMPC) as a chiral selector. The thermodynamic and structural parameters obtained via density functional theory (DFT) calculations pointed out the chiral discrimination as well as the enantiomeric elution order of PZQ, thus elucidating the experimental data and validating our proposed method. Finally, the hydrogen bonds and π-π stacking interactions played a key role in the discrimination between the PZQ diastereomeric complexes formed.     

Isothermal titration calorimetry for chiral chemistry

One of the most powerful techniques that are currently available to measure thermodynamic parameters such as enthalpy (ΔH), Gibbs free energy (ΔG), entropy changes (ΔS), and binding affinity in chemical reactions is isothermal titration calorimetry (ITC). Recent advances in instrumentation have facilitated the development of ITC as a very essential analytical tool in biology and chemistry. In this article, we will focus on a review of the literature on the application of ITC for the study of chiral systems and chiral interactions. We present studies in which the ITC technique is used to study chiral interactions, for instance in chiral solutions, chiral organometallic complexes, guest‐host chiral binding interactions, and biological macromolecules. Finally, we put strong emphasis on the most recent application of ITC for the study of chirality in nanosystems and at the nanoscale.