Ligand Diffusion Research Articles

Application of CoLD-CoP to Detecting Competitively and Cooperatively Binding Ligands.

NMR utilization in fragment-based drug discovery requires techniques to detect weakly binding fragments and to subsequently identify cooperatively binding fragments. Such cooperatively binding fragments can then be optimized or linked in order to develop viable drug candidates. Similarly, ligands or substrates that bind macromolecules (including enzymes) in competition with the endogenous ligand or substrate are valuable probes of macromolecular chemistry and function. The lengthy and costly process of identifying competitive or cooperative binding can be streamlined by coupling computational biochemistry and spectroscopy tools. The Clustering of Ligand Diffusion Coefficient Pairs (CoLD-CoP) method, previously developed by Snyder and co-workers, detects weakly binding ligands by analyzing pairs of diffusion spectra, obtained in the absence and the presence of a protein. We extended the CoLD-CoP method to analyze spectra pairs (each in the presence of a protein) with or without a critical ligand, to detect both competitive and cooperative binding.

Abstract 7362: Integrated analysis of scRNAseq and spatial omics in brain metastatic lung cancer tumor tissue

Abstract Spatial omics technologies have made significant advances in recent years, improving our understanding of the spatial localization of cells and intercellular interactions. Intercellular interactions are essential for maintaining proper tissue function and homeostasis, and dysregulation of these interactions can contribute to various diseases, including cancer and autoimmune disorders. Ligand proteins, one of the signaling molecules responsible for cell-cell interactions, bind to cell surface receptors and trigger intracellular signaling pathways. The effective range of ligand signaling, i.e. the extent to which a cell spatially and directly transmits information via the ligand, has not been systematically studied, although it may determine the occurrence of cell-cell interactions. The authors have previously developed methodologies combining spatial transcriptomics and single-cell RNA sequencing to analyze intercellular interactions at the single-cell level in spatial dimensions. Additionally, we have devised a technique to model the spatial diffusion of ligands from spatial transcriptomics and estimate the spatial range of ligand action. In this study, we used these developed methods to elucidate events in the tumor microenvironment of brain metastatic lung cancer tissue. Specifically, an integrated analysis of metastatic brain tumor samples was performed using visium and single-cell data from the same patient. The results suggest the presence of a heterogeneous microglial subpopulation, including clusters enriched in cytokines and chemokines for angiogenesis and wound healing, clusters associated with immune tolerance via IL-10 signaling, clusters enriched in gene sets related to phagocytosis, antigen processing, and antigen presentation, and clusters related to clearance of pathogens and residues. The presence of homogeneous microglial subpopulations was suggested. Furthermore, these subpopulations exhibited different spatial distributions, suggesting that they interact with surrounding cancer cells through different mechanisms. Citation Format: Haruka Hirose, Takahiro Tsuji, Yasuhiro Kojima, Akihiko Yoshizawa, Yoshiki Arakawa, Hiroaki Ozasa, Hiroaki Wake, Teppei Shimamura. Integrated analysis of scRNAseq and spatial omics in brain metastatic lung cancer tumor tissue [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7362.

Nanoimaging of Facet-Dependent Adsorption, Diffusion, and Reactivity of Surface Ligands on Au Nanocrystals.

Analysis of the influence of dissimilar facets on the adsorption, stability, mobility, and reactivity of surface ligands is essential for designing ligand-coated nanocrystals with optimal functionality. Herein, para-nitrothiophenol and nitronaphthalene were chemisorbed and physisorbed, respectively, on Au nanocrystals, and the influence of different facets within a single Au nanocrystal on ligands properties were identified by IR nanospectroscopy measurements. Preferred adsorption was probed on (001) facets for both ligands, with a lower density on (111) facets. Exposure to reducing conditions led to nitro reduction and diffusion of both ligands toward the top (111) facet. Nitrothiophenol was characterized with a diffusivity higher than that of nitronaphthalene. Moreover, the strong thiol-Au interaction led to the diffusion of Au atoms and the formation of thiol-coated Au nanoparticles on the silicon surface. It is identified that the adsorption and reactivity of surface ligands were mainly influenced by the atomic properties of each facet, while diffusion was controlled by ligand-metal interactions.

Understanding the ligand-assisted reprecipitation of CsPbBr3 nanocrystals via high-throughput robotic synthesis approach

•High-throughput automated experimental workflow for LARP-PNC synthesis is employed •Effects of chemical and processing parameters on PNC functionalities are explored •SHAP, a machine learning method, assesses the impact of synthesis parameters •Ligand diffusion during reaction determines the functionalities of PNCs Inorganic cesium lead bromide (CsPbBr3) perovskite nanocrystals (PNCs) have shown promise in optoelectronic applications. A simpler method of synthesizing high-quality PNCs is the ligand-assisted reprecipitation (LARP) method, but it is susceptible to instability. This study used a high-throughput automated experimental platform to explore the growth behaviors and colloidal stability of LARP-synthesized PNCs. The influence of ligands on particle growth and functionalities was systematically explored using two distinctive acid-base pairs. The study found that short-chain ligands cannot make functional PNCs with the desired sizes and shapes, whereas long-chain ligands provide homogeneous and stable PNCs. The study also found that excessive amines or polar antisolvents can cause PNCs to transform into a Cs-rich non-perovskite structure with poorer emission functionalities and larger size distributions. The diffusion of ligands in a reaction system is crucial in determining the structures and functionalities of the PNCs. This study provides detailed guidance on synthesis routes for desired PNCs. Inorganic cesium lead bromide (CsPbBr3) perovskite nanocrystals (PNCs) have shown promise in optoelectronic applications. A simpler method of synthesizing high-quality PNCs is the ligand-assisted reprecipitation (LARP) method, but it is susceptible to instability. This study used a high-throughput automated experimental platform to explore the growth behaviors and colloidal stability of LARP-synthesized PNCs. The influence of ligands on particle growth and functionalities was systematically explored using two distinctive acid-base pairs. The study found that short-chain ligands cannot make functional PNCs with the desired sizes and shapes, whereas long-chain ligands provide homogeneous and stable PNCs. The study also found that excessive amines or polar antisolvents can cause PNCs to transform into a Cs-rich non-perovskite structure with poorer emission functionalities and larger size distributions. The diffusion of ligands in a reaction system is crucial in determining the structures and functionalities of the PNCs. This study provides detailed guidance on synthesis routes for desired PNCs.

JINXED: just in time crystallization for easy structure determination of biological macromolecules.

Macromolecular crystallography is a well established method in the field of structural biology and has led to the majority of known protein structures to date. After focusing on static structures, the method is now under development towards the investigation of protein dynamics through time-resolved methods. These experiments often require multiple handling steps of the sensitive protein crystals, e.g. for ligand-soaking and cryo-protection. These handling steps can cause significant crystal damage, and hence reduce data quality. Furthermore, in time-resolved experiments based on serial crystallography, which use micrometre-sized crystals for short diffusion times of ligands, certain crystal morphologies with small solvent channels can prevent sufficient ligand diffusion. Described here is a method that combines protein crystallization and data collection in a novel one-step process. Corresponding experiments were successfully performed as a proof-of-principle using hen egg-white lysozyme and crystallization times of only a few seconds. This method, called JINXED (Just IN time Crystallization for Easy structure Determination), promises high-quality data due to the avoidance of crystal handling and has the potential to enable time-resolved experiments with crystals containing small solvent channels by adding potential ligands to the crystallization buffer, simulating traditional co-crystallization approaches.

Determine ligand binding kinetics to a membrane protein using Brownian dynamics simulation.

Molecular diffusion controls the kinetics of protein-ligand binding in various biological processes. Determining the reaction rate between proteins and ligands is crucial in understanding these processes and in designing novel strategies to enhance or disrupt binding. Most previous studies focus on ligand diffusion in a three-dimensional bulk space. However, with the rapid growth of membrane protein research, a comprehensive understanding of molecular diffusion toward membrane-bound organelles or biomolecules tethered on a planar scaffold is essential. In this work, we developed a method that can predict the association rate constant of a ligand-membrane protein binding reaction according to trajectories from Brownian dynamics simulations. Our approach can be divided into two parts: 1) analytically determine the ligand association rate to a hemispherical region surrounding the membrane protein, and 2) compute the protein-ligand binding probability by Brownian dynamics simulations. We applied the method to calculate the reaction rate of biological systems with different charges. We found that the presence of a membrane does affect ligand diffusion, especially when the ligand moves close to the membrane. The critical aspects of surface diffusion, such as the forbidden zone, edge effect, and simulation criteria, were also discussed. Although the current development is based on a coarse-grained model, our method is still useful in understanding the binding kinetics of a highly complicated biological system.

Synergistic effect of naphthalenediimide and squaraine ligand targeting G-quadruplex DNA in cancer cells

Targeting and stabilizing nonclassical DNA G-quadruplexes (G4s) with a ligand to inhibit cell proliferation is a very promising approach for cancer treatment. Here, we demonstrate that the combination of a naphthalenediimide (NDI) ligand and a squaraine ligand significantly improves the anticancer activity of either ligand alone. The NDI ligand binds the 5′-terminal of hybrid-type G4s and induces the topological conversion from a metastable hybrid to a stable parallel conformation, which allows the end-stacking of the squaraine ligand on the 3′-terminal of the resultant parallel-type G4 structure. Moreover, the NDI ligand promotes the diffusion of the squaraine ligand into the nucleus, and the synergistic effect of the two ligands improves the stability of G4s in cancer cells, blocks the cell cycle in the sub-G1 phase, and induces the DNA damage response. These findings will be helpful in the development of combinational ligands targeting DNA G4s with enhanced bioactivity toward the inhibition of cancer cell proliferation.

A novel binding site in the nicotinic acetylcholine receptor for MB327 can explain its allosteric modulation relevant for organophosphorus-poisoning treatment

Organophosphorus compounds (OPCs) are highly toxic compounds that can block acetylcholine esterase (AChE) and thereby indirectly lead to an overstimulation of muscarinic and nicotinic acetylcholine receptors (nAChRs). The current treatment with atropine and AChE reactivators (oximes) is insufficient to prevent toxic effects, such as respiratory paralysis, after poisonings with various OPCs. Thus, alternative treatment options are required to increase treatment efficacy. Novel therapeutics, such as the bispyridinium non-oxime MB327, have been found to reestablish neuromuscular transmission by interacting directly with nAChR, probably via allosteric mechanisms. To rationally design new, more potent drugs addressing nAChR, knowledge of the binding mode of MB327 is fundamental. However, the binding pocket of MB327 has remained elusive. Here, we identify a new potential allosteric binding pocket (MB327-PAM-1) of MB327 located at the transition of the extracellular to the transmembrane region using blind docking experiments and molecular dynamics simulations. MB327 forms striking interactions with the receptor at this site. The interacting amino acids are highly conserved among different subunits and different species. Correspondingly, MB327 can interact with several nAChR subtypes from different species. We predict by rigidity analysis that MB327 exerts an allosteric effect on the orthosteric binding pocket and the transmembrane domain after binding to MB327-PAM-1. Furthermore, free ligand diffusion MD simulations reveal that MB327 also has an affinity to the orthosteric binding pocket, which agrees with recently published results that related bispyridinium compounds show inhibitory effects via the orthosteric binding site. The newly identified binding site allowed us to predict structural modifications of MB327, resulting in the more potent resensitizers PTM0062 and PTM0063.

The Release of a Highly Cytotoxic Paullone Bearing a TEMPO Free Radical from the HSA Hydrogel: An EPR Spectroscopic Characterization.

This study shows the potential of a thermally induced human serum albumin (HSA) hydrogel to serve as a drug depot for sustained release of a highly cytotoxic modified paullone ligand bearing a TEMPO free radical (HL). The binding of HL to HSA was studied by electron paramagnetic resonance (EPR) spectroscopy and imaging. The EPR protocol was also implemented for the study of matrix degradation, and ligand diffusion rate, in two additional spin-labeled hydrogels, containing 5-doxylstearate and 3-carbamoyl-proxyl. The results showed that the hydrogel is an efficient HL reservoir as it retained 60% of the ligand during 11 days of dialysis in physiological saline. Furthermore, upon incubation with Colo 205 human colon adenocarcinoma cells for 3 days, the HL/HSA hydrogel did not exhibit cytotoxic activity, demonstrating that it is also an efficient ligand depot in the presence of living cells. It was observed that the percentage of HL release is independent of its initial concentration in the hydrogel, suggesting that HSA possesses a specific binding site for the ligand, most likely Sudlow site 2, as predicted by molecular docking. The intrinsic property of albumin to bind and transport various substances, including hydrophobic drugs, may be fine-tuned by appropriate physical/chemical hydrogel preparation procedures, providing optimal drug delivery.

Solvent's Role in Cavity-Ligand Recognition Would Depend on the Mode of Ligand Diffusion.

Solvent is known to play crucial roles in dictating the thermodynamics and kinetics of the biomolecular recognition process. Here, we show that the extent of significance of water in modulating the ligand recognition process is critically contingent on the ligand diffusion and on the constraints introduced on it. Toward the end, we use a well-known prototypical system of spherical ligand diffusing freely toward a hydrophobic concave cavity in explicit water. We analyze a large series of adaptively sampled unbiased molecular dynamics simulation trajectories within the framework of time-structured independent component analysis (TICA). Our quantitative investigations reveal that water would play a significant role in the ligand recognition process, provided that the ligand is constricted to diffuse along a centro-symmetric fashion. On the contrary, water's contribution in the ligand recognition process would diminish to a negligible value if the ligand freely diffuses toward the pocket. A Markov state model (MSM) constructed using the simulated trajectories identifies a set of transiently populated metastable states comprising partially ligand-unbound macro states, alongside ligand-bound and ligand-unbound pose and gives rise to multiple transition paths of ligand in its way to the hydrophobic cavity. Lifting the restriction on ligand movement changes its binding pathway, time scales, and the extent of the role of solvent in modulating the recognition process.

An on-demand, drop-on-drop method for studying enzyme catalysis by serial crystallography

Serial femtosecond crystallography has opened up many new opportunities in structural biology. In recent years, several approaches employing light-inducible systems have emerged to enable time-resolved experiments that reveal protein dynamics at high atomic and temporal resolutions. However, very few enzymes are light-dependent, whereas macromolecules requiring ligand diffusion into an active site are ubiquitous. In this work we present a drop-on-drop sample delivery system that enables the study of enzyme-catalyzed reactions in microcrystal slurries. The system delivers ligand solutions in bursts of multiple picoliter-sized drops on top of a larger crystal-containing drop inducing turbulent mixing and transports the mixture to the X-ray interaction region with temporal resolution. We demonstrate mixing using fluorescent dyes, numerical simulations and time-resolved serial femtosecond crystallography, which show rapid ligand diffusion through microdroplets. The drop-on-drop method has the potential to be widely applicable to serial crystallography studies, particularly of enzyme reactions with small molecule substrates.

The Pleiotropic Intricacies of Hedgehog Signaling: From Craniofacial Patterning to Carcinogenesis.

Hedgehog signaling was discovered more than 40 years ago in experiments demonstrating that it is a fundamental mediator of limb development. Since that time, it has been shown to be important in development, homeostasis, and disease. The hedgehog pathway proceeds through a pathway highly conserved throughout animals beginning with the extracellular diffusion of hedgehog ligands, proceeding through an intracellular signaling cascade, and ending with the activation of specific target genes. A vast amount of research has been done elucidating hedgehog signaling mechanisms and regulation. This research has found a complex system of genetics and signaling that helps determine how organisms develop and function. This review provides an overview of what is known about hedgehog genetics and signaling, followed by an in-depth discussion of the role of hedgehog signaling in craniofacial development and carcinogenesis.

Dependence of phase transition uniformity on crystal sizes characterized using birefringence.

Solid–solid phase transitions (SSPTs) have been widely observed in crystals of organic or inorganic small-molecules. Although SSPTs in macromolecular crystals have been reported, the majority involve local atomic changes, such as those induced by changes in hydration. SSPTs driven by large conformational changes, however, can be more difficult to characterize since they often significantly disrupt lattice packing interactions. Such drastic changes make the cooperativity of molecular motion at the atomic level less easily achieved and more dependent on intrinsic properties of the crystal that define lattice order. Here, we investigate the effect of crystal size on the uniformity of SSPT in thin plate-like crystals of the adenine riboswitch aptamer RNA (riboA) by monitoring changes in crystal birefringence upon the diffusion of adenine ligand. The birefringence intensity is directly related to molecular order and the concurrent changes to polarizability of molecules that results from structural changes throughout the phase transition. The riboA crystals were loosely grouped into three categories (small, medium, and large) based on the surface area of the crystal plates. The time width of transition increased as a function of crystal size, ranging from ∼13 s for small crystals to ∼40 s for the largest crystal. Whereas the transitions in small crystals (<10 μm2) were mostly uniform throughout, the medium and large crystals exhibited large variations in the time and width of the transition peak depending on the region of the crystal being analyzed. Our study provides insight into the spatiotemporal behavior of phase transitions in crystals of biological molecules and is of general interest to time-resolved crystallographic studies, where the kinetics of conformational changes may be governed by the kinetics of an associated SSPT.

Structural insights into the ligand recognition and catalysis of the key aminobutanoyltransferase CntL in staphylopine biosynthesis

Staphylopine (StP) and other nicotianamine-like metallophores are crucial for many pathogens to acquire the transition metals from hosts during invasion. CntL from Staphylococcus aureus (SaCntL) catalyzes the condensation of the 2-aminobutyrate (Ab) moiety of S-adenosylmethionine (SAM) with D-histidine in the biosynthesis of StP. Here, we report the crystal structures of SaCntL in complex with either SAM or two products. The structure of SaCntL consists of an N-terminal four-helix bundle (holding catalytic residue E84) and a C-terminal Rossmann fold (binding the substrates). The sequence connecting the N- and C-terminal domains (N-C linker) in SaCntL was found to undergo conformational alternation between open and closed states. Our structural and biochemical analyses suggested that this intrinsically dynamic interdomain linker forms an additional structural module that plays essential roles in ligand diffusion, recognition, and catalysis. We confirmed that SaCntL stereoselectively carries out the catalysis of D-His but not its enantiomer, L-His, and we found that the N-C linker and active site of SaCntL could accommodate both enantiomers. SaCntL is likely able to bind L-His without catalysis, and as a result, L-His could show inhibitory effects toward SaCntL. These findings provide critical structural and mechanistic insights into CntL, which facilitates a better understanding of the biosynthesis of nicotianamine-like metallophores and the discovery of inhibitors of this process.

Diversity and robustness of bone morphogenetic protein pattern formation.

ABSTRACTPattern formation by bone morphogenetic proteins (BMPs) demonstrates remarkable plasticity and utility in several contexts, such as early embryonic development, tissue patterning and the maintenance of stem cell niches. BMPs pattern tissues over many temporal and spatial scales: BMP gradients as short as 1-2 cell diameters maintain the stem cell niche of the Drosophila germarium over a 24-h cycle, and BMP gradients of several hundred microns establish dorsal-ventral tissue specification in Drosophila, zebrafish and Xenopus embryos in timescales between 30 min and several hours. The mechanisms that shape BMP signaling gradients are also incredibly diverse. Although ligand diffusion plays a dominant role in forming the gradient, a cast of diffusible and non-diffusible regulators modulate gradient formation and confer robustness, including scale invariance and adaptability to perturbations in gene expression and growth. In this Review, we document the diverse ways that BMP gradients are formed and refined, and we identify the core principles that they share to achieve reliable performance.

Statistics of Reaction Flux and Dynamical Activity Associated with a Diffusion-Influenced Ligand-Binding Reaction.

In this paper, we consider a macromolecule with two competitive binding sites where a ligand can bind to and gives rise to a unicyclic reaction network consisting of four states-(i) a single state with both binding sites vacant, (ii) two states with one bound site and one free binding site, and (iii) an another single state with both sites occupied. We obtain probability densities of the time-integrated current along the clockwise direction and the dynamical activity or mean number of jumps between different states for finite times at a fast diffusion limit. On the other hand, in the diffusion-limited case, ligand diffusion between the two binding sites directly connects the mono-ligated states-changing the reaction scheme. Addition of the new reaction channel alters the precision of ligand occupancy to a single site, the mean dynamical activity, and the mean entropy production rate. All of these quantities are calculated with varying degrees of competition between the two sites for ligands, and we find that increase in the competition between the two sites decreases all above-mentioned additive functionals. The upper bound of precision associated with a single-site ligand occupancy for a diffusion-influenced reaction network is set by the mean dynamical activity (mean entropy production rate) at small (large) ligand concentrations at the steady-state limit.

Binding of Folate-G4-PAMAM dendrimer conjugate with indomethacin via ligand diffusion MD simulations

Preceding experimental findings revealed that the release of indomethacin decreased when a folate conjugate G4-PAMAM (folate-G4-PAMAM) dendrimer was used compared with its unconjugated dendrimer (G4-PAMAM). Further, better encapsulation of the conjugated dendrimer was achieved, information useful for elucidating the structural and energetic basis of indomethacin on folate-G4-PAMAM encapsulation. In this study, we employed a ligand diffusion molecular dynamic simulations (LDMDSs) strategy combined with the molecular mechanics-generalized-born surface area (MMGBSA) approach to explore the mechanism by which indomethacin conjugated to folate-G4-PAMAM dendrimer forms complexes better than G4-PAMAM dendrimer. To this, we first constructed and equilibrated the folate-G4-PAMAM dendrimer, then, this system was submitted to docking and molecular dynamics (MD) simulation to evaluate its ability to form a stable complex with the folate receptor (FR). We observed that the folate-G4-PAMAM dendrimer was able to bind FR with higher affinity than free folic acid. Based on these results, we further performed LDMDSs to assess folate-G4-PAMAM dendrimer and G4-PAMAM dendrimer contacts with indomethacin. Our results correlate with experimental data, which confirm that folate-G4-PAMAM dendrimers are capable of most rapidly binding greater numbers of indomethacin molecules than G4-PAMAM, which suggests better loading and slower release occurs when the functionalized G4-PAMAM dendrimer is used. The simulations further revealed that van der Waals interactions govern the affinity. Communicated by Ramaswamy H. Sarma

Change in phytoextraction of Cd by rapeseed (Brassica napus L.) with application rate of organic acids and the impact of Cd migration from bulk soil to the rhizosphere

Adding exogenous low-molecular weight organic acids is an effective technique to improve phytoremediation of Cd-contaminated soil and has been well documented, but how acid application rate affects remediation efficiency and its underlying limiting factors remains elusive. We investigated this using pot experiments with rapeseed (Brassica napus L.) as the model plant. Plastic pots packed with a sandy loam contaminated by Cd at 4.838 mg/kg were amended with acetic acid, oxalic acid, citric acid, malic acid and tartaric acid, respectively, at an application rate gradient varying from 0.0 to 12.0 mmol/kg. Plants in each pot were harvested after growing for five months, and we then measured the exchangeable, carbonate, Fe–Mn oxide, organic and residual Cd in the rhizosphere, as well as Cd in both roots and shoots. The results showed that all organic acids improved plant uptake of Cd and, compared with the control without acid addition, they could improve Cd uptake by more than 100%. The enhanced Cd extraction was due to the increase in exchangeable Cd in the rhizosphere. Plant Cd was weakly correlated to the amount of Cd lost from a unit volume of the rhizosphere due to root extraction (R2 = 0.06), but a good negative correlation was found between them after normalizing the lost Cd by root biomass (R2 = 0.36). Mass balance analysis revealed that the average Cd content in soil (rhizosphere and bulk soils combined) was much higher than the Cd content in the rhizosphere, and the improved Cd mobility after acid addition was thus due to the increased chelation. As diffusion of ligands in water is one order in magnitude smaller than diffusion of Cd ions, our results suggested that Cd migration from the bulk soil into the rhizosphere was a major factor limiting Cd phytoextraction by rapeseed after adding the exogenous organic acids.

Tracking the Effects of Ligands on Oxidative Etching of Gold Nanorods in Graphene Liquid Cell Electron Microscopy.

Surface ligands impact the properties and chemistry of nanocrystals, but observing ligand binding locations and their effect on nanocrystal shape transformations is challenging. Using graphene liquid cell electron microscopy and the controllable, oxidative etching of gold nanocrystals, the effect of different ligands on nanocrystal etching can be tracked with nanometer spatial resolution. The chemical environment of liquids irradiated with high-energy electrons is complex and potentially harsh, yet it is possible to observe clear evidence for differential binding properties of specific ligands to the nanorods' surface. Exchanging CTAB ligands for PEG-alkanethiol ligands causes the nanorods to etch at a different, constant rate while still maintaining their aspect ratio. Adding cysteine ligands that bind preferentially to nanorod tips induces etching predominantly on the sides of the rods. This etching at the sides leads to Rayleigh instabilities and eventually breaks apart the nanorod into two separate nanoparticles. The shape transformation is controlled by the interplay between atom removal and diffusion of surface atoms and ligands. These in situ observations are confirmed with ex situ colloidal etching reactions of gold nanorods in solution. The ability to monitor the effect of ligands on nanocrystal shape transformations will enable future in situ studies of nanocrystals surfaces and ligand binding positions.

Ligand Diffusion Enables Force-Independent Cell Adhesion via Activating α5β1 Integrin and Initiating Rac and RhoA Signaling.

Cells reside in a dynamic microenvironment in which adhesive ligand availability, density, and diffusivity are key factors regulating cellular behavior. Here, the cellular response to integrin-binding ligand dynamics by directly controlling ligand diffusivity via tunable ligand-surface interactions is investigated. Interestingly, cell spread on the surfaces with fast ligand diffusion is independent of myosin-based force generation. Fast ligand diffusion enhances α5β1 but not αvβ3 integrin activation and initiates Rac and RhoA but not ROCK signaling, resulting in lamellipodium-based fast cell spreading. Meanwhile, on surfaces with immobile ligands, αvβ3 and α5β1 integrins synergistically initiate intracellular-force-based canonical mechanotransduction pathways to enhance cell adhesion and osteogenic differentiation of stem cells. These results indicate the presence of heretofore-unrecognized pathways, distinct from canonical actomyosin-driven mechanisms, that are capable of promoting cell adhesion.