Dynamic Binding Mechanism Research Articles

Lignin-based vitrimer containing dynamic borate ester bonds with intrinsic photoconversion and excellent photothermal remoldability

The development of photoresponsive shape memory materials based on the photothermal conversion properties of lignin and the low activation energy of the dynamic covalent borate bond is of great importance. In this paper, a kind of lignin-based vitrimer polymer (LBP) containing dynamic boronic ester bonds was prepared by a “sulfhydryl-epoxy” click reaction and etherification reaction. The results show that the rigid segment EP-EL (lignin-based epoxy resin) and BDB (2,2′-(1,4-phenylene)-bis-[4-mercapto-1,3,2-dioxaneborane]) with benzene ring structure can impart tensile strength (20.8 MPa) to the LBP, while the flexible segment PEG imparts good elongation at break (15 %). The dynamic binding and dissociation exchange mechanism of the boronic ester bonds enables LBP to exhibit thermal remodelling properties (up to 36.2 %) and water-assisted self-healing properties at room temperature (up to 49.0 %). In addition, LBP exhibits excellent thermal and light-responsive shape memory properties due to its own photothermal conversion performance (photothermal conversion efficiency up to 18.2 %) and the dynamic boronic ester bond thermal activation bond exchange mechanism. The insulating properties of LBP make it suitable for use in high temperature protection circuit devices and light-responsive circuit devices. This study provides new insights into the design and application of Vitrimer and photoresponsive shape memory polymers, and also offers a new avenue for high-value utilization of lignin.

Multivalent lectin-carbohydrate interactions: Energetics and mechanisms of binding.

The biological signaling properties of lectins, which are carbohydrate-binding proteins, are due to their ability to bind and cross-link multivalent glycoprotein receptors on the surface of normal and transformed cells. While the cross-linking properties of lectins with multivalent carbohydrates and glycoproteins are relatively well understood, the mechanisms of binding of lectins to multivalent glycoconjugates are less well understood. Recently, the thermodynamics of binding of lectins to synthetic clustered glycosides, a multivalent globular glycoprotein, and to linear glycoproteins (mucins) have been described. The results are consistent with a dynamic binding mechanism in which lectins bind and jump from carbohydrate to carbohydrate epitope in these molecules. Importantly, the mechanism of binding of lectins to mucins is similar to that for a variety of protein ligands binding to DNA. Recent analysis also shows that high-affinity lectin-mucin cross-linking interactions are driven by favorable entropy of binding that is associated with the bind and jump mechanism. The results suggest that the binding of ligands to biopolymers, in general, may involve a common mechanism that involves enhanced entropic effects which facilitate binding and subsequent complex formation including enzymology.

Investigating the Dynamic Binding Behavior of PMX53 Cooperating with Allosteric Antagonist NDT9513727 to C5a Anaphylatoxin Chemotactic Receptor 1 through Gaussian Accelerated Molecular Dynamics and Free-Energy Perturbation Simulations.

C5a anaphylatoxin chemotactic receptor 1 (C5aR1) is an important target in anti-inflammatory therapeutics. The cyclic peptide antagonist PMX53 binds to the orthosteric site located in the extracellular vestibule of C5aR1, and the non-peptide antagonist NDT9513727 binds to the allosteric site formed by the middle region of TM3 (trans-membrane helix), TM4, and TM5. We catch a sight of the variational binding mode of PMX53 during the Gaussian accelerated molecular dynamic (GaMD) simulations. In the binary complex of C5aR1 and PMX53, the PMX53 takes a dynamic binding mechanism during the simulation. Namely, the side chain of Arg6 of PMX53 extends to TM6-TM7 (pose 1) or swings to TM5 (pose 2), forming a salt bridge with Glu199. Meanwhile, in the ternary complex of C5aR1 with PMX53 and NDT9513727, the side chain of Arg6 of PMX53 swings to TM5 (pose 2) from extending to TM6-TM7 (pose 1) at the beginning of the GaMD simulation. In subsequent simulation, PMX53 stabilizes in the pose 2 binding mode by forming a stable salt bridge with Glu199. The free-energy perturbation (FEP) calculations demonstrate that pose 1 (ΔGbinding = -10.94 kcal/mol) is more stable in the binary complex and pose 2 (ΔGbinding = -7.91 kcal/mol) is unstable because of highly dynamic TM5. NDT9513727 interacts directly with TM4 and TM5 and stabilizes the hydrophobic stack between the extracellular sides of the two helices. Therefore, pose 2 (ΔGbinding = -16.27 kcal/mol) is notably stable than pose 1 (ΔGbinding = -9.78 kcal/mol) in the ternary complex. The identification of a novel binding mode of PMX53 and the detailed structural information of PMX53 interacting with a receptor obtained by GaMD simulations will be helpful in designing potent antagonists of C5aR1.

Multiple Molecular Dynamics Simulations and Energy Analysis Unravel the Dynamic Properties and Binding Mechanism of Mutants HIV-1 Protease with DRV and CA-p2.

ABSTRACTPRS17, a variant of human immunodeficiency virus type I protease (HIV-1 PR), has 17 mutated residues showing high levels of multidrug resistance. To describe the effects of these mutated residues on the dynamic properties and the binding mechanism of PR with substrate and inhibitor, focused on six systems (two complexes of WT PR and PRS17 with inhibitor Darunavir (DRV), two complexes of WT PR and PRS17 with substrate analogue CA-p2, two unligand WT PR and PRS17), we performed multiple molecular dynamics (MD) simulations combined with MM-PBSA and solvated interaction energy (SIE) methods. For both the unligand PRs and ligand-PR complexes, the results from simulations revealed 17 mutated residues alter the flap-flap distance, the distance from flap regions to catalytic sites, and the curling degree of the flap tips. These mutated residues changed the flexibility of the flap region in PR, and thus affected its binding energy with DRV and CA-p2, resulting in differences in sensitivity. Hydrophobic cavity makes an important contribution to the binding of PR and ligands. And most noticeable of all, the binding of the guanidine group in CA-p2 and Arg8’ of PRS17 is useful for increasing their binding ability. These results have important guidance for the further design of drugs against multidrug resistant PR.IMPORTANCE Developing effective anti-HIV inhibitors is the current requirement to cope with the emergence of the resistance of mutants. Compared with the experiments, MD simulations along with energy calculations help reduce the time and cost of designing new inhibitors. Based on our simulation results, we propose two factors that may help design effective inhibitors against HIV-1 PR: (i) importance of hydrophobic cavity, and (ii) introduction of polar groups similar to the guanidine group.

Mechanism of Mucin Recognition by Lectins: A Thermodynamic Study.

Isothermal titration microcalorimetry (ITC) can directly determine the thermodynamic binding parameters of biological molecules including affinity constant, binding stoichiometry, heat of binding (enthalpy) and indirectly the entropy, and free energy of binding. ITC has been extensively used to study the binding of lectins to mono- and oligosaccharides, but limitedly in applications to lectin-glycoprotein interactions. Inherent experimental challenges to ITC include sample precipitation during the experiment and relative high amount of sample required, but careful design of experiments can minimize these problems and allow valuable information to be obtained. For example, the thermodynamics of binding of lectins to multivalent globular and linear glycoproteins (mucins) have been described. The results are consistent with a dynamic binding mechanism in which lectins bind and jump from carbohydrate to carbohydrate epitope in these molecules leading to increased affinity. Importantly, the mechanism of binding of lectins to mucins appears similar to that for a variety of protein ligands binding to DNA. Recent results also show that high-affinity lectin-mucin cross-linking interactions are driven by favorable entropy of binding that is associated with the bind and jump mechanism. The results suggest that the binding of ligands to biopolymers, in general, may involve a common mechanism that involves enhanced entropic effects that facilitate binding interactions.

A small molecule stabilises the disordered native state of the Alzheimer's Aβ peptide

The stabilisation of native states of proteins is a powerful drug discovery strategy. It is still unclear, however, whether this approach can be applied to intrinsically disordered proteins. Here we report a small molecule that stabilises the native state of the Aβ42 peptide, an intrinsically disordered protein fragment associated with Alzheimer9s disease. We show that this stabilisation takes place by a dynamic binding mechanism, in which both the small molecule and the Aβ42 peptide remain disordered. This disordered binding mechanism involves enthalpically favourable local π-stacking interactions coupled with entropically advantageous global effects. These results indicate that small molecules can stabilise disordered proteins in their native states through transient non-specific interactions that provide enthalpic gain while simultaneously increasing the conformational entropy of the proteins.

The Mechanism of Quorum Sensing Inhibition in Streptococcus pyogenes by the Phage Protein Paratox

Streptococcus pyogenes is a causative agent of pharyngitis and necrotizing fasciitis. Key to its pathogenicity are numerous prophages spread throughout its genome that encode deadly toxins. These prophages also encode several proteins whose biological function is unknown. Of particular interest is the conserved phage protein paratox (Prx), which is genetically linked to phage toxin genes. Our past results have shown that Prx expression is regulated by the natural competence ComRS quorum sensing pathway, and that Prx itself is a negative regulator of ComRS. Prx directly binds the transcription factor and quorum sensing receptor ComR and inhibits its ability to bind DNA by an unknown mechanism. As ComR undergoes a significant conformational change upon binding the peptide pheromone XIP, we hypothesize that Prx employs a novel mechanism of protein-protein binding and inhibition. Using a combination of structural biology and biochemistry, including X-ray crystallography, small-angle X-ray scattering (SAXS), and various fluorescence assays, we have been able to elucidate the molecular details of how Prx manipulates the conformation of ComR to prevent activation by the XIP pheromone. Our results not only reveal a dynamic protein-protein binding mechanism, but further demonstrate the myriad roles that phage proteins have evolved to regulate the pathways of their hosts for self-preservation.

Bioactive flavonoids from Rubus corchorifolius inhibit α-glucosidase and α-amylase to improve postprandial hyperglycemia

This research established an optimized method for the extraction and enrichment of flavonoids from R. corchorifolius fruit. Under the optimized extraction conditions, 12 flavonoids (1–12) were isolated, of which six (2–4, 9–10, 12) were obtained from R. corchorifolius for the first time. Compound 4 showed significant α-glucosidase (4.96 μM) and α-amylase (8.04 μM) inhibitory effects. Molecular modeling revealed that compound 4 exhibits strong binding with the active sites of α-glucosidase and α-amylase. Lineweaver-Burk plot analysis and surface plasmon resonance revealed the possible dynamic binding mechanism of the flavonoids with α-glucosidase and α-amylase. The enriched flavonoids and compound 4 showed significant hypoglycemic effects in mice administered a high dose of glucose. In this study, a variety of flavonoids with hypoglycemic activity were found for the first time, revealing the rich chemical composition of R. corchorifolius fruit and highlighting the potential value of R. corchorifolius fruit flavonoids as dietary supplements.

A CFI Countermeasure Against GOT Overwrite Attacks

In the Unix-like system, the Global Offset Table (GOT) overwrite attack is a long-lasting control flow hijacking attack. The attack, by leveraging the dynamic symbol binding mechanism, overwrites any GOT entry into the attacker's target address to take the execution flow on the library function call. Recently, Full Relro (Relocation Read only), which arranges the GOT section as read-only at program startup, is regarded as most useful against the threat. However, it entails nontrivial loading overhead and is not applicable to libraries. Furthermore, many software packages are currently distributed without Full Relro. As a result, programs are still exposed to the risk of GOT attacks. In this paper, we propose a CFI-based protection scheme against the GOT overwrite attack. Using dynamically bound function symbols as branch identifiers, the scheme secures inter-module function calls on PLT (Procedure Linkage Table) effectively with little performance overhead. Our LLVM based implementation and evaluation on binutils-gdb show that the branch protection scheme is difficult to bypass, fast, and compatible with existing library programs.

New views into class B GPCRs from the crystal structure of PTH1R.

The parathyroid hormone 1 receptor (PTH1R) is a major regulator of mineral ion homeostasis and bone metabolism and is thus considered an attractive drug target for the treatment of disorders in calcium metabolism and bone-related diseases such as osteoporosis. PTH1R is a member of the class B of GPCRs, which all share a dynamic multidomain binding mechanism to the peptide hormone. For a long time, these complexes have been recalcitrant to structural studies despite their great therapeutic relevance. Through extensive engineering of both the receptor and the peptide agonist ligand, we were able to determine the first high-resolution structure of a PTH1R-agonist complex. Comparisons of the PTH1R crystal structure with subsequently reported cryo-electron microscopy structures of the same receptor in complex with a G protein, as well as with other class B GPCR structures bound to antagonists, reveal new insights into the two-step activation mechanism of class B GPCRs and extend our understanding of the precise molecular rearrangements during receptor activation.

Formation of a Secretion-Competent Protein Complex by a Dynamic Wrap-around Binding Mechanism

Bacterial virulence is typically initiated by translocation of effector or toxic proteins across host cell membranes. A class of gram-negative pathogenic bacteria including Yersinia pseudotuberculosis and Yersinia pestis accomplishes this objective with a protein assembly called the type III secretion system. Yersinia effector proteins (Yop) are presented to the translocation apparatus through formation of specific complexes with their cognate chaperones (Syc). In the complexes where the structure is available, the Yops are extended and wrap around their cognate chaperone. This structural architecture enables secretion of the Yop from the bacterium in early stages of translocation. It has been shown previously that the chaperone-binding domain of YopE is disordered in its isolation but becomes substantially more ordered in its wrap-around complex with its chaperone SycE. Here, by means of NMR spectroscopy, small-angle X-ray scattering and molecular modeling, we demonstrate that while the free chaperone-binding domain of YopH (YopHCBD) adopts a fully ordered and globular fold, it populates an elongated, wrap-around conformation when it engages in a specific complex with its chaperone SycH2. Hence, in contrast to YopE that is unstructured in its free state, YopH transits from a globular free state to an elongated chaperone-bound state. We demonstrate that a sparsely populated YopHCBD state has an elevated affinity for SycH2 and represents an intermediate in the formation of the protein complex. Our results suggest that Yersinia has evolved a binding mechanism where SycH2 passively stimulates an elongated YopH conformation that is presented to the type III secretion system in a secretion-competent conformation.

Exploration of binding and inhibition mechanism of a small molecule inhibitor of influenza virus H1N1 hemagglutinin by molecular dynamics simulation

Influenza viruses are a major public health threat worldwide. The influenza hemagglutinin (HA) plays an essential role in the virus life cycle. Due to the high conservation of the HA stem region, it has become an especially attractive target for inhibitors for therapeutics. In this study, molecular simulation was applied to study the mechanism of a small molecule inhibitor (MBX2329) of influenza HA. Behaviors of the small molecule under neutral and acidic conditions were investigated, and an interesting dynamic binding mechanism was found. The results suggested that the binding of the inhibitor with HA under neutral conditions facilitates only its intake, while it interacts with HA under acidic conditions using a different mechanism at a new binding site. After a series of experiments, we believe that binding of the inhibitor can prevent the release of HA1 from HA2, further maintaining the rigidity of the HA2 loop and stabilizing the distance between the long helix and short helices. The investigated residues in the new binding site show high conservation, implying that the new binding pocket has the potential to be an effective drug target. The results of this study will provide a theoretical basis for the mechanism of new influenza virus inhibitors.

Crystal structure of FabZ-ACP complex reveals a dynamic seesaw-like catalytic mechanism of dehydratase in fatty acid biosynthesis.

Fatty acid biosynthesis (FAS) is a vital process in cells. Fatty acids are essential for cell assembly and cellular metabolism. Abnormal FAS directly correlates with cell growth delay and human diseases, such as metabolic syndromes and various cancers. The FAS system utilizes an acyl carrier protein (ACP) as a transporter to stabilize and shuttle the growing fatty acid chain throughout enzymatic modules for stepwise catalysis. Studying the interactions between enzymatic modules and ACP is, therefore, critical for understanding the biological function of the FAS system. However, the information remains unclear due to the high flexibility of ACP and its weak interaction with enzymatic modules. We present here a 2.55 Å crystal structure of type II FAS dehydratase FabZ in complex with holo-ACP, which exhibits a highly symmetrical FabZ hexamer-ACP3 stoichiometry with each ACP binding to a FabZ dimer subunit. Further structural analysis, together with biophysical and computational results, reveals a novel dynamic seesaw-like ACP binding and catalysis mechanism for the dehydratase module in the FAS system, which is regulated by a critical gatekeeper residue (Tyr100 in FabZ) that manipulates the movements of the β-sheet layer. These findings improve the general understanding of the dehydration process in the FAS system and will potentially facilitate drug and therapeutic design for diseases associated with abnormalities in FAS.

Communicating machines as a dynamic binding mechanism of services

Distributed software is becoming more and more dynamic to support applications able to respond and adapt to the changes of their execution environment. For instance, service-oriented computing (SOC) envisages applications as services running over globally available computational resources where discovery and binding between them is transparently performed by a middleware. Asynchronous Relational Networks (ARNs) is a well-known formal orchestration model, based on hypergraphs, for the description of service-oriented software artefacts. Choreography and orchestration are the two main design principles for the development of distributed software. In this work, we propose Communicating Relational Networks (CRNs), which is a variant of ARNs, but relies on choreographies for the characterisation of the communicational aspects of a software artefact, and for making their automated analysis more efficient.

Molecular recognition of avirulence protein (avrxa5) by eukaryotic transcription factor xa5 of rice (Oryza sativa L.): Insights from molecular dynamics simulations

The avirulence gene avrxa5 of bacterial blight pathogen Xanthomonas oryzae pv. oryzae (Xoo) recognized by the resistant rice lines having corresponding resistance (xa5) gene in a gene–for–gene manner. We used a combinatorial approach involving protein–protein docking, molecular dynamics (MD) simulations and binding free energy calculations to gain novel insights into the gene-for-gene mechanism that governs the direct interaction of R-Avr protein. From the best three binding poses predicted by molecular docking, MD simulations were performed to explore the dynamic binding mechanism of xa5 and avrxa5. Molecular Mechanics/Poisson Boltzmann Surface Area (MM/PBSA) techniques were employed to calculate the binding free energy and to uncover the thriving force behind the molecular recognition of avrxa5 by eukaryotic transcription factor xa5. Binding free energy analysis revealed van der Waals term as the most constructive component that favors the xa5 and avrxa5 interaction. In addition, hydrogen bonds (H-bonds) and essential electrostatic interactions analysis highlighted amino acid residues Lys54/Asp870, Lys56/Ala868, Lys56/Ala866, Lys56/Glu871, Ile59/His862, Gly61/Phe858, His62/Arg841, His62/Leu856, Ser101/Ala872 and Ser105/Asp870 plays pivotal role for the energetically stability of the R-Avr complex. Insights gained from the present study are expected to unveil the molecular mechanisms that define the transcriptional activator mediated transcriptome modification in host plants.

Cognitive resource-aware unobtrusive service provisioning in ambient intelligence environments

The cognitive load placed on users by both the proactive and spontaneous provisioning of service functionality and by the physical activities performed in ambient intelligence environments can lead to the depletion of their mental resources. This paper demonstrates how burdening the inappropriate selection of service functionality can be for users by conducting a semi-naturalistic and controlled user test to investigate the significance of the cognitive resource depletion problem in specific ambient intelligence environments. A dynamic service binding and scheduling mechanism is provided based on different types of interference and on mental resources and their demand requirements. A technical evaluation is conducted by simulating the mechanism over a set of various abstract service compositions, making use of real datasets of user interactions with diverse HCI services and daily physical activities. The results show that this mechanism ensures less cognitively taxing, unobtrusive service composition provisioning.

Probing lectin-mucin interactions by isothermal titration microcalorimetry.

Isothermal titration microcalorimetry (ITC) can directly determine the thermodynamic binding parameters of biological molecules including affinity constant, binding stoichiometry, and heat of binding (enthalpy) and indirectly the entropy and free energy of binding. ITC has been extensively used to study the binding of lectins to mono- and oligosaccharides, but limited applications to lectin-glycoprotein interactions. Inherent experimental challenges to ITC include sample precipitation during the experiment and relative high amount of sample required, but careful design of experiments can minimize these problems and allow valuable information to be obtained. For example, the thermodynamics of binding of lectins to multivalent globular and linear glycoproteins (mucins) have been described. The results are consistent with a dynamic binding mechanism in which lectins bind and jump from carbohydrate to carbohydrate epitope in these molecules leading to increased affinity. Importantly, the mechanism of binding of lectins to mucins appears similar to that for a variety of protein ligands binding to DNA. Recent results also show that high affinity lectin-mucin cross-linking interactions are driven by favorable entropy of binding that is associated with the bind and jump mechanism. The results suggest that the binding of ligands to biopolymers, in general, may involve a common mechanism that involves enhanced entropic effects that facilitate binding interactions.

An Integrated Approach to Developing Self-Adaptive Software *

One of the main challenges of developing self-adaptive systems in open environment comes from uncertain self-adaptation requirements due to the unpredictability of environment changes and its co-existence with well-defined self-adaptation requirements in self-adaptive systems. This paper presents an integrated approach that combines offline and on-line self-adaptation together in a unified technical framework to support the development and running of such systems. We consider self-adaptive system as a multi- agent organization and propose a novel dynamic binding self-adaptation mechanism inspired from organization metaphors to specify and analyze self-adaptation. A description language, SADL, is designed to program well-defined self-adaptation logic at design- time and implement off-line self-adaptation. In order to deal with uncertain self-adaptation, a reinforcement learning method is incorporated with the dynamic binding mechanism, which enables software agents to make decisions on self-adaptation at runtime and implement on-line self-adaptation. Our approach provides a unified frame-work to accommodate off-line and on-line approaches and a general-purpose methodology to develop complex self-adaptive systems in a systematic way. A supported platform called SADE+ is developed and a case is studied to illustrate the proposed approach.

Model-driven geospatial web service composition

Abstract. A lot of work has been done on the geospatial service composition to support advanced processing, spatial calculation, and invoking of heterogeneous data. However, the quality of service chain is rarely considered and the process model cannot be reused. A modeldriven way of geospatial web service composition is proposed in this work, the service composition is treated as an optimization problem by GwcsFlow model and dynamic binding mechanism. The case of facility location analysis is provided to demonstrate the improvements in geospatial service composition through optimization algorithms.

Application of Workflow Management Systems in E-Services

Workflow management systems, a relatively recent technology, are designed to make work more efficient, integrate heterogeneous application systems, and support inter-organizational processes in electronic commerce applications. This paper presents an infrastructure and a mechanism for achieving dynamic Inter-enterprise workflow management using e-services provided by collaborative e-business enterprises. E-services are distributed services that can be accessed programmatically on the Internet, using SOAP messages and the HTTP protocol. In this work, we categorize e-services according to their business types. E-service requests are specified in the activities of a process model according to some standardized e-service templates and are bound to the proper service providers at run-time by using a constraint-based, dynamic binding mechanism.