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We demonstrate the transfer of a cesium frequency standard steered to UTC(NIST) over 20 km of dark telecom optical fiber. Our dissemination scheme uses an active stabilization technique with a phase-locked voltage-controlled oscillator. Out-of-loop characterization of the optical fiber link performance is done with dual-fiber and single-fiber transfer schemes. We observe a fractional frequency instability of 1.5 × 10 -12 and 2 × 10 -15 at averaging intervals of 1 s and 10 5 s, respectively, for the link. Both schemes are sufficient to transfer the cesium clock reference without degrading the signal, with nearly an order of magnitude lower fractional frequency instability than the cesium clocks over all time scales. The simplicity of the two-fiber technique may be useful in future long-distance applications where higher stability requirements are not paramount, as it avoids technical complications involved with the single-fiber scheme.

Optical frequencies of the D line transitions in ^{9}Be^{+} were measured with a relative uncertainty of Δν/ν=5×10^{-11}. The results represent the highest accuracy achieved on a broad electric dipole-allowed (E1) transition in a trapped ion experiment to date, enabled in part by detailed consideration of photon recoil and quantum interference. Measurements were made on a single laser-cooled ion stored in a radio frequency Paul trap, using a spectroscopy laser stabilized to an optical frequency comb and referenced to UTC (NIST). The uncertainties in the D_{1} and D_{2} lines have been reduced by a factor of 10 and 30, respectively, compared to previous work. We have extracted the ^{2}P fine structure splitting, Δν_{fs}=197 064.54(7)  MHz, and the ^{2}P_{1/2} hyperfine constant, A_{P_{1/2}}=-117.92(4)  MHz.

Macrophages mediate key antimicrobial responses against intracellular bacterial pathogens, such as Salmonella enterica . Yet, they can also act as a permissive niche for these pathogens to persist in infected tissues within granulomas, which are immunological structures composed of macrophages and other immune cells. We apply single-cell transcriptomics to investigate macrophage functional diversity during persistent S. enterica serovar Typhimurium ( S Tm) infection in mice. We identify determinants of macrophage heterogeneity in infected spleens and describe populations of distinct phenotypes, functional programming, and spatial localization. Using an S Tm mutant with impaired ability to polarize macrophage phenotypes, we find that angiotensin-converting enzyme (ACE) defines a granuloma macrophage population that is nonpermissive for intracellular bacteria, and their abundance anticorrelates with tissue bacterial burden. Disruption of pathogen control by neutralizing TNF is linked to preferential depletion of ACE + macrophages in infected tissues. Thus, ACE + macrophages have limited capacity to serve as cellular niche for intracellular bacteria to establish persistent infection.

We report the first operation of a Ra^{+} optical clock, a promising high-performance clock candidate. The clock uses a single trapped ^{226}Ra^{+} ion and operates on the 7s ^{2}S_{1/2}→6d ^{2}D_{5/2} electric quadrupole transition. By self-referencing three pairs of symmetric Zeeman transitions, we demonstrate a frequency instability of 1.1×10^{-13}/sqrt[τ], where τ is the averaging time in seconds. The total systematic uncertainty is evaluated to be Δν/ν=9×10^{-16}. Using the clock, we realize the first measurement of the ratio of the D_{5/2} state to the S_{1/2} state Landé g-factors: g_{D}/g_{S}=0.598 805 3(11). A Ra^{+} optical clock could improve limits on the time variation of the fine structure constant, α[over ˙]/α, in an optical frequency comparison. The ion also has several features that make it a suitable system for a transportable optical clock.

Iron-catalyzed C-C coupling reactions of pyrrole provide a unique alternative to the traditional Pd-catalyzed counterpart. However, many details regarding the actual mechanism remain unknown. A series of macrocyclic iron(III) complexes were used to evaluate specifics related to the role of O 2 , radicals, and μ -oxodiiron-complex participation in the catalytic cycle. It was determined that the mononuclear tetra-azamacrocyclic complex is a true catalyst and not a stoichiometric reagent, while more than one equivalent of a sacrificial oxidant is needed. Furthermore, the reaction does not proceed through an organic radical pathway. μ -Oxodiiron complexes are not involved in the main catalytic pathway, and the dimers are, in fact, off-cycle species that decrease catalytic efficiency., Competing Interests: The authors declare no competing financial interest.

Sensing and responding to environmental signals is critical for bacterial pathogens to successfully infect and persist within hosts. Many bacterial pathogens sense temperature as an indication they have entered a new host and must alter their virulence factor expression to evade immune detection. Using secondary structure prediction, we identified an RNA thermosensor (RNAT) in the 5' untranslated region (UTR) of tviA encoded by the typhoid fever-causing bacterium Salmonella enterica serovar Typhi (S. Typhi). Importantly, tviA is a transcriptional regulator of the critical virulence factors Vi capsule, flagellin, and type III secretion system-1 expression. By introducing point mutations to alter the mRNA secondary structure, we demonstrate that the 5' UTR of tviA contains a functional RNAT using in vitro expression, structure probing, and ribosome binding methods. Mutational inhibition of the RNAT in S. Typhi causes aberrant virulence factor expression, leading to enhanced innate immune responses during infection. In conclusion, we show that S. Typhi regulates virulence factor expression through an RNAT in the 5' UTR of tviA. Our findings demonstrate that limiting inflammation through RNAT-dependent regulation in response to host body temperature is important for S. Typhi's "stealthy" pathogenesis., Competing Interests: The authors have declared that no competing interests exist.

Laser decoherence limits the stability of optical clocks by broadening the observable resonance linewidths and adding noise during the dead time between clock probes. Correlation spectroscopy avoids these limitations by measuring correlated atomic transitions between two ensembles, which provides a frequency difference measurement independent of laser noise. Here, we apply this technique to perform stability measurements between two independent clocks based on the ^{1}S_{0}↔^{3}P_{0} transition in ^{27}Al^{+}. By stabilizing the dominant sources of differential phase noise between the two clocks, we observe coherence between them during synchronous Ramsey interrogations as long as 8 s at a frequency of 1.12×10^{15}  Hz. The observed contrast in the correlation spectroscopy signal is consistent with the 20.6 s ^{3}P_{0} state lifetime and represents a measurement instability of (1.8±0.5)×10^{-16}/sqrt[τ/s] for averaging periods longer than the probe duration when dead time is negligible.

We identify Ba^{4+} (Te-like) as a promising candidate for a high-accuracy optical clock. The lowest-lying electronic states are part of a ^{3}P_{J} fine structure manifold with anomalous energy ordering, being nonmonotonic in J. We propose a clock based on the 338.8 THz electric quadrupole transition between the ground (^{3}P_{2}) and first-excited (^{3}P_{0}) electronic states. We perform relativistic many-body calculations to determine relevant properties of this ion. The lifetime of the excited clock state is found to be several seconds, accommodating low statistical uncertainty with a single ion for practical averaging times. The differential static scalar polarizability is found to be small and negative, providing suppressed sensitivity to blackbody radiation while simultaneously allowing cancellation of Stark and excess micromotion shifts. With the exception of Hg^{+} and Yb^{+}, sensitivity to variation of the fine structure constant is greater than other optical clocks thus far demonstrated.

In mammalian cells, inflammatory caspases detect Gram-negative bacterial invasion by binding lipopolysaccharides (LPS). Murine caspase-11 binds cytosolic LPS, stimulates pyroptotic cell death, and drives sepsis pathogenesis. Extracellular priming factors enhance caspase-11-dependent pyroptosis. Herein we compare priming agents and demonstrate that IFN γ priming elicits the most rapid and amplified macrophage response to cytosolic LPS. Previous studies indicate that IFN-induced expression of caspase-11 and guanylate binding proteins (GBPs) are causal events explaining the effects of priming on cytosolic LPS sensing. We demonstrate that these events cannot fully account for the increased response triggered by IFN γ treatment. Indeed, IFN γ priming elicits higher pyroptosis levels in response to cytosolic LPS when macrophages stably express caspase-11. In macrophages lacking GBPs encoded on chromosome 3, IFN γ priming enhanced pyroptosis in response to cytosolic LPS as compared with other priming agents. These results suggest an unknown regulator of caspase-11-dependent pyroptosis exists, whose activity is upregulated by IFN γ ., Competing Interests: The authors declare no competing interests., (© 2020 The Authors.)

The various sub-species of Salmonella enterica cause a range of disease in human hosts. The human-adapted Salmonella enterica serovar Typhi enters the gastrointestinal tract and invades systemic sites to cause enteric (typhoid) fever. In contrast, most non-typhoidal serovars of Salmonella are primarily restricted to gut tissues. Across Africa, invasive non-typhoidal Salmonella (iNTS) have emerged with an ability to spread beyond the gastrointestinal tract and cause systemic bloodstream infections with increased morbidity and mortality. To investigate this evolution in pathogenesis, we compared the genomes of African iNTS isolates with other Salmonella enterica serovar Typhimurium and identified several macA and macB gene variants unique to African iNTS. MacAB forms a tripartite efflux pump with TolC and is implicated in Salmonella pathogenesis. We show that macAB transcription is upregulated during macrophage infection and after antimicrobial peptide exposure, with macAB transcription being supported by the PhoP/Q two-component system. Constitutive expression of macAB improves survival of Salmonella in the presence of the antimicrobial peptide C18G. Furthermore, these macAB variants affect replication in macrophages and influence fitness during colonization of the murine gastrointestinal tract. Importantly, the infection outcome resulting from these macAB variants depends upon both the Salmonella Typhimurium genetic background and the host gene Nramp1, an important determinant of innate resistance to intracellular bacterial infection. The variations we have identified in the MacAB-TolC efflux pump in African iNTS may reflect evolution within human host populations that are compromised in their ability to clear intracellular Salmonella infections., Competing Interests: I have read the journal's policy and the authors of this manuscript have the following competing interests: Rocío Canals currently works for GSK Vaccines Institute for Global Health. All other authors have no competing interests.

Many Gram-negative bacterial pathogens antagonize anti-bacterial immunity through translocated effector proteins that inhibit pro-inflammatory signaling. In addition, the intracellular pathogen Salmonella enterica serovar Typhimurium initiates an anti-inflammatory transcriptional response in macrophages through its effector protein SteE. However, the target(s) and molecular mechanism of SteE remain unknown. Here, we demonstrate that SteE converts both the amino acid and substrate specificity of the host pleiotropic serine/threonine kinase GSK3. SteE itself is a substrate of GSK3, and phosphorylation of SteE is required for its activity. Remarkably, phosphorylated SteE then forces GSK3 to phosphorylate the non-canonical substrate signal transducer and activator of transcription 3 (STAT3) on tyrosine-705. This results in STAT3 activation, which along with GSK3 is required for SteE-mediated upregulation of the anti-inflammatory M2 macrophage marker interleukin-4Rα (IL-4Rα). Overall, the conversion of GSK3 to a tyrosine-directed kinase represents a tightly regulated event that enables a bacterial virulence protein to reprogram innate immune signaling and establish an anti-inflammatory environment., (Copyright © 2019 The Authors. Published by Elsevier Inc. All rights reserved.)

Many intracellular bacteria can establish chronic infection and persist in tissues within granulomas composed of macrophages. Granuloma macrophages exhibit heterogeneous polarization states, or phenotypes, that may be functionally distinct. Here, we elucidate a host-pathogen interaction that controls granuloma macrophage polarization and long-term pathogen persistence during Salmonella Typhimurium (STm) infection. We show that STm persists within splenic granulomas that are densely populated by CD11b + CD11c + Ly6C + macrophages. STm preferentially persists in granuloma macrophages reprogrammed to an M2 state, in part through the activity of the effector SteE, which contributes to the establishment of persistent infection. We demonstrate that tumor necrosis factor (TNF) signaling limits M2 granuloma macrophage polarization, thereby restricting STm persistence. TNF neutralization shifts granuloma macrophages toward an M2 state and increases bacterial persistence, and these effects are partially dependent on SteE activity. Thus, manipulating granuloma macrophage polarization represents a strategy for intracellular bacteria to overcome host restriction during persistent infection., (Copyright © 2019 Elsevier Inc. All rights reserved.)

Inflammasomes are a formidable armada of intracellular pattern recognition receptors. They recognize determinants of infection, such as foreign entities or danger signals within the host cell cytosol, rapidly executing innate immune defenses and initiating adaptive immune responses. Although inflammasomes are implicated in many diseases, they are especially critical in host protection against intracellular bacterial pathogens. Given this role, it is not surprising that many pathogens have evolved effective strategies to evade inflammasome activation. In this review, we will provide a brief summary of inflammasome activation during infection with the intent of highlighting recent advances in the field. Additionally, we will review known bacterial evasion strategies and countermeasures that impact pathogenesis., (Copyright © 2019 Elsevier Ltd. All rights reserved.)

The pyridinophane molecule L2 (3,6,9,15-tetraazabicyclo[9.3.1]penta-deca-1(15),11,13-trien-13-ol) has shown promise as a therapuetic for neurodegenerative diseases involving oxidative stress and metal ion misregulation. Protonation and metal binding stability constants with Mg 2+ , Ca 2+ , Cu 2+ , and Zn 2+ ions were determined to further explore the therapeutic and pharmacological potential of this water soluble small molecule. These studies show that incorporation of an -OH group in position 4 of the pyridine ring decreases the pI values compared to cyclen and L1 (3,6,9,15-tetraazabicyclo[9.3.1]penta-deca-1(15),11,13-triene). Furthermore, this approach tunes the basicity of the tetra-aza macrocyclic ligand through the enhanced resonance stabilization of the -OH in position 4 and rigidity of the pyridine ring such that L2 has increased basicity compared to previously reported tetra-aza macrocycles. A metal binding preference for Cu 2+ , a redox cycling agent known to produce oxidative stress, indicates that this would be the in vivo metal target of L2. However, the binding constant of L2 with Cu 2+ is moderated compared to cyclen due to the rigidity of the ligand and shows how ligand design can be used to tune metal selectivity. An IC 50 = 298.0 μM in HT-22 neuronal cells was observed. Low metabolic liability was determined in both Phase I and II in vitro models. Throughout these studies other metal binding systems were used for comparison and as appropriate controls. The reactivity reported to date and pharmacological features described herein warrant further studies in vivo and the pursuit of L2 congeners using the knowledge that pyridine substitution in a pyridinophane can be used to tune the structure of the ligand and retain the positive therapeutic outcomes.

We describe a framework for calculating the frequency shift and uncertainty of trapped-ion optical atomic clocks caused by background-gas collisions, and apply this framework to an 27 Al + clock to enable a total fractional systematic uncertainty below 10 -18 . For this clock, with 38(19) nPa of room-temperature H 2 background gas, we find that collisional heating generates a non-thermal distribution of motional states with a mean time-dilation shift of order 10 -16 at the end of a 150 ms probe, which is not detected by sideband thermometry energy measurements. However, the contribution of collisional heating to the spectroscopy signal is highly suppressed and we calculate the BGC shift to be -0.6(2.4) × 10 -19 , where the shift is due to collisional heating time dilation and the uncertainty is dominated by the worst case ± π /2 bound used for collisional phase shift of the 27 Al + superposition state. We experimentally validate the framework and determine the background-gas pressure in situ using measurements of the rate of collisions that cause reordering of mixed-species ion pairs.

We describe an optical atomic clock based on quantum-logic spectroscopy of the ^{1}S_{0}↔^{3}P_{0} transition in ^{27}Al^{+} with a systematic uncertainty of 9.4×10^{-19} and a frequency stability of 1.2×10^{-15}/sqrt[τ]. A ^{25}Mg^{+} ion is simultaneously trapped with the ^{27}Al^{+} ion and used for sympathetic cooling and state readout. Improvements in a new trap have led to reduced secular motion heating, compared to previous ^{27}Al^{+} clocks, enabling clock operation with ion secular motion near the three-dimensional ground state. Operating the clock with a lower trap drive frequency has reduced excess micromotion compared to previous ^{27}Al^{+} clocks. Both of these improvements have led to a reduced time-dilation shift uncertainty. Other systematic uncertainties including those due to blackbody radiation and the second-order Zeeman effect have also been reduced.

Macrocyclic ligands have been explored extensively as scaffolds for transition metal catalysts for oxygen and hydrogen atom transfer reactions. C-C reactions facilitated using earth abundant metals bound to macrocyclic ligands have not been well-understood but could be a green alternative to replacing the current expensive and toxic precious metal systems most commonly used for these processes. Therefore, the yields from direct Suzuki-Miyaura C-C coupling of phenylboronic acid and pyrrole to produce 2-phenylpyrrole facilitated by eight high-spin iron complexes ([Fe 3+ L1(Cl) 2 ] + , [Fe 3+ L4(Cl) 2 ] + , [Fe 2+ L5(Cl)] + , [Fe 2+ L6(Cl) 2 ], [Fe 3+ L7(Cl) 2 ] + , [Fe 3+ L8(Cl) 2 ] + , [Fe 2+ L9(Cl)] + , and [Fe 2+ L10(Cl)] + ) were compared to identify the effect of structural and electronic properties on catalytic efficiency. Specifically, catalyst complexes were compared to evaluate the effect of five properties on catalyst reaction yields: (1) the coordination requirements of the catalyst, (2) redox half-potential of each complex, (3) topological constraint/rigidity, (4) N atom modification(s) increasing oxidative stability of the complex, and (5) geometric parameters. The need for two labile cis-coordination sites was confirmed based on a 42% decrease in catalytic reaction yield observed when complexes containing pentadentate ligands were used in place of complexes with tetradentate ligands. A strong correlation between iron(III/II) redox potential and catalytic reaction yields was also observed, with [Fe 2+ L6(Cl) 2 ] providing the highest yield (81%, -405 mV). A Lorentzian fitting of redox potential versus yields predicts that these catalysts can undergo more fine-tuning to further increase yields. Interestingly, the remaining properties explored did not show a direct, strong relationship to catalytic reaction yields. Altogether, these results show that modifications to the ligand scaffold using fundamental concepts of inorganic coordination chemistry can be used to control the catalytic activity of macrocyclic iron complexes by controlling redox chemistry of the iron center. Furthermore, the data provide direction for the design of improved catalysts for this reaction and strategies to understand the impact of a ligand scaffold on catalytic activity of other reactions.

We report on Raman sideband cooling of ^{25}Mg^{+} to sympathetically cool the secular modes of motion in a ^{25}Mg^{+}-^{27}Al^{+} two-ion pair to near the three-dimensional (3D) ground state. The evolution of the Fock-state distribution during the cooling process is studied using a rate-equation simulation, and various heating sources that limit the efficiency of 3D sideband cooling in our system are discussed. We characterize the residual energy and heating rates of all of the secular modes of motion and estimate a secular motion time-dilation shift of -(1.9±0.1)×10^{-18} for an ^{27}Al^{+} clock at a typical clock probe duration of 150 ms. This is a 50-fold reduction in the secular motion time-dilation shift uncertainty in comparison with previous ^{27}Al^{+} clocks.

The Flaviviridae are a family of viruses that cause severe human diseases. For example, dengue virus (DENV) is a rapidly emerging pathogen causing an estimated 100 million symptomatic infections annually worldwide. No approved antivirals are available to date and clinical trials with a tetravalent dengue vaccine showed disappointingly low protection rates. Hepatitis C virus (HCV) also remains a major medical problem, with 160 million chronically infected patients worldwide and only expensive treatments available. Despite distinct differences in their pathogenesis and modes of transmission, the two viruses share common replication strategies. A detailed understanding of the host functions that determine viral infection is lacking. Here we use a pooled CRISPR genetic screening strategy to comprehensively dissect host factors required for these two highly important Flaviviridae members. For DENV, we identified endoplasmic-reticulum (ER)-associated multi-protein complexes involved in signal sequence recognition, N-linked glycosylation and ER-associated degradation. DENV replication was nearly completely abrogated in cells deficient in the oligosaccharyltransferase (OST) complex. Mechanistic studies pinpointed viral RNA replication and not entry or translation as the crucial step requiring the OST complex. Moreover, we show that viral non-structural proteins bind to the OST complex. The identified ER-associated protein complexes were also important for infection by other mosquito-borne flaviviruses including Zika virus, an emerging pathogen causing severe birth defects. By contrast, the most significant genes identified in the HCV screen were distinct and included viral receptors, RNA-binding proteins and enzymes involved in metabolism. We found an unexpected link between intracellular flavin adenine dinucleotide (FAD) levels and HCV replication. This study shows notable divergence in host-depenency factors between DENV and HCV, and illuminates new host targets for antiviral therapy.

Penning traps are made extremely compact by embedding rare-earth permanent magnets in the electrode structure. Axially-oriented NdFeB magnets are used in unitary architectures that couple the electric and magnetic components into an integrated structure. We have constructed a two-magnet Penning trap with radial access to enable the use of laser or atomic beams, as well as the collection of light. An experimental apparatus equipped with ion optics is installed at the NIST electron beam ion trap (EBIT) facility, constrained to fit within 1 meter at the end of a horizontal beamline for transporting highly charged ions. Highly charged ions of neon and argon, extracted with initial energies up to 4000 eV per unit charge, are captured and stored to study the confinement properties of a one-magnet trap and a two-magnet trap. Design considerations and some test results are discussed.

Optical frequencies of the D lines of (6,7)Li were measured with a relative accuracy of 5 × 10⁻¹¹ using an optical comb synthesizer. Quantum interference in the laser induced fluorescence for the partially resolved D2 lines was found to produce polarization dependent shifts as large as 1 MHz. Our results resolve large discrepancies among previous experiments and between all experiments and theory. The fine-structure splittings for ⁶Li and ⁷Li are 10052.837(22) MHz and 10053.435(21) MHz. The splitting isotope shift is 0.599(30) MHz, in reasonable agreement with recent theoretical calculations.

Phosphorylation of the cardiac troponin complex by PKA at S22 and S23 of troponin I (TnI) accelerates Ca(2+) release from troponin C (TnC). The region of TnI around the bisphosphorylation site binds to, and stabilizes, the Ca(2+) bound N-terminal domain of TnC. Phosphorylation interferes with this interaction between TnI and TnC resulting in weaker Ca(2+) binding. In this study, we used (1)H-(15)N-HSQC NMR to investigate at the atomic level the interaction between an N-terminal fragment of TnI consisting of residues 1-64 of TnI (I1-64) and TnC. We produced several mutants of I1-64, TnI, and TnC to test the contribution of certain residues to the transmission of the phosphorylation signal in both NMR experiments and functional assays. We also investigated how phosphorylation of the PKC sites in I1-64 (S41 and S43) affects the interaction of I1-64 with TnC. We found that phosphorylation of S22 and S23 produced only localized effects in the structure of I1-64 between residues 24 and 34. Residues 1-17 of I1-64 did not bind to TnC, and residues 38-64 bound tightly to the C-terminal domain of TnC regardless of phosphorylation. Residues 22-34 bound weakly to TnC in a phosphorylation sensitive manner. Bisphosphorylation prevented this phosphorylation switch region from interacting with TnC. Systematic mutation of residues in the phosphorylation switch did not prevent PKA phosphorylation from accelerating Ca(2+) release from troponin. We conclude that the phosphorylation switch binds to TnC via an extended interaction site spanning residues R19 to A34.

The N-terminal extension of cardiac troponin I (TnI) is bisphosphorylated by protein kinase A in response to beta-adrenergic stimulation. How this signal is transmitted between TnI and troponin C (TnC), resulting in accelerated Ca(2+) release, remains unclear. We recently proposed that the unphosphorylated extension interacts with the N-terminal domain of TnC stabilizing Ca(2+) binding and that phosphorylation prevents this interaction. We now use (1)H NMR to study the interactions between several N-terminal fragments of TnI, residues 1-18 (I1-18), residues 1-29 (I1-29), and residues 1-64 (I1-64), and TnC. The shorter fragments provide unambiguous information on the N-terminal regions of TnI that interact with TnC: I1-18 does not bind to TnC whereas the C-terminal region of unphosphorylated I1-29 does bind. Bisphosphorylation greatly weakens this interaction. I1-64 contains the phosphorylatable N-terminal extension and a region that anchors I1-64 to the C-terminal domain of TnC. I1-64 binding to TnC influences NMR signals arising from both domains of TnC, providing evidence that the N-terminal extension of TnI interacts with the N-terminal domain of TnC. TnC binding to I1-64 broadens NMR signals from the side chains of residues immediately C-terminal to the phosphorylation sites. Binding of TnC to bisphosphorylated I1-64 does not broaden these NMR signals to the same extent. Circular dichroism spectra of I1-64 indicate that bisphosphorylation does not produce major secondary structure changes in I1-64. We conclude that bisphosphorylation of cardiac TnI elicits its effects by weakening the interaction between the region of TnI immediately C-terminal to the phosphorylation sites and TnC either directly, due to electrostatic repulsion, or via localized conformational changes.

Phosphorylation of the unique N-terminal extension of cardiac troponin I (TnI) by PKA modulates Ca(2+) release from the troponin complex. The mechanism by which phosphorylation affects Ca(2+) binding, however, remains unresolved. To investigate this question, we have studied the interaction of a fragment of TnI consisting of residues 1-64 (I1-64) with troponin C (TnC) by isothermal titration microcalorimetry and cross-linking. I1-64 binds extremely tightly to the C-terminal domain of TnC and weakly to the N-terminal domain. Binding to the N-domain is weakened further by phosphorylation. Using the heterobifunctional cross-linker benzophenone-4-maleimide and four separate cysteine mutants of I1-64 (S5C, E10C, I18C, R26C), we have probed the protein-protein interactions of the N-terminal extension. All four I1-64 mutants cross-link to the N-terminal domain of TnC. The cross-linking is enhanced by Ca(2+) and reduced by phosphorylation. By introducing the same monocysteine mutations into full-length TnI, we were able to probe the environment of the N-terminal extension in intact troponin. We find that the full length of the extension lies in close proximity to both TnC and troponin T (TnT). Ca(2+) enhances the cross-linking to TnC. Cross-linking to both TnC and TnT is reduced by prior phosphorylation of the TnI. In binary complexes the mutant TnIs cross-link to both the isolated TnC N-domain and whole TnC. Cyanogen bromide digestion of the covalent TnI-TnC complex formed from intact troponin demonstrates that cross-linking is predominantly to the N-terminal domain of TnC.