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Real time observation of chemical reactions of individual noble metal nanoparticles (MNPs) is fundamentally important to their controlled synthesis, chemical sensing and catalysis applications. Here, with a simple and high-throughput single-molecule darkfield spectral imaging technique, we demonstrate that the reaction-induced plasmonic resonance variations of multiple MNPs could be monitored in parallel. Oxidation kinetics of individual gold nanorods (AuNRs), either immobilized on a glass substrate or moving freely in homogeneous solution, was recorded successfully. Heterogeneous reaction pathways and intermediate states unobsorvable in ensemble UV-visible measurements were revealed. Interestingly, the oxidation rate of individual immobilized AuNRs was much slower than that of the bulk AuNR solution, which implies the existence of a novel self-catalysis mechanism. This high-throughput darkfield spectral imaging technique could be applied to chemical reaction kinetics and heterogeneous catalysis studies of other MNPs at single particle level. 10.1021/ac101933y

Research has been conducted on Escherichia coli cyclic AMP receptor protein. The intermolecular communication mechanism and the covalent linkage properties have been investigated via the study of the functional and structural properties of the protein's DNA- and cyclic AMP-binding domains and the details are presented.

An iron-EDTA-mediated protein footprinting technique was utilized in the investigation of the conformational changes in the catalytic subunit of the cyclic AMP-dependent protein kinase upon substrate binding. Solvent-accessible enzyme surfaces as well as the structural dynamics of the catalytic domain were monitored during the footprinting process. Results reveal that the structural changes in the catalytic domain involve the transition from an open to a close conformation.

Research was conducted to determine the structural elements associated in the coupling of interfacial interactions by glycine 141 mutation in Escherichia coli cAMP receptor protein. Wild-type caMP receptor proteins were determined from temperature-induced Escherichia coli cells while their quaternary structure was monitored by sedimentation equilibrium. Results showed that the mutation differentially perturbed the network involving the interfacial relations between subunits and domains.

The communication between domains induced by cAMP binding can be dissociated from the proper subunit realignment of the cAMP receptor protein (CRP) dimer that is necessary for the activation of CRP. The mutations at position 128 were analyzed in order to identify the partial reactions in the activation pathway. The results indicate that mutations of Ser 128 to Ala or Pro does not disturb the overall secondary structure as monitored by circular synchronism in any significant ways.

Type-II DNA-(cytosine-5)-methyltransferase (M.HhaI) gene was transfected and overexpressed in Escherichia coli and purified using a salt back-extraction technique. The extracted M.HhaI can be isolated as pure molecules or complexed with S-adenosylmethionine, its cofactor. The cofactor-bound form can methylate nucleic acid. The enzyme kinetics of the purified M.HhaI were also reported. Crystallographic analysis of the enzyme revealed its growth along a monoclinic space group. Dimensions for each unit cell are presented.

Investigates the energetics of subunit dimerization and unfolding in the cyclic adenosine monophosphate (CAMP) binding domain and the CAMP receptor protein (CRP) of Escherichia coli. Structural and functional analysis of renatured CRP and CAMP binding domains; Conditions for reversible denaturation of CRP; Energetics of intra- and intersubunit interactions in CRP.

The translational and rotational dynamics of anisotropic optical nanoprobes revealed in single particle tracking (SPT) experiments offer molecular-level information about cellular activities. Here, we report an automated high-speed multidimensional SPT system integrated with a deep learning algorithm for tracking the 3D orientation of anisotropic gold nanoparticle probes in living cells with high localization precision (<10 nm) and temporal resolution (0.9 ms), overcoming the limitations of rotational tracking under low signal-to-noise ratio (S/N) conditions. This method can resolve the azimuth (0°-360°) and polar angles (0°-90°) with errors of less than 2° on the experimental and simulated data under S/N of ∼4. Even when the S/N approaches the limit of 1, this method still maintains better robustness and noise resistance than the conventional pattern matching methods. The usefulness of this multidimensional SPT system has been demonstrated with a study of the motions of cargos transported along the microtubules within living cells.

PCIF1 and FTO are a pair of human mRNA cap-specific modification enzymes that have opposing activities. PCIF1 adds a methyl group to the N6-position of 2' O -methyladenosine (A m ), generating N6, 2' O -dimethyladenosine (m 6 A m ), when A m is the cap-proximal nucleotide. FTO removes the N6-methyl group from m 6 A m . In addition, FTO has a demethylase activity on a broad spectrum of various RNA substrates, as well as on D NA N6-methyldeoxyadenosine (m 6 dA). While the existence of m 6 dA in mammalian D NA remains controversial, we show here that PCIF1 has significant methylation activity on single stranded DNA deoxyadenosine, double stranded RNA/DNA hybrids, and double stranded DNA, though with lower catalytic efficiency than that on its preferred RNA substrate. PCIF1 has activities in the order ssRNA > RNA/DNA hybrid > ssDNA > dsDNA. We discuss the implications of PCIF1 generation, and FTO removal, of DNA adenine methylation.

Understanding the selectivity of methyltransferase inhibitors is important to dissecting the functions of each methyltransferase target. From this perspective, we report a chemoproteomic study to profile the selectivity of a potent protein N-terminal methyltransferase 1 (NTMT1) bisubstrate inhibitor NAH-C3-GPKK ( K i, app = 7 ± 1 nM) in endogenous proteomes. First, we describe the rational design, synthesis, and biochemical characterization of a new chemical probe 6 , a biotinylated analogue of NAH-C3-GPKK. Next, we systematically analyze protein networks that may selectively interact with the biotinylated probe 6 in concert with the competitor NAH-C3-GPKK. Besides NTMT1, the designated NTMT1 bisubstrate inhibitor NAH-C3-GPKK was found to also potently inhibit a methyltransferase complex HemK2-Trm112 (also known as KMT9-Trm112), highlighting the importance of systematic selectivity profiling. Furthermore, this is the first potent inhibitor for HemK2/KMT9 reported until now. Thus, our studies lay the foundation for future efforts to develop selective inhibitors for either methyltransferase.

Nanoconfinement imposes physical constraints and chemical effects on reactivity in nanoporous catalyst systems. In the present study, we lay the groundwork for quantitative single-molecule measurements of the effects of chemical environment on heterogeneous catalysis in nanoconfinement. Choosing hydrophobicity as an exemplary chemical environmental factor, we compared a range of essential parameters for an oxidation reaction on platinum nanoparticles (NPs) confined in hydrophilic and hydrophobic nanopores. Single-molecule experimental measurements at the single particle level showed higher catalytic activity, stronger adsorption strength, and higher activation energy in hydrophobic nanopores than those in hydrophilic nanopores. Interestingly, different dissociation kinetic behaviors of the product molecules in the two types of nanopores were deduced from the single-molecule imaging data.

The active sites of hundreds of human α-ketoglutarate (αKG) and Fe(II)-dependent dioxygenases are exceedingly well preserved, which challenges the design of selective inhibitors. We identified a noncatalytic cysteine (Cys481 in KDM5A) near the active sites of KDM5 histone H3 lysine 4 demethylases, which is absent in other histone demethylase families, that could be explored for interaction with the cysteine-reactive electrophile acrylamide. We synthesized analogs of a thienopyridine-based inhibitor chemotype, namely, 2-((3-aminophenyl)(2-(piperidin-1-yl)ethoxy)methyl)thieno[3,2- b]pyridine-7-carboxylic acid (N70) and a derivative containing a (dimethylamino)but-2-enamido)phenyl moiety (N71) designed to form a covalent interaction with Cys481. We characterized the inhibitory and binding activities against KDM5A and determined the cocrystal structures of the catalytic domain of KDM5A in complex with N70 and N71. Whereas the noncovalent inhibitor N70 displayed αKG-competitive inhibition that could be reversed after dialysis, inhibition by N71 was dependent on enzyme concentration and persisted even after dialysis, consistent with covalent modification.

An ultrabroadband all-dielectric planar Luneburg lens has been designed and fabricated in this study, which is in the form of a radial gradient lightweight honeycomb column. Because of the novel design of a radial symmetric honeycomb-like microstructure in the subwavelength dimension and the radial gradient configuration according to the refractive index distribution of Luneburg lens, the present lens can focus incident plane waves on the opposite side with high convergence, and its operating frequency range is rather broadband, spanning from 6 to 16 GHz. Besides, the all-dielectric honeycomb-like lens is lightweight with a mass density of 0.23 g/cm 3 , and its broadband transmittance is higher than the reported cases consisting of metallic metamaterial or gradient photonic crystal structures. A prototype of the lens is fabricated by using 3D printing techniques, on which the electric near-field distribution and far-field radiation pattern measurements have been carried out, and the aforementioned performances were demonstrated experimentally. It was also observed that for two point sources placed at the edge of the lens whose intersection angle with the center of the lens is 90°, the far-field radiation pattern was still kept highly directional, which means that the lens can generate two highly directional beams simultaneously, and is an efficient double input-double output device.

Isomers of chiral drugs can exhibit marked differences in biological activities. We studied the binding and inhibitory activities of 12 compounds against KDM5A. Among them are two pairs of enantiomers representing two distinct inhibitor chemotypes, namely, ( R)- and ( S)-2-((2-chlorophenyl)(2-(piperidin-1-yl)ethoxy)methyl)-1 H-pyrrolo[3,2- b]pyridine-7-carboxylic acid (compounds N51 and N52) and ( R) - and ( S) -N-(1-(3-isopropyl-1 H-pyrazole-5-carbonyl)pyrrolidin-3-yl)cyclopropanecarboxamide (compounds N54 and N55). In vitro, the S enantiomer of the N51/N52 pair (N52) and the R enantiomer of the N54/N55 pair (N54) exhibited about 4- to 5-fold greater binding affinity. The more potent enzyme inhibition of KDM5A by the R-isoform for the cell-permeable N54/N55 pair translated to differences in growth inhibitory activity. We determined structures of the KDM5A catalytic domain in complex with all 12 inhibitors, which revealed the interactions (or lack thereof) responsible for the differences in binding affinity. These results provide insights to guide improvements in binding potency and avenues for development of cell permeable inhibitors of the KDM5 family.

EPAC proteins are therapeutic targets for the potential treatment of cardiac hypertrophy and cancer metastasis. Several laboratories use a tetrahydroquinoline analog, CE3F4, to dissect the role of EPAC1 in various disease states. Here, we report SAR studies with tetrahydroquinoline analogs that explore various functional groups. The most potent EPAC inhibitor 12a exists as a mixture of inseparable E (major) and Z (minor) rotamers. The rotation about the N -formyl group indeed impacts the activity against EPAC., Competing Interests: The authors declare no competing financial interest.

Optical super-resolution imaging has gained momentum in investigations of heterogeneous and homogeneous chemical reactions at the single-molecule level. Thanks to its exceptional spatial resolution and ability to monitor dynamic systems, much detailed information on single-molecule reaction/adsorption processes and single-particle catalytic processes has been revealed, including chemical kinetics and reaction dynamics; active-site distributions on single-particle surfaces; and size-, shape-, and facet-dependent catalytic activities of individual nanocatalysts. In this review, we provide an overview of recent advances in super-resolution chemical imaging of surface reactions.

N,N-Diphenylamines were discovered as potent and selective EPAC2 inhibitors. A study was conducted to determine the structure-activity relationships in a series of inhibitors of which several compounds displayed submicromolar potencies. Selectivity over the related EPAC1 protein was also demonstrated. Computational modeling reveals an allosteric site that is distinct from the cAMP binding domain shared by both EPAC isoforms, providing a theory with regards to subtype selectivity.

Exchange proteins directly activated by cAMP (EPAC) as guanine nucleotide exchange factors mediate the effects of the pivotal second messenger cAMP, thereby regulating a wide variety of intracellular physiological and pathophysiological processes. A series of novel 2-(isoxazol-3-yl)-2-oxo-N'-phenyl-acetohydrazonoyl cyanide EPAC antagonists was synthesized and evaluated in an effort to optimize properties of the previously identified high-throughput (HTS) hit 1 (ESI-09). Structure-activity relationship (SAR) analysis led to the discovery of several more active EPAC antagonists (e.g., 22 (HJC0726), 35 (NY0123), and 47 (NY0173)) with low micromolar inhibitory activity. These inhibitors may serve as valuable pharmacological probes to facilitate our efforts in elucidating the biological functions of EPAC and developing potential novel therapeutics against human diseases. Our SAR results have also revealed that further modification at the 3-, 4-, and 5-positions of the phenyl ring as well as the 5-position of the isoxazole moiety may allow for the development of more potent EPAC antagonists.

Circular permutation of the NADPH-dependent oxidoreductase Old Yellow Enzyme from Saccharomyces pastorianus (OYE1) can significantly enhance the enzyme's catalytic performance. Termini relocation into four regions of the protein (sectors I-IV) near the active site has proven effective in altering enzyme function. To better understand the structural consequences and rationalize the observed functional gains in these OYE1 variants, we selected representatives from sectors I-III for further characterization by biophysical methods and X-ray crystallography. These investigations not only show trends in enzyme stability and quaternary structure as a function of termini location, but also provide a possible explanation for the catalytic gains in our top-performing OYE variant (new N-terminus at residue 303; sector III). Crystallographic analysis indicates that termini relocation into sector III affects the loop β6 region (amino acid positions: 290-310) of OYE1 which forms a lid over the active site. Peptide backbone cleavage greatly enhances local flexibility, effectively converting the loop into a tether and consequently increasing the environmental exposure of the active site. Interestingly, such active site remodeling does not negatively impact the enzyme's activity and stereoselectivity, nor does it perturb the conformation of other key active site residues with the exception of Y375. These observations were confirmed in truncation experiments, deleting all residues of the loop β6 region in our OYE variant. Intrigued by the finding that circular permutation leaves most of the key catalytic residues unchanged, we also tested OYE permutants for possible additive or synergistic effects of amino acid substitutions. Distinct functional changes in these OYE variants were detected upon mutations at W116, known in native OYE1 to cause inversion of diastereo-selectivity for ( S )-carvone reduction. Our findings demonstrate the contribution of loop β6 toward determining the stereoselectivity of OYE1, an important insight for future OYE engineering efforts.

Spectral chemical sensing with digital color analysis by using consumer imaging devices could potentially revolutionize personalized healthcare. However, samples with small spectral variations often cannot be differentiated in color due to the nonlinearity of color appearance. In this study, we address this problem by exploiting the color image formation mechanism in digital photography. A close examination of the color image processing pipeline emphasizes that although the color can be represented digitally, it is still a reproducible subjective perception rather than a measurable physical property. That makes it possible to physically manage the color appearance of a nonradiative specimen through engineered illumination. By using scattering light imaging of gold nanoparticles (GNPs) as a model system, we demonstrated via simulation that enlarged color difference between spectrally close samples could be achieved with actively controlled illumination of multiple narrow-band light sources. Experimentally, darkfield imaging results indicate that color separation of single GNPs with various sizes can be significantly improved and the detection limit of GNP aggregation-based colorimetric assays can be much reduced when the conventional spectrally continuous white light was replaced with three independently intensity-controlled laser beams, even though the laser lines were uncorrelated with the LSPR maxima of the GNPs. With low-cost narrow-band light sources widely available today, this actively controlled illumination strategy could be utilized to replace the spectrometer in many spectral sensing applications.

We present a high-throughput strategy for sensitive detection of H2S by using individual spherical Au-Ag core-shell plasmonic nanoparticles (PNPs) as molecular probes. This method is based on quantification of color variation of the single PNPs resulting from formation of Ag2S on the particle surface. The spectral response range of the 51 nm PNP was specifically designed to match the most sensitive region of color cameras. A high density of immobilized PNPs and rapid color RGB (red/green/blue) analysis allow a large number of individual PNPs to be monitored simultaneously, leading to reliable quantification of color change of the PNPs. A linear logarithmic dependence on sulfide concentrations from 50 nM to 100 μM was demonstrated by using this colorimetric assay. By designing PNPs with various surface chemistries, similar strategies could be developed to detect other chemically or biologically important molecules.

3',5'-Cyclic adenosine monophosphate (cAMP) is a pivotal second messenger that regulates numerous biological processes under physiological and pathological conditions, including cancer, diabetes, heart failure, inflammation, and neurological disorders. In the past, all effects of cAMP were initially believed to be mediated by protein kinase A (PKA) and cyclic nucleotide-regulated ion channels. Since the discovery of exchange proteins directly activated by cyclic adenosine 5'-monophosphate (EPACs) in 1998, accumulating evidence has demonstrated that the net cellular effects of cAMP are also regulated by EPAC. The pursuit of the biological functions of EPAC has benefited from the development and applications of a growing number of pharmacological probes targeting EPACs. In this review, we seek to provide a concise update on recent advances in the development of chemical entities including various membrane-permeable analogues of cAMP and newly discovered EPAC-specific ligands from high throughput assays and hit-to-lead optimizations.

We have developed a high-resolution nonfluorescent imaging method based on superlocalization of gold nanorods (AuNRs). By taking advantage of their anisotropic optical property of the plasmonic scattering of AuNRs, selective imaging of only a fraction of AuNRs can be achieved by rotating the sample relative to the linear polarized illumination under cross-polarization microscopy with a high NA objective. The AuNR positions obtained from a series of images could then be used to reconstruct the overall image. Two AuNRs with center-to-center distances of 80 nm were successfully resolved. This simple but deterministic super-resolution imaging technique can potentially be used to fingerprint optically anisotropic metal nanoparticles and their assemblies for labeling, sensing, and encryption applications.

DNA methyltransferases (DNMTs) are important enzymes involved in epigenetic control of gene expression and represent valuable targets in cancer chemotherapy. A number of nucleoside DNMT inhibitors (DNMTi) have been studied in cancer, including in cancer stem cells, and two of them (azacytidine and decitabine) have been approved for treatment of myelodysplastic syndromes. However, only a few non-nucleoside DNMTi have been identified so far, and even fewer have been validated in cancer. Through a process of hit-to-lead optimization, we report here the discovery of compound 5 as a potent non-nucleoside DNMTi that is also selective toward other AdoMet-dependent protein methyltransferases. Compound 5 was potent at single-digit micromolar concentrations against a panel of cancer cells and was less toxic in peripheral blood mononuclear cells than two other compounds tested. In mouse medulloblastoma stem cells, 5 inhibited cell growth, whereas related compound 2 showed high cell differentiation. To the best of our knowledge, 2 and 5 are the first non-nucleoside DNMTi tested in a cancer stem cell line.

The Zfp57 gene encodes a KRAB (Krüppel-associated box) domain-containing C2H2 zinc finger transcription factor that is expressed in early development. Zfp57 protein recognizes methylated CpG dinucleotide within GCGGCA elements at multiple imprinting control regions. In the previously determined structure of the mouse Zfp57 DNA-binding domain in complex with DNA containing 5-methylcytosine (5mC), the side chains of Arg178 and Glu182 contact the methyl group via hydrophobic and van der Waals interactions. We examined the role of Glu182 in recognition of 5mC by mutagenesis. The majority of mutants examined lose selectivity of methylated (5mC) over unmodified (C) and oxidative derivatives, 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxylcytosine (5caC), suggesting that the side chain of Glu182 (the size and the charge) is dispensable for methyl group recognition but negatively impacts the binding of unmodified cytosine as well as oxidized derivatives of 5mC to achieve 5mC selectivity. Substitution of Glu182 with its corresponding amide (E182Q) had no effect on methylated DNA binding but gained significant binding affinity for 5caC DNA, resulting in a binding affinity for 5caC DNA comparable to that of the wild-type protein for 5mC. We show structurally that the uncharged amide group of E182Q interacts favorably with the carboxylate group of 5caC. Furthermore, introducing a positively charged arginine at position 182 resulted in a mutant (E182R) having higher selectivity for the negatively charged 5caC.

EPAC1 and EPAC2, two isoforms of exchange proteins directly activated by cAMP (EPAC), respond to the second messenger cAMP and regulate a wide variety of intracellular processes under physiological and pathophysiological circumstances. Herein, we report the chemical design, synthesis, and pharmacological characterization of three different scaffolds (diarylsulfones, N,N-diarylamines, and arylsulfonamides) as highly potent and selective antagonists of EPAC2. Several selective EPAC2 antagonists have been identified including 20i (HJC0350), which has an apparent IC(50) of 0.3 μM for competing with 8-NBD-cAMP binding of EPAC2 and is about 133-fold more potent than cAMP. Compounds 1 (ESI-05), 14c (HJC0338), and 20i, selected from each series, have exhibited no inhibition of EPAC1-mediated Rap1-GDP exchange activity at 25 μM, indicating that they are EPAC2-specific antagonists. Moreover, live-cell imaging studies using EPAC1, EPAC2, or PKA FRET sensor also demonstrate that 20i functions as an EPAC2 specific antagonist.

Herein, we demonstrated a new optical microscopy method to selectively image small-size gold nanoparticles (GNPs) inside noisy living cells through determination of the difference image between the probe beam (illuminated at the resonance wavelength of GNPs, 532 nm) and the reference beam (illuminated at 473 nm). From computer simulation and single-particle imaging experiments, we demonstrated that GNPs with a diameter of 45 nm could be selectively imaged in the GNPs/cell lysates mixture and inside living cells by dual-wavelength difference (DWD) imaging. The diffusion dynamics of nucleic acids functionalized GNPs on cell membranes and the internalization kinetics of these GNPs by living cells were explored with this method. Our real-time tracking experiments showed that statistically 80% of GNPs were under restricted diffusion on the cell membrane. The cell cytoskeleton fence effect, as observed in the single-particle tracking experiments, may be one of the main factors for the restricted diffusion mode.

One of the most fundamental questions in the control of gene expression in mammals is how epigenetic methylation patterns of DNA and histones are established, erased, and recognized. This central process in controlling metazoan gene expression includes coordinated covalent modifications of DNA and its associated histones. This review focuses on recent developments in characterizing the functional links between the methylation status of the DNA and of two particularly important histone marks. Mammalian DNA methylation is intricately connected to the presence of unmodified lysine 4 and methylated lysine 9 residues in histone H3. An interconnected network of methyltransferases, demethylases, and accessory proteins is responsible for changing or maintaining the modification status of specific regions of chromatin. The structural and functional interactions among members of this network are critical to processes that include imprinting and differentiation, dysregulation of which is associated with disorders ranging from inflammation to cancer.

Protein arginine methyltransferases (PRMTs) are a group of eukaryotic enzymes that catalyze the methylation of Arg residues in a variety of proteins (e.g., histones H3 and H4), and their activities influence a wide range of cellular processes, including cell growth, RNA splicing, differentiation, and transcriptional regulation. Dysregulation of these enzymes has been linked to heart disease and cancer, suggesting this enzyme family as a novel therapeutic target. To aid the development of PRMT inhibitors, we characterized the substrate specificity of both the rat and human PRMT1 orthologues using histone based peptide substrates. N- and C-terminal truncations to identify a minimal peptide substrate indicate that long-range interactions between enzyme and substrate are important for high rates of substrate capture. The importance of these long-range interactions to substrate capture were confirmed by "mutagenesis" experiments on a minimal peptide substrate. Inhibition studies on S-adenosyl-homocysteine, thioadenosine, methylthioadenosine, homocysteine, and sinefungin suggest that potent and selective bisubstrate analogue inhibitor(s) for PRMT1 can be developed by linking a histone based peptide substrate to homocysteine or sinefungin. Additionally, we present evidence that PRMT1 utilizes a partially processive mechanism to dimethylate its substrates.

Exchange proteins directly activated by cAMP (Epac) make up a family of cAMP binding domain-containing proteins that play important roles in mediating the effects of cAMP through the activation of downstream small GTPases, Ras-proximate proteins. To delineate the mechanism of Epac activation, we probed the conformation and structural dynamics of Epac using amide hydrogen-deuterium (H-D) exchange coupled with Fourier transform infrared spectroscopy (FT-IR) and structural modeling. Our studies show that unlike that of cAMP-dependent protein kinase (PKA), the classic intracellular cAMP receptor, binding of cAMP to Epac does not induce significant changes in overall secondary structure and structural dynamics, as measured by FT-IR and the rate of H-D exchange, respectively. These results suggest that Epac activation does not involve significant changes in the amount of exposed surface areas as in the case of PKA activation, and conformational changes induced by cAMP in Epac are most likely confined to small local regions. Homology modeling and comparative structural analyses of the CBDs of Epac and PKA lead us to propose a model of Epac activation. On the basis of our model, Epac activation by cAMP employs the same underlying structural principal utilized by PKA, although the detailed structural and conformational changes associated with Epac and PKA activation are significantly different. In addition, we predict that during Epac activation the first beta-strand of the switchboard switches its conformation to a alpha-helix, which folds back to the beta-barrel core of the CBD and interacts directly with cAMP to form the base of the cAMP-binding pocket.

Although individual structures of cAMP-dependent protein kinase (PKA) catalytic (C) and regulatory (R) subunits have been determined at the atomic level, our understanding of the effects of cAMP activation on protein dynamics and intersubunit communication of PKA holoenzymes is very limited. To delineate the mechanism of PKA activation and structural differences between type I and II PKA holoenzymes, the conformation and structural dynamics of PKA holoenzymes Ialpha and IIbeta were probed by amide hydrogen-deuterium exchange coupled with Fourier transform infrared spectroscopy (FT-IR) and chemical protein footprinting. Binding of cAMP to PKA holoenzymes Ialpha and IIbeta leads to a downshift in the wavenumber for both the alpha-helix and beta-strand bands, suggesting that R and C subunits become overall more dynamic in the holoenzyme complexes. This is consistent with the H-D exchange results showing a small change in the overall rate of exchange in response to the binding of cAMP to both PKA holoenzymes Ialpha and IIbeta. Despite the overall similarity, significant differences in the change of FT-IR spectra in response to the binding of cAMP were observed between PKA holoenzymes Ialpha and IIbeta. Activation of PKA holoenzyme Ialpha led to more conformational changes in beta-strand structures, while cAMP induced more apparent changes in the alpha-helical structures in PKA holoenzyme IIbeta. Chemical protein footprinting experiments revealed an extended docking surface for the R subunits on the C subunit. Although the overall subunit interfaces appeared to be similar for PKA holoenzymes Ialpha and IIbeta, a region around the active site cleft of the C subunit was more protected in PKA holoenzyme Ialpha than in PKA holoenzyme IIbeta. These results suggest that the C subunit assumes a more open conformation in PKA holoenzyme IIbeta. In addition, the chemical cleavage patterns around the active site cleft of the C subunit were distinctly different in PKA holoenzymes Ialpha and IIbeta even in the presence of cAMP. These observations provide direct evidence that the R subunits may be partially associated with the C subunit with the pseudosubstrate sequence docked in the active site cleft in the presence of cAMP.