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  • Article
    Piëch V, Li W, Reeke GN, Gilbert CD.
    Proc Natl Acad Sci U S A. 2013 Oct 22;110(43):E4108-17.
    The visual system uses continuity as a cue for grouping oriented line segments that define object boundaries in complex visual scenes. Many studies support the idea that long-range intrinsic horizontal connections in early visual cortex contribute to this grouping. Top-down influences in primary visual cortex (V1) play an important role in the processes of contour integration and perceptual saliency, with contour-related responses being task dependent. This suggests an interaction between recurrent inputs to V1 and intrinsic connections within V1 that enables V1 neurons to respond differently under different conditions. We created a network model that simulates parametrically the control of local gain by hypothetical top-down modification of local recurrence. These local gain changes, as a consequence of network dynamics in our model, enable modulation of contextual interactions in a task-dependent manner. Our model displays contour-related facilitation of neuronal responses and differential foreground vs. background responses over the neuronal ensemble, accounting for the perceptual pop-out of salient contours. It quantitatively reproduces the results of single-unit recording experiments in V1, highlighting salient contours and replicating the time course of contextual influences. We show by means of phase-plane analysis that the model operates stably even in the presence of large inputs. Our model shows how a simple form of top-down modulation of the effective connectivity of intrinsic cortical connections among biophysically realistic neurons can account for some of the response changes seen in perceptual learning and task switching.
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  • Article
    Smithies O.
    Proc Natl Acad Sci U S A. 2003 Apr 01;100(7):4108-13.
    Current interpretations of kidney function in terms of a coarse filter followed by a fine filter have difficulty explaining why the glomerulus does not clog. I propose, as an alternative, a semiquantitative hypothesis that assumes that the size-selective property of the glomerulus is a consequence of the limited fraction of space in the glomerular basement membrane (a concentrated gel) into which macromolecules can permeate. The glomerular epithelial cell slits and slit diaphragms are assumed to impose substantial resistance to liquid flow across the glomerulus without acting as a molecular sieve. Calculations based on gel behavior show that proteins cross the glomerular basement membrane mainly by diffusion rather than by liquid flow, whereas water crosses entirely by flow. Thus, diffusion provides most of the protein, whereas flow provides the diluent. As a result, the single-nephron glomerular filtration rate (GFR) becomes a prime factor in (inversely) determining the concentration of proteins in early proximal tubular fluid. Because the reabsorption of proteins from the tubules is a saturable process, the gel permeationdiffusion hypothesis readily accounts for the albuminuria observed when single-nephron GFR is substantially reduced by severe pathological decreases in slit diaphragm length, such as occur in minimal-change nephrotic syndrome in humans, in animals treated with puromycin aminonucleoside, or in humans or animals with mutations in the gene coding for nephrin. My hypothesis predicts that albuminuria will ensue, even with a normal kidney, if the single-nephron GFR falls below approximately 50% of normal.
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  • Article
    Sharf Y, Seo Y, Eliav U, Akselrod S, Navon G.
    Proc Natl Acad Sci U S A. 1998 Apr 14;95(8):4108-12.
    A technique is described for displaying distinct tissue layers of large blood vessel walls as well as measuring their mechanical strain. The technique is based on deuterium double-quantum-filtered (DQF) spectroscopic imaging. The effectiveness of the double-quantum filtration in suppressing the signal of bulk water is demonstrated on a phantom consisting of rat tail tendon fibers. Only intrafibrillar water is displayed, excluding all other signals of water molecules that reorient isotropically. One- and two-dimensional spectroscopic imaging of bovine aorta and coronary arteries show the characteristic DQF spectrum of each of the tissue layers. This property is used to obtain separate images of the outer layer, the tunica adventitia, or the intermediate layer, the tunica media, or both. To visualize the effect of elongation, the average residual quadrupole splitting <delta nu q> is calculated for each pixel. Two-dimensional deuterium quadrupolar splitting images are obtained for a fully relaxed and a 55% elongated sample of bovine coronary artery. These images indicate that the strong effect of strain is associated with water molecules in the tunica adventitia whereas the DQF NMR signal of water in the tunica media is apparently strain-insensitive. After appropriate calibration, these average quadrupolar splitting images can be interpreted as strain maps.
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  • Article
    Arnal JF, Clamens S, Pechet C, Negre-Salvayre A, Allera C, Girolami JP, Salvayre R, Bayard F.
    Proc Natl Acad Sci U S A. 1996 Apr 30;93(9):4108-13.
    Estradiol is known to exert a protective effect against the development of atherosclerosis, but the mechanism by which this protection is mediated is unclear. Since animal studies strongly suggest that production of endothelium-derived relaxing factor is enhanced by estradiol, we have examined the effect of estrogens on nitric oxide (NO) synthase (NOS) activity, protein, and mRNA in cultured bovine aortic endothelial cells. In reporter cells rich in guanylate cyclase, it has been observed that long-term treatment (> or = 24 hr) with ethinylestradiol (EE2) dose-dependently increased guanylate cyclase-activating factor activity in the conditioned medium of endothelial cells. However, conversion of L-[14C]arginine to L-[14C]citrulline by endothelial cell homogenate or quantification of nitrite and nitrate released by intact cells in the conditioned medium did not reveal any change in NOS activity induced by EE2 treatment. Similarly, Western and Northern blot analyses did not reveal any change in the endothelial NOS protein and mRNA content in response to EE2. However, EE2 dose- and time-dependently decreased superoxide anion production in the conditioned medium of endothelial cells with an EC50 value (0.1 nM) close to that which increased guanylate cyclase-activating factor activity (0.5 nM). Both of these effects were completely prevented by the antiestrogens tamoxifen and RU54876. Thus, endothelium exposure to estrogens appears to induce a receptor-mediated antioxidant effect that enhances the biological activity of endothelium-derived NO. These effects could account at least in part for the vascular protective properties of these hormones.
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  • Article
    Trentini DB, Pecoraro M, Tiwary S, Cox J, Mann M, Hipp MS, Hartl FU.
    Proc Natl Acad Sci U S A. 2020 02 25;117(8):4099-4108.
    Mammalian cells present a fingerprint of their proteome to the adaptive immune system through the display of endogenous peptides on MHC-I complexes. MHC-I-bound peptides originate from protein degradation by the proteasome, suggesting that stably folded, long-lived proteins could evade monitoring. Here, we investigate the role in antigen presentation of the ribosome-associated quality control (RQC) pathway for the degradation of nascent polypeptides that are encoded by defective messenger RNAs and undergo stalling at the ribosome during translation. We find that degradation of model proteins by RQC results in efficient MHC-I presentation, independent of their intrinsic folding properties. Quantitative profiling of MHC-I peptides in wild-type and RQC-deficient cells by mass spectrometry showed that RQC substantially contributes to the composition of the immunopeptidome. Our results also identify endogenous substrates of the RQC pathway in human cells and provide insight into common principles causing ribosome stalling under physiological conditions.
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  • Article
    Gojobori T, Moriyama EN, Ina Y, Ikeo K, Miura T, Tsujimoto H, Hayami M, Yokoyama S.
    Proc Natl Acad Sci U S A. 1990 Jun;87(11):4108-11.
    From what viruses the human immunodeficiency viruses (HIVs) originated is an extremely controversial question. To address this question, we have analyzed nucleotide sequences of simian immunodeficiency viruses (SIVs) and HIVs by using the techniques for understanding molecular evolution. In particular, we compared the nucleotide sequences of whole genomes, gene region by gene region, between a given pair of viruses, including four types of SIVs--isolated from mandrills (Papio sphinx), African green monkeys (Cercopithecus aethiops), sooty mangabeys (Cercocebus atys), and rhesus macaques (Macaca mulatta)--as well as HIVs. Phylogenetic trees for all gene regions examined showed that the present HIVs may have emerged as different variants of SIVs of Old World monkeys, possibly from recombination between viruses related to SIVs.
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  • Article
    Schroeder JI, Raschke K, Neher E.
    Proc Natl Acad Sci U S A. 1987 Jun;84(12):4108-12.
    Stomatal pores in leaves enable plants to regulate the exchange of gases with their environment. Variations of the pore aperture are mediated by controlled changes of potassium salt concentrations in the surrounding guard cells. The voltage-dependent gating of K(+)-selective channels in the plasma membrane (plasmalemma) of cell-wall-free guard cells (protoplasts) was studied at the molecular level in order to investigate the regulation of K(+) fluxes during stomatal movements. Inward and outward K(+) currents across the plasmalemma of guard cells were identified by using the whole-cell configuration of the patch-clamp technique. Depolarizations of the membrane potential from a holding potential of -60 mV to values more positive than -40 mV produced outward currents that were shown to be carried by K(+). Hyperpolarizations elicited inward K(+) currents. Inward and outward currents were selective for K(+) over Na(+) and could be partially blocked by exposure to extracellular Ba(2+). In cell-attached and excised membrane patches, previously identified K(+)-selective single channels in guard cells were studied. Averaging of single-channel currents during voltage pulses resulted in activation and deactivation kinetics that were similar to corresponding kinetics of inward and outward currents in whole cells, showing that K(+)-selective channels were the molecular pathways for the K(+) currents recorded across the plasmalemma of single guard-cell protoplasts. Estimates demonstrate that K(+) currents through the voltage-gated K(+) channels recorded in whole guard cells can account for physiological K(+) fluxes reported to occur during stomatal movements in leaves.
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  • Article
    Novick RP, Adler GK, Majumder S, Khan SA, Carleton S, Rosenblum WD, Iordanescu S.
    Proc Natl Acad Sci U S A. 1982 Jul;79(13):4108-12.
    pT181 is a 4.4-kilobase plasmid from Staphylococcus aureus specifying tetracycline resistance and present in about 20 copies per cell. The existence of a diffusible pT181 product required for plasmid replication has been proposed on the basis of trans-complementable thermosensitive mutants defective in plasmid maintenance (phenotype Tsr). In this report, the Tsr mutants are shown to have primary replication defects, and the genetic complementation data are confirmed biochemically. All of five mutations are in a single cistron, the repC cistron; interruption of the plasmid DNA molecule at any of three neighboring restriction sites inactivates repC function. Analysis of the DNA sequence in this region reveals an open reading frame of 939 base pairs which encodes the repC product, a 313-amino acid protein. pT181 replication has been demonstrated in cell-free extracts to require specifically a pT181-coded protein of approximately the same size, and it is proposed that this protein is, indeed, the repC product. Preliminary evidence is discussed suggesting that the pT181 replication rate is controlled at the level of synthesis of the repC protein.
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  • Article
    Birchmeier C, Kreis TE, Eppenberger HM, Winterhalter KH, Birchmeier W.
    Proc Natl Acad Sci U S A. 1980 Jul;77(7):4108-12.
    The distributions of both fibronectin (LETS, CSP) fibers and focal contacts to the substratum, as viewed by fluorescence and reflection contrast microscopy, respectively, have been compared in freshly plated WI-38 human fibroblasts. Most frequently, the actual focal attachment plaques did not contain fibronectin fluorescence and, furthermore, fibronectin spots and fibers often alternated with focal contacts. Overlap, however, was observed between focal contacts and the endings of actin-containing stress fibers [see also Wehland, J., Osborn, M. & Weber, K. (1979) J. Cell Sci. 37, 257-273]. Thus, the fibroblast attachment membrane might best be described as a corrugated sheet that undulates between alternating microfilaments and fibronectin fibers, at the points of closest and farthest distance to the substratum, respectively.
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  • Article
    Pishesha N, Thiru P, Shi J, Eng JC, Sankaran VG, Lodish HF.
    Proc Natl Acad Sci U S A. 2014 Mar 18;111(11):4103-8.
    Mouse models have been used extensively for decades and have been instrumental in improving our understanding of mammalian erythropoiesis. Nonetheless, there are several examples of variation between human and mouse erythropoiesis. We performed a comparative global gene expression study using data from morphologically identical stage-matched sorted populations of human and mouse erythroid precursors from early to late erythroblasts. Induction and repression of major transcriptional regulators of erythropoiesis, as well as major erythroid-important proteins, are largely conserved between the species. In contrast, at a global level we identified a significant extent of divergence between the species, both at comparable stages and in the transitions between stages, especially for the 500 most highly expressed genes during development. This suggests that the response of multiple developmentally regulated genes to key erythroid transcriptional regulators represents an important modification that has occurred in the course of erythroid evolution. In developing a systematic framework to understand and study conservation and divergence between human and mouse erythropoiesis, we show how mouse models can fail to mimic specific human diseases and provide predictions for translating findings from mouse models to potential therapies for human disease.
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  • Article
    Unadkat HV, Hulsman M, Cornelissen K, Papenburg BJ, Truckenmüller RK, Carpenter AE, Wessling M, Post GF, Uetz M, Reinders MJ, Stamatialis D, van Blitterswijk CA, de Boer J.
    Proc Natl Acad Sci U S A. 2011 Oct 04;108(40):16565-70.
    It is increasingly recognized that material surface topography is able to evoke specific cellular responses, endowing materials with instructive properties that were formerly reserved for growth factors. This opens the window to improve upon, in a cost-effective manner, biological performance of any surface used in the human body. Unfortunately, the interplay between surface topographies and cell behavior is complex and still incompletely understood. Rational approaches to search for bioactive surfaces will therefore omit previously unperceived interactions. Hence, in the present study, we use mathematical algorithms to design nonbiased, random surface features and produce chips of poly(lactic acid) with 2,176 different topographies. With human mesenchymal stromal cells (hMSCs) grown on the chips and using high-content imaging, we reveal unique, formerly unknown, surface topographies that are able to induce MSC proliferation or osteogenic differentiation. Moreover, we correlate parameters of the mathematical algorithms to cellular responses, which yield novel design criteria for these particular parameters. In conclusion, we demonstrate that randomized libraries of surface topographies can be broadly applied to unravel the interplay between cells and surface topography and to find improved material surfaces.
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  • Article
    Kim JC, Orr-Weaver TL.
    Proc Natl Acad Sci U S A. 2011 Oct 04;108(40):16681-6.
    To investigate the properties of metazoan replication origins, recent studies in cell culture have adopted the strategy of identifying origins using genome-wide approaches and assessing correlations with such features as transcription and histone modifications. Drosophila amplicon in follicle cells (DAFCs), genomic regions that undergo repeated rounds of DNA replication to increase DNA copy number, serve as powerful in vivo model replicons. Because there are six DAFCs, compared with thousands of origins activated in the typical S phase, close molecular characterization of all DAFCs is possible. To determine the extent to which the six DAFCs are different or similar, we investigated the developmental and replication properties of the newly identified DAFC-34B. DAFC-34B contains two genes expressed in follicle cells, although the timing and spatial patterns of expression suggest that amplification is not a strategy to promote high expression at this locus. Like the previously characterized DAFC-62D, DAFC-34B displays origin activation at two separate stages of development. However, unlike DAFC-62D, amplification at the later stage is not transcription-dependent. We mapped the DAFC-34B amplification origin to 1 kb by nascent strand analysis and delineated cis requirements for origin activation, finding that a 6-kb region, but not the 1-kb origin alone, is sufficient for amplification. We analyzed the developmental localization of the origin recognition complex (ORC) and the minichromosome maintenance (MCM)2-7 complex, the replicative helicase. Intriguingly, the final round of origin activation at DAFC-34B occurs in the absence of detectable ORC, although MCMs are present, suggesting a new amplification initiation mechanism.
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  • Article
    Roberts JJ, Wood RA, Haszeldine RS.
    Proc Natl Acad Sci U S A. 2011 Oct 04;108(40):16545-8.
    Industrialized societies which continue to use fossil fuel energy sources are considering adoption of Carbon Capture and Storage (CCS) technology to meet carbon emission reduction targets. Deep geological storage of CO(2) onshore faces opposition regarding potential health effects of CO(2) leakage from storage sites. There is no experience of commercial scale CCS with which to verify predicted risks of engineered storage failure. Studying risk from natural CO(2) seeps can guide assessment of potential health risks from leaking onshore CO(2) stores. Italy and Sicily are regions of intense natural CO(2) degassing from surface seeps. These seeps exhibit a variety of expressions, characteristics (e.g., temperature/flux), and location environments. Here we quantify historical fatalities from CO(2) poisoning using a database of 286 natural CO(2) seeps in Italy and Sicily. We find that risk of human death is strongly influenced by seep surface expression, local conditions (e.g., topography and wind speed), CO(2) flux, and human behavior. Risk of accidental human death from these CO(2) seeps is calculated to be 10-8 year-1 to the exposed population. This value is significantly lower than that of many socially accepted risks. Seepage from future storage sites is modeled to be less that Italian natural flux rates. With appropriate hazard management, health risks from unplanned seepage at onshore storage sites can be adequately minimized.
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  • Article
    Wesolowski D, Tae HS, Gandotra N, Llopis P, Shen N, Altman S.
    Proc Natl Acad Sci U S A. 2011 Oct 04;108(40):16582-7.
    Basic peptides covalently linked to nucleic acids, or chemically modified nucleic acids, enable the insertion of such a conjugate into bacteria grown in liquid medium and mammalian cells in tissue culture. A unique peptide, derived from human T cells, has been employed in a chemical synthesis to make a conjugate with a morpholino oligonucleotide. This new conjugate is at least 10- to 100-fold more effective than previous peptides used in altering the phenotype of host bacteria if the external guide sequence methodology is employed in these experiments. Bacteria with target genes expressing chloramphenicol resistance, penicillin resistance, or gyrase A function can effectively be reduced in their expression and the host cells killed. Several bacteria are susceptible to this treatment, which has a broad range of potency. The loss in viability of bacteria is not due only to complementarity with a target RNA and the action of RNase P, but also to a non-gene-specific tight binding of the complexed nontargeted RNA to the basic polypeptide-morpholino oligonucleotide.
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  • Article
    Dey S, Matsunami H.
    Proc Natl Acad Sci U S A. 2011 Oct 04;108(40):16651-6.
    A variety of social behaviors like intermale aggression, fear, and mating rituals are important for sustenance of a species. In mice, these behaviors have been implicated to be mediated by peptide pheromones that are sensed by a class of G protein-coupled receptors, vomeronasal receptor type 2 (V2Rs), expressed in the pheromone detecting vomeronasal organ. Matching V2Rs with their cognate ligands is required to learn what receptors the biologically relevant pheromones are acting on. However, this feat has been greatly limited by the unavailability of appropriate heterologous tools commonly used to study ligand receptor specificity, because this family of receptors fails to traffic to the surface of heterologous cells. Here we show that calreticulin, a housekeeping chaperone commonly expressed in most eukaryotic cells, is sparsely expressed in the vomeronasal sensory neurons (VSNs). Correspondingly, knockdown of calreticulin in commonly available cell lines enables V2Rs to efficiently target to the cell membrane. Using this knowledge, we have now been able to successfully surface express receptors and functionally identify cognate ligands. Additionally, calreticulin4, a homolog of calreticulin shows restricted and enriched expression in the VSNs. Interestingly, in heterologous cells, calreticulin4 does not inhibit surface expression of V2Rs and can in part carry out functions of calreticulin. On the basis of our data, we postulate that V2Rs may use a unique trafficking mechanism whereby an important and more commonly expressed chaperone is deleterious for membrane export and is replaced by a functionally equivalent homolog that does not inhibit export while carrying out its functions.
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  • Article
    Le Floch R, Chiche J, Marchiq I, Naiken T, Naïken T, Ilc K, Ilk K, Murray CM, Critchlow SE, Roux D, Simon MP, Pouysségur J.
    Proc Natl Acad Sci U S A. 2011 Oct 04;108(40):16663-8.
    Malignant tumors exhibit increased dependence on glycolysis, resulting in abundant export of lactic acid, a hypothesized key step in tumorigenesis. Lactic acid is mainly transported by two H(+)/lactate symporters, MCT1/MCT4, that require the ancillary protein CD147/Basigin for their functionality. First, we showed that blocking MCT1/2 in Ras-transformed fibroblasts with AR-C155858 suppressed lactate export, glycolysis, and tumor growth, whereas ectopic expression of MCT4 in these cells conferred resistance to MCT1/2 inhibition and reestablished tumorigenicty. A mutant-derivative, deficient in respiration (res(-)) and exclusively relying on glycolysis for energy, displayed low tumorigenicity. These res(-) cells could develop resistance to MCT1/2 inhibition and became highly tumorigenic by reactivating their endogenous mct4 gene, highlighting that MCT4, the hypoxia-inducible and tumor-associated lactate/H(+) symporter, drives tumorigenicity. Second, in the human colon adenocarcinoma cell line (LS174T), we showed that combined silencing of MCT1/MCT4 via inducible shRNA, or silencing of CD147/Basigin alone, significantly reduced glycolytic flux and tumor growth. However, both silencing approaches, which reduced tumor growth, displayed a low level of CD147/Basigin, a multifunctional protumoral protein. To gain insight into CD147/Basigin function, we designed experiments, via zinc finger nuclease-mediated mct4 and basigin knockouts, to uncouple MCTs from Basigin expression. Inhibition of MCT1 in MCT4-null, Basigin(high) cells suppressed tumor growth. Conversely, in Basigin-null cells, in which MCT activity had been maintained, tumorigenicity was not affected. Collectively, these findings highlight that the major protumoral action of CD147/Basigin is to control the energetics of glycolytic tumors via MCT1/MCT4 activity and that blocking lactic acid export provides an efficient anticancer strategy.
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  • Article
    Lott GA, Perdomo-Ortiz A, Utterback JK, Widom JR, Aspuru-Guzik A, Marcus AH.
    Proc Natl Acad Sci U S A. 2011 Oct 04;108(40):16521-6.
    By applying a phase-modulation fluorescence approach to 2D electronic spectroscopy, we studied the conformation-dependent exciton coupling of a porphyrin dimer embedded in a phospholipid bilayer membrane. Our measurements specify the relative angle and separation between interacting electronic transition dipole moments and thus provide a detailed characterization of dimer conformation. Phase-modulation 2D fluorescence spectroscopy (PM-2D FS) produces 2D spectra with distinct optical features, similar to those obtained using 2D photon-echo spectroscopy. Specifically, we studied magnesium meso tetraphenylporphyrin dimers, which form in the amphiphilic regions of 1,2-distearoyl-sn-glycero-3-phosphocholine liposomes. Comparison between experimental and simulated spectra show that although a wide range of dimer conformations can be inferred by either the linear absorption spectrum or the 2D spectrum alone, consideration of both types of spectra constrain the possible structures to a "T-shaped" geometry. These experiments establish the PM-2D FS method as an effective approach to elucidate chromophore dimer conformation.
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  • Article
    Kim G, Kronenberg M.
    Proc Natl Acad Sci U S A. 2011 Oct 04;108(40):16493-4.
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  • Article
    Feduccia A.
    Proc Natl Acad Sci U S A. 2011 Oct 04;108(40):16487-8.
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  • Article
    Jha SK, Ji M, Gaffney KJ, Boxer SG.
    Proc Natl Acad Sci U S A. 2011 Oct 04;108(40):16612-7.
    Understanding how electric fields and their fluctuations in the active site of enzymes affect efficient catalysis represents a critical objective of biochemical research. We have directly measured the dynamics of the electric field in the active site of a highly proficient enzyme, Δ(5)-3-ketosteroid isomerase (KSI), in response to a sudden electrostatic perturbation that simulates the charge displacement that occurs along the KSI catalytic reaction coordinate. Photoexcitation of a fluorescent analog (coumarin 183) of the reaction intermediate mimics the change in charge distribution that occurs between the reactant and intermediate state in the steroid substrate of KSI. We measured the electrostatic response and angular dynamics of four probe dipoles in the enzyme active site by monitoring the time-resolved changes in the vibrational absorbance (IR) spectrum of a spectator thiocyanate moiety (a quantitative sensor of changes in electric field) placed at four different locations in and around the active site, using polarization-dependent transient vibrational Stark spectroscopy. The four different dipoles in the active site remain immobile and do not align to the changes in the substrate electric field. These results indicate that the active site of KSI is preorganized with respect to functionally relevant changes in electric fields.
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