Understanding noncovalent interactions: ligand binding energy and catalytic efficiency from ligand-induced reductions in motion within receptors and enzymes

The weak magnetic field inhibits the supramolecular self-ordering of chiral molecules

The magnetic field can affect processes in the non-magnetic systems, including the biochemical reactions in the living cells. This phenomenon becomes possible due to the fermionic nature of an electron and significant energy gain provided by the exchange interactions. Here we report the inhibition effect of the magnetic field on the processes of the chiral supramolecular, i.e., macroscopic self-ordering in the non-magnetic model system. The observed effect is in tune with the reports on the influence of the magnetic field on the adsorption of the chiral molecules, which was explained by the effect of the chirally-induced spin-selectivity and the inhibition of the chemical reactions caused by the singlet-triplet conversion. The magneto sensitivity of the process of the chiral self-ordering directly indicates its spin-polarization nature. Tacking together all of the results in the field, we can propose that the chirality-driven exchange interactions guide the selection of the chiral molecules and explain their prevalence in the living matter. It is also probable that these forces have played a critical role in the origin of life on Earth.

A defined structural unit enables de novo design of small-molecule-binding proteins

The de novo design of proteins that bind highly functionalized small molecules represents a great challenge. To enable computational design of binders, we developed a unit of protein structure-a van der Mer (vdM)-that maps the backbone of each amino acid to statistically preferred positions of interacting chemical groups. Using vdMs, we designed six de novo proteins to bind the drug apixaban; two bound with low and submicromolar affinity. X-ray crystallography and mutagenesis confirmed a structure with a precisely designed cavity that forms favorable interactions in the drug-protein complex. vdMs may enable design of functional proteins for applications in sensing, medicine, and catalysis.

Halogen Bonds in Protein Nucleic Acid Recognition

Identifying new binding forces between electron donor and acceptor entities is key to properly understanding molecular recognition and aggregation phenomena, which are of inmense importance to biology. For decades, the halogenation of DNA/RNA bases has been routinely carried out to solve solid state structures of nucleic acids (NA). However, the effects of this modification might be deeper than just a simple atom substitution since halogens are also known to undergo noncovalent binding (halogen bonding). Herein we show that halogenated NAs with either Br or I atoms are able to establish halogen bonds with properly disposed protein residues. An inspection of the Protein Data Bank (PDB) reveals several examples involving 5-iodo/5-bromouracil, 8-bromoadenine, and 5-iodocytosine bases that are consistent with the halogen bond geometry features. Computations reveal the favorable and moderately strong nature of this interaction, thus confirming the ability of halogenated bases to actively participate in protein-NA binding.

Dramatic Enhancement of Binding Affinities Between Foldamer-Based Receptors and Anions by Intra-Receptor π-Stacking

As a synthetic model for intra-protein interactions that reinforce binding affinities between proteins and ligands, the energetic interplay of binding and folding was investigated using foldamer-based receptors capable of adopting helical structures. The receptors were designed to have identical hydrogen-bonding sites for anion binding but different aryl appendages that simply provide additional π-stacking within the helical backbones without direct interactions with the bound anions. In particular, the presence of electron-deficient aryl appendages led to dramatic enhancements in the association constant between the receptor and chloride or nitrate ions, by up to three orders of magnitude. Extended stacking within the receptor contributes to the stabilization of the entire folding structure of complexes, thereby enhancing binding affinities.

Toward Simple, Predictive Understanding of Protein-Ligand Interactions: Electronic Structure Calculations on Torpedo Californica Acetylcholinesterase Join Forces with the Chemist's Intuition

Contemporary efforts for empirically-unbiased modeling of protein-ligand interactions entail a painful tradeoff - as reliable information on both noncovalent binding factors and the dynamic behavior of a protein-ligand complex is often beyond practical limits. We demonstrate that information drawn exclusively from static molecular structures can be used for reproducing and predicting experimentally-measured binding affinities for protein-ligand complexes. In particular, inhibition constants (Ki) were calculated for seven different competitive inhibitors of Torpedo californica acetylcholinesterase using a multiple-linear-regression-based model. The latter, incorporating five independent variables - drawn from QM cluster, DLPNO-CCSD(T) calculations and LED analyses on the seven complexes, each containing active amino-acid residues found within interacting distance (3.5 Å) from the corresponding ligand - is shown to recover 99.9% of the sum of squares for measured Ki values, while having no statistically-significant residual errors. Despite being fitted to a small number of data points, leave-one-out cross-validation statistics suggest that it possesses surprising predictive value (Q2LOO=0.78, or 0.91 upon removal of a single outlier). This thus challenges ligand-invariant definitions of active sites, such as implied in the lock-key binding theory, as well as in alternatives highlighting shape-complementarity without taking electronic effects into account. Broader implications of the current work are discussed in dedicated appendices.

Off-Pocket Activity Cliffs: A Puzzling Facet of Molecular Recognition

While accurate quantitative prediction of ligand-protein binding affinity remains an elusive goal, high-affinity ligands to therapeutic targets are being designed through heuristic optimization of ligand-protein contacts. However, herein, through large-scale data mining and analyses, we demonstrate that a ligand's binding can also be strongly affected through modifying its solvent-exposed portion that does not make contacts with the protein, thus resulting in "off-pocket activity cliffs" (OAC). We then exposed the roots of the OAC phenomenon by means of molecular dynamics (MD) simulations and MD data analyses. We expect OAC to extend our knowledge of molecular recognition and enhance the drug designer's toolkit.

Strong Adverse Contribution of Conformational Dynamics to Streptavidin-Biotin Binding

Molecular dynamics plays an important role for the biological function of proteins. For protein ligand interactions, changes of conformational entropy of protein and hydration layer are relevant for the binding process. Quasielastic neutron scattering (QENS) was used to investigate differences in protein dynamics and conformational entropy of ligand-bound and ligand-free streptavidin. Protein dynamics were probed both on the fast picosecond time scale using neutron time-of-flight spectroscopy and on the slower nanosecond time scale using high-resolution neutron backscattering spectroscopy. We found the internal equilibrium motions of streptavidin and the corresponding mean square displacements (MSDs) to be greatly reduced upon biotin binding. On the basis of the observed MSDs, we calculated the difference of conformational entropy ΔS_conf of the protein component between ligand-bound and ligand-free streptavidin. The rather large negative ΔS_conf value (-2 kJ mol^-1 K^-1 on the nanosecond time scale) obtained for the streptavidin tetramer seems to be counterintuitive, given the exceptionally high affinity of streptavidin-biotin binding. Literature data on the total entropy change ΔS observed upon biotin binding to streptavidin, which includes contributions from both the protein and the hydration water, suggest partial compensation of the unfavorable ΔS_conf by a large positive entropy gain of the surrounding hydration layer and water molecules that are displaced during ligand binding.

Salen‑manganese complexes for controlling ROS damage: Neuroprotective effects, antioxidant activity and kinetic studies

A new manganese(III) complex [MnL¹(DCA)(H₂O)](H₂O)_,1 [H₂L¹ is the chelating ligand N,N'-bis(2-hydroxy-3-methoxybenzylidene)-1,2-diaminopropane, and DCA is dicyanamide], has been prepared and characterized by different analytical and spectroscopic techniques. The tetragonally elongated octahedral geometry for the manganese coordination sphere was revealed by X-ray diffraction studies for 1. The antioxidant behavior of this complex and other manganese(III)-salen type complexes was tested through superoxide dismutase and catalase probes, and through the study of their neuroprotective effects in SH-SY5Y neuroblastoma cells. In this human neuronal model, these model complexes were found to improve cell survival in an oxidative stress model. During studies aimed to getting a better understanding of the kinetics of the processes involved in this antioxidant behavior, an important effect on the solvent in the kinetics of reaction of the complexes with H₂O₂ was revealed that suggests a change in the mechanism of reaction of the complexes. The kinetic data in methanol and buffered aqueous solutions correlate well with the results of the test of catalase activity, thus showing that the rate determining step in the catalytic cycle corresponds to the initial reaction of the complexes with H₂O₂.

Targeting the Bacterial Transglycosylase: Antibiotic Development from a Structural Perspective

One of the major threats to human life nowadays is widespread antibiotic resistance. Antibiotics are used to treat bacterial infections by targeting their essential pathways, such as the biosynthesis of bacterial cell walls. Bacterial transglycosylase, particularly glycosyltransferase family 51 (GT51), is one critical player in the cell wall biosynthesis and has long been known as a promising yet challenging target for antibiotic development. Here, we review the structural studies of this protein and summarize recent progress in developing its specific inhibitors, including synthetic substrate analogs and novel compounds identified from high-throughput screens. A detailed analysis of the protein-ligand interface has also provided us with valuable insights into the future antibiotic development against the bacterial transglycosylase.

Theoretical explanation for the pharmaceutical incompatibility through the cooperativity effect of the drug-drug intermolecular interactions in the phenobarbital∙∙∙paracetamol∙∙∙H2O complex

In order to reveal the essence of the pharmaceutical incompatibility, the cooperativity effects of the drug-drug intermolecular π∙∙∙π and H∙∙∙O H-bonding interactions involving hydration were evaluated in the phenobarbital∙∙∙paracetamol∙∙∙H₂O complex at the M06-2X/6-311++G** and MP2/6-311++G** levels. The thermodynamic cooperativity effects were also investigated by the statistical thermodynamic method. The results show that the π∙∙∙π stacking ternary complexes with the moderate anti-cooperativity effects are dominant in controling the aggregation process of phenobarbital, paracetamol, and H₂O, as is confirmed by the atoms-in-molecules (AIM) and reduced density gradient (RDG) analyses. Therefore, it can be inferred that the anti-cooperativity effect plays an important role in forming the pharmaceutical incompatibility, and thus a deduction on the formation process of the pharmaceutical incompatibility between phenobarbital and paracetamol, with the hydration effect, is given. Several valuable models that relate the features of molecular surface electrostatic potentials or their statistical parameters, such as the surface areas, average values ([Formula: see text]), variances ([Formula: see text], [Formula: see text] and [Formula: see text]), and product of [Formula: see text] and electrostatic balance parameter (ν) ([Formula: see text]ν), to the values of the cooperativity effects were predicted. The formation of the pharmaceutical incompatibility is a thermodynamic cooperativity process driven by the enthalpy change. Graphical abstract Anti-cooperativity effect plays an important role in forming the pharmaceutical incompatibility.

Catalysis by Networks of Cooperative Hydrogen Bonds

The main paradigm of today's chemistry is sustainability. In pursuing sustainability, we need to learn from chemical processes carried out by Nature and realize that Nature does not use either strong acids, or strong bases or fancy reagents to achieve outstanding chemical processes. Instead, enzyme activity leans on the cooperation of several chemical entities to avoid strong acids or bases or to achieve such an apparently simple goal as transferring a proton from an NuH unit to an E unit (NuH + E → Nu–EH). Hydrogen bond catalysis emerged strongly two decades ago in trying to imitate Nature and avoid metal catalysis. Now to mount another step in pursuing the goal of sustainability, the focus is upon cooperativity between the different players involved in catalysis. This chapter looks at the concept of cooperativity and, more specifically, (a) examines the role of cooperative hydrogen bonded arrays of the general type NuH⋯(NuH)n⋯NuH (i.e. intermolecular cooperativity) to facilitate general acid–base catalysis, not only in the solution phase but also under solvent-free and catalyst-free conditions, and, most important, (b) analyzes the capacity of designer chiral organocatalysts displaying intramolecular networks of cooperative hydrogen bonds (NCHBs) to facilitate enantioselective synthesis by bringing conformational rigidity to the catalyst in addition to simultaneously increasing the acidity of key hydrogen atoms so to achieve better complementarity in the highly polarized transition states.

Aromatically functionalized pseudo-crown ethers with unusual solvent response and enhanced binding properties

Conformational flexibility in the host's structure is often considered detrimental to its binding. Flexible pseudo-crown ethers with aromatic donor/acceptor groups at the chain ends, however, displayed enhanced binding affinity and selectivity, particularly when the direct binding interactions were compromised by unfavorable solvents.

Synergistic promotion by intramolecular hydrogen bonding: a bi-functionally catalyzed cascade reaction for the synthesis of enantiopure chromenopyrrolidines

An effective organocatalytic asymmetric cascade reaction of o-hydroxy aromatic aldimines and β,γ-unsaturated-α-ketoesters was developed.

Exploiting the biomimetic and luminescence properties of multivalent dendrimer-semiconductor nanohybrid materials in the ultra-low level determination of folic acid

In view of the enhanced generation of folate receptors in cancerous cells and diseases linked to the deficiency of folic acid, such as anemia, mental devolution, congenital malformation, etc., the development of a simple method for the ultra-sensitive determination of folic acid remains a long-standing issue for practical applications in medicine and biotechnology. Thus, the proposed luminescence based strategy involving multifunctional poly(amidoamine) (PAMAM) dendrimer encapsulated quantum dots (QDs) as a probe provides a simple, fast and efficient method for the selective determination of folic acid at the nano-molar level. Absorption and Fourier transform infra-red (FTIR) spectroscopy provide evidence of the binding of folic acid with dendrimer amine groups. The emission quenching of dendrimer encapsulated CdS QDs follows a linear Stern-Volmer plot with an exceedingly high value of the Stern-Volmer constant (K_SV = 8.4 × 10⁶ M^-1) facilitating a higher detection efficiency. Similar quenching analysis with dendrimer-ZnS QDs showed a slightly lower Stern-Volmer constant (K_SV = 2.29 × 10⁶ M^-1). The lower probing efficiency of the protein or amino acid capping of QDs has been explained through zeta potential measurements. The solvent polarity dependence suggests a charge transfer process responsible for the emission quenching of CdS QDs, which is static in nature as revealed by lifetime measurements. The determination of folic acid at this low level is not affected by possible interfering molecules, such as vitamin C, vitamin B₁₂ and uric acid. Calorimetric measurements showed that the exothermic binding of folic acid with a dendrimer follows enthalpy-entropy compensation. The detailed mechanistic aspect of interactions of folic acid with the QD probe helps in a better understanding of the detection process, which in turn can assist in developing a dendrimer based material for image analysis and drug delivery in folate receptor rich cells.

Molecular Recognition of a Thomsen-Friedenreich Antigen Mimetic Targeting Human Galectin-3

Overexpression of the Thomsen-Friedenreich (TF) antigen in cell membrane proteins occurs in 90 % of adenocarcinomas. Additionally, the binding of the TF antigen to human galectin-3 (Gal-3), also frequently overexpressed in malignancy, promotes cancer progression and metastasis. In this context, structures that interfere with this specific interaction have the potential to prevent cancer metastasis. A multidisciplinary approach combining the optimized synthesis of a TF antigen mimetic with NMR, X-ray crystallography methods, and isothermal titration calorimetry assays was used to unravel the molecular structural details that govern the Gal-3/TF mimetic interaction. The TF mimetic has a binding affinity for Gal-3 similar to that of the TF natural antigen and retains the binding epitope and bioactive conformation observed for the native antigen. Furthermore, from a thermodynamic perspective, a decrease in the enthalpic contribution was observed for the Gal-3/TF mimetic complex; however, this behavior is compensated by a favorable gain in entropy. From a structural perspective, these results establish our TF mimetic as a scaffold to design multivalent solutions to potentially interfere with Gal-3 aberrant interactions and for likely use in hampering Gal-3-mediated cancer cell adhesion and metastasis.

The recognition of glycans by protein receptors. Insights from NMR spectroscopy

Carbohydrates (glycans, saccharides, sugars) are everywhere. In fact, glycan-protein interactions are involved in many essential processes of life and disease. The understanding of the key structural details at the atomic and molecular level is of paramount importance to effectively design molecules for therapeutic purposes. Different approximations may be employed to decipher these molecular recognition processes with high resolution. Advances in cryo-electron microscopy are providing exquisite details on different biological mechanisms involving sugars, while better and better protocols for structural refinement in the application of X-ray methods for protein-sugar complexes and glycoproteins are also permitting fantastic advances in the glycoscience arena. Alternatively, NMR spectroscopy remains as one of the most rewarding techniques to explore protein-carbohydrate interactions. In fact, given the intrinsic dynamic nature of saccharides, NMR can afford exquisite structural information at the atomic detail, not accessible by other techniques. However, the access to this information is sometimes intricate, and requires careful analysis and well-defined strategies. In this review, we have highlighted these issues and presented an overview of different modern NMR approaches with a focus on the latest developments and challenges.

Mechanical Cooperativity in DNA Cruciform Structures

Unlike short-range chemical bonds that maintain chemical properties of a biological molecule, long-range mechanical interactions determine mechanochemical properties of molecules. Limited by experimental approaches, however, direct quantification of such mechanical interactions is challenging. Using magneto-optical tweezers, herein we found torque can change the topology and mechanochemical property of DNA cruciform, a naturally occurring structure consisting of two opposing hairpin arms. Both mechanical and thermodynamic stabilities of DNA cruciforms increase with positive torque, which have been attributed to the topological coupling between DNA template and the cruciform. The coupling exists simultaneously in both arms of a cruciform, which coordinates the folding and unfolding of the cruciform, leading to a mechanical cooperativity not observed previously. As DNA torque readily varies during transcriptions, our finding suggests that DNA cruciforms can modulate transcriptions by adjusting their properties according to the torque.

Cooperativity Principles in Self-Assembled Nanomedicine

Nanomedicine is a discipline that applies nanoscience and nanotechnology principles to the prevention, diagnosis, and treatment of human diseases. Self-assembly of molecular components is becoming a common strategy in the design and syntheses of nanomaterials for biomedical applications. In both natural and synthetic self-assembled nanostructures, molecular cooperativity is emerging as an important hallmark. In many cases, interplay of many types of noncovalent interactions leads to dynamic nanosystems with emergent properties where the whole is bigger than the sum of the parts. In this review, we provide a comprehensive analysis of the cooperativity principles in multiple self-assembled nanostructures. We discuss the molecular origin and quantitative modeling of cooperative behaviors. In selected systems, we describe the examples on how to leverage molecular cooperativity to design nanomedicine with improved diagnostic precision and therapeutic efficacy in medicine.

Structural insight into the antagonistic action of diarylheptanoid on human estrogen receptor alpha

Estrogen receptor α (ER α) is an important therapeutic target in the regulation of ligand dependent signaling in breast cancer. The current study investigates the anti-estrogenic potential of the Diarylheptanoid, 5-hydroxy-7-(4-hydroxy-3 methoxyphenyl)-1-phenyl-3-heptanone (DAH) in silico. Rigid Docking analysis of DAH at the ligand binding domain (LBD) of ER α showed hydrogen bond interactions with Arg394 and Glu353 at the active site, similar to the positive controls 4-Hydroxy Tamoxifen (4-OHT) and Fulvestrant (FUL). The protein and the protein-DAH complexes were further analyzed using molecular dynamics simulations for a time scale of 50 ns using GROMACS. Root mean square fluctuation (RMSF) analysis showed large fluctuations at the N-terminal region of Helices (H) 3, 9 and at the C-terminal region of H11, which could be involved in the antagonistic conformational change. Interestingly, H12 appeared to move away from the ligand binding pocket and occupy the co-activator binding groove at the LBD of ER α. Secondary structure analysis of the protein upon binding of DAH and CUR showed structural change from α-helix to Turn conformation at H4. We hypothesize that this structural change at H4, similar to the positive control, could hinder the activity of AF-2 by blocking the binding of co-activator. These conformational changes in ER α indicate an anti-estrogenic and therapeutic potential of the DAH.

The electron's spin and molecular chirality - how are they related and how do they affect life processes?

The recently discovered chiral induced spin selectivity (CISS) effect gives rise to a spin selective electron transmission through biomolecules. Here we review the mechanism behind the CISS effect and its implication for processes in Biology. Specifically, three processes are discussed: long-range electron transfer, spin effects on the oxidation of water, and enantioselectivity in bio-recognition events. These phenomena imply that chirality and spin may play several important roles in biology, which have not been considered so far.

Intramolecularly enhanced molecular tweezers with unusually strong binding for aromatic guests in unfavorable solvents

Molecular tweezers using aromatic interactions for binding normally work best in polar instead of nonpolar solvents due to the strong solvophobic effect in the binding.

High-affinity and selective detection of pyrophosphate in water by a resorcinarene salt receptor

Pyrophosphate (PPi) is a byproduct of DNA and RNA synthesis, and abnormal levels are indicative of disease. We report the high-affinity binding of PPi in water by N-alkyl ammonium resorcinarene chloride receptors. Experimental analysis using ¹H and ³¹P NMR, isothermal titration calorimetry, mass spectrometry, and UV-vis spectroscopy all support exceptional selectivity of these systems for PPi in water. The measured affinity of K₁ = 1.60 × 10⁷ M^-1 for PPi is three orders of magnitude larger than that observed for binding to another phosphate, ATP. This exceptional anion-binding affinity in water is explored through a detailed density functional theory computational study. These systems provide a promising avenue for the development of future innovative medical diagnostic tools.

Direction-dependent force-induced dissociation dynamics of an entropic-driven lock-and-key assembly

The unbinding dynamics of a nanosized sphere-and-cavity assembly under the pulling of constant force and constant loading rate is explored by dissipative particle dynamics simulations. The formation of this matched lock-and-key pair in a polymer solution is driven by the depletion attraction. The two-dimensional free energy landscape U(x,z) associated with this assembly is constructed. Our results indicate that the unbinding pathway along the orientation of the assembly is unfavorable due to the relatively high energy barrier compared to that along the tortuous minimum path whose energy barrier is not high. It is also found that the dissociation rate depends on the direction of the external force (θ) with respect to the assembly orientation. The presence of the force component perpendicular to the assembly orientation can reduce the bond lifetime significantly by driving the key particle to approach the minimum path. Moreover, the dissociation dynamics can be facilitated even by a pushing force compared to the spontaneous dissociation (without forces). To elucidate the effective pathway under pulling, the escaping position is analyzed and its mean direction with respect to the assembly orientation rises generally with increasing θ, revealing that the presence of the force component along the minimum pathway is helpful. The importance of the direction of the external pulling has been demonstrated in our simple system. Therefore, this effect should be considered in more complicated unbinding experiments.

Host-guest interactions between sildenafil and cyclodextrins: Spectrofluorometric study and molecular dynamic modeling

Sildenafil (SF) was included in cyclodextrins (CD) to enhance its solubility. Spectrofluorometry was used to confirm the complexation constant (stability constant). The orientations of SF inside the β-CDs and γ-CDs were fully illustrated. Molecular dynamics simulations were performed on two inclusion complexes (β-CD/SF and γ-CD/SF) in the aqueous system. The polar methylpiperazine group was found to locate inside the β-CD cavity, both in the wide and narrow side and was positioned 2°A from the center. In contrast, the methylpiperazine group did not fit well within the γ-CD cavity. Moreover, these results also confirmed hydrogen bonding that the highest number of bonding formed between the polar methylpiperazine sulfonyl structure and the hydroxyl group of β-CD. The simulated binding free energy of the methylpiperazine-β-CD inclusion complex (-6.01kcal/mol), featured a large contribution from electrostatic and van der Waals forces, which was the most stable complex. The association constant of β-CD/SF (12.3) was higher than γ-CD/SF (3.3) and confirmed with in silico measurements of binding free energy. In summary, SF forms a stable complex with β-CD.

CH2 Linkage Effects on the Reactivity of Bis(aminophosphine)-Ruthenium Complexes for Selective Hydrogenation of Esters into Alcohols

A novel ruthenium complex binding to two subtly different aminophosphine ligands, (o-PPh2C6H4CH2NH2)(o-PPh2C6H4NH2)RuCl2, was successfully isolated. This bis(aminophosphine)-ruthenium complex shows efficient activity in both dimethyl oxalate (DMO) and methyl benzoate (MB) hydrogenation. On the contrast, similar complexes (o-PPh2C6H4NH2)2RuCl2 and (o-PPh2C6H4CH2NH2)2RuCl2, can only effectively catalyze the hydrogenation of DMO and MB, respectively. Our experimental studies in combination of theoretical calculations reveal that the remarkable substrate selectivity in the hydrogenation of esters arises from the nonbonding interactions operated by the CH2 linkage of the ligand.

Mapping a protein recognition centre with chiral photoactive ligands. An integrated approach combining photophysics, reactivity, proteomics and molecular dynamics simulation studies

A multidisciplinary strategy to obtain structural information on the intraprotein region is described here. As probe ligands, (S)- and (R)-CPFMe (the methyl esters of the chiral drug carprofen) have been selected, while bovine α1-acid glycoprotein (BAAG) has been chosen as a biological host. The procedure involves the separate irradiation of the BAAG/(S)-CPFMe and BAAG/(R)-CPFMe complexes, coupled with fluorescence spectroscopy, laser flash photolysis, proteomic analysis, docking and molecular dynamics simulations. Thus, irradiation of the BAAG/CPFMe complexes at λ = 320 nm was followed by fluorescence spectroscopy. The intensity of the emission band obtained after irradiation indicated photodehalogenation, whereas its structureless shape suggested covalent binding of the resulting radical CBZMe˙ to the biopolymer. After gel filtration chromatography, the spectra still displayed emission, in agreement with covalent attachment of CBZMe˙ to BAAG. Stereodifferentiation was observed in this process. After trypsin digestion and ESI-MS/MS, the incorporation of CBZMe was detected at Phe68. Docking and molecular dynamics simulation studies, which were carried out using a homology model of BAAG, reveal that the closer proximity of the aromatic moiety of the (S)-enantiomer to the phenyl group of Phe68 would be responsible for the experimentally observed, more effective chemical modification of the protein. The proposed tridimensional structure of BAAG covalently modified by the two enantiomers is also provided. In principle, this approach can be extended to a variety of protein/ligand complexes.

Chirality-induced spin polarization places symmetry constraints on biomolecular interactions

Noncovalent interactions between molecules are key for many biological processes. Necessarily, when molecules interact, the electronic charge in each of them is redistributed. Here, we show experimentally that, in chiral molecules, charge redistribution is accompanied by spin polarization. We describe how this spin polarization adds an enantioselective term to the forces, so that homochiral interaction energies differ from heterochiral ones. The spin polarization was measured by using a modified Hall effect device. An electric field that is applied along the molecules causes charge redistribution, and for chiral molecules, a Hall voltage is measured that indicates the spin polarization. Based on this observation, we conjecture that the spin polarization enforces symmetry constraints on the biorecognition process between two chiral molecules, and we describe how these constraints can lead to selectivity in the interaction between enantiomers based on their handedness. Model quantum chemistry calculations that rigorously enforce these constraints show that the interaction energy for methyl groups on homochiral molecules differs significantly from that found for heterochiral molecules at van der Waals contact and shorter (i.e., ∼0.5 kcal/mol at 0.26 nm).

Molecular cloning, expression profile, odorant affinity, and stability of two odorant-binding proteins in Macrocentrus cingulum Brischke (Hymenoptera: Braconidae)

The polyembryonic endoparasitoid wasp Macrocentrus cingulum Brischke (Hymenoptera: Braconidae) is deployed successfully as a biocontrol agent for corn pest insects from the Lepidopteran genus Ostrinia in Europe and throughout Asia, including Japan, Korea, and China. The odorants are recognized, bound, and solubilized by odorant-binding protein (OBP) in the initial biochemical recognition steps in olfaction that transport them across the sensillum lymph to initiate behavioral response. In the present study, we examine the odorant-binding effects on thermal stability of McinOBP2, McinOBP3, and their mutant form that lacks the third disulfide bonds. Real-time PCR experiments indicate that these two are expressed mainly in adult antennae, with expression levels differing by sex. Odorant-binding affinities of aldehydes, terpenoids, and aliphatic alcohols were measured with circular dichroism spectroscopy based on changes in the thermal stability of the proteins upon their affinities to odorants. The obtained results reveal higher affinity of trans-caryophelle, farnesene, and cis-3-Hexen-1-ol exhibits to both wild and mutant McinOBP2 and McinOBP3. Although conformational flexibility of the mutants and shape of binding cavity make differences in odorant affinity between the wild-type and mutant, it suggested that lacking the third disulfide bond in mutant proteins may have chance to incorrect folded structures that reduced the affinity to these odorants. In addition, CD spectra clearly indicate proteins enriched with α-helical content.

In silico analysis of interaction pattern switching in ligand⋯receptor binding in Golgi α-mannosidase II induced by the protonated states of inhibitors

Different binding modes for charge-neutral and protonated inhibitor forms in Golgi α-mannosidase II active sites may influence their biological activities.

Nanorings with copper(ii) and zinc(ii) centers: forcing copper porphyrins to bind axial ligands in heterometallated oligomers

The affinity of copper(ii) porphyrins for pyridine ligands is extremely weak, but oligo-pyridine templates can be used to direct the synthesis of Cu-containing cyclic porphyrin oligomers when they also have Zn centers. We report the synthesis of two heterometallated nanorings: a six-porphyrin ring prepared from a Zn/Cu/Zn linear trimer and a ten-porphyrin ring prepared from a Zn/Zn/Cu/Zn/Zn pentamer. Both these macrocycles have copper porphyrins at two specific positions across the diameter of the ring and zinc at other sites. The presence of a paramagnetic metal results in broadening of the 1H NMR spectra and reduces the relaxation time constants (T1 and T2). The changes in T1 provide quantitative information on the distance of each proton from the copper atom. The Zn/Zn/Cu/Zn/Zn linear porphyrin pentamer binds strongly to a penta-pyridyl template, despite the weakness of the Cu-N interaction, because of the chelate cooperativity of the neighboring Zn-N coordination. The stabilities of a family of four linear porphyrin pentamer complexes were determined by UV-vis-NIR titration and analyzed using a chemical double-mutant cycle. The results show that the free energy of interaction of a copper center to axial pyridine ligands is -6.2 kJ mol-1 when the entropy cost of bringing together the two molecules has already been paid by pyridine-zinc interactions. The development of template-directed approaches to the synthesis of nanorings with combinations of different metals at specific positions around the ring opens up many possibilities for controlling the photophysical behavior of these supramolecular systems and for probing their conformations by EPR.