Multiple Binding Modes Research Articles

Insight into the interaction between amino acids and SO2: Detailed bonding modes.

Amino acids are a highly effective and environmentally friendly adsorbent for SO2. However, there has been no comprehensive study of the binding modes between amino acids and SO2 at the molecular level. In this paper, the binding modes of three amino acids (Asp, Lys, and Val) with SO2 are studied comprehensively and in detail using quantum chemical calculations. The results indicate that each amino acid has multiple binding modes: 22 for Asp, 49 for Lys, and 10 for Val. Both the amino and carboxyl groups in amino acids, as well as those in side chains, can serve as binding sites for chalcogen bonds. The binding energies range from - 6.42 to - 1.06kcal/mol for Asp, - 12.43 to - 1.63kcal/mol for Lys, and - 7.42 to - 0.60kcal/mol for Val. Chalcogen and hydrogen bonds play a crucial role in the stronger binding modes. The chalcogen bond is the strongest when interacting with an amino group, with an adiabatic force constant of 0.475 mDyn/Å. Energy decomposition analysis indicates that the interaction is primarily electrostatic attraction, with the orbital and dispersive interactions dependent on the binding mode. Amino acids and complexes of amino acids with SO2 were used to do semi-empirical MD using Molclus combined with xtb at the GFN2 level. Optimization and frequency calculations of the structures were conducted using density-functional theory (DFT) B3LYP/6-311G* (with DFT-D3 correction). Single-point energy calculations were performed for all structures using DLPNO-CCSD(T)/aug-cc-pVTZ with tightPNO. Further analysis of the structures was conducted using ESP, AIM, IGMH, and sob-EDA to gain a deeper understanding of the interactions between amino acids and SO2.

A polyurethane elastomer combining high strength and excellent self‐healing properties for waterproofing coatings

AbstractSelf‐healing materials have not been able to solve the problem of the coexistence of mechanical strength and self‐healing function. Despite years of research, high‐strength self‐healing materials still require external factors to accelerate their self‐healing process. For this reason, in this study, two kinds of chain extenders were inserted into the hard segment to design the molecular structure of polyurethane. The introduction of two chain extenders not only provided multiple binding modes for hydrogen bond recombination, but also formed more types of hydrogen bonds. Based on the design, a polyurethane elastomer PUGI‐D3B2 with high strength and excellent self‐healing properties was synthesized. Data such as FTIR and 1H NMR spectra clearly demonstrate the successful synthesis of PUGI‐D3B2. The mechanical strength of PUGI‐D3B2 is 15.34 MPa, and its surface scratches can completely disappear after self‐healing at 60°C for 10 h，and 98.02% of the mechanical strength is restored after 12 h of heal. Therefore, combining the excellent self‐healing properties of PUGI‐D3B2, we prepared a multifunctional superhydrophobic material (SHN‐SiO2/PUGI‐D3B2). It can be used in a wide range of applications such as waterproof coatings, biomedicine and flexible electronics, which provides a new idea for the future direction of multifunctional materials.

Polydopamine Adhesion: Catechol, Amine, Dihydroxyindole, and Aggregation Dynamics.

While polydopamine (PDA) possesses the surface-independent adhesion property of mussel-binding proteins, significant differences exist between them. Particularly, PDA's short and rigid backbone differs from the long and flexible protein sequence of mussel-binding proteins. Given that adhesion relies on achieving a conformal contact with large surface coverage, PDA has drawbacks as an adhesive. In our study, we investigated the roles of each building block of PDA to build a better understanding of their binding mechanisms. Initially, we anticipated that catecholamine oligomers form specific binding with substrates. However, our study showed that the universal adhesion of PDA is initiated by the solubility limit of growing oligomers by forming agglomerates, complemented by multiple binding modes of catechol. Notably, in the absence of amines, poly(catechol) either remained in solution or formed minor suspensions without any surface coating, underscoring the essential role of amines in the adhesion process by facilitating insoluble aggregate formation. To substantiate our findings, we induced poly(catechol) aggregation using quaternized poly(4-vinylpyridine) (qPVP), leading to subsequent surface adhesion upon agglomerate formation.

Structural Adaptation of Secondary p53 Binding Sites on MDM2 and MDMX

The thermodynamics of secondary p53 binding sites on MDM2 and MDMX were evaluated using p53 peptides containing residues 16–29, 17–35, and 1–73. All the peptides had large, negative heat capacity (ΔCp), consistent with the burial of p53 residues F19, W23, and L26 in the primary binding sites of MDM2 and MDMX. MDMX has a higher affinity and more negative ΔCp than MDM2 for p5317-35, which is due to MDMX stabilization and not additional interactions with the secondary binding site. ΔCp measurements show binding to the secondary site is inhibited by the disordered tails of MDM2 for WT p53 but not a more helical mutant where proline 27 is changed to alanine. This result is supported by all-atom molecular dynamics simulations showing that p53 residues 30–35 turn away from the disordered tails of MDM2 in P27A17-35 and make direct contact with this region in p5317-35. Molecular dynamics simulations also suggest that an intramolecular methionine-aromatic motif found in both MDM2 and MDMX structurally adapts to support multiple p53 binding modes with the secondary site. ΔCp measurements also show that tighter binding of the P27A mutant to MDM2 and MDMX is due to increased helicity, which reduces the energetic penalty associated with coupled folding and binding. Our results will facilitate the design of selective p53 inhibitors for MDM2 and MDMX.

Anillin-related Mid1 as an adaptive and multimodal contractile ring anchoring protein: A simulation study

Cytokinesis of animal and fungi cells depends crucially on the anillin scaffold proteins. Fission yeast anillin-related Mid1 anchors cytokinetic ring precursor nodes to the membrane. However, it is unclear if both of its Pleckstrin Homology (PH) and C2 C-terminal domains bind to the membrane as monomers or dimers, and if one domain plays a dominant role. We studied Mid1 membrane binding with all-atom molecular dynamics near a membrane with yeast-like lipid composition. In simulations with the full C terminal region started away from the membrane, Mid1 binds through the disordered L3 loop of C2 in a vertical orientation, with the PH away from the membrane. However, a configuration with both C2 and PH initially bound to the membrane remains associated with the membrane. Simulations of C2-PH dimers show extensive asymmetric membrane contacts. These multiple modes of binding may reflect Mid1's multiple interactions with membranes, node proteins, and ability to sustain mechanical forces.

MFG-E8: a model of multiple binding modes associated with ps-binding proteins.

Membrane-binding proteins often associate with lipid membranes through a singular binding interface which is generally modeled as a two-state system: bound or unbound. However, even a single interface can engage with more than one mode of binding since a variety of interactions can contribute to the binding event. Unfortunately, the ability to clearly delineate the different binding modes of a singular binding interface has been elusive with existing models. Here, we present a study on milk fat globule EGF factor 8 (MFG-E8), which belongs to a class of proteins that identifies and binds phosphatidylserine (PS). These proteins detect membrane dysregulation implicated in exposed PS in apoptosis and malignant cells. In order to elucidate the factors affecting the binding of MFG-E8, we used a model system consisting of a series of lipid vesicles with varying PS mole fraction to identify the sensitivity of MFG-E8's binding affinity to changes in electrostatics using a tryptophan fluorescence spectral shift assay. Using a newly developed model, we experimentally identified three binding modes, each associated with a different number of PS lipids, with its cooperativity for binding being enhanced by the availability of negatively charged lipids. X-ray reflectivity experiments additionally suggest that MFG-E8's binding modes are influenced by membrane packing. The protocols established for elucidating MFG-E8's interaction with lipid membranes under different membrane conditions can be applied to the study of other membrane-binding proteins that target specific membrane attributes, such as fluidity and electrostatics, and help elucidate these membrane targeting mechanisms and their subsequent binding events.

Anisotropic dynamics of an interfacial enzyme active site observed using tethered substrate analogs and ultrafast 2D IR spectroscopy.

Enzymes accelerate the rates of biomolecular reactions by many orders of magnitude compared to bulk solution, and it is widely understood that this catalytic effect arises from a combination of polar pre-organization and electrostatic transition state stabilization. A number of recent reports have also implicated ultrafast (femtosecond-picosecond) timescale motions in enzymatic activity. However, complications arising from spatially-distributed disorder, the occurrence of multiple substrate binding modes, and the influence of hydration dynamics on solvent-exposed active sites still confound many experimental studies. Here we use ultrafast two-dimensional infrared (2D IR) spectroscopy and covalently-tethered substrate analogs to examine dynamical properties of the promiscuous Pyrococcus horikoshii ene-reductase (PhENR) active site in two binding configurations mimicking proposed "inactive" and "reactive" Michaelis complexes. Spectral diffusion measurements of aryl-nitrile substrate analogs reveal an end-to-end tradeoff between fast (sub-ps) and slow (>5ps) motions. Fermi resonant aryl-azide analogs that sense interactions of coupled oscillators are described. Lineshape and quantum beat analyses of these probes reveal characteristics that correlate with aryl-nitrile frequency fluctuation correlation functions parameters, demonstrating that this anisotropy is an intrinsic property of the water-exposed active site, where countervailing gradients of fast dynamics and disorder in the reactant ground state are maintained near the hydration interface. Our results suggest several plausible factors leading to state-selective rate enhancement and promiscuity in PhENR. This study also highlights a strategy to detect perturbations to vibrational modes outside the transparent window of the mid-IR spectrum, which may be extended to other macromolecular systems.

Synthesis and Electrochemical Investigation of Phosphine Substituted Diiron Phosphadithiolate Complexes

AbstractThis work reports on ligand exchange reactions between a [FeFe] hydrogenase model containing the higher homologue (PhosDT) and phosphines selected to cover a variety of electronic properties and possible coordination modes. Additionally, the amount of the phosphines and the reaction temperature were varied to study the formation of complexes with multiple phosphines or altered binding modes. Due to steric effects caused by the position of the bridgehead, the phosphines bind preferentially at the more accessible iron centre on the phosphinate averted side. While all ligand exchanges resulted in a ligand‐specific main product at room temperature, reflux conditions induced decomposition in case of PhosDT‐(κ2‐dppe) and PhosDT‐(κ2‐dppv) and a change in the binding mode for the dppm containing complex. Moreover, we highlight two novel iron complexes obtained as side products of the reactions with dppe and dppv, while in case of dppm an additional model with two bridging phosphine ligands was generated. Finally, the six novel phosphine substituted PhosDT models were electrochemically investigated, revealing a cathodic shift compared to the starting material due to the increased electron density at the iron atoms. Moreover, the models with monodentate ligands exhibit a different CV pattern for the FeIFeI/FeIFe0 process than complexes with bidentate phosphines.

Analyzing barium titanate TiO2 surface interactions with tert-butylphosphonic acid using density functional theory

Barium titanate (BTO) is a widely researched ferroelectric useful for energy storage. While BTO’s surface chemistry is commonly studied using density functional theory, little has been published on the TiO2 surface. Here, we determined that BTO’s surface response can be decoupled from the ferroelectric response by using a pre-optimized ferroelectric slab and allowing only the top three atomic z-layers to respond to ligand binding. Multiple favorable binding modes were identified for hydrogen, hydroxyl, water, and tert-butyl phosphonic acid on BTO’s TiO2 surface. Of these ligands, tBuPA dominates surface binding with binding energies as low as − 2.61 eV for its nine configurations.Graphical abstract

Osmium ester-hinged chlorin dimers

A bis(dihydroxychlorin) osmate ester is formed as a side product in the osmylation of meso-tetraphenylporphyrin. The product can also be formed in good yield along well-known reaction pathways of osmate esters by treatment of the monomeric chlorin diol osmate ester bispyridine complex with acid. The dimer was spectroscopically characterized. The free base dimer can be metalated with zinc(II). The bis([dihydroxychlorinato]zinc) osmate ester dimer was spectroscopically and structurally characterized, showing its clamshell architecture with a 42[Formula: see text] angle between the mean planes of the two metallochlorin chromophores and a 9.11 Å zinc-to-zinc separation. Upon reaction with dimethylaminopyridine (DMAP), the clamshell structure pivots around the osmium center and arranges the two chromophores, each zinc center coordinated to DMAP, in maximum separation from each other, as shown by structural analysis. Preliminary 1H NMR titration data are presented that show the bis-zinc clamshell structure to form a 1:1 supramolecular complex with diethylenetriamine (DETA), expressing a three-point recognition motive: the terminal amine functionalities coordinate to the zinc ions in each half-shell, thus bridging both chromophores, and the central amine functionality was deduced to be H-bonded to the osmium oxo group pointing toward the inside of the host. The UV-vis spectroscopic response upon DETA binding shows greater complexity in the interaction at higher ligand:host ratios, suggesting multiple binding modes. A similarly complex binding situation is also observed for the interactions of the chlorin osmate ester monomer with DETA.

DNA binding properties and cell viabilities of metal complexes derived from (E)-2-hydroxy-N'-((thiophen-2-yl)methylene)benzohydrazone and (E)-N'-((thiophen-2-yl)methylene)isonicotinylhydrazone.

This study aims to investigate the CT-DNA (Calf thymus DNA) binding properties and HeLa cell viabilities of metal complexes derived from (E)-2-hydroxy-N'-((thiophen-2-yl)methylene)benzohydrazone (H2L1) and (E)-N'-((thiophen-2-yl)methylene)isonicotinylhydrazone (HL2). A series of metal complexes derived from (E)-2-hydroxy-N'-((thiophen-2-yl)methylene)benzohydrazone (H2L1) and (E)-N'-((thiophen-2-yl)methylene)isonicotinylhydrazonewere (HL2) were synthesized, and their structures were characterized through FT-IR, ESI-MS, elemental analysis, molar conductivities and X-ray diffraction. DNA binding properties between CT-DNA and metal complexes were investigated by UV-Vis spectrophotometry and viscosity titration. The toxicological properties of compounds on HeLa cell were measured in vitro. Ligand H2L1 or HL2 exhibits a tridentate and anion ligand and uses oxygen anion, nitrogen atom and sulfur atom to coordinate with metal ions. When coordinated with metal ions, the unit O=C-NH- of each ligand has been enolized and deprotonated into -O-C=N-. The suggested chemical formulas of metal complexes are: [Co(HL1)2], [Ni(HL1)2], [Cu(HL1)2], [Co(L2)2], [Cu(L2)2], [Zn(L2)2], [ScL2(NO3)2(H2O)2], [Pr(L2)2(NO3)] and [Dy(L2)2(NO3)]. Both ligands and their metal complexes can bind strongly to CT-DNA through hydrogen bond and intercalation with Kb of 104~105 L mol-1 compared to ethidium bromide [classical DNA intercalator, Kb(EB-DNA) = 3.068 × 104 L mol-1]; however, the groove pattern cannot be excluded. The coexistence of multiple binding modes may be a common form of drug binding to DNA. HeLa cell shows lower viabilities in the presence of [Ni(HL1)2] and [Cu(HL1)2] (*p < 0.05) compared to the other compounds, with the LC50 of 2.6 μmol L-1 and 2.2 μmol L-1, respectively. These compounds, especially [Ni(HL1)2] and [Cu(HL1)2], will be promising for anti-tumor drugs, which should be further studied.

Multiple Modes of Zinc Binding to Histatin 5 Revealed by Buffer-Independent Thermodynamics.

Histatin 5 (Hist5) is an antimicrobial peptide found in human saliva as part of the innate immune system. Hist5 can bind several metal ions in vitro, and Zn2+ has been shown to function as an inhibitory switch to regulate the peptide's biological activity against the opportunistic fungal pathogen Candida albicans in cell culture. Here, we studied Zn2+ binding to Hist5 at four temperatures from 15 to 37 °C using isothermal titration calorimetry to obtain thermodynamic parameters that were corrected for competing buffer effects. Hist5 bound Zn2+ with a buffer-dependent association constant of ∼105 M-1 and a buffer-independent association constant of ∼6 × 106 M-1 at pH 7.4 and at all temperatures tested. Zn2+ binding was both enthalpically and entropically favorable, with larger entropic contributions at 15 °C and larger enthalpic contributions at 37 °C. Additionally, the Zn:Hist5 binding stoichiometry increased from 1:1 to 2:1 as temperature increased. The enthalpy-entropy compensation and the variable stoichiometry lead us to propose a model in which the Zn-Hist5 complex exists in an equilibrium between two distinct binding modes with different Zn:Hist5 stoichiometries. The in-depth thermodynamic analysis presented herein may help illuminate the biophysical basis for Zn-dependent changes in the antifungal activity of Hist5.

FuzPred: a web server for the sequence-based prediction of the context-dependent binding modes of proteins.

Proteins form complex interactions in the cellular environment to carry out their functions. They exhibit a wide range of binding modes depending on the cellular conditions, which result in a variety of ordered or disordered assemblies. To help rationalise the binding behavior of proteins, the FuzPred server predicts their sequence-based binding modes without specifying their binding partners. The binding mode defines whether the bound state is formed through a disorder-to-order transition resulting in a well-defined conformation, or through a disorder-to-disorder transition where the binding partners remain conformationally heterogeneous. To account for the context-dependent nature of the binding modes, the FuzPred method also estimates the multiplicity of binding modes, the likelihood of sampling multiple binding modes. Protein regions with a high multiplicity of binding modes may serve as regulatory sites or hot-spots for structural transitions in the assembly. To facilitate the interpretation of the predictions, protein regions with different interaction behaviors can be visualised on protein structures generated by AlphaFold. The FuzPred web server (https://fuzpred.bio.unipd.it) thus offers insights into the structural and dynamical changes of proteins upon interactions and contributes to development of structure-function relationships under a variety of cellular conditions.

Natural silk nanofibers as building blocks for biomimetic aerogel scaffolds

Protein nanofibers offer great promise for tissue engineering scaffolds owing to biomimetic architecture and exceptional biocompatibility. Natural silk nanofibrils (SNFs) are promising but unexplored protein nanofibers for biomedical applications. In this study, the SNF-assembled aerogel scaffolds with ECM-mimicking architecture and ultra-high porosity are developed based on a polysaccharides-assisted strategy. The SNFs exfoliated from silkworm silks can be utilized as building blocks to construct 3D nanofibrous scaffolds with tunable densities and desirable shapes on a large scale. We demonstrate that the natural polysaccharides can regulate SNF assembly through multiple binding modes, endowing the scaffolds with structural stability in water and tunable mechanical properties. As a proof of concept, the biocompatibility and biofunctionality of the chitosan-assembled SNF aerogels were investigated. The nanofibrous aerogels have excellent biocompatibility, and their biomimetic structure, ultra-high porosity, and large specific surface area endow the scaffolds with enhanced cell viability to mesenchymal stem cells. The nanofibrous aerogels were further functionalized by SNF-mediated biomineralization, demonstrating their potential as a bone-mimicking scaffold. Our results show the potential of natural nanostructured silks in the field of biomaterials and provide a feasible strategy to construct protein nanofiber scaffolds.

Structure-Activity Relationships of Ligand Binding to Oxysterol-Binding Protein (OSBP) and OSBP-Related Protein 4.

Oxysterol-binding protein (OSBP) and OSBP-related protein 4 (ORP4) have emerged as potentially druggable targets in antiviral and precision cancer drug development. Multiple structurally diverse small molecules function through targeting the OSBP/ORP family of proteins, including the antiviral steroidal compounds OSW-1 and T-00127-HEV2. Here, the structure-activity relationships of oxysterols and related compound binding to human OSBP and ORP4 are characterized. Oxysterols with hydroxylation at various side chain positions (i.e., C-20, C-24, C-25, and C-27)─but not C-22─confer high affinity interactions with OSBP and ORP4. A library of 20(S)-hydroxycholesterol analogues with varying sterol side chains reveal that side chain length modifications are not well tolerated for OSBP and ORP4 interactions. This side chain requirement is contradicted by the high affinity binding of T-00127-HEV2, a steroidal compound lacking the side chain. The binding results, in combination with docking studies using homology models of OSBP and ORP4, suggest multiple modes of steroidal ligand binding to OSBP and ORP4.

Structures of calmodulin–melittin complexes show multiple binding modes lacking classical anchoring interactions

Calmodulin (CaM) is a Ca2+ sensor protein found in all eukaryotic cells that regulates a large number of target proteins in a Ca2+ concentration-dependent manner. As a transient type hub protein, it recognizes linear motifs of its targets, though for the Ca2+-dependent binding no consensus sequence was identified. Its complex with melittin, a major component of bee venom, is often used as a model system of protein - protein complexes. Yet, the structural aspects of the binding are not well understood, as only diverse, low-resolution data are available concerning the association. We present the crystal structure of melittin in complex with Ca2+-saturated calmodulins from two, evolutionarily distant species, Homo sapiens and Plasmodium falciparum representing three binding modes of the peptide. Results - augmented by molecular dynamics simulations - indicate that multiple binding modes can exist for CaM-melittin complexes, as an intrinsic characteristic of the binding. While the helical structure of melittin remains, swapping of its salt bridges and partial unfolding of its C-terminal segment can occur. In contrast to the classical way of target recognition by CaM, we found that different sets of residues can anchor at the hydrophobic pockets of CaM, which were considered as main recognition sites. Finally, the nanomolar binding affinity of the CaM-melittin complex is created by an ensemble of arrangements of similar stability - tight binding is achieved not by optimized specific interactions but by simultaneously satisfying less optimal interaction patterns in co-existing different conformers.

Mining the Protein Data Bank to inspire fragment library design.

The fragment approach has emerged as a method of choice for drug design, as it allows difficult therapeutic targets to be addressed. Success lies in the choice of the screened chemical library and the biophysical screening method, and also in the quality of the selected fragment and structural information used to develop a drug-like ligand. It has recently been proposed that promiscuous compounds, i.e., those that bind to several proteins, present an advantage for the fragment approach because they are likely to give frequent hits in screening. In this study, we searched the Protein Data Bank for fragments with multiple binding modes and targeting different sites. We identified 203 fragments represented by 90 scaffolds, some of which are not or hardly present in commercial fragment libraries. By contrast to other available fragment libraries, the studied set is enriched in fragments with a marked three-dimensional character (download at 10.5281/zenodo.7554649).

Structural predictions of protein-DNA binding: MELD-DNA.

Structural, regulatory and enzymatic proteins interact with DNA to maintain a healthy and functional genome. Yet, our structural understanding of how proteins interact with DNA is limited. We present MELD-DNA, a novel computational approach to predict the structures of protein-DNA complexes. The method combines molecular dynamics simulations with general knowledge or experimental information through Bayesian inference. The physical model is sensitive to sequence-dependent properties and conformational changes required for binding, while information accelerates sampling of bound conformations. MELD-DNA can: (i) sample multiple binding modes; (ii) identify the preferred binding mode from the ensembles; and (iii) provide qualitative binding preferences between DNA sequences. We first assess performance on a dataset of 15 protein-DNA complexes and compare it with state-of-the-art methodologies. Furthermore, for three selected complexes, we show sequence dependence effects of binding in MELD predictions. We expect that the results presented herein, together with the freely available software, will impact structural biology (by complementing DNA structural databases) and molecular recognition (by bringing new insights into aspects governing protein-DNA interactions).

Modeling binding plasticity in BET proteins through simulations and NMR.

The bromo and extraterminal (BET) family of proteins play an important role in regulating the expression of immune response genes—and has also been associated to multiple types of cancers and virus attack. The extra terminal domain (ET) of BET proteins acts as an interaction hub to accommodate binding to multiple host and viral proteins. Surprisingly, it interacts with these proteins through multiple binding modes, where peptide epitopes can bind as single strands, hairpins in different orientations and helices.

Equilibrium binding equations for peripheral membrane-binding proteins.

Peripheral Membrane-Binding Proteins underlie and regulate many important physiological functions such as the clearance of apoptotic cells, immune activation, and synaptic pruning. Lipid composition and membrane physical properties allow these proteins to distinguish target from non-target cell membranes. However, a general model describing this sensitivity to membrane composition and properties has yet to be developed. Instead, in the literature, different equations are used on a case-by-case basis to measure binding constants that are highly contextual at best and ambiguous at worst, making it difficult to compare results obtained from different studies. Here, we present a general model underlying the association of this class of proteins with lipid membranes that, when applied to a given system, produces the appropriate equation for the lipid composition dependence with well-defined parameters such as dissociation constants. This model allows us to derive the equations commonly used in the field and establish how their parameters are related. Using examples of phosphatidylserine-binding proteins, we show how this model can potentially reveal multiple binding modes, account for calcium coordination between a given protein and its associated lipids, as well as sensitivity for additional lipid species.