The Role of Conformational Changes in Molecular Recognition

Current Advances in Aptamer-based Biomolecular Recognition and Biological Process Regulation

The interaction between biomolecules with their target ligands plays a great role in regulating biological functions. Aptamers are short oligonucleotide sequences that can specifically recognize target biomolecules via structural complementarity and thus regulate related biological functions. In the past ten years, aptamers have made great progress in target biomolecule recognition, becoming a powerful tool to regulate biological functions. At present, there are many reviews on aptamers applied in biomolecular recognition, but few reviews pay attention to aptamer-based regulation of biological functions. Here, we summarize the approaches to enhancing aptamer affinity and the advancements of aptamers in regulating enzymatic activity, cellular immunity and cellular behaviors. Furthermore, this review discusses the challenges and future perspectives of aptamers in target recognition and biological functions regulation, aiming to provide some promising ideas for future regulation of biomolecular functions in a complex biological environment.

Binding-Induced Unfolding of 1-Bromopropane in α-Cyclodextrin

Raman multivariate curve resolution vibrational spectroscopy and X-ray crystallography are used to quantify changes in the gauche-trans conformational equilibrium of 1-bromopropane (1-BP) upon binding to α-cyclodextrin (α-CD). Both conformers of 1-BP are found to bind to α-CD, although binding favors the unfolded trans conformation. Temperature-dependent measurements of the binding-induced change in the 1-BP conformation equilibrium constant indicate that the trans conformer is both enthalpically and entropically stabilized in the host cavity.

Increasing the Affinity of an O-Antigen Polysaccharide Binding Site in Shigella flexneri Bacteriophage Sf6 Tailspike Protein

Broad and unspecific use of antibiotics accelerates spread of resistances. Sensitive and robust pathogen detection is thus important for a more targeted application. Bacteriophages contain a large repertoire of pathogen-binding proteins. These tailspike proteins (TSP) often bind surface glycans and represent a promising design platform for specific pathogen sensors. We analysed bacteriophage Sf6 TSP that recognizes the O-polysaccharide of dysentery-causing Shigella flexneri to develop variants with increased sensitivity for sensor applications. Ligand polyrhamnose backbone conformations were obtained from 2D 1 H,1 H-trNOESY NMR utilizing methine-methine and methine-methyl correlations. They agreed well with conformations obtained from molecular dynamics (MD), validating the method for further predictions. In a set of mutants, MD predicted ligand flexibilities that were in good correlation with binding strength as confirmed on immobilized S. flexneri O-polysaccharide (PS) with surface plasmon resonance. In silico approaches combined with rapid screening on PS surfaces hence provide valuable strategies for TSP-based pathogen sensor design.

Relative Principal Components Analysis: Application to Analyzing Biomolecular Conformational Changes

A new method termed “Relative Principal Components Analysis” (RPCA) is introduced that extracts optimal relevant principal components to describe the change between two data samples representing two macroscopic states. The method is widely applicable in data-driven science. Calculating the components is based on a physical framework that introduces the objective function (the Kullback–Leibler divergence) appropriate for quantifying the change of the macroscopic state affected by the changes in the microscopic features. To demonstrate the applicability of RPCA, we analyze the thermodynamically relevant conformational changes of the protein HIV-1 protease upon binding to different drug molecules. In this case, the RPCA method provides a sound thermodynamic foundation for analyzing the binding process and thus characterizing both the collective and the locally relevant conformational changes. Moreover, the relevant collective conformational changes can be reconstructed from the informative latent variables to exhibit both the enhanced and the restricted conformational fluctuations upon ligand association.

Intermolecular distance measurement with TNT suppressor on the M13 bacteriophage-based Förster resonance energy transfer system

An M13 bacteriophage-based Förster resonance energy transfer (FRET) system is developed to estimate intermolecular distance at the nanoscale using a complex of CdSSe/ZnS nanocrystal quantum dots, genetically engineered M13 bacteriophages labeled with fluorescein isothiocyanate and trinitrotoluene (TNT) as an inhibitor. In the absence of trinitrotoluene, it is observed that a significant spectral shift from blue to green occur, which represents efficient energy transfer through dipole-dipole coupling between donor and acceptor, or FRET-on mode. On the other hand, in the presence of trinitrotoluene, the energy transfer is suppressed, since the donor-to-acceptor intermolecular distance is detuned by the specific capturing of TNT by the M13 bacteriophage, denoted as FRET-off mode. These noble features are confirmed by changes in the fluorescence intensity and the fluorescence decay curve. TNT addition to our system results in reducing the total energy transfer efficiency considerably from 16.1% to 7.6% compared to that in the non-TNT condition, while the exciton decay rate is significantly enhanced. In particular, we confirm that the energy transfer efficiency satisfies the original intermolecular distance dependence of FRET. The relative donor-to-acceptor distance is changed from 70.03 Å to 80.61 Å by inclusion of TNT.

Diversification of Device Platforms by Molecular Layers: Hybrid Sensing Platforms, Monolayer Doping, and Modeling

Inorganic materials such as semiconductors, oxides, and metals are ubiquitous in a wide range of device technologies owing to the outstanding robustness and mature processing technologies available for such materials. However, while the important contribution of inorganic materials to the advancement of device technologies has been well established for decades, organic-inorganic hybrid device systems, which merge molecular functionalities with inorganic platforms, represent a newer domain that is rapidly evolving at an increasing pace. Such devices benefit from the great versatility and flexibility of the organic building blocks merged with the robustness of the inorganic platforms. Given the overwhelming wealth of literature covering various approaches for modifying and using inorganic devices, this feature article selectively highlights some of the advances made in the context of the diversification of devices by surface chemistry. Particular attention is given to oxide-semiconductor systems and metallic surfaces modified with organic monolayers. The inorganic device components, such as semiconductors, metals, and oxides, are modified by organic monolayers, which may serve as either active, static, or sacrificial components. We portray research directions within the broader field of organic-inorganic hybrid device systems that can be viewed as specific examples of the potential of such hybrid device systems given their comprehensive capabilities of design and diversification. Monolayer doping techniques where sacrificial organic monolayers are introduced into semiconducting elements are reviewed as a specific case, together with associated requirements for nanosystems, devices, and sensors for controlling doping levels and doping profiles on the nanometric scale. Another series of examples of the flexibility provided by the marriage of organic functional monolayers and inorganic device components are represented by a new class of biosensors, where the organic layer functionality is exploited in a functioning device for sensing. Considerations for relying on oxide-terminated semiconductors rather than the pristine semiconductor material as a platform both for processing and sensing are discussed. Finally, we cover aspects related to the use of various theoretical and computational approaches to model organic-inorganic systems. The main objectives of the topics covered here are (i) to present the advances made in each respective domain and (ii) to provide a comprehensive view of the potential uses of organic monolayers and self-assembly processes in the rapidly evolving field of molecular-inorganic hybrid device platforms and processing methodologies. The directions highlighted here provide a perspective on a future, not yet fully realized, integrated approach where organic monolayers are combined with inorganic platforms in order to obtain versatile, robust, and flexible systems with enhanced capabilities.

Elucidating the energetic contributions to the binding free energy

New exact equations are derived for the terms contributing to the binding free energy (ΔG⁰) of a ligand-receptor pair using our recently introduced formalism which we here call perturbation-divergence formalism (PDF). Specifically, ΔG⁰ equals the sum of the average of the perturbation (pertaining to new interactions) and additional dissipative terms. The average of the perturbation includes the sum of the average receptor-ligand interactions and the average of the change of solvation energies upon association. The Kullback-Leibler (KL) divergence quantifies the energetically dissipative terms, which are due to the configurational changes and, using the chain rule of KL divergence, can be decomposed into (i) dissipation due to limiting the external liberation (translation and rotation) of the ligand relative to the receptor and (ii) dissipation due to conformational (internal) changes inside the receptor and the ligand. We also identify all exactly canceling energetic terms which do not contribute to ΔG⁰. Furthermore, the PDF provides a new approach towards dimensionality reduction in the representation of the association process and towards relating the dynamic (high dimensional) with the thermodynamic (one-dimensional) changes.