Role In Molecular Recognition Research Articles

Conformational and Electron Density Analysis of Bicyclo[3.1.0] hexanes: All Roads Lead to Boats

In view of the existence of an optimal conformation for molecular recognition and bearing in mind that nucleosides exhibit a broad range of pharmaceutical properties, whereby their conformation has a key role in molecular recognition, the tendency of the pseudosugar moiety in carbanucleosides to adopt a boat‐like conformation has been studied on the basis of a bicyclo[3.1.0]hexane system, resulting in versatile druglike scaffolds to increase molecular recognition. It is already known that using this system as a pseudosugar can fix the conformation in the northern or southern geometry required for biological activity, according to the relative position of the three‐membered ring. By mapping their energy potential surface, we investigated the preference for boat‐like conformers in bicyclo[3.1.0]hexanes. DFT was utilized alongside NBO analysis to explore the enhanced stability of boat‐like conformers, also considering the influence of oxygen, sulfur, and selenium heteroatoms. Additionally, charge density distribution analysis using QTAIM identified key atoms contributing to stability changes. These findings will help to comprehend this behavior in the drug discovery process when conformationally restricted nucleosides are involved.

De novo design of buttressed loops for sculpting protein functions.

In natural proteins, structured loops have central roles in molecular recognition, signal transduction and enzyme catalysis. However, because of the intrinsic flexibility and irregularity of loop regions, organizing multiple structured loops at protein functional sites has been very difficult to achieve by de novo protein design. Here we describe a solution to this problem that designs tandem repeat proteins with structured loops (9-14 residues) buttressed by extensive hydrogen bonding interactions. Experimental characterization shows that the designs are monodisperse, highly soluble, folded and thermally stable. Crystal structures are in close agreement with the design models, with the loops structured and buttressed as designed. We demonstrate the functionality afforded by loop buttressing by designing and characterizing binders for extended peptides in which the loops form one side of an extended binding pocket. The ability to design multiple structured loops should contribute generally to efforts to design new protein functions.

A data-driven exploration of the complexity of the phosphorus-centered pnictogen bonds

Phosphorus-centered pnictogen bonds, similar to well-studied halogen bonds, play a vital role in molecular recognition and assembly. This study aims to explain how pnictogen bonds interact with other noncovalent interactions. A model system, phosphines (PH3), which is also present in phosphorus cycles and reduces planetary atmospheres, is examined. The investigation of the phosphorus trifluoride (PF3) molecule explores its substituent effects. To generate a broad spectrum of molecular configurations, a specially tailored protocol for sampling and optimisation was implemented. The configurations were refined to uncover primary interaction patterns, and a clustering algorithm revealed unique interaction patterns. This report presents the energy stability and distribution of all the clusters. Our findings verify the prevalent presence of pnictogen bonds, identified by their geometric characteristics and co-occurrence with hydrogen bonds, which show an almost linear correlation. Another significant discovery is the correlation between various energy decomposition elements, especially regarding the electrostatic energy and overall binding energy. These results are anticipated to significantly contribute towards our comprehension of non-covalent interactions among phosphorus-containing molecules and the formulation of empirical models having physical interpretations.

The C-terminal Region of D-DT Regulates Molecular Recognition for Protein-Ligand Complexes.

Systematic analysis of molecular recognition is critical for understanding the biological function of macromolecules. For the immunomodulatory protein D-dopachrome tautomerase (D-DT), the mechanism of protein-ligand interactions is poorly understood. Here, 17 carefully designed protein variants and wild type (WT) D-DT were interrogated with an array of complementary techniques to elucidate the structural basis of ligand recognition. Utilization of a substrate and two selective inhibitors with distinct binding profiles offered previously unseen mechanistic insights into D-DT-ligand interactions. Our results demonstrate that the C-terminal region serves a key role in molecular recognition via regulation of the active site opening, protein-ligand interactions, and conformational flexibility of the pocket's environment. While our study is the first comprehensive analysis of molecular recognition for D-DT, the findings reported herein promote the understanding of protein functionality and enable the design of new structure-based drug discovery projects.

Conformer-Selective Photoelectron Circular Dichroism.

Conformational flexibility and chirality both play a key role in molecular recognition. It is therefore very useful to develop spectroscopic methods that simultaneously probe both properties. It has been theoretically predicted that photoelectron circular dichroism (PECD) should be very sensitive to conformational isomerism. However, experimental proof has been less forthcoming and only exists for a very few favorable cases. Here, we present a new PECD scheme based on resonance-enhanced two-photon ionization (RE2PI) using UV/Vis nanosecond laser excitations. The spectral resolution obtained thereby guarantees conformer-selectivity by inducing resonant conformer-specific ππ* S1←S0 transitions. We apply this experimental scheme to the study of chiral 1-indanol, which exists in two conformers linked by a ring inversion and defined by the position of the hydroxyl group, namely axial and equatorial. We show that the PECD of the equatorial and axial forms considerably differ in sign, magnitude and shape. We also discuss the influence of the total ionization energy, vibronic excitation of intermediate and final states, and relative polarization of the excitation and ionization lasers. Conformer-specificity adds a new dimension to the applications of PECD in analytical chemistry addressing now the general case of floppy systems.

Conformer‐Selective Photoelectron Circular Dichroism

AbstractConformational flexibility and chirality both play a key role in molecular recognition. It is therefore very useful to develop spectroscopic methods that simultaneously probe both properties. It has been theoretically predicted that photoelectron circular dichroism (PECD) should be very sensitive to conformational isomerism. However, experimental proof has been less forthcoming and only exists for a very few favorable cases. Here, we present a new PECD scheme based on resonance‐enhanced two‐photon ionization (RE2PI) using UV/Vis nanosecond laser excitations. The spectral resolution obtained thereby guarantees conformer‐selectivity by inducing resonant conformer‐specific ππ* S1←S0 transitions. We apply this experimental scheme to the study of chiral 1‐indanol, which exists in two conformers linked by a ring inversion and defined by the position of the hydroxyl group, namely axial and equatorial. We show that the PECD of the equatorial and axial forms considerably differ in sign, magnitude and shape. We also discuss the influence of the total ionization energy, vibronic excitation of intermediate and final states, and relative polarization of the excitation and ionization lasers. Conformer‐specificity adds a new dimension to the applications of PECD in analytical chemistry addressing now the general case of floppy systems.

Insights into the mechanism of binding of doxorubicin and a chlorin compound with 22-mer c-Myc G quadruplex

BackgroundThe interaction of small molecules with G quadruplexes is in focus due to its role in molecular recognition and therapeutic drug design. Stabilization of G-quadruplex structures in the promoter regions of oncogenes by small molecule binding has been demonstrated as a potential approach for cancer therapy. MethodsIn this study, electronic spectroscopy (ultraviolet-visible, fluorescence, circular dichroism), differential scanning calorimetry, and molecular modeling were employed to explore the interactions between the chemotherapy drug doxorubicin and a chlorin compound 5,10,15,20-tetraphenyl-[2,3]-[bis(carboxy)-methano]chlorin (H2TPC(DAC)), and the c-Myc 22-mer G quadruplex DNA. ResultsSpectroscopic studies indicated external binding of the compounds with partial stacking at the end quartets. Calorimetric studies and temperature dependent circular dichroism data displayed increased melting temperatures of G quadruplex structure on binding with the compounds. Circular dichroism spectra indicated that the G quadruplex structure is intact upon ligand binding. Both the compounds showed binding affinities of the order of 106 M−1. Fluorescence lifetime studies revealed static quenching as major mechanism for fluorescence quenching. Polymerase chain reaction stop assay hinted that binding of both ligands under study could inhibit the amplification of the DNA sequence. ConclusionResults show that doxorubicin and H2TPC(DAC) bind to the 22-mer c-Myc quadruplex structure with good affinity and induce stability. SignificanceDoxorubicin and H2TPC(DAC) have demonstrated their affinity towards c-Myc G quadruplex DNA, stabilizing it and inhibiting expression and polymerization. The results can be of practical use in designing new analogs for the two compounds, which can become potent anti-cancer agents targeting the c-Myc GQ structure.

A Novel “Turn‐On” Fluorescent Sensor for Screening Triplex DNA Binder Based upon Molecular Beacon

AbstractTriplex DNA plays an essential role in molecular recognition, gene regulation, diagnosis, and treatment of genetic diseases. However, triplex DNA has some shortcomings, such as poor internal Hoogsteen hydrogen bond stability and the difficult formation of parallel triplex DNA under physiological conditions, limiting its applications to a certain extent. Therefore, it is crucial to screen intercalators to enhance triplex DNA stability. Herein, we established a novel “turn‐on” fluorescence sensor for screening triplex DNA binders based upon molecular beacon. Eight different organic small molecules were screened. The fluorescence of the sensor was significantly enhanced in the presence of berberine, coralyne, palmatine, and neomycin. These four small molecules affect stabilizing triplex DNA as an intercalator; the other four small molecules, kanamycin, tetracycline, ethidium bromide, and 4 ′, 6‐diamidino‐2‐phenylindole did not show any noticeable intercalation effect. The results of circular dichroism and melting curve were consistent with those of the fluorescence spectrum.

Evolution of Br⋯Br contacts in enantioselective molecular recognition during chiral 2D crystallization

Halogen-mediated interactions play an important role in molecular recognition and crystallization in many chemical and biological systems, whereas their effect on homochiral versus heterochiral recognition and crystallization has rarely been explored. Here we demonstrate the evolution of Br⋯Br contacts in chiral recognition during 2D crystallization. On Ag(100), type I contacts prevail at low coverage and lead to homochiral recognition and the formation of 2D conglomerates; whereas type II contacts mediating heterochiral recognition are suppressed at medium coverage and appear in the racemates induced by structural transitions at high coverage. On Ag(111), type I contacts dominate the 2D crystallization and generate 2D conglomerates exclusively. DFT calculations suggest that the energy difference between type I and type II contacts is reversed upon adsorption due to the substrate induced mismatch energy penalty. This result provides fundamental understanding of halogen-mediated interactions in molecular recognition and crystallization on surface.

Probing terahertz dynamics of multidomain protein in cell-like confinement

The development of meaningful descriptions of multidomain proteins exhibiting complex inter-domain dynamics modes is a key challenge for understanding their roles in molecular recognition and signalling processes. Here we developed a generally applicable approach for probing the low frequency collective hydration dynamics of multidomain proteins that uses terahertz spectroscopy of a protein molecule confined in a phospholipid reverse micelles environment (named Droplet THz). With the combination of normal mode analysis, we demonstrated the binding of calcium ions modulates the local inter-domain motion of the human coagulant factor VIII protein in a concentration-dependent manner. These findings highlight the Droplet THz as a valuable tool for dissecting the ultrafast dynamics of domain motion in the multidomain proteins and suggest a modulating mechanism of calcium ions on the structural flexibility and function of human coagulant proteins.

Conformational dynamics promotes disordered regions from function-dispensable to essential in evolved site-specific DNA recombinases

Protein intrinsically disordered regions (IDRs) play pivotal roles in molecular recognition and regulatory processes through structural disorder-to-order transitions. To understand and exploit the distinctive functional implications of IDRs and to unravel the underlying molecular mechanisms, structural disorder-to-function relationships need to be deciphered. The DNA site-specific recombinase system Cre/loxP represents an attractive model to investigate functional molecular mechanisms of IDRs. Cre contains a functionally dispensable disordered N-terminal tail, which becomes indispensable in the evolved Tre/loxLTR recombinase system. The difficulty to experimentally obtain structural information about this tail has so far precluded any mechanistic study on its involvement in DNA recombination. Here, we use in vitro and in silico evolution data, conformational dynamics, AI-based folding simulations, thermodynamic stability calculations, mutagenesis and DNA recombination assays to investigate how evolution and the dynamic behavior of this IDR may determine distinct functional properties. Our studies suggest that partial conformational order in the N-terminal tail of Tre recombinase and its packing to a conserved hydrophobic surface on the protein provide thermodynamic stability. Based on our results, we propose a link between protein stability and function, offering new plausible atom-detailed mechanistic insights into disorder-function relationships. Our work highlights the potential of N-terminal tails to be exploited for regulation of the activity of Cre-like tyrosine-type SSRs, which merits future investigations and could be of relevance in future rational engineering for their use in biotechnology and genomic medicine.

Correlated Response of Protein Side-Chain Fluctuations and Conformational Entropy to Ligand Binding.

The heterogeneous fast side-chain dynamics of proteins plays crucial roles in molecular recognition and binding. Site-specific NMR experiments quantify these motions by measuring the model-free order parameter (Oaxis2) on a scale of 0 (most flexible) to 1 (least flexible) for each methyl-containing residue of proteins. Here, we have examined ligand-induced variations in the fast side-chain dynamics and conformational entropy of calmodulin (CaM) using five different CaM-peptide complexes. Oaxis2 of CaM in the ligand-free (Oaxis,U2) and ligand-bound (Oaxis,B2) states are calculated from molecular dynamics trajectories and conformational energy surfaces obtained using the adaptive biasing force (ABF) method. ΔOaxis2 = Oaxis,B2 - Oaxis,U2 follows a Gaussian-like unimodal distribution whose second moment is a potential indicator of the binding affinity of these complexes. The probability for the binding-induced Oaxis,U2 → Oaxis,B2 transition decreases with increasing magnitude of ΔOaxis2, indicating that large flexibility changes are improbable for side chains of CaM after ligand binding. A linear correlation established between ΔOaxis2 and the conformational entropy change of the protein makes possible the determination of the conformational entropy of binding of protein-ligand complexes. The results not only underscore the functional importance of fast side-chain fluctuations but also highlight key motional and thermodynamic correlates of protein-ligand binding.

Intrinsic Conformational Preferences of the Charged Amino Acids in Disordered Proteins

Conformational equilibria in the unfolded states of proteins have many important biological roles, from regulating how some proteins fold and maintain structural stability, to describing the macromolecular details of intrinsically disordered proteins (IDPs), a protein class that does not adopt physiologically stable structures and instead utilizes unfolded states to facilitate their functions. Recently, to better understand the structural properties of IDPs, we analyzed both the sequence dependence to the mean hydrodynamic size of IDPs in water, as well as the impact of heat on the coil dimensions, showing that the sequence dependence and thermodynamic energies associated with intrinsic biases for the polyproline II (PPII) backbone conformation could be obtained. This result is important because PPII is used biologically for protein–protein and protein–nucleic acid interactions and thus has a role in molecular recognition. Experiments that evaluate how the hydrodynamic size changes with compositional changes in the IDP revealed amino acid-specific preferences for PPII that were in excellent quantitative agreement with calorimetry-measured values from small unfolded peptides and also those inferred by a survey of the protein coil library. Here, a set of charge-substitution experiments were used to measure the intrinsic preferences of the charged amino acids (i.e., lysine, arginine, glutamic acid, and aspartic acid) for the PPII backbone conformation, the results of which provide insight into how long-range charge-charge interactions and short-range effects, such as hydration and sterics, can modulate the structural and dynamical properties of IDPs, an increasingly important protein class in cell function.

Investigation of the structure of regulatory proteins interacting with glycosaminoglycans by combining NMR spectroscopy and molecular modeling- the beginning of a wonderful friendship.

The interaction of regulatory proteins with extracellular matrix or cell surface-anchored glycosaminoglycans (GAGs) plays important roles in molecular recognition, wound healing, growth, inflammation and many other processes. In spite of their high biological relevance, protein-GAG complexes are significantly underrepresented in structural databases because standard tools for structure determination experience difficulties in studying these complexes. Co-crystallization with subsequent X-ray analysis is hampered by the high flexibility of GAGs. NMR spectroscopy experiences difficulties related to the periodic nature of the GAGs and the sparse proton network between protein and GAG with distances that typically exceed the detection limit of nuclear Overhauser enhancement spectroscopy. In contrast, computer modeling tools have advanced over the last years delivering specific protein-GAG docking approaches successfully complemented with molecular dynamics (MD)-based analysis. Especially the combination of NMR spectroscopy in solution providing sparse structural constraints with molecular docking and MD simulations represents a useful synergy of forces to describe the structure of protein-GAG complexes. Here we review recent methodological progress in this field and bring up examples where the combination of new NMR methods along with cutting-edge modeling has yielded detailed structural information on complexes of highly relevant cytokines with GAGs.

Recent Force Field Strategies for Intrinsically Disordered Proteins.

Intrinsically disordered proteins (IDPs) are widely distributed across eukaryotic cells, playing important roles in molecular recognition, molecular assembly, post-translational modification, and other biological processes. IDPs are also associated with many diseases such as cancers, cardiovascular diseases, and neurodegenerative diseases. Due to their structural flexibility, conventional experimental methods cannot reliably capture their heterogeneous structures. Molecular dynamics simulation becomes an important complementary tool to quantify IDP structures. This review covers recent force field strategies proposed for more accurate molecular dynamics simulations of IDPs. The strategies include adjusting dihedral parameters, adding grid-based energy correction map (CMAP) parameters, refining protein-water interactions, and others. Different force fields were found to perform well on specific observables of specific IDPs but also are limited in reproducing all available experimental observables consistently for all tested IDPs. We conclude the review with perspective areas for improvements for future force fields for IDPs.

Fabrication of a near-infrared excitation surface molecular imprinting ratiometric fluorescent probe for sensitive and rapid detecting perfluorooctane sulfonate in complex matrix

Construction of fluorescent probe for highly sensitive and selective detection of perfluorooctane sulfonate (PFOS) in water and biological samples is a very important strategy in related pollutant monitoring and environmental health risk appraisal. To overcome the drawback of low sensitivity caused by high-back ground signal of the conventional sensor, a molecularly imprinted near-infrared excitation ratiometric fluorescent probe was constructed and employed to determine PFOS. The sensing process was achieved through the selectively recognition of specific cavities in the probe surface with analyte, accompanied by fluorescence quenching due to the photoinduced electron transfer effect between upconversion materials and PFOS. Under optimized experimental conditions, the fluorescence quenching efficiency of the probe has good linearity against the concentrations of PFOS response divided into two segments within linear ranges of 0.001–0.1 nmol/L and 0.1–1 nmol/L, respectively, with low detection limit of 1 pmol/L. Selective experiment results indicate that the C-F chain length plays a dominant role in molecular recognition and high sensitively detection. The fabricated probe shows well detection performance in a wide pH range. Furthermore, real samples analyses indicate that such an efficient fluorescent probe has potentials in PFOS determination in surface water, human serum and egg extract sample analyses.

Novel, Chiral, and Enantiopure C2‐Symmetric Thioureas Promote Asymmetric Protio‐Pictet‐Spengler Reactions by Anion‐Binding Catalysis

AbstractAlthough anion‐binding processes are well‐known for their crucial role in molecular recognition, they have only recently been utilized for catalysis. Herein, a new class of chiral, enantiopure C2‐symmetrical thioureas that, in combination with 4‐methoxybenzoic acid, promotes the enantioselective protio‐Pictet‐Spengler reaction to provide unprotected tetrahydro‐β‐carbolines in good yields (40–93 %) and moderate‐to‐high enantioselectivities (34–95 % ee) in one step from tryptamine and aldehyde derivatives is described. The formation of a chiral catalyst‐anion complex was explored by 1H NMR.

Solution Structure and Conformational Dynamics of a Doublet Acyl Carrier Protein from Prodigiosin Biosynthesis.

The acyl carrier protein (ACP) is an indispensable component of both fatty acid and polyketide synthases and is primarily responsible for delivering acyl intermediates to enzymatic partners. At present, increasing numbers of multidomain ACPs have been discovered with roles in molecular recognition of trans-acting enzymatic partners as well as increasing metabolic flux. Further structural information is required to provide insight into their function, yet to date, the only high-resolution structure of this class to be determined is that of the doublet ACP (two continuous ACP domains) from mupirocin synthase. Here we report the solution nuclear magnetic resonance (NMR) structure of the doublet ACP domains from PigH (PigH ACP1-ACP2), which is an enzyme that catalyzes the formation of the bipyrrolic intermediate of prodigiosin, a potent anticancer compound with a variety of biological activities. The PigH ACP1-ACP2 structure shows each ACP domain consists of three conserved helices connected by a linker that is partially restricted by interactions with the ACP1 domain. Analysis of the holo (4'-phosphopantetheine, 4'-PP) form of PigH ACP1-ACP2 by NMR revealed conformational exchange found predominantly in the ACP2 domain reflecting the inherent plasticity of this ACP. Furthermore, ensemble models obtained from SAXS data reveal two distinct conformers, bent and extended, of both apo (unmodified) and holo PigH ACP1-ACP2 mediated by the central linker. The bent conformer appears to be a result of linker-ACP1 interactions detected by NMR and might be important for intradomain communication during the biosynthesis. These results provide new insights into the behavior of the interdomain linker of multiple ACP domains that may modulate protein-protein interactions. This is likely to become an increasingly important consideration for metabolic engineering in prodigiosin and other related biosynthetic pathways.

Molecular Recognition at Septin Interfaces: The Switches Hold the Key

The assembly of a septin filament requires that homologous monomers must distinguish between one another in establishing appropriate interfaces with their neighbors. To understand this phenomenon at the molecular level, we present the first four crystal structures of heterodimeric septin complexes. We describe in detail the two distinct types of G-interface present within the octameric particles, which must polymerize to form filaments. These are formed between SEPT2 and SEPT6 and between SEPT7 and SEPT3, and their description permits an understanding of the structural basis for the selectivity necessary for correct filament assembly. By replacing SEPT6 by SEPT8 or SEPT11, it is possible to rationalize Kinoshita's postulate, which predicts the exchangeability of septins from within a subgroup. Switches I and II, which in classical small GTPases provide a mechanism for nucleotide-dependent conformational change, have been repurposed in septins to play a fundamental role in molecular recognition. Specifically, it is switch I which holds the key to discriminating between the two different G-interfaces. Moreover, residues which are characteristic for a given subgroup play subtle, but pivotal, roles in guaranteeing that the correct interfaces are formed.

Исчерпывающее окисление декагидроксипиллар[5]арена нитратами меди(II) и железа(III)

Pillar[n]arenes are suitable synthetic platforms for synthesis of functionalized p-cyclophanes, versatile building blocks for creating supramolecular polymers and (pseudo)rotaxanes. The presence of hydroquinone fragments in unsubstituted pillar[n]arene derivatives opens wide opportunities for their application in electrochemical sensors and for their use as reducing agents for synthesis of hybrid materials. Macrocyclic cavity plays the key role in molecular recognition, supramolecular self-assembly of pillararenes, and therefore possibility of switching electron donor properties of aromatic moieties, forming macrocyclic cavity presents specific interest. Synthesis of pillar[n]quinones is non-trivial goal, usually, it requires expensive reagents (сerium(IV) ammonium nitrate). As an oxidized compound alkoxy-derivatives of pillararenes are used. While possibility of red-ox transitions of decahydroxypillar[5]arene are well known, to the date in literature there are no examples of total oxidation of decahydroxypillar[5]arene. We have studied interaction of decahydroxy-pillar[5]arene with a row of inorganic oxidants: catalytic oxidation with air oxygen in presence of copper(II) and iron(III) nitrates, and oxidation with ammonium persulfate. In order to find the optimal conditions for oxidation of pillar[5]arene the series of solvents were tried (proton donor alcohols and acetic acid, proton acceptor dimethylformamide and dimethylsulfoxide). It was established that using glacial acetic acid as a solvent with ultrasonication leads to total oxidation of pillar[5]arene to pillar[5]quinone. This fact is explained by strong proton-donor properties of glacial acetic acid, to prevent formation of insoluble quinhydrone complexes of pillar[5]arene oxidation products. Using ammonium persulfate does not lead to the product of total oxidation.